Electronic Energy transfer through a molecular wire: a semi-classical perspective

Aarti Sindhu and Amber Jain

E-mail: (Will be shown in the real poster)

The mechanism of electronic energy transfer (EET) in a molecular wire is one of the crucial phenomena occurring in the whole process of photosynthesis. From recent experimental as well as theoretical studies, it has been shown that the coherences play a vital role in the EET of FMO (a molecular wire in green sulfur bacteria). In the present work, we have simulated the molecular wire (with FMO parameters as a probe) using a semi-classical method called surface hopping and compared the results with the exact numerical method available in the literature. For simplicity, first, we worked on a model Hamiltonian with only two and three sites. Through careful analysis of the results obtained, we could understand the role of coherences in the dynamics. Moreover, due to these coherences, a diabatic coupling as small as 5 cm^-1 has a significant effect on the dynamics. The findings of the work have potential applications in designing artificial solar cells.

References:

1. S. Engel, T. R. Calhoun, E. L. Read, T.-K.Ahn,T. Mančal, Y.-C.Cheng, R. E. Blankenship, G. R. Fleming, Nature 2007, 446, 782
2. Ishizaki, G. R. Fleming, Proc. Natl. Acad. Sci. USA 2009, 106, 17255
3. Sindhu, A. Jain. ChemPhysChem 2022: e202200392.

Phonon transport in Janus monolayer siblings: a comparison of 1T and 2H-ISbTe

Viet-Ha Chu^a Tien-Ha Le^b Truong-Tho Pham^c,d and Duc-Long Nguyen^c,d
a) Department of Physics, TNU-University of Education, Thai Nguyen, Vietnam
b) Institute of Sciences and Technology, TNU-University of Sciences, Thai Nguyen, Vietnam
c) Laboratory of Applied Physics, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam
d) Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam
E-mail: (Will be shown in the real poster)

The study of two-dimensional (2D) Janus materials has gained considerable attention in recent years due to their asymmetrical structures and resulting unique quantum features. Despite extensive research on phonon transport in Janus monolayers, Janus materials with different crystal prototypes have received little attention. In this study, we perform an in-depth investigation of the phonon transport in two distinct Janus materials, 1T and 2H-ISbTe, using first-principles calculations and a machine learning-accelerated Boltzmann transport equation. Our results reveal that 2H-ISbTe exhibits a low lattice thermal conductivity of 1.5 W mK−1, 2.3 times lower than that of its 1T counterpart, due to its covalent bonding and low elastic constants. A detailed examination of phonon group velocity, phonon lifetime, and heat carrier identification is also carried out to gain a better understanding of the thermal transport characteristics of these Janus materials. The results of this study provide new insights into the diverse thermal transport behavior of Janus ISbTe monolayers and offer promising prospects for their application in thermal management and thermoelectric devices.

Novel Polycarbonate Material Design of Light-Resistance: a Theoretical Investigation

Xiao Huang, Yuuichi Orimoto, Yuriko Aoki

Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Japan

 We studied the mechanism of polycarbonate (PC) photodegradation using a simplified model bisphenol-A hydrogen carbonate (BPAHC) at first, and the results showed that the PhO-COO- bond cleavage can be explained from two electronic excitations. The well-known one is the electronic excitation from oxygen (within carbonate group) lone pair to the carbonate group that stabilizes the orbital energy of carbonate π anti-bonding, and the newly proposed one is the electronic excitation from oxygen lone pair to phenyl (adjacent to carbonate) group that generates a quinoidal structure; the structure forces Ph=O double bond and induces Ph=O∙∙∙COO- cleavage.^[1]

To further design more novel light-resistant PC materials, on the basis of the above mechanism, the detailed mechanism of photodegradation for donor/acceptor-substituted PCs was investigated with quantum chemical methods with considering the effect of electron-donating and electron-withdrawing groups. The results showed that the PhO-COO- bond cleavage is promoted when introducing the electron-donating group on BPAHC, because the above-mentioned excitations are enhanced, finally generating a quinoidal structure and stabilizing the orbital energy of carbonate π anti-bonding. On the contrary, the PhO-COO- bond cleavage is suppressed when introducing the electron-withdrawing group on BPAHC, because the concentrated excitations are reduced compared to BPAHC.

Reference

[1] Xiao Huang, Yuuichi Orimoto, and Yuriko Aoki. Theoretical Analysis of Properties of Ground and Excited States for Photodissociation of the C-O Bond in Polycarbonates. J. Phys. Chem. A, 125, 6662-6673 (2021).

Structural, electronic, and electron transport properties of the pentagonal PdSe₂ nanotubes

Nguyen Thanh Tien¹, Pham Thi Bich Thao¹, and Le Nhat Thanh¹

¹College of Natural Science, Can Tho University, Vietnam 

Two-dimensional novel pentagonal materials (2Dpenta) have gained a lot of attention being a new class of materials with unique properties that could influence future technologies. In this report, we have systematically investigated the structural, electronic, and transport properties of pentagonal PdSe₂ nanotubes (p-PdSe₂ NT). The stability and electronic properties of p-PdSe₂ NTs with different tube sizes and under uniaxial small strain are investigated by using density functional theory. The studied structures experience an indirect to direct band gap transition with slight variation of the band gap as the tube size increases. Specifically, (5×5) p-PdSe2 NT, (6×6) p-PdSe2 NT, (7×7) p-PdSe2 NT, (8×8) p-PdSe2 NT possess indirect bandgap semiconductors, while (9×9) p-PdSe2 NT exhibits a direct band gap. The (9×9) p-PdSe2 NT structure is the most stable structure with the lowest binding energy of -2.020 eV. In addition, under uniaxial small strain, the survey structures are stable and can still keep the pentagonal ring structure. The structures are unstable with tensile strain from 24%, compression from -18% for sample (5×5) and -20% for sample (9×9). The electronic band structure and band gap are strongly affected by the uniaxial compressive strain. The evolution of band gap versus the strain as linear. The band gap of p-PdSe2 NT experiences an indirect-direct-indirect or a direct-indirect-direct transition when axial strain is applied. The results of this investigation bring a better understanding of the p-PdSe2 NT, opens up potential applications in next generation electronic devices and electromechanical sensors.

A NOVEL DESIGNATION OF HETEROCIRCULENE STRUCTURES TO GIANT COVALENT FRAMEWORK

Lam H. Nguyen^a,b,c,*

^a.Institute for Computational Science and Technology, Ho Chi Minh City, Viet Nam.

^b.Faculty of Chemistry, University of Science, Ho Chi Minh City, Viet Nam.

^c.Vietnam National University, Ho Chi Minh City, Vietnam

A number of hybrid flowers from four main circulene classes: Oxiflowers, Sulflowers, Pyrroflowers, and Phosphoflower have been created, called SILKY flowers. The structures of these flowers have also been tested under different spin states, and it is found that there are planar molecules at the singlet state, but several forms are distorted in triplet and quintet ones. Moreover, the frontier orbital energies and the HOMO-LUMO gaps are promising to be developed for semi-conductor material design. Especially the size of a circulene structure is opened higher than eight fused rings, spreading from nine to twelve fused rings by mixing thiophene, furan, and pyrrole. Interestingly, a new type of giant covalent framework has been created by connecting the SILKY flowers via saturated carbon chains. This finding promises a new trend in studying the circulene structure and giant covalent framework.

Ab initio Study of the Electronic Structure and UV-vis Absorption Spectra of Metalloporphyrins with Multireference Perturbation Theory Methods

Gaurab Ganguly, Jan Plutner, Josef Michl, and Zdenek Havlas

Institute of Organic Chemistry and Biochemistry, Flemingovo Nam. 2, 16610 Prague 6, Czech Republic

Porphyrin-based dyes are efficient light harvesters and have been used as sensitizers in dye-sensitized solar cells (DSSCs), therefore, their photophysical properties are of particular interest. The UV-vis (12500 – 48000 cm^-1) absorption spectra of porphyrin-based systems are composed of three major regions including four characteristic bands: the low-energy Q-band, the most intense B-band and the shoulder on its highenergy tail or the N-band, and lastly the weak and broad L-band. However, the presence of 26 π-electrons in 24 π-orbitals in the porphyrin-based systems in general, and additional open d-shell in transition metal containing porphyrins cause a severe challenge for spectra simulations with ab initio wavefunction theory calculations. In this work, a systematic theoretical study of the UV-vis spectroscopy of a series of metalloporphyrin (M = Mg, Fe, Co, Ni, Cu, Zn) has been carried out using restricted active space (RAS) self-consistent field (SCF) approach. Multireference Perturbation Theory (MRPT) calculations have been performed on the optically-allowed valence excited states to assign the four lowest features of the spectra. The choice of active space and the accuracy of the two most popular MRPT methods, namely, the complete active space second-order perturbation theory (CASPT2) and the N-electron valence state second-order perturbation theory (NEVPT2) were assessed in predicting accurate vertical excitation energies. Both the CASPT2 and NEVPT2 results are in good qualitative agreement with the in-house experimental data. However, the quantitative accuracy of CASPT2 turns out to be superior in predicting the position of the Qband, while the improved performance of NEVPT2 was noted in predicting the position of the B-band. These results may help understand the photophysics of other metalloporphyrins used in DSSCs.

Quantum monodromy in effective polyad breaking Hamiltonian

Ishita Ghorai

School of Physical Sciences, Indian Institute of Technology Mandi, Himachal Pradesh, India

Monodromy is a classical property of two or more degrees of freedom of integrable dynamical systems that creates a distinctive pattern on the distribution of quantum mechanical eigenvalues. The concept of quantum monodromy was recently developed and demonstrated to be an important qualitative feature of numerous realistic models. From these examples, new qualitative features of molecular systems are used to naturally lead to generalized monodromy notions. Finally, in extremely complex systems, a relationship or link between phyllotaxis and monodromy is possible.

As spectroscopy becomes more advanced and also the theory of anharmonic systems and nonlinear systems have resulted in a renewed and acute appreciation of the complexity and subtlety of molecular vibrational motion in recent years. Quantum monodromy concept will play a crucial and important role in the understanding of these complex motions.

COMPUTATION-EXPERIMENT CORRELATION IN INHIBITABILITY OF PLANT-BASED COMPOSITION AND PROTEIN-RELATED STRUCTURES

Thanh Q. Bui¹, Phan Tu Quy², Nguyen Thi Thanh Hai¹, and Nguyen Thi Ai Nhung^1*

¹Department of Chemistry, University of Sciences, Hue University, Hue, Vietnam

²Department of Natural Sciences & Technology, Tay Nguyen University, Buon Ma Thuot, Vietnam

*Email: (Will be shown in the real poster)

Data-driven and Machine Learning Modelling of Melanin Absorption Spectra

 Arpan Choudhury¹, Raghunathan Ramakrishnan²*, Debashree Ghosh¹*

¹ School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India

² Tata Institute of Fundamental Research Hyderabad, Hyderabad-500046, India

Elucidation of melanin structure by experimental approaches faced continuous adversity due to its extreme heterogeneity. Eumelanin, one of the variants of melanin, is best known for its photo-protective properties and is characterized by a broadband featureless absorption spectrum spanning most of the UV and visible region of light. Although there are several computational studies to address the seriosity of structural heterogeneity in the absorption spectrum, a complete structure-property relationship is still missing. Here we propose a data-driven and machine learning modelling of melanin spectra to arrive at a clear picture of its underlying chemistry.

 References:

1. G. Prota, Melanins and Melanogenesis, Academic Press, 2012.
2. E. Kaxiras, A. Tsolakidis,  G. Zonios, S. Meng, Physical review letters, 2006, 97, 218102.
3. D. Ghosh, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2021,11,e1505.
4. A. Choudhury, D. Ghosh, Chemical Communications, 2020,56,10481.

Adsorption Mechanism of Pyrrole, Furan and Thiophene on Fe(110) Surface: A DFT Study

Thong Le Minh Pham^1,2_, Thanh Khoa Phung^3,4, Ho Viet Thang⁵

¹Institute of Research and Development, Duy Tan University, Da Nang City 550000, Viet Nam.

²Faculty of Environmental and Chemical Engineering, Duy Tan University, Da Nang, 550000, Viet Nam

³Department of Chemical Engineering, School of Biotechnology, International University, Ho Chi Minh City, Vietnam

⁴Vietnam National University, Ho Chi Minh City, Vietnam.

⁵The University of Da-Nang, University of Science and Technology, 54 Nguyen Luong Bang, Da-Nang 550000, Vietnam

Understanding the interaction of pyrrole, furan, and thiophene with Fe(110) surface is essential for designing novel inhibitors against the corrosion of steel. Herein, we present DFT calculated results for the adsorption of pyrrole, furan, and thiophene on Fe(110) surface. It was found that the studied molecules prefer to adsorb at the hollow site by forming covalent bonds with four Fe atoms on Fe(110) surface. The chemisorptions of pyrrole, furan, and thiophene on Fe(110) surface are demonstrated by large adsorption energies and charge transfers from the surface to the molecules. Moreover, vdW corrections in the DFT calculations have a minimal effect on the adsorption geometry while it significantly increases the adsorption energy of the molecules. The energetic and structural analysis shows large molecular distortions induced by the interactions with Fe(110) surface. Among the studied molecules, thiophene experiences the least molecular distortions by the adsorption, thereby having the largest adsorption energy. The nature of bonding of the adsorbates and Fe(110) surface was also elucidated by analyzing the density of states, the charge density difference plot, and the Bader charge.

References

1. Thong Le Minh Pham, Thanh Khoa Phung, Ho Viet Thang, DFT insights into the adsorption mechanism of five-membered aromatic heterocycles containing N, O, or S on Fe(110) surface, Volume 583, 2022, 152524.

Computational Study of  pK_a Shift of Aspartate Residue in Thioredoxin: Role of Configurational Sampling and Solvent Model                      

Shivani Verma and Nisanth N. Nair*

Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India

Alchemical free energy calculations are widely used in predicting pK_a in biomolecular systems. These calculations are carried out using either Free Energy Perturbation (FEP) or Thermodynamic Integration (TI). In these methods, free energy differences are calculated by introducing some non-physical intermediate states between two physically relevant states. When applied to condensed matter systems, the predictive power of these methods is affected by the slow convergence in the free energy estimates, mainly due to the drastic environmental changes while moving from one state to the other. [3] Numerous efforts have been made to improve the accuracy and efficiency of such calculations, especially by boosting conformational sampling. [4, 5] In this work, we use a technique that enhances the conformational sampling by temperature acceleration of collective variables for alchemical transformations and applies it to the prediction of pK_a of the buried Asp₂₆ residue in thioredoxin protein. It shows the importance of enhanced sampling and effect of solvent models in the pK_a calculations. [6]                                       

References:

[3] Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167–4180.

[4] Cuendet, M. A.; Tuckerman, M. E. J. Chem. Theory Comput. 2012, 8, 3504-3512.

[5] Meng, Y.; Sabri Dashti, D.; Roitberg, A. E. J. Chem. Theory Comput. 2011, 7, 2721–2727.

[6] S. Verma, N. N. Nair. arXiv:2211.13637v1

Machine learning methods for successfully predicting the enantioselectivity of Pauson-Khand reactions 

Neha Rani

Department of Chemistry, Indian Institute of Technology Jammu, India

Machine Learning (ML) methods can be reliably used for successful prediction of unknown reaction outcomes which can provide significant momentum to current efforts in design of novel catalysts without the need of extensive experimentation thus saving manpower, energy, money, and chemical waste.  In this regard, we have developed a novel machine learning protocol that can successfully predict the enantiomeric excess (%ee) of the bicyclopentenone products arising from transition-metal catalyzed asymmetric Pauson-Khand reaction between an 1,6-enyne and carbon monoxide (CO). A set of calculated molecular descriptors has been selected which contain 102 parameters from the substrate enyne and [2,2′-bis(diphenylphosphino)-1,1′-binaphthyl]-based ligand present on the catalytic core. We have considered global parameters e.g. sterimol (L1, B1, B5) and rotational constants (RCx, RCy, RCz). The non-molecular descriptors e.g. temperature, CO pressure, catalyst concentration, and solvent dielectric constant have been included as well. A reliable model was developed by training on the known chemical systems: a total of 216 unique chemical reactions from combination of 16 BINAP-based ligands and 48 enyne substrates.  Synthetic Minority Oversampling Technique was applied to take care of the imbalanced data to avoid biasness of the data towards high %ee (>70%). Different ML algorithms, e.g. the neural network (NN), decision tree (DT), logistic regression (LR) and Random forest (RF), were applied to analyze the importance of our calculated descriptors in determining the %ee of the reaction products. For further validation, we tested our newly-developed protocol on a total of 25 out-of-bag samples which constitute a set of 25 unique reactions that do not appear in the training sets. Reasonable accuracy was found that proved the robustness of our model.

Computational Approach for Molecular Design with High Hole Mobilities using Random Forest Technique and Computer Simulation Method

Toshio Asada^1,2,*, Keijin Nakaguro¹, Takashi Yamaguchi¹, Tomohiro Oshiyama³ and Yuki Mitsuta^1,2

¹Department of Chemistry, Osaka Metropolitan University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531 Japan.
 ²RIMED, Osaka Metropolitan University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531 Japan.
  ³Konica Minolta, Inc., 2970, Ishikawa-machi, Hachioji, Tokyo, 192-8505 Japan.

Hole mobility in the amorphous phase is one of an important physical property for designing hole transport layers in electronic devices such as the organic light emitted diode. However, the new molecules have been discovered by trial-and-error approaches. Recently, the theoretical and computational approaches have been developed to evaluate the hole mobility for a given molecule. We have previously proposed the successive conduction (SC) model, which is a statistical approach to evaluate hole mobility in the amorphous phase using a limited number of evaluated kinetic rate constants by the molecular orbital calculations and the Marcus theory. While the SC model can evaluate hole mobility when the molecular structure is provided, it is difficult to propose the reliable molecules to realize the desired hole mobility.

In order to realize the automated system for the molecular design with a desired hole mobility, the random forest approach of the machine learning techniques have been applied in this study. We have constructed a data base with hole mobilities for 321 molecules from the published papers. The new molecules have been designed using the ChemTS python module proposed by Tsuda et al., which is the combined approach of Monte Carlo tree search and recurrent neural networks. The hole mobilities of generated molecules have been evaluated by both the random forest model and the SC model. Since some novel molecules with high hole mobilities could be automatically proposed, we will discuss the techniques in this conference.

A parameter free approach for core level spectroscopy without core-hole reference states

Bibek Samal, Vamsee K. Voora

Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India

X-ray spectroscopy provides valuable information about the local chemical environment of atoms in molecules by probing core-electronic structure. However, modeling core-electronic structure is challenging owing to large orbital-relaxation effects and relativistic corrections. We overcome these challenges by combining GKS-spRPA with (perturbative) X2C approach to study the K- and L-edge X-ray photoelectron spectroscopy (XPS) and nonresonant X-ray emission spectroscopy (XES) of molecular systems. The core and valence-electron one-particle states, required for the computation of the XES and XPS spectra, are obtained directly in a single calculation of the neutral system without any use of core-hole reference states.  A systematic analysis of the accuracy of the X2C-GKS-spRPA method shows that, for K-edge spectroscopy of third-period elements, MAEs of less than 1 eV are observed. We also show that an analytic continuation technique, with a O(N⁴) computational cost, can be used to obtain highly accurate X-ray emission spectra of molecules such as C₆₀ and S₈ with multiple core-hole states. 

 References:

1. K. Voora; R. Galhenage; J. C. Hemminger; F. Furche. Effective one-particle energies from generalized kohn–sham random phase approximation: A direct approach for computing and analyzing core ionization energies. J. Chem. Phys., 151(13), 134106, (2019).
2. J. Franzke; N. Middendorf; F. Weigend. Efficient implementation of one- and two-component analytical energy gradients in exact two-component theory. J. Chem. Phys., 148, 104110, (2018).

Machine Learning Frontier Orbital Energies of Nanodiamonds

Thorren Kirschbaum, Börries von Seggern, Joachim Dzubiella, Annika Bande, Frank Noé

Simulation of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
Institute of Mathematics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany

Machine learning (ML) of chemical properties represents a powerful tool for high-throughput-screening of materials for a plethora of applications.^[1] For nanomaterials, however, datasets on which such approaches can be performed are quite sparse. Therefore, we present the ND5k dataset, consisting of 5,089 diamondoid and nanodiamond (ND) structures that are optimized via tight binding density functional theory (DFTB) and their frontier orbital energies computed at DFT/PBE0 level of theory. The ND5k dataset provides a natural extension of the existing databases of organic molecules (QM7b,^[2] QM9,^[3] OE62,^[4] etc.) towards larger and more complex carbon-based structures. We compare different ML algorithms for predicting the frontier orbital energies of the ND5k structures and for extrapolating their predictions to larger NDs: Kernel ridge regression (KRR) using the smooth overlap of atomic positions (SOAP) descriptor,^[5] an edge-conditioned graph neural network with set2set pooling (enn-s2s),^[6] and the graph neural networks SchNet^[7] and PaiNN.^[8] Furthermore, we develop a variant of the enn-s2s that replaces the generic atom-type-specific graph node embeddings with precise atomic descriptors. Here, we use the SOAP atomic descriptors, and the principal component analysis-reduced SOAP descriptors, as initial hidden node states of the molecular graphs. While the PaiNN model achieves top performances, our modified enn-s2s variant yields the overall second-best results. The network extension presented by us is general and can straightforwardly be applied to enhance other graph neural networks architectures as well.

References
[1] P. O. Dral, J. Phys. Chem. Lett. 2020, 11, 2336–2347.
[2] G. Montavon, M. Rupp, V. Gobre, A. Vazquez-Mayagoitia, K. Hansen, A. Tkatchenko, K.-R. Müller, O. Anatole von Lilienfeld, New J. Phys. 2013, 15, 095003.
[3] R. Ramakrishnan, P. O. Dral, M. Rupp, O. A. von Lilienfeld, Sci. Data 2014, 1, 140022.
[4] A. Stuke, C. Kunkel, D. Golze, M. Todorović, J. T. Margraf, K. Reuter, P. Rinke, H. Oberhofer, Sci. Data 2020, 7, 58.
[5] A. P. Bartók, R. Kondor, G. Csányi, Phys. Rev. B 2013, 87, 184115.
[6] J. Gilmer, S. S. Schoenholz, P. F. Riley, O. Vinyals, G. E. Dahl, in Proceedings of the 34th International Conference on Machine Learning, PMLR 2017, 1263–1272.
[7] K. T. Schütt, H. E. Sauceda, P.-J. Kindermans, A. Tkatchenko, K.-R. Müller, J. Chem. Phys. 2018, 148, 241722.
[8] K. Schütt, O. Unke, M. Gastegger, in Proceedings of the 38th International Conference on Machine Learning, PMLR 2021, 9377–9388.

What can superatoms do for you?

Celina Sikorska ^a,✉, Emma Vincent ^a, Iwona Anusiewicz ^b, Nicola Gaston ^a

^a) The MacDiarmid Institute for Advanced Materials and Nanotechnology, Department of Physics, The University of Auckland Private Bag 92019, Auckland 1142, New Zealand
^b) Faculty of Chemistry, University of Gdansk, Fahrenheit Union of Universities in Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland

✉ Will be shown in the poster at the conference

Superatoms are clusters of atoms that act like a single atom. They have unique properties, including diverse functionalization, redox activity, and magnetic ordering. Materials made up of superatoms, so-called cluster-assembled solids, hold the promise of high tunability, atomic precision, and robust architectures. Superalkalis are a class of superatoms that have extremely low ionization energy and might serve as catalysts. Carbon dioxide (CO₂) is a major greenhouse gas, yet is a cheap carbon feedstock. Developing efficient catalysts that convert CO₂ into fuel is vital to addressing the energy crisis and global warming. The high stability of CO₂ makes the conversion difficult. Our goal is to design and explore superatoms for CO₂ activation and transformation, using computational chemistry with quantum chemistry techniques. We believe that the electronic properties of superalkalis can predict the efficiency of superalkali/CO₂ complex formation. We investigate the influence of electronic structure, ionization energy, and ligation on the stability and selectivity of superalkali/CO₂ complexes.

We believe that our results will be useful for understanding CO₂ conversion into fuels and value-added chemicals.

P_n ring size dependence on NHC-induced ring contraction reactions of [CoCp′′′(η⁴-P₄] and [FeCp^*(η⁵-P₅)]. A DFT Study.

Gaurav Joshi, M. N. Sreerag, Eluvathingal D. Jemmis* and John F. Nixon

Department of Inorganic and Physical Chemistry, Indian Institute of Science Bengaluru

Email:(Will be shown in the poster at the conference)

Cyclopolyphosphorus rings (cyclo-P_n) as ligands, isolobal to aromatic carbon rings, have intrigued chemists for the past few decades.^1-3 The reactivity of transition metal stabilized cyclo-P_n [TM-cyclo-P_n] through phosphorus has led to several facile transformations with retention, expansion, fragmentation, and even contraction of the ring.^4-9 In a recent report, Sheer et al. observed carbene induced facile ring contraction of [CoCp′′′(η⁴-P₄)], and [Ta(CO)₂Cp′′(η⁴-P₄)] (Cp′′′ = 1,2,4-tri-tert-butyl-cyclopentadienyl, Cp′′ = 1,3-di-tert-butyl-cyclopentadienyl).^5,6 However, a similar reaction with [FeCp^*(η⁵-P₅)] ends up giving an intermediate with ring retention.⁸ In order to answer these discrepancies, arising as the ring size increases, we have computed the energetics for the ring contraction with variation in ring size (Figure 1). We have employed different theoretical tools for a qualitative picture of the overall reaction. It is observed that the inherent ring strain in the P_n ring plays a decisive role in determining the ring contraction capability of [TM-cyclo-P_n] complex. We have further analysed the role of different metal, nucleophile on the ring-contraction energetics. An isolobal perspective on these reactions affords a more simplistic picture of the overall reaction.¹⁰

We also report the mechanism of ring contraction by NHC in triple decker complexes with varying valence electron count (VEC), the role of halogens in inducing ring contraction and product distribution in double decker and triple decker complexes.^5,11,12

Figure 1. Free energy landscape for the carbene induced ring-contraction reaction of [CoCp(η⁴-P₄)] and [FeCp(η⁵-P₅)] computed at B3LYP/Def2SVP level of theory with the IEFPCM solvation model for THF solvent at 298 K.

References:

1. P. Ginsberg and W. E. Lindsell, J. Am. Chem. Soc., 1971, 93, 2082–2084.
2. Peresypkina, A. Virovets and M. Scheer, Coord. Chem. Rev., 2021, 446, 213995.
3. M. Hoidn, D. J. Scott and R. Wolf, Chem. – A Eur. J., 2021, 27, 1886–1902.
4. A. Ghilardi, S. Midollini, A. Orlandini and L. Sacconi, Inorg. Chem., 1980, 19, 301–306.
5. Piesch, S. Reichl, M. Seidl, G. Balázs and M. Scheer, Angew. Chemie Int. Ed., 2019, 58, 16563–16568.
6. Riedlberger, S. Todisco, P. Mastrorilli, A. Y. Timoshkin, M. Seidl and M. Scheer, Chem. – A Eur. J., 2020, 26, 16251–16255.
7. Riedlberger, M. Seidl and M. Scheer, Chem. Commun., 2020, 56, 13836–13839.
8. Piesch, M. Seidl and M. Scheer, Chem. Sci., 2020, 11, 6745–6751.
9. B. Clendenning, P. B. Hitchcock, J. F. Nixon and L. Nyulászi, Chem. Commun., 2000, 1305–1306
10. Joshi, M. N. Sreerag, E. D. Jemmis and J. F. Nixon, Inorg. Chem., 2022, 61, 15822-15830. 
11. Brake, E. Peresypkina, A. V. Virovets, M. Piesch, W. Kremer, L. Zimmermann, C. Klimas and M. Scheer, Angew. Chem. Int. Ed. 2020, 59, 16241–16246.
12. ‌A. Garbagnati, M. Seidl, G. Balázs and M. Scheer,  – A Eur. J., 2022, DOI:10.1002/chem.202200669.

A DFT investigation of CO₂ activation on transition metals doped thin film ZnO

Ho Viet Thang

The University of Danang, University of Science and Technology, 54 Nguyen Luong Bang, Lien Chieu, Danang 550000, Vietnam

Email: (Will be shown in the poster at the conference)

CO₂ is the primary greenhouse gas causing global warming and its concentration in the atmosphere has increased yearly¹. Many efforts have been dedicated to capturing and converting CO₂ into value-added products, aiming at reducing the impact of CO₂ in the enviroment. It is well known that CO₂ is a linear and chemically inert molecule and  CO₂ activation is the key step in converting CO₂ processes^2,3. This study investigates CO₂ activation on M transition metals (M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu) doped ultra-thin film ZnO using density functional theory. Analyzing the geometrical structure, bond order, Bader charge, magnetic moment, the density of states, and charge density difference, the adsorption energy of adsorbed CO₂ on M-doped ZnO reveals that among transition metals doped ZnO, Sc, Ti, V, and Cr can activate CO₂, while the rest of the transition metals are unable to activate CO₂. The driving force that gives rise to the CO₂ activation on Sc, Ti, V, and Cr-doped ZnO is due to the charge transfer from the doped metal to the π* antibonding orbital of CO₂. This results in bending and lowering the bond order of CO₂ molecules compared to free CO₂ with linear geometry. This study will provide useful information on CO₂ activation on transition metal-doped ZnO, to capture and convert CO₂ into valuable chemicals.

 References

1. T. J. Crowley. Causes of Climate Change over the Past 1000 Years. Science, 2000, 289, 270–277.
2. Y. Chen et al. CO₂ capture and conversion to value-added products promoted by MXene-based materials. Green Energy & Environment, 2022, 7, 394-410.
3. A. Adamu, F. Russo-Abegão, K. Boodhoo. Process intensification technologies for CO₂ capture and conversion – a review. BMC Chemical Engineering. 2020, 2, 1-18.

Through-space/Through-bond method for analyzing molecular orbital interactions and its application to DNA mutations

Mariia Ivonina, Yuuichi Orimoto, Yuriko Aoki

Kyushu University, Kasuga, Japan

Being able to quantify molecular orbital interactions is helpful for studying properties of molecular systems such as stability, reactivity, chemical bonds pattern, etc. For this purpose, we developed an ab initio approach for analyzing various molecular orbital interactions that occur through space and through bond, the so-called “Through-space/Through-bond” (TS/TB) method.

Highly Accurate Buried Surface Area for Protein Docking by FFT Convolution of Grid-Based Shrake-Rupley Surfaces

James Tufts, Hong Ha Nguyen, David D. L. Minh*

*Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA

The Fast Fourier Transform (FFT) is the foundation of many protein and fragment docking algorithms, as it enables efficient interaction energy evaluation at regular spatial intervals. In an attempt to improve predictions of the nonpolar solvation free energy, we developed an algorithm to reproduce the buried surface area. Highly accurate protein-protein buried surface areas were obtained through two convolutions of a Shrake-Rupley solvent accessible surface area (SASA) grid with water shell grids. Using the 179 systems of the Protein-Protein Affinity Benchmark v2, an R2 value of 0.99 for the linear correlation between the grid-based SASA scoring function and the Shrake-Rupley SASA (Receptor+Ligand-Complex) using the top 1000 highest scores for 101 rotations per system, including the native rotation. We also evaluate protein binding free energies using the grid-based SASA along with electrostatics and Lennard-Jones energies. 

Grafting Methionine on 1F1 Antibody Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza A Viruses

Hoa Thanh Le^1,2, Phuc-Chau Do^3,4, and Ly Le⁵

¹Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam

²Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam

³School of Biotechnology, International University, Ho Chi Minh City, Vietnam

⁴Vietnam National University, Ho Chi Minh City, Vietnam

⁵Vingroup Big Data Institute, Hanoi, Vietnam

Email: (Will be shown in the poster at the conference)

A high level of mutation enables the influenza A virus to resist antibiotics targeting influenza A virus, causing annual, costly and time-consuming redevelopment of anti-flu vaccine. We derived peptide inhibitors from antibody complementarity-determining regions and broadened their spectrum to H1, H2, H3 strains by grafting hotspot amino acid capable of forming favorable contact with structurally conserved regions on HA of these strains. A portion of the structure of hemagglutinin (HA) is assumed to be well-conserved to maintain its biological role, and structure tends to be more conserved than sequence. Structurally conserved residues on HA were identified by structural alignment. Hotspot amino acids and anti-HA antibody fragments able to bind to the conserved residues were identifed by molecular docking. The structure of hotspot-grafted fragments were modeled and validated for binding ability to HA conserved residues by docking with HA of H1, H2 and H3 strains. Most of the conserved and strongly similar residues are located in the receptor-binding and esterase regions on the HA1 domain. Methionine amino acid achieved the best docking score within the 2.8 Å Van der Waals radius. Our peptide inhibitor was able to form in silico contact with a structurally conserved region across H1, H2, and H3 HA, with the binding site at the boundary between HA1 and HA2 domains, spreading across different monomers, suggesting a new target for designing broad-spectrum antibody and vaccine. This research presents an affordable method to design broad-spectrum peptide inhibitors based on antibody fragments.

Quantum and quasiclassical dynamical simulations for the Ar₂H⁺ on a new global analytical potential energy surface

Significance of Sub-pico-newton Forces on the Folding-Unfolding of TrpZip2 β-Hairpin

1. G.Govind, EC.Nayana, and P.Anjukandi, J. Biomol. Struct. Dyn. (2021) 1-7.
2. Gomez, D., Peña Ccoa, W.J., Singh, Y., Rojas, E. and Hocky, G.M., J. Phys. Chem. B (2021) 125,12115-12124
3. EC.Nayana, A.G.Nair, P.Anjukandi,Is the Multifaceted Folding-Unfolding Landscape a Manifestation of Sub-pico-newton Mechanical Tension? A TrpZip2 β–Hairpin Perspective, Submitted (2022).

High- vs. low-spin Ni²⁺ in elongated octahedral environments: Sr₂NiO₂Cu₂S₂ , Sr₂NiO₂Cu₂Se₂

Ziyu Lu, Simon J. Clarke and John E. McGrady.^a*

Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK

Email: (Will be shown in the poster at the conference)

The two layered materials, Sr₂NiO₂Cu₂S₂ and Sr₂NiO₂Cu₂Se₂­, consisting of alternating [Sr₂NiO₂]²⁺ and [Cu₂S₂]^2-(or [Cu₂Se₂]^2-) layers, have been investigated using X-ray and neutron diffraction as well as density functional theory. The results for Sr₂NiO₂Cu₂Se₂­ are unambiguous, in that the distended octahedral environment supports a high-spin (S = 1) configuration at Ni²⁺. The situation in Sr₂NiO₂Cu₂S₂ is, however, much less clear-cut, with measured lattice parameters and bond lengths apparently midway between typical values for high- and low-spin configurations. The measured data are, however, essentially independent of temperature, apparently excluding an equilibrium between these two spin states. A detailed series of DFT calculations (VASP, plane-wave basis) on Sr₂NiO₂Cu₂S₂ converges on two distinct solutions whose energies are very dependent on the chosen value of U, one with all Ni²⁺ high-spin, the other where they are all low-spin, neither of which matches the experiment. Finally, we located an even more stable ‘mixed’ solution where high- and low-spin centers co-exist in a 50:50 ratio (Figure 1), and this solution provides a remarkably good match to all the available experimental data. The co-existence of both high- and low-spin configurations in a stable structure is a remarkable consequence of the very distended octahedral geometry, where long axial Ni-S distances are imposed by the 3-dimensional lattice.

Figure 1 Structure of Sr₂NiO₂Cu₂S₂(Sr₂NiO₂Cu₂Se₂) and checkerboard arrangement of Ni²⁺ in the mixed model

Acknowledgement Thank Rob Smyth and Jack Blandy for the synthesis and characterise Sr₂NiO₂Cu₂S₂ and Sr₂NiO₂Cu₂Se₂ samples.

[1] R. D. Smyth, J. N. Blandy, Z. Yu, S. Liu, C. V. Topping, S. J. Cassidy, C. F. Smura, D. N. Woodruff, P. Manuel, C. L. Bull, N. P. Funnell, C. J. Ridley, J. E. McGrady and S. J. Clarke, Chem. Mater. 2022, 34, 21, 9503–9516

Investigating the structural features of SRAS-CoV-2 Mpro binding site bound covalent ligands at phyiological temperature

Hien T. T. Lai, Agata Kranjc, Toan T. Nguyen

Key Laboratory for Multiscale Simulation of Complex Systems, and Department of Theoretical Physics, University of Science, Vietnam National University – Hanoi
334 Nguyen Trai street, Thanh Xuan, Hanoi, Vietnam

The SARS-CoV-2 pandemic was firstly detected at the end of December 2019 in China and quickly spread around the world, has been heavy threating global health. Although various COVID-19 vaccines and drugs are approved, developing antiviral drugs and vaccines against COVID-19 virus with high effectiveness is a long-term measure. The SARS-CoV-2 Mpro protein plays important role in the replication and transcription of this viral cycle life, together with three other targets for developing potential drugs treatment for COVID-19 patients. In this research, we investigate the SARS-CoV-2 Mpro binding site bound ligand 11a at physiology temperature (310K) using all-atom simulations, then compare to their X-ray experimental structures (at 273K) for understanding the thermal-dynamic features. We found that conformations of both the Mpro proteins and the ligand are stable during 500ns of the simulation time. In the case of the side chain of residue H41 is the same in the experimental Mpro structure, the cyclohexyl ring of the ligand 11a is bent perpendicularly to adapt to the side chain of H41. Oppositely, the side chain of H41 is turned over and has one Hbond with the catalytic water, the conformations of 11a are more stable during MD simulation. So, not only the catalytic dyad C145 – H41, but also the catalytic water and conformations of H41 play a role in the functions of the Mpro receptor. These results are a root for studying candidate drugs against SARS-CoV-2.

Sorting and Counting Peptide Aggregates

Amol Tagad, Reman Kumar Singh and G. Naresh Patwari

Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076 INDIA

Although protein aggregation is a frequently occurring complex phenomenon in biological processes, methods to analyze aggregation process  are not reliable. Conventional methods such as center-of-mass to center-of-mass (COM−COM) distance, the radius of gyration (Rg), hydrogen bonding (HB), and solvent accessible surface area (SASA) are not reliable due to a variety of reasons. To fill in the lacuna of availability of robust method to analyze peptide and protein aggregation, we developed a new method wherein a binary aggregation matrix (AM) is generated by considering the interpeptide Cα−Cα cutoff distances, which are encoded to 0 and 1 depending on the distance cutoff. The aggregation propensity of six LCD peptides to form dimers, trimers, and tetramers was examined using a newly developed AM methodology. This method allows counting and sorting peptide aggregates using the aggregation matrix wherein the ordered conformations such as parallel/antiparallel or shifted parallel/antiparallel were obtained by analyzing the diagonal/antidiagonal and shifted diagonal/antidiagonal, respectively. Further, in a system consisting of multiple peptide units, the aggregation was decomposed into dimer formation, which allows usage of two-dimensional matrices for a useful and inexpensive method to analyze aggregation propensity in the MD trajectory, which is its unique selling point over all the existing methods.

Combined In Situ XAS and DFT Studies on the Role of Pt in Zeolite-Supported Metal Catalysts for Selective n-Hexane Isomerization

Yuwanda Injongkol¹, Pongtanawat Khemthong^{2, 3}*, and Siriporn Jungsuttiwong¹*

¹ Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand

 ² National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand

³ Center of Excellence in Environmental Catalysis and Adsorption, Thammasat University, Pathum Thani 12120, Thailand

*Corresponding address (E-mail: Will be shown in the poster at the conference)

In this study, we used several in situ, and spectroscopy analyses to investigate the roles of platinum (Pt) in zeolite-supported Pt catalysts for selective n-alkane isomerization. Catalytic testing at 300 and 450  used hydrogen gas as both reactant and carrier. Typically, HY zeolites have proved to be active hydrocarbon cracking catalysts. The particular challenge is to find an effective catalyst, which favors the isomerization of n-alkanes without too much cracking. In this work, adding Pt atoms to HY zeolite provides an enhanced multifunctional catalyst for converting n-alkanes to branched hydrocarbons. To understand the effect of Pt, we further investigated the reaction mechanism of n-hexane isomerization to 2 methylpentane (2MP) and 3-methylpentane (3MP) by DFT simulations, using a cluster of 30T HY zeolite modeled through B3LYP+3D calculations. We found that, at 450 , the isomerization on Pt-HY gives higher cracking products. Decreasing temperature to 300  yielded greater selectivity of branched hydrocarbons. In addition, DFT calculations demonstrate that the 2MP production via route A1 (C3‒C4 bond activation) and a rate-determining step of 0.97 eV proved more thermodynamically and kinetically favorable than the 3MP product. This agrees well with our experimental observations. Consequently, the presence of Pt on the HY zeolite plays an essential role in both C‒C forming and breaking. Finally, the Pt HY zeolite is an efficient catalyst for petroleum production, improving the octane number for catalytic performance and product selectivity by isomerizing straight-chain alkanes to their branched chain isomers.

Keywords: Hexane isomerization; Pt-HY zeolite; In situ CO₂-TPD; DFT; In situ XAS                                          

DFT Study on doped Argyrodite LPSC Solid Electrolyte with Enhanced Ionic Conductivity and Moisture Stability

Yu-Ching Yang, Santhanamoorthi Nachimuthu, and Jyh-Chiang Jiang*

Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan 106335

E-mail：(Will be shown in the poster at the conference)

Lithium-ion batteries (LIBs) have high energy density and long cycle life. However, they still pose a critical safety issue due to their use of flammable organic liquid electrolytes. Ceramic electrolytes can improve safety over liquid electrolytes, and solid-state sulfide electrolytes, in particular have taken center stage due to comparable ionic conductivity to commercial organic liquid electrolytes. For instance, the lithium ionic conductivity of argyrodite Li₆PS₅Cl (LPSC) is around 0.34 mS/cm, ^[1] while LISICON-like Li₁₀GeP₂S₁₂ is around 12 mS/cm. ^[2] However, they have some drawbacks, such as the production of a toxic gas H₂S ^[3] and as a result a decrease in ionic conductivity. Hence, developing LPSC-based electrolytes with high ionic conductivity and outstanding chemical stability is essential. This study aimed to enhance the ionic conductivity and moisture stability of LPSC. Herein, we considered doping of different elements on both Li and Cl sites of the LPSC and investigated their moisture stability and lithium ionic diffusivity using density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD) calculations. We have used the bonding energies to explore the moisture stability and found that Ti, La, and Y atom substitutions improved stability. The amounts of Li and Cl atoms in LPSC affect the overall ionic conductivity, with La and Y atoms substitutions at the Cl site and Ti substitutions at the Li site having the highest ionic conductivities. This theoretical study sheds new light on developing novel Solid-State electrolytes for future All-solid-state batteries.

References

Relativistic Density Functional Theory Calculations of the Concentration Dependence of ²⁰⁷Pb NMR in Lead Nitrate Aqueous Solution

Yoshimitsu Asakura¹, Daisuke Kuwahara¹, Naoya Nakagawa¹

¹Graduate School of Informatics and Engineering, the University of Electro-Communications, 1-5-1 Chofugaoka, Chofu City, Tokyo

The chemical shifts in nuclear magnetic resonance spectroscopy for metal ions in aqueous solutions of inorganic salts often change with the solution concentration. These changes are referred to herein as dilution–concentration (dc) shifts. For main-group elements, the dc shifts generally increase with increasing atomic number. We calculated the dc shifts for various metal and nonmetal ions in aqueous nitrate solutions of elements in periods 5 and 6 by the density functional theory method based on the spin–orbit zeroth-order regular approximation Hamiltonian. The calculation results revealed that the dc shifts of metal and nonmetal ions with the outermost shell electron configuration of 6s² are primarily determined by the changes in the spin–orbit interaction terms of the shielding constants. Furthermore, the spin densities of the Pb(II) ions in aqueous lead nitrate solutions under an external magnetic field were calculated using the matrix/modified Dirac–Kohn–Sham Hamiltonian, which confirmed the presence of Fermi contacts between the spin-polarized electrons and the lead nucleus. When a suitable isovalue for visualizing the spin density was set, there was no Fermi contact in the infinite dilution state, whereas the upward-spin electron was in Fermi contact with the lead nucleus in the saturation state. There have been few reports of the NMR chemical shifts of heavy atoms in terms of Fermi contacts with relativistically spin-polarized electrons. We succeeded in clarifying how the dc shifts occur on the hydrated ions of heavy atoms by visualizing the Fermi contact of spin-polarized electrons with heavy-metal nuclei.

Realization of Electrochromic Materials by Electronic Structure Informatics – Optimization of Hue and Oxidation Potential

Daisuke Goto^{1, 2}, Hirotoshi Mori¹

E-mail: (Will be shown in the real poster)

1: Graduate School of Science and Engineering, Department of Applied Chemistry, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan

2: Research and Development Group, Ricoh Company, Ltd., 2-7-1 Izumi, Ebina, 243-0437, Japan

Materials informatics (MI) is a powerful tool for discovering new materials. One of the crucial challenges for future MI is to sufficiently reduce costs and accelerate the creation of feature variables from scientific and industrial standpoints. However, the current MI forces us to perform time-consuming high-precision electronic structure calculations or experiments.

Electrochromic (EC) materials have also been considered a good target for the extensive application of MI for their development. EC materials are already employed in practical applications such as residential and aircraft windows, automotive anti-glare mirrors, color signages, displays, filters, sunglasses that can switch instantly between colored and uncolored states depending on whether a person is indoors or outdoors, and medical lenses that become transparent when uncolored. Electrochromism occurs when a reversible color change occurs due to the radical species produced via electrochemical reduction-oxidation. In open-shell systems with singly occupied molecular orbitals (SOMOs), electronic transitions occur with a highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gap smaller than the average; this principle drives the color change in EC materials.     Here we propose employing the semi-empirical molecular orbital method to accelerate further material developments with an example of pure process magenta and yellow with well-tuned oxidation potentials EC materials. Applying “the ultra-high-speed search” method to 1.2 million molecules and subsequently targeted syntheses, ordinarily pure uncolored process magenta (hue angle = 348^o) and yellow (hue angle = 92 ^o and E_ox = 0.16V) EC materials were realized with 100 times development speed faster than conventional methods. Due to the universality of the electronic structure theory, this method would open a new dimension for EC and any other materials design.

Symmetry-Breaking Mechanisms of the SARS-CoV-2 Main Protease

Hong Ha Nguyen, James Tufts, David D. L. Minh*

*Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA

The coronavirus 3C-like main protease (MPro) – an essential target of COVID-19 drugs – has approximately half of the activity and an asymmetric dimer structure at certain pH, suggesting that only one catalytic site is active at a time. However, the mechanism that leads to this asymmetry is unknown. Prior to the COVID-19 pandemic, previous modeling studies that investigated the asymmetry of MPro were only about 148 ns long. In the last few years, several groups have produced much longer simulations of MPro and released them to the public for detailed analysis. Here, we analyze a 100-microsecond simulation produced by D.E. Shaw Research (DESRES) and a series of trajectories with an aggregate time of 2.9-millisecond produced by Folding@Home to investigate the mechanism by which asymmetry emerges. The D.E. Shaw simulation reveals a domino chain initiated by breaking the salt-bridge Arg4*-Glu290 that propagates to alternate conformations of the catalytic sites. Markov state model analysis of the Folding@Home simulations reveals that transitions between active and inactive conformations in two subunits are reversible and that one subunit is preferentially in an active conformation. 

Structure and Dynamics of the Isozymes II and IX of Human Carbonic Anhydrase

Divya Rai, Satyajit Khatua and Srabani Taraphder

Department of Chemistry, Indian Institute of Technology Kharagpur 721302, India

Email and Mobile: (Will be shown in the real poster)

1. Kazokaite, J.; Niemans, R.; Dudutiene, V.; et al. Oncotarget, 9 (2018) 26800–26816.
2. Fisher, S. Z.; Maupin, C. M.; Budayova-Spano, M.; et al. Biochemistry, 46 (2007) 2930–2937.

Time-dependent Hartree-Fock-Bogoliubov method: An alternative excited-state methodology including static electron correlation

Masatsugu Nishida¹, Tomoko Akama², Masato Kobayashi^2,3, Tetsuya Taketsugu^2,3

¹Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 10 Nishi 8, Kita-ku, 060-0810 Sapporo, Hokkaido, Japan

²WPI-ICReDD, Hokkaido University, Kita 21 Nishi 10, Kita-ku,001-0021, Sapporo, Hokkaido, Japan

³Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, 060-0810, Sapporo, Hokkaido, Japan

An accurate evaluation of excitation energies for molecules is challenging because it requires the description of both ground and excited states having different correlation energies with similar accuracy. If the ground state of a target system has large static correlation energy, a multi-configurational reference state is required for the qualitative description. The most popular method for such a system is the CASSCF method. However, the scope of its application is limited because its computational cost increases with the size of the active space. We focused on the Hartree–Fock–Bogoliubov (HFB) method.^1-3 This method treats the interaction between electrons as quasiparticles and thus can handle static electron correlations without losing the simplicity of the independent particle approximation.

In this study, we formulate the Real-Time Time-Dependent (RT-TD) HFB method for molecular systems as a simple method for calculating excited states that can consider static electron correlations. The RT-TDHFB method has the disadvantage that the HFB wave function is not necessarily an eigenfunction of the number operator; therefore, the electron number changes during time evolution. To avoid this, we focus on applying the canonical basis (Cb)-TDHFB method⁴ developed in nuclear physics.

We show the Cb-TDHFB calculation result for the H₂ molecule (r = 2.6 Å). Fig. 1 shows the HF canonical MOs with their HFB occupation, absorption spectrum, and contribution of transitions between MOs. Excitations occur even from orbitals that are unoccupied in the HF ground state. It suggests that the Cb-TDHFB method can calculate excited states incorporating static correlations.

References

[1] J.-P. Blaizot and G. Ripka, Quantum Theory of Finite Systems, (MIT Press, Cambridge, 1986).

[2] V.N. Staroverov and G.E. Scuseria, J. Chem. Phys. 117, 11107 (2002).

[3] M. Kobayashi, J. Chem. Phys. 140, 084115 (2014).

[4] S. Ebata et al., Phys. Rev. C. 82, 034306 (2010).

[5] M. Nishida, T. Akama, M. Kobayashi, and T. Taketsugu, submitted.

Quantum chemical calculation of excited states using variational quantum deflation method and applications to photocatalyst modeling

Soichi Shirai¹, Takahiro Horiba¹, and Hirotoshi Hirai¹

¹ Toyota Central R&D Labs., Inc., Nagakute, Aichi, Japan

The possibility of performing quantum chemical calculations using quantum computers has attracted much interest of scientists. Variational quantum deflation (VQD) is a quantum-classical hybrid algorithm for the calculation of excited states with noisy intermediate-scale quantum devices. In the VQD framework, the excited states are sequentially calculated through minimizing the cost function. The weighting coefficients determine the magnitude of the penalty terms. Although the weighting coefficients should be appropriately chosen for desired calculations, they have been empirically estimated. In this study, the VQD calculations of the core-excited and core-ionized states for common molecules were examined focusing on the effects of the penalty terms of the cost function [1]. They were conducted using the quantum circuit simulator with a classical computer. Adopting a simplified procedure for estimating the weighting coefficients allowed these core-level states to be successfully calculated (Table 1). The relationship between the weighting coefficients and the resulting ansatz states was systematically examined through calculations of the O 1s core-ionized state for a water molecule. The application of this technique to functional materials was demonstrated by calculating the core-level states for titanium dioxide (TiO₂) and nitrogen-doped TiO₂ models. The results were consistent with experimental findings, indicating that VQD calculations employing an appropriate cost function can be applied to the analysis of functional materials in conjunction with an experimental approach.

Table 1. Weighting coefficients in the cost function for the VQD calculations: overlap weights (β), s2 number weights (w₁), sz number weights (w₂) and particle number weights (w₃); and core excitation/ionization energies calculated using orbital-optimized-VQD with cc-pVQZ. Available experimental values are also shown. Values in parentheses are deviations from the experimental values.

[1] Shirai, S.; Horiba, T.; Hirai, H., ACS Omega 2022, 7 (12), 10840−10853.

Chlorpyrifos Insecticide Oxidation by Hydroxyl Radicals in the Environment: Mechanistic, Kinetics, and Ecotoxicity Evaluation

Dinh Hieu Truong,^1,2,* Duy Quang Dao,^1,2 Sonia Taamalli,³ Florent Louis,³ Thi Chinh Ngo, ^1,2 Thi Le Anh Nguyen, ^1,2 Hisham K. Al Rawas,³ Nissrin Alharzali,³ Abderrahman El Bakali,³ Marc Ribaucour,³ Ivan Černuśák⁴

¹ Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam

² Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Viet Nam

³ Université de Lille, CNRS, UMR 8522 – PC2A – PhysicoChimie des Processus de Combustion et de l’Atmosphère, 590000 Lille, France

⁴ Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia

Chlorpyrifos (CPF) is a white-like-solid insecticide used on crops, animals, and buildings in different environments. Long-term exposure to this pesticide has adverse effects on human health, including neurological effects, persistent developmental disorders, and autoimmune disorders, and therefore, its use has been banned in many parts of the world. In this research, the initial oxidation of CPF by hydroxyl radicals (HO^Ÿ) was theoretically investigated in both gas and aqueous phases using density functional theory (DFT) at the M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G(d) level of theory. Radical adduct formation (RAF), single electron transfer (SET), and different abstraction reactions, including hydrogen-, chlorine-, and sulfur-abstraction, were systematically studied. The results showed that the H-abstraction reactions, which occur at H-position belonging to ethyl functional groups, are the most crucial in the oxidizing process with the low Gibbs free energies of activation and high rate constants. The main products of H-abstraction reactions are found in the reactions that occur in methylene functional groups with the branching ratios being 55.44 and 29.43% in the gas phase, and 31.84 and 29.07% in the aqueous one. The overall rates at 298.15 K are equal to 1.25 × 10¹⁰ and 4.76 × 10⁸ M^-1s^-1 in the gas and aqueous phase, respectively. Overall, CPF has a high potential to be oxidized by HO^Ÿ radicals at multiple sites with high rates. The ecotoxicity estimation of CPF and its essential degraded products to aquatic organisms suggests that they are harmful or toxic substances.

* Corresponding authors: (Will be shown in the real poster) (T.D.H)

Parallelization for Valence Bond Calculation

Fuming Ying, Wei Wu

College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China

Various parallelization techniques are applied in modern computational chemistry programs, where Message passing interface (MPI) and OpenMP are the widely used. OpenMP is thread-based and lightweight but limited in a single node while MPI is process-based and available for computations with multiple nodes. By combining MPI and OpenMP, a quantum chemistry programs would benefit from the advantages of both sides, e.g. available for use of multiple nodes and with lightweight parallelization within each node. Recently, such hybrid parallelization is implemented  in our XMVB program, which is an ab initio valence bond program. Test calculations validate the efficient acceleration of  strategy. In some cases, the speedup is close to linear.

Theoretical insights into the radical scavenging activity of natural feruloylmonotropeins

Nguyen Quang Trung,^1,2* Quan V. Vo³

¹The University of Danang ‒ University of Science and Education, Da Nang 550000, Vietnam.

²Quality assurance and Testing center 2, Da Nang 550000, Vietnam.

³The University of Danang ‒ University of Technology and Education, Danang 550000, Vietnam.

*Corresponding authors: (Will be shown in the real poster)

Paederia scandens (Lour.) is one of popular plants which is used as traditional medicine in Vietnam, China, India, and Japan for the treatment of various diseases, such as toothache, chest pains, piles, inflammation of the spleen… Several studies on the constitution of its extracts along with their numerous biological activities, including anti‒nociceptive, antiviral, antitumor, and anti‒inflammatory. Two iridoid glucosides including 6’‒O‒E‒feruloylmonotropein (6‒FMT) and 10’‒O‒E‒feruloylmonotropein (10‒FMT) which were isolated from the MeOH extract of P. scandens, were predicted to be engaged in their antioxidant activity. In this study, the hydroperoxyl scavenging activity of 6‒FMT and 10‒FMT was examined by using density functional theory. These FMT are supposed to be a weak antioxidant in non‒polar environments, whereas an excellent HOO^• scavenging in the polar environment (pH=7.4) with k_overall = 3.66×10⁷ M^‒1 s^‒1 and 9.45×10⁶ M^‒1 s^‒1, respectively, better than that of the typical antioxidant such as Trolox and nearly equivalent to ascorbic acid and resveratrol. Their hydroperoxyl scavenging activity was concentrated by the di‒anion form of FMT in water at physiological pH following the single electron transfer mechanism.

Keywords: feruloylmonotropeins, DFT study, antiradical activity, kinetic study

New Insights into the interfacial Lithium-ion diffusion in the argyrodite Li₆PS₅Cl Solid electrolyte- Effects of Mg-compound as a buffer layer

 Li-Han Wang, Santhanamoorthi Nachimuthu, and Jyh-Chiang Jiang*

Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan 106335

Increasing the safety of conventional lithium-ion batteries (LIBs) has drawn more attention in recent years due to the increase in demand for electronic vehicles (EVs). All-solid-state lithium batteries (ASSLBs) have been considered to be safer and more reliable due to their nonflammable inorganic solid electrolytes. However, the ASSBs also faced the practical challenges of low ionic conductivity and inferior interfacial stability between electrodes and solid electrolytes (SEs). It has been reported that modifying the surface by adding intermediate layers between the SEs and the anode surface is an effective approach to ameliorating the interface stability. Thus, in this study, we considered MgS and MgF₂ as buffer layers to pre-react with the lithium anode and studied the SEI formation using density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD) calculations. Snapshots of AIMD simulations reveal the formation of SEI components such as Li₂S and LiF and Mg-Li alloy. Furthermore, we explored the interfacial properties of Li₂S/Li₆PS₅Cl and LiF/Li₆PS₅Cl interface systems, and nudged elastic band (NEB) method is used to determine the possible Li-ion diffusion pathways within the SE and at the interface systems. The energy barriers for Li-ion diffusion are calculated, and we find that the Li-diffusion along the interface is the rate-determining step. Our results also show that Mg-Li alloys can cause localized lithium deposition in the early stage of the reaction. This work on the atomic scale will offer a useful perspective for improving the ionic conductivity of ASSBs.

References

[1] Guo-Ran Li, Xue-Ping Gao, et al. Lithium–Magnesium Alloy as a Stable Anode for Lithium–Sulfur Battery. Advanced Functional Materials, 2019, 29: 1808756

[2] M. Helen, Maximilian Fichtner. Magnesium Sulphide as Anode Material for Lithium-Ion Batteries. Electrochimica Acta, 2015,169: 180-185

[3] Wei Chen, Qinfen Gu, Dalin Sun, and Xuebin Yu, et al. Controlled-Size Hollow Magnesium Sulfide Nanocrystals Anchored on Graphene for Advanced Lithium Storage. ACS Nano, 2018, 12: 12741-12750

[4] Hongyu Zhang, Shunlong Ju, et al. Dendrite-Free Li-Metal Anode Enabled by Dendritic Structure. Advanced Functional Materials, 2021, 31: 2009712

­­THEORETICAL STUDY OF LITHIUM ADSORPTION IN SILICON NANOSTRUCTURES FOR APPLICATION AS ANODES IN LITHIUM-ION BATTERIES

Fadjar Mulya, Vudhichai Parasuk^*

Center of Excellence in Computational Chemistry (CECC), Department of Chemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand

Corresponding author: (Will be shown in the real poster)

ABSTRACT

Structural and electronic properties and lithium adsorptions of hydrogenated silicon nanostructures were studied using density functional theory (DFT) with M06-2X hybrid functional and 6-31G+(d) basis set. Ten sizes of silicon quantum dots (SiQDs) used as a model of nanostructures (Si₁₀H₁₆, Si₁₄H₂₀, Si₁₈H₂₄, Si₂₂H₂₈, Si₂₆H₃₀, Si₃₀H₃₄, Si₃₅H₃₆, Si₃₉H₄₀, Si₄₄H₄₂, and Si₄₈H₄₆) and three adsorption sites (tetrahedral inner (Td_inner), tetrahedral surface (Td_surface), and hexagonal (Hex)) were investigated. Effects of cluster size and adsorption sites of SiQDs on binding energy, molecular volume, and energy gap were monitored. In addition, the two and three lithium atoms adsorptions on SiQDs were addressed. Binding energies per atom of the double adsorptions are 0.60 – 0.65 eV, while those of the triple adsorptions are 0.72 – 1.12 eV. Thus, the adsorption complex (adplex) becomes more stable as more Li atoms are adsorbed on SiQDs. The adsorption behavior is in good agreement with previous theoretical and experimental studies. The change of molecular volume had been achieved lower than 0.5% both single and multiple adsorptions. Increasing Si number in SiQDs can reduce the change of molecular volume. Furthermore, the change energy gap of SiQDs both single and multiple lithium adsorptions are in the range of 44.5 and 67.7 % which means the adsorption of lithium on the SiQDs significantly affected to the electronic properties. Therefore, SiQDs might be suitable to be used as anode materials of lithium-ion rechargeable battery with high-energy-density and long cycle-life.

Keywords: DFT; Lithium-ion battery; Adsorption; Molecular Volume; Electronic properties.

Prioritizing the best molecules in drug discovery

Boyli Ghosh, Jennifer Brookes, Mark D Mackey

Cresset, Cambridgeshire, UK

Free Energy Perturbation (FEP) methods make important contributions to drug discovery projects by reliably predicting the relative binding affinity of molecules which can then be used to help prioritize synthesis and testing. Alchemical free-energy calculations compute the relative binding free energy of closely-related compounds by gradually morphing them through a number of artificial (‘alchemical’) intermediate states controlled by a λ switching function.

One barrier to using FEP can be the time constraints and the difficulties in setting up the calculation. In this poster, we will show how Flare™ FEP can be used to efficiently create a perturbation network for a congeneric series of ligands which automatically includes intermediate ligands when needed, and adaptively assigning the number of λ windows for each link in the network. This allows for the accurate calculation of the binding affinity for the ligand series against the protein target of interest.

A DFT study of the molecular and electronic structures
of cis‑dioxidomolybdenum (VI) complex of 8‑hydroxyquinoline and 4‑benzoyl‑3‑methyl‑1‑phenyl‑2‑pyrazolin‑5‑one with water

Huu Tho Nguyen,¹ Thanh Q. Bui,² Pham Vu Nhat,³  Do Thi Phuong Lan,⁴ Nguyen Thi Ai Nhung^2,*

¹Faculty of Natural Sciences Education, Sai Gon University, Ho Chi Minh City 700000, Vietnam

²Department of Chemistry, University of Sciences, Hue Univerisity, Hue City 530000, Vietnam

³Department of Chemistry, Can Tho University, Can Tho 94000, Vietnam

⁴Tran Quoc Toan secondary school, Bao Loc City, Lam Dong Province 670000, Vietnam

Density functional theory approaches are employed to elucidate the structural features and electronic properties of cis-dioxidomolybdenum(VI) complexes with water, 8-hydroxyquinoline and 4-benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one. Geometrical parameters are optimized using B3PW91, B3LYP functionals in conjunction with def2-TZVP, LanL2DZ and 6-311 + G basis sets. Computed results show that the complex energetically prefers a pseudo-pentagonal bipyramidal shape in the ground state. The nature of intramolecular interactions between Mo(VI) and ligands is evaluated by analyzing the natural bond orbital and quantum theory of atoms in molecules. The Mo–OH₂ interaction is rather weak with an average distance of 2.445 Å and a very low Mayer bond order of 0.235. The vibrational signatures and vertical electronic transitions of some excitations are examined and compared to available experimental data. The most favorable sites for electrophilic, nucleophilic attack or protonation are also identified using the noncovalent interaction method.

Keywords: DFT, B3PW91, Molybdenum, 8-Hydroxyquinoline, 4-Benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one

Implementation of picture-change corrected density functional theory based on infinite-order two-component relativistic method  into GAMESS program

Chinami Takashima,¹ Junji Seino,^1,2 Hiromi Nakai^1,2

¹Department of Chemistry and Biochemistry, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan

²Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan

Relativistic effect is important in quantum chemical calculations of heavy-element compounds. Our group developed accurate and efficient methods based on the infinite-order two-component (IOTC) method [1], which is one of the most accurate two-component (2c) relativistic method. The local unitary transformation (LUT) [2,3] achieved linear-scaling relativistic transformations of one- and two-electron operators in the IOTC method. We also developed the picture-change correction (PCC) for density functional theory (DFT), which performed relativistic transformation to density operator [4]. The PCC is inevitable for 2c DFT as well as one- and two-electron operators. In 2016, the one-electron LUT scheme for energy and analytical energy gradient calculations were implemented into the public version of GAMESS program [5]. Recently, we implemented the LUT-IOTC method for two-electron operator and PCC for 2c DFT into GAMESS (2022 R1) [6]. In this presentation, we will present the overview of these methods and performances of the program in terms of accuracy and efficiency.

[1] M. Barysz and A. J. Sadlej, J. Chem. Phys. 116, 2696 (2002).

[2] J. Seino and H. Nakai, J. Chem. Phys. 136, 244102 (2012).

[3] J. Seino and H. Nakai, J. Chem. Phys. 137, 144101 (2012).

[4] Y. Ikabata, T. Oyama, M. Hayami, J. Seino, and H. Nakai, J. Chem. Phys. 150, 164104 (2019).

[5] Y. Nakajima, J. Seino, M. W. Schmidt, and H. Nakai, J. Comput. Chem. Jpn. 15, 68 (2016).

[6] C. Takashima, J. Seino, and H. Nakai, J. Comput. Chem. Jpn. 19, 128 (2020).

DFT – Proposed Mechanism of Friedel–Crafts Acylation of Indole Using Metal Triflate Catalysts

 Kieu Van Thuy Nguyen¹, Nguyen Nguyen Pham Tran^1,2

 ¹Computational Chemistry Lab, VNUHCM–University of Science, Ho Chi Minh City 700000, Vietnam

 ²Institute for Computational Science and Technology, Ho Chi Minh City 700000, Vietnam

Email: (Will be shown in the real poster)

Friedel–Crafts acylation of indole with propionic anhydride base on the metal triflate catalyst is a fast and green method to synthesize 3-acylindole without the protection of the NH position [1][2]. However, the role and effect of metal triflate catalyst for regioselective substitution of acyl group on the indole remain a question. This study was undertaken to elucidate the reaction mechanisms of regioselective acylation of indole in the 3-position for copper and some rare-earth metal triflates catalysts. All calculations were performed at the B3LYP/6-31+G(d,p) level of theory. The regioselectivity reactions in the non-catalytic and catalytic conditions were carried out. Specifically, in catalytic conditions, the symmetries of triflate ligands in the transition state complex were counted and it seems affected the rate of the reaction. The energy profiles showed that the standard Gibbs energy of the activated transition state of Y(OTf)₃ catalyst with symmetric triflate ligands is the most favorable (7.34 kcal/mol). Our calculated results are consistent with the experimental work [3]. 

Keywords: catalytic mechanism, Friedel–Crafts acylation, metal triflate catalyst, indole.

References

[1] J. Ross and J. Xiao, Green Chem 2002, 4, (2), 129–133

[2] J. Wu, D. Wang, F. Wu, and B. Wan, J. Org. Chem 2013, 78, (11), 5611–5617.

[3] Tran PH, Tran HN, Hansen PE, Do MH, and Le TN, Molecules 2015, 20, 19605-19619.

Methane Oxidation to Methanol catalyzed by Copper Oxide clusters supported in MIL-53(Al) – A DFT study

Chun-Wei Yeh, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang*

Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei, Taiwan

Email:(Will be shown in the real poster)

As the global environment changes, reducing greenhouse gases or converting them into fuels and chemicals with added value is essential for the environment. Methane oxidation to methanol is of particular interest because it represents a significant challenge in catalysis due to the difficulty in activating strong C–H bond. Metal-organic frameworks (MOFs) have recently received much attention, particularly as catalysts, due to their high porosity, thermal stability, and even tunable metal sites or linker structures. In addition, the enzyme, particulate methane monooxygenase (pMMO), ^[1] has been reported to convert methane into methanol by copper oxide cluster ^[2] of their active sites. Inspired by these, in this study, we considered the well-known MIL-53(Al), a kind of MOF, as support for copper oxide clusters and explored their reactivity towards methane oxidation by Density Functional Theory (DFT) calculations. First, we investigate the formation of Cu₂O₂ clusters on MIL-53(Al) by oxidizing Cu₂ with O₂ or N₂O, in which O₂ has the lowest energy barrier of 0.13 eV. The barrier for initial C-H bond activation on Cu₂O₂/MIL-53(Al) is 0.70 eV, which is the rate-determining step in the overall methane conversion to methanol reactions. Our results suggest that the conversion of methane to methanol over Cu₂O₂/MIL-53(Al) is more favorable than the conversion of methane to formaldehyde. The desorption energy of the methanol over the Cu₂O₂/MIL-53(Al) is 0.71eV. Furthermore, we considered the different oxidants and proposed the reaction pathways for regenerating the active copper oxide clusters to explore the prospect of catalyst reusability.

References:

[1]Yoshizawa K, Shiota Y. Conversion of methane to methanol at the mononuclear and dinuclear copper sites of particulate methane monooxygenase (pMMO): a DFT and QM/MM study. JACS. 2006;128(30):9873-81.

[2]Li G, Vassilev P, Sanchez-Sanchez M, Lercher JA, Hensen EJ, Pidko EA. Stability and reactivity of copper oxo-clusters in ZSM-5 zeolite for selective methane oxidation to methanol. J Catal. 2016;338:305-12.

Application of the Most Stable Reaction Pathway Search (MSRP) method to the synthesis route of flutolanil

Yujirou Matsuo¹, Toru Yamaguchi¹, Eri Maeyama Kawahara², Ayako Sakata¹, Kenji Hori^1,2

¹ Division of Computational Chemistry, Transition State Technology Co. Ltd., 2-16-1 Tokiwadai, Ube, Yamaguchi 755-8611, Japan

² Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube, Yamaguchi 755-8611, Japan

The Transition State Database (TSDB) is a cloud-based database system that stores results of quantum mechanical calculations for chemical reactions (structures such as transition states (TS), reactants and products, activation free energies, reaction free energies, etc.). The TSDB currently has more than 2000 TS structures which are used to locate other TS structures. All the TS structures have special 3D areas, called TS Motifs, and those belonging to same name reactions are similar to each other regardless of sizes of molecules. We can use the TS motifs to easily and rapidly locate complicated TS structure from a simple one. Although there are many TS conformations for molecules with many substituents, this method is unlikely to produce the most stable TS conformation. It is because optimized TS conformation is essentially the same as that of an initial one created from the TS motif method. Therefore, it is essential to search for the most stable conformation of TS involved in the reaction. In this study, we will present a method to search reaction pathways with this property (the Most Stable Reaction Pathway, MSRP) and results applied to a condensation reaction in the synthetic route of Flutolanil, an acid amide fungicide.

Insight into the excited-state intramolecular proton transfer of Paratrimerin C – A TD-DFT study

Thi Le Anh Nguyen,^1,2 Dinh Hieu Truong,^1,2 Thi Chinh Ngo,^1,2 Duy Quang Dao^1,2

¹Institute of Research and Development, Duy Tan University, Da Nang, 550000, Viet Nam

²Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam

Email: (Will be shown in the real poster)

Paratrimerin C is a natural acridone antioxidant that is also potent as an anti-UV agent. The photophysical process of Paratrimerin C, including the absorption and emission and the excited state intramolecular proton transfer (ESIPT) mechanism, is studied herein with time-dependent density functional theory. The solvent effect on ESIPT is analyzed with the Integral Equation Formalism Polarization Continuum Model solvent for polar and non-polar solvents. Adding up to three molecules of water and benzene around the Paratrimerin C was investigated for an explicit approach. The normal and tautomer forms of the Paratrimerin C at the ground- and excited-state structures are studied at the M06-2X/6-311++G(d,p) level of theory. The excitation energy of the complexes is calculated using TD-DFT at the same level of theory, showing the UV-Vis absorption in 450-200 nm. The potential energy curves along the reaction coordinates indicate that the ESIPT is a barrier-less reaction, and the variation of O_d-O_a distance in the excited state shows significant molecular structure deformation along the proton transfer process following the normal-to-tautomerism pathway. The results suggest using other acridone derivatives as efficient and tunable bioactive fluorescence molecules.[1]

References:

[1]. Nguyen, T. L. A., Truong, D. H., Ngo, T. C., Dao, D. Q., Int. J. Quantum Chem. 2022, e27032. https://doi.org/10.1002/qua.27032

Metastable XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn) Compounds with Ng-C/F and Ng-N Bonds and Possible Isomerization therein

Gourhari Jana¹, Ranita Pal², and Pratim Kumar Chattaraj^*,3

¹ Department of Chemical Engineering and Materials Science, Michigan State University, East Landing MI, 48823, USA.

²Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, India

³Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India

While noble gas (Ng) compounds with either Ng-C or Ng-N bonds are reported in the literature, those containing both are rare. We have predicted a set of compounds with C-Ng-N bonding unit where its presence produces reasonably stable Ng-inserted compounds. The general bonding in Ng-inserted compounds consists of covalent bond on one side of Ng, and ionic on the other side. However, in the present case, Ng forms partial covalent bonds with the elements located on either side. Moreover, our chosen parent compound, HCCNSi was reported to be found spectroscopically. We have investigated how the presence of Ng improves the possibility of detection of the HCCSiN isomer. The F analogue of the aforementioned Ng-insertion compound is also studied to understand the influence of the presence of an electronegative element on its structure and bonding. XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn) compounds are thermochemically stable concerning all possible dissociation channels except two two-body Ng-release processes which are kinetically protected by substantial activation barriers. A detailed bonding study reveals that both the Ng-X and Ng-N bonds are partially covalent. An ab-initio molecular dynamics simulation reveals the thermodynamic and kinetic stability of the studied compounds.

Insights into Titan’s atmospheric chemistry of HCN and ammonia

Sunanda Panda¹, Anoop Ayyappan¹

¹Department of Chemistry, IIT Kharagpur, 721302

E-mail: (Will be shown in the real poster)

Biomarkers like HCN are observed in the stratosphere  of Titan (Saturn’s moon) in the form of a haze layer^[1]. As it resembles early earth atmosphere^[2], in this work we have done unbiased chemical space search of HCN and ammonia.  Artificial force induced automated search for reaction of  HCN with NH₃ using PyAR (Python based aggregator and reactor), followed by transition state search of the  reaction paths have been performed. Thereafter the kinetic study was done to get the probable products. The reactions here resulted in compounds containing imine, nitrile, and amine functional groups, and some N-heterocycles. Higher population of polyamines, polyimines and  N-heterocyclic compounds obtained here may aid the formation of self-replicating RNA precursors^[3,4]  and thus can lead to life on Titan.                                                                                           

[1] Wilson, E.H. and Atreya, S.K., Chemical sources of haze formation in Titan’s atmosphere. Planetary and Space Science, 2003,  51(14-15), 1017-1033.

[2] Trainer, M.G.,  Pavlov, A.A.., DeWitt, H.L., Jimenez, J.L., McKay, C.P.,  Toon, O.B., and  Tolbert, M.A., Proceedings of the National Academy of Sciences, 2006, 103(48), 18035-18042.

[3] R. A., Sanchez, J. P., Ferbis, L. E. and Orgel.,L., Journal of molecular biology, 1967, 30(2), 223–253.

[4] Ferris, J. P.; Orgel, L., An unusual photochemical rearrangement in the synthesis of adenine from hydrogen cyanide1. Journal of the American Chemical Society 1966, 88, 1074–1074.

Density functional theory study of secondary metal cation effects on nickel-alkali catalysts for ethylene polymerization

Pavee Apilardmongkol¹, Manussada Ratanasak², Jun-ya Hasegawa², and Vudhichai Parasuk¹*

¹ Center of Excellence in Computational Chemistry,
Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand

Email: (Will be shown in the real poster)

 ² Institute for Catalysis, Hokkaido University,
Kita21, Nishi10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan

Email: (Will be shown in the real poster)

*Corresponding address ((Will be shown in the real poster))

The reaction mechanism of heterobimetallic nickel phenoxyphosphine polyethylene glycol (Ni-PEG) with alkali metal (M = Li, Na, K, and Cs) catalysts for ethylene polymerization were investigated using the Density Functional Theory (DFT) calculations with ωB97XD/6-31G(d) and effective core potential (ECP)/SDD for heavy metals. Potential energy profiles show that the isomerization step is a necessary step for this reaction. The activation energies of Ni-PEG systems with different alkali metals in the favorable pathway were calculated. The energy difference between the reactant and transition states for polymerization shows the following trend, Ni-PEG(Li) < Ni-PEG(Na) < Ni-PEG(K) < Ni-PEG(Cs), which corresponds to experimentally observed activities. Moreover, the roles of secondary metals in Ni-PEG catalysts in terms of steric, electronic, electrostatic effects were elucidated. The DFT results suggested that the cooperative metal-metal/metal-ligand interactions in the catalyst should be strong and the catalyst should have a less positive charge on the secondary metal cation of the PEG group to enhance the polymerization rate. Finally, the effect of catalyst structure on experimental activity was investigated to find key factors for designing new catalysts, and the Ni-PEG catalysts with Be, Mg, Co, and Zn as the secondary metals were suggested.

λ-DFVB(U): A hybrid density functional valence bond method based on unpaired electron density

Peikun Zheng, Zixi Gan, Chen Zhou*, Peifeng Su, Wei Wu*

College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China

Here we introduce a hybrid density functional valence bond method based on unpaired electron density, called λ-DFVB(U), which is a combination of the valence bond self-consistent field (VBSCF) method and Kohn–Sham density functional theory. In λ-DFVB(U), the double-counting error of electron correlation is mitigated by a linear decomposition of the electron-electron interaction using a parameter λ, which is a function of an index based on the number of effectively unpaired electrons. In addition, λ-DFVB(U) is based on the approximation that correlation functionals in KS-DFT only cover dynamic correlation and exchange functionals mimic some amount of static correlation. Furthermore, effective spin densities constructed from unpaired density are used to address the symmetry dilemma problem in λ-DFVB(U). The method is applied to test calculations of atomization energies, atomic excitation energies, and reaction barriers. It is shown that the accuracy of λ-DFVB(U) is comparable to that of CASPT2, while its computational cost is approximately the same as VBSCF.

Complexes of carbon dioxide with methanol and its monohalogen-substituted: beyond the tetrel bond

Cam-Tu Phan Dang,^1,2,* Nguyen Tien Trung³

¹Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam

²Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam

³Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon university, Viet Nam

Applicability domain for machine-learned electron correlation model

Ryo Fujisawa,¹ Mikito Fujinami,¹ Junji Seino,^1,2 Yasuhiro Ikabata,^3,4 Hiromi Nakai^*1,2

¹Department of Chemistry and Biochemistry, Waseda University, Tokyo, Japan. ²Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan. ³Information and media center, Toyohashi University of Technology, Aichi, Japan. ⁴Department of Computer Science and Engineering, Toyohashi University of Technology, Aichi, Japan.

*Email: (Will be shown in the real poster)

Accurate calculations of electron correlation energies are essential tasks in quantum chemistry, which encouraged to develop various correlation models such as perturbation theory and coupled-cluster (CC) method as well as density functional theory (DFT). In the trend of incorporating artificial intelligence (AI) technique into theoretical chemistry, we proposed a machine-learned electron correlation (ML-EC) model, [1,2] which adopted electron densities and their derivatives at the HF/DZ level as descriptors and learns correlation energy densities at the CCSD(T)/CBS level as objective variables. Numerical demonstrations clarified that the ML-EC model evaluated more accurate reaction energies than those of DFT calculations. However, the validity of the ML-EC model might depend on learned and applied systems, namely, training and test data. In this study, we adopted an applicability domain (AD) technique, namely, Jackknife aggregating (Jagging) method, [3] for the diagnostic of the ML-EC model. Numerical applications of the Jagging method clarified the reasonable AD, which lead to reasonably improve the accuracy of the ML-EC model by adding data points outside of the AD.

[1] T. Nudejima, Y. Ikabata, J. Seino, T. Yoshikawa, and H. Nakai, J. Chem. Phys. 151, 024104 (2019).

[2] Y. Ikabata, R. Fujisawa, J. Seino, T. Yoshikawa, and H. Nakai, J. Chem. Phys. 153, 184108 (2020).

[3] H. Kaneko and K. Funatsu, J. Chem. Inf. Model. 54, 2469 (2014).

Oxidized Bridged Carbenes as Viable Intermediates in Fe(III) Catalyzed C-H Functionalization of Indoles

Reena Balhara and Garima Jindal*

Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, India-560012

Direct C-H functionalization is effectively accomplished by Fe-catalyzed carbene insertion processes.[1] Fe(III) presents several advantages over the frequently used Fe(II).[2] However, Fe(III) complexes’ mechanistic understanding is significantly behind that of Fe(II) complexes. The formation of bridged versus terminal metallocarbenes is one of the main unresolved problems.[3] Despite being isolated and discovered to be thermodynamically more stable, the oxidized bridged carbenes are typically regarded as a dead end for the catalytic cycle. In the present study, we investigate the formation and subsequent reactions of the bridged carbenes for the Fe(TPP)Cl catalyzed C(sp2)-H insertion. We demonstrate via DFT calculations that mono and bis-oxidized bridged carbenes are involved in the lowest energy pathway. Importantly, we propose a mechanistic investigation demonstrating that these bridged carbenes are not the dead end in Fe catalysis and may be more prevalent than currently thought in other reactions. Our research will have significant repercussions for using Fe(III) complexes in various insertion processes, particularly those involving heme-containing enzymes that must be conducted under anaerobic/reducing conditions.

References

A minimal structure model for steered molecular dynamics simulation 

Ho Anh Kiet,¹ Truong Duc Toan¹ and Minh Tho Nguyen^1,2

^­1 Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, Vietnam

² Department of Chemistry, KU Leuven, B-3001 Leuven, Belgium

Over two decades, Steered Molecular Dynamics method has been proposed and continuously increasing accuracy. Accompanying that, requirements of the data’s abundance, storage capacity have increased. Therefore, we propose a more compact SMD procedure for receptor-ligand interaction studies by truncating unnecessary parts of the receptor while maintaining accuracy and economy. In this project, we reduced the simulation time up to 6 times and the rupture force’s and pulling work’s deviations of the cut configurations show a converging trend in diameter from 1.4nm onwards. This suggests that we can use an offset to approximate the results as when using the original configuration.

Keywords. Steered molecular dynamics, SMD simulation, truncation, optimizing conformations.

Decoding Regioselective Reaction Mechanism of the Gentisic Acid Catalyzed by Gentisate 1,2-Dioxygenase Enzyme

Rounak Nath, Rabindranath Manna, Ankan Paul*

School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, India

Gentisate 1,2-dioxygenase (GDO), a non-heme ring-fission dioxygenase metalloenzyme has emerged as an effective catalyst for both intra and extradiol cleavage for the aerobic catabolism of the toxic and xenobiotic compounds.^1,2 GDO enzyme can selectively cleave aromatic C-C bonds of gentisic acid (GTQ) and converts it to less toxic compounds in presence of the molecular oxygen. Regioselectivity appears when 2-oxo-4-hydroxyhepta-3,5-dienedioic acid (maleylpyruvic acid) is formed as a major and 2,7-dioxo-3,6-dihydroxyhepta-3,5-dienoic acid as a minor product.^2,3 The former product is generated due to the intradiol clevage of the aromatic C-C bond bearing the –OH and –COOH groups and the dissolution of the bond adjacent to the –OH moiety through the extra diol cleavage is responsible for the minor product formation. We have explored the presence of three water molecules in the active site with pivotal roles in the oxidative cleavage of the GTQ using classical molecular dynamics simulation of the wild type GTQ-GDO and its mutated variants.⁴ Herein, mutations have been performed to elucidate the catalysing role of 174^th residue at the active site of the GDO enzyme. We have used hybrid QM/MM calculations to probe three distinct reaction mechanisms for the regioselective reaction of the GTQ catalysed by GDO enzyme. The most favourable pathway is predicted to have a rate determining barrier of 21.4 kcal/mol associated with the alkylperoxo intermediate formation at the uB3LYP-D3/def2-TZVP/OPLS level of theory on the quintet spin surface.⁴

References

¹Rahaman et al. Angew. Chem. Int. Ed. 2016, 55, 13838.

²Eppinger et al. Biochim. Biophys. Acta. 2015, 1854, 1425.

³Harpel et al. J. Bio. chem. 1990, 265, 22187.

⁴Nath et al. Catal. Sci. Technol. 2022, 12, 5742.

Controlling Tunneling Oscillation and Quantum Localization in an Asymmetric Double-Well Potential: A Bohmian Perspective

Interaction of hydrated M³⁺(H₂O)_5-6 ions (M = Fe, Ru, and Os) with the primary alcohols and the hydroxyl groups of cellulose chain: A theoretical investigation

Dang T. Nguyen¹

^{1 Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, 41 Dinh Tien Hoang, Ben Nghe Ward, District 1, Ho Chi Minh City 700000, Vietnam}

(*) E-mail: (Will be shown in the real poster)

Interaction of hydrated M³⁺(H₂O)_5-6 ions (where M = Fe, Ru, and Os) with the primary alcohols were investigated by using density functional theory (DFT) method at the B3LYP/6-311+g(d,p) level, the PBEPBE/6-311+g(d,p) level. The results indicated that the adjacent dissociation Gibbs energy (E_AB) depended significantly on the molecular volume (V_m) of primary alcohols and the inductive effects of substituent R in primary alcohol R-CH₂OH (R: H, CH₃, CH₃CH₂, CH₃CH₂CH₂, Cl-CH₂, F-CH₂). The two-layer ONIOM approach and the local softness (s⁺_o) analysis were employed for the hydroxyl groups of cellulose chain (1G, 2G, 3G) at the B3LYP/6-311+g(d,p):HF/6-31g* level. The affinity of M³⁺(H₂O)₅ ions with the sixth water molecule in gas phase reduced in the order as follows: Fe³⁺ > Ru³⁺ > Os³⁺, which were determined by the E_AB values, bond lengths (r_AB) of M³⁺-O distance at the B3LYP/LANL2DZ/6-311+g(d,p) level (LANL2DZ basis set for the metal atoms). The water solvent make the E_AB values of Fe³⁺(H₂O)₆ ions and Fe³⁺(H₂O)₅(CH₃OH) ions change completely in the case of the polarizable continuum model (PCM) while the Onsager model give the good agreement with the gas phase model.

The influence of 1,1,2,2-Tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether as a diluent on solvation structure and reduction behavior in carbonate-electrolytes of lithium-ion batteries: Insights from AIMD Simulations

Hui-Tzu Lai, Kuan-Yu Lin, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang*

Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei, Taiwan

e-mail: (Will be shown in the real poster)

The electrolyte is critical to the performance and cycling stability of high-voltage lithium-ion batteries (LIBs). High-concentration electrolytes (HCEs) (typically > 3M) have shown promising potential in improving the cyclic stabilities of anode materials under stringent conditions compared to conventional electrolytes (typically > 1~2 M). However, HCEs face several challenges in practical applications, including high viscosity, poor wettability, low ionic conductivity, poor low-temperature performance, and high costs, which are attributed to a unique solvation structure.¹ To further advance HCEs, localized high-concentration electrolytes (LHCEs) have been developed by introducing diluent into HCEs. Herein, an advanced electrolyte is considered that includes the addition of 1,1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether (TTE) as a diluent in LiTFSI/EC-EMC salt/carbonate-solvent-based electrolytes. We explore the solvation structure formation with different salt concentrations such as conventional electrolyte (2M LiTFSI/EC/EMC), HCE (6M LiTFSI/EC/EMC), and LHCE (2M LiTFSI/EC/EMC/TTE) using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Due to the high salt content and a denser solvation structure, there is no free solvent, and have a 31.67% lower ion dissociation rate in HCEs. Diluent, TTEs has the weakest interaction with Li⁺ ions and surrounds the one shell solvation structure in LHCE. As a result, altering TTEs content can effectively influence electrolyte coordination behavior. Moreover, our AIMD results show that salt clusters aggregate easily in HCEs and form a three-dimensional network structure, which prevents Li⁺ transport and the presence of TTEs can break these aggerate networks in HCE and effectively increase the Li⁺ diffusion.

References

1. Cao, X.; Jia, H.; Xu, W.; Zhang, J.-G., Review—Localized High-Concentration Electrolytes for Lithium Batteries. Journal of The Electrochemical Society 2021, 168, 010522.

Curvature and external electric field effects on Graphene Quantum Dots

Theoretical models on formation of the hydroperoxy radical (HOO·) in water solution: application to sterilization

Trinh Le Huyen,^1,2 Minh Tho Nguyen,³ M. C. Lin^1*

¹ Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan

²Department of Chemical Engineering, The University of Da Nang – University of Science and Technology, Da Nang 550000, Vietnam.

³ Institute for Computational Science and Technology (ICST), Ho Chi Minh City, Vietnam.

*E-mail: (Will be shown in the real poster)

The O₂^•− (g) anion produced by low-power microwave discharge of air has been known to be effective for sterilization in water solution. The mechanism and kinetics of the reactions of the hydrated superoxide anion (O₂^•−).(H₂O)₄ with the protonated water clusters (H⁺).(H₂O)₄ were determined by quantum chemical computations using both hybrid density functional (B3LYP) and wavefunction CCSD(T)) methods in combination with the 6-311++G(3df,2p) basis set, embedded in a continuum of aqueous solution simulated by the PCM method for handling electronic structures in solution. These reactions occur with a sequential hydrogen atom transfers effectively controlled by diffusion according to our kinetic evaluation. The predicted equilibrium constant for the HOO^.(H₂O)₈  ↔ O₂^•− (H₂O)₄ + H⁺(H₂O)₄ reaction is in good accord with reported experimental values.

References

Development of a nanoscale excited-state nuclear–electronic dynamics simulation method and application to charge transfer in organic solar cells

Predicting functional liquid properties by effective fragment potential: Osmolyte and gas absorbing liquid

Nahoko KUROKI,^1,2 Hirotoshi MORI¹

¹ Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University,  1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan

² Japan Science and Technology Agency, ACT-X, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

Chemical processes are unit operations with phase transitions such as fluid transportation, separation extraction, and gas absorption that contribute to chemical engineering.  It is necessary to understand states of matter and physicochemical properties when developing or designing chemical processes.  All matters exist as gases, liquids, or solids.  The stable phase of the matter can be controlled by changing pressure and temperature conditions.  Since gases and liquids, including supercritical fluids, can change their shapes by external forces, these states are called “fluids” and distinguished from the corresponding “solids.”  With the high flowabilities, the fluids can often be mixed up with the other fluids or even dissolve solids if suitable fluids are chosen.  Thus, understanding the properties of fluids with proper molecular-level insights is essential in the fields of physical chemistry and chemical engineering.  This study aims to develop novel simulation methods with high chemical accuracy and low computational cost for predicting the static structures and transport properties of fluids in an ab initio manner.  This study systematically investigated the applicability of ab initio molecular dynamics simulation with effective fragment potential (EFP).

Predicting Acidity in Non-Aqueous Solvents:
An Electronic Structure Informatics

Rima Suzuki¹, Nahoko Kuroki^1,2, Hirotoshi Mori^*,1

 ¹ Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan

² JST, ACT-X, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

*E-mail: (Will be shown in the real poster)

From semiconductor processing to drug discovery, acids are often used in various non-aqueous solutions. On the other hand, generally, acidity in water is also used as the standard in any other solvents. Acidities in aqueous and non-aqueous environments have a nonlinear relationship. This fact leads to difficulties in practical acid applications in many fields. With the background, various quantum chemical methods have been developed to predict acidity with high precision in arbitrary solvents. However, the high computational cost of these methods limits the number of molecules that can be considered. In other words, no theoretical method has yet been developed to predict acidity rapidly in arbitrary solvents.

In this study, we developed a method to determine acidity in arbitrary non-aqueous environments with high accuracy and rapidity using an electronic structure informatics approach that combines quantum chemical calculations and machine learning. The developed method was applied to cyclopentadiene derivatives (25 million molecules) which show strong acidities by the formation of stable conjugate base. We explored how the acidity changes in arbitrary non-aqueous solvents. On the day, we will discuss the possibility of on-demand acid design using this method and a unified interpretation of the solvent dependence of acidity in non-aqueous environments.

A Matrix Feature Based Machine Learning Approach for Screening of Mn-PNP Catalysts for Homogeneous CO₂ Hydrogenation Reaction

Amitabha Das^†, Biswarup Pathak^†,*

^†Department of Chemistry, Indian Institute of Technology Indore, M.P.-453552, India

^*E-mail: (Will be shown in the real poster)

Homogeneous CO₂ reduction reaction can be a promising approach to produce carbon neutral fuels (COOH, CH₃OH).^[1,2] The earth abundant Mn-based aromatic PNP pincer catalysts are found to be efficient for this reaction. The presence of different ligands in the PNP pincer catalyst can tune the activity of the active metal center.^[3,4] In light of the possible combinations of ligand-catalyst pairs utilizing the experimentally reported ligands for PNP pincer catalysts, are quite large making it difficult to screen experimentally or using DFT methods in order to discover the best or optimal set of ligand combinations for this reaction. Herein, we implemented machine learning (ML) based screening of ligands in the 1^st region (-H, -Me, -CF₃ -Et, -OMe, -OEt, -Pr, –ⁱPr, –^tBu) and 2^nd region (-H, -Me, -Et, -Pr, –ⁱPr, –^tBu) of the Mn-based aromatic PNP pincer catalysts (Figure 1). For the first time, we employed the matrix-based features as an input parameter rather than the costly DFT or elemental features. Free energy change and the activation barrier for the important heterolytic hydrogen cleavage and the hydride transfer are considered to be the appropriate descriptor for the overall reaction. The ML based Kernel Ridge Regression (KRR) method shows superior predictive capability for a set of 330 catalysts. The predicted free energy change and activation barriers for specific catalysts are found to be in good agreement with DFT validated results. The proposed method is expected to escalate the design of suitable catalysts for the CO₂ reduction reaction.

Figure 1: Considered Mn-based aromatic PNP catalysts with possible ligands.

References

1. 1. K. S. Rawat, S. C. Mandal and B. Pathak, Acta, 2019, 297, 606–612.
2. 2. Das, S. C. Mandal and B. Pathak, Catal. Sci. Technol., 2021, 11, 1375–1385.
3. 3. M. Mastalir, M. Glatz, B. Stöger, M. Weil, E. Pittenauer, G. Allmaier and K. Kirchner, Chim. Acta, 2017, 455, 707−714.
4. 4. -Q. Zou, S. Chakraborty, A. Nerush, D. Oren, Y. DiskinPosner, Y. Ben-David and D. Milstein, ACS Catal., 2018, 8, 8014–8019

Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, But The Omicron Variant Reduces Its Neutralizing Ability

Hung Nguyen¹, Pham Dang Lan^2,3, Daniel A. Nissley⁴, Edward P. O’Brien^{5, 6, 7}, and Mai Suan Li^1,2

¹Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland

²Life Science Lab, Institute for Computational Science and Technology, Quang Trung

Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam

³Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam

⁴Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom

⁵Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States

⁶Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States

⁷Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, United States

 A promising approach to combat Covid-19 infections is the development of effective antiviral antibodies that target the SARS-CoV-2 spike protein. Understanding the structures and molecular mechanisms underlying the binding of antibodies to SARS-CoV-2 can contribute to quickly achieving this goal. Recently, a cocktail of REGN10987 and REGN10933 antibodies was shown to be an excellent candidate for the treatment of Covid-19. Here, using all-atom steered molecular dynamics and coarse-grain umbrella sampling we examine the interactions of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein with REGN10987 and REGN10933 separately as well as together. Both computational methods show that REGN10933 binds to RBD more strongly than REGN10987. Importantly, the cocktail binds to RBD (simultaneous binding) more strongly than its components. The dissociation constants of REGN10987-RBD and REGN10933-RBD complexes calculated from the coarse-grained simulations are in good agreement with the experimental data. Thus, REGN10933 is probably a better candidate for treating Covid-19 than REGN10987, although the cocktail appears to neutralize the virus more efficiently than REGN10933 or REGN10987 alone. REGN10987’s association with RBD is driven by van der Waals interactions, while the electrostatic interactions dominate in the case of REGN10933 and the cocktail. We also studied the effectiveness of these antibodies on the two most dangerous variants Delta and Omicron. Consistent with recent experimental reports, our results confirmed that the Omicron variant reduces the neutralizing activity of REGN10933, REGN10987, and REGN10933+REGN10987 with the K417N, N440K, L484A, and Q498R mutations playing a decisive role, while the Delta variant slightly changes their activity.

Keywords:  SARS-CoV-2, RBD, Covid-19, REGN-COV2, REGN10933, REGN10987, antibody cocktail, SMD simulation, Coarse-grained simulation, Delta variant, Omicron variant.

How are Hydroxyl Groups localized on a Graphene Sheet?

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On the improved use of the Jarzynski’s equality for molecular dynamics simulations

Truong Duc Toan^1,2

^­1 Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam

² Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam

Since the equilibrium binding free energy keeps an important role in ranking the protein – ligand binding affinities, to obtain the ∆G_eq in recent day is always challenging. Previously we used the non – equillibrium one basing on the advantages of method: fast and quite accurate. Performing a small number of trajectories, we have successfully determined the free energy profile and the binding/unbinding free energy barriers in different biomolecular systems. However, we found that a rare pulling work can appear arbitrarily and its small value would exponentially dominate the reliability of obtained data. The result wouldn’t be right reflected. Thus, in this scheme, we focus to minimize the bad influence of these unexpected events by applying the block – averaged method. The block averaging is chosen due to its economic, fast calculation and friendly application. Better correlation values are collected, R = 0.9; 0.89 in case of thrombin and HIV-1 complexes, respectively. Our goal is rather to improve the tool which could help us to rank the binding affinities more correctly.

Boron(III) complexes bearing halogenated quinolin-8-ol derivatives: A simple procedure to prepare new fluorescence ‘turn-off’ sensor probe for sensitive and selective detection of Cu²⁺ in aqueous media

A THEORETICAL STUDY OF THE ADSORPTION AND OXIDATION OF BENZENE (C₆H₆) ON THE MANGANESE OXIDE CATALYSTS

Structure and vibrational spectroscopy of ReSi_x⁺ clusters

Roshan Singh ^a*, André Fielicke ^b*, Ewald Janssens ^c*, Peter Lievens ^c*, John E. McGrady.^a*

a*:Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK

b*: Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany

c*: Quantum Solid State Physics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200 D, B-3001 Leuven, Belgium. 

Email: (Will be shown in the real poster)

The electronic and structural properties of mixed metal-silicon clusters are of great interest because of the opportunity to explore how metal-silicon and, potentially, metal-metal, bonding influences geometry and vibrational spectroscopy. Beyond the intrinsic interest in the nature of the chemical bonds in these clusters, they can be viewed as minimal models for transition metals impurities in bulk silicon, an issue of considerable commercial significance in the semi-conductor industry. The clusters of immediate interest are species such as ReSi_x⁺, x = 3-9, which have been studied in the groups of Fielicke (Berlin) and Janssens (Leuven). The clusters are generated in the gas phase and their vibrational spectra measured indirectly through multi-photon desorption techniques. In this work, we use density functional theory in combination with a particle-swarm algorithm^[1] to identify low-energy isomers of these clusters and calculate their vibrational spectrum. Through symmetry-based analysis, we have been able to decode the vibrational spectra to show that the Re atom sits outside a growing Si_x net, rather than being encapsulated by it, as is the case for smaller Mn clusters^[2] , making the data much more useful than simply a fingerprint. The strong dependence of spin state on the choice of functional is a well-known problem in DFT studies of transition metals, and so we have also explored the use of DLPNO coupled-cluster theory (CCSD(T)) as an alternative approach to computing accurate energetics.                                   

Figure 1 Vibrational spectra of Re@Si₃ + and stretching mode related to the high intensity vibration.

References

1 Vaibhav Khanna. (2022). Evolution of vibrational spectra in the manganesesilicon clusters mn2sin, N = 10, 12, and 13, and cationic [MN2SI13]+. The Journal of Physical Chemistry , 126 (10), 1617–1626. https://doi.org/10.1021/acs.jpca.1c10027.s003 

2 Wang, Y., Lv, J., Zhu, L., & Ma, Y. (2012). Calypso: A method for crystal structure prediction. Computer Physics Communications, 183(10), 2063–2070. https://doi.org/10.1016/j.cpc.2012.05.008 

need to include some of your results here (an optimised structure plus arrows showing displacement for the major peak. You also need to include the x axis!

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Chromium-doped silicon clusters: chiral structures and high magnetism

Alternating enhancement of bonds by π and σ delocalized electrons in the ribbon model

Long Van Duong,^1,2,* Nguyen Ngoc Tri,³ Nguyen Phi Hung,⁴ and Minh Tho Nguyen⁵

¹ Atomic Molecular and Optical Physics Research Group, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam

² Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam

³ Department of Chemistry, Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam

⁴ Department of Chemistry, Faculty of Natural Sciences, Quy Nhon University, Quy Nhon , Vietnam

⁵ Department of Chemistry, Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam

Boron-doped ribbon-like structures  has emerged as a wire structure. The stability of the ribbon structure has been investigated according to the ribbon model. Accordingly, the delocalized electron distribution leads to a shortening of the distances between atoms at the ends of the structure and causes an increase in the potential barrier at the ends of the structure. The subsequent effect of increasing the potential barrier at the ends is that the π and σ delocalized electrons can be viewed as freely moving along the structure as a particle moving in a one-dimensional potential well. The close relationship between π and σ electron distributions with the stability of ribbon structures is presented in the poster.

One application of the ribbon model presented in the poster is to explain the stability of the B₂Si₃^q and B₃Si₂^p structures through competition with the Hückel model.

Modeling the Electronic Properties of
Cyano Polycyclic Aromatic Hydrocarbons: a machine learning-based Quantitative Structure−Property Relationships approach

Tuan H. Nguyen^1,2 , Khang M. Le³ , Lam H. Nguyen^1,3 , and Thanh N. Truong^4,*

¹ Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam

² Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, Ho Chi Minh City, Vietnam

³ Faculty of Chemistry, VNUHCM-University of Science, Ho Chi Minh City, Vietnam

⁴ Department of Chemistry, University of Utah, Salt Lake City, Utah, United States

Corresponding author’s contact information: (Will be shown in the real poster)

Cyano substitution to PAH molecules introduces multiple improvements to the PAH as organic semiconductors, such as ease of fabrication, stability against heat, and oxidizing agents, etc. This calls for a Quantitative Structure-Property Relationship (QSPR) model for predicting the electronic properties of this chemical class as a means of computer-aid material screening. We shown that such a model is constructed by a pair of descriptors: the Degree of p -orbital overlap (DPO) descriptor, which has been used to build QSPR model for PAHs previously, and a new descriptor for including the effect of the cyano substituents. Moreover, the proposed model is automatic as the truncated form of the DPO descriptor can be automatically extracted from the molecules stored as SMILES strings, and the descriptor parameter can be optimized in a machine learning-like manner. The dataset of 926 cyano-substituted PAHs whose electronic properties are calculated at the B3LYP/6-31+G(d) of the DFT level theory is used to train and assessed the model. The pair of descriptors are shown to correlate linearly with the three modeled electronic properties, namely bandgap, ionization potential, and electron affinity of CN-PAHs. Consequently, model testing suggests that our model has an accuracy of within 2 eV for all multi-substituted CN-PAHs and 0.2 eV for the mono-substituted CN-PAH subclass.

Key words: quantitative structure-property relationships (QSPR), machine learning (ML), truncated degree of π-orbital overlap (DPO), cyano polycyclic aromatic hydrocarbon (CN-PAH).

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Guiding the deep learning-based scoring function through data augmentations

Seokhyun Moon,¹ Woo Youn Kim*^1,2,3

¹Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

²HITS Incorporation, 124 Teheran-ro, Gangnam-gu, Seoul 06234, Republic of Korea

³KI for Artificial Intelligence, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

Drug-target interaction (DTI) prediction is a challenging problem in structure-based drug discovery. Deep learning(DL)-based scoring functions recently got attention for fast and accurate DTI prediction. However, unlike other fields where DL achieved remarkable success, the DL for estimating binding affinity showed unsatisfactory results due to the scarcity of data. Thus to overcome data deficiency issues, previous methods utilized various computer-generated binding poses for each complex for training as data augmentation. Nevertheless, it is currently unclear how data augmentations affect the model performance. In this light, our study focused on acquiring insights from the prediction results of the DL-based scoring function to figure out how the model learns data augmentations and influences performance. We compared the distribution of the predicted values of DL models trained with different data to verify the effect of each data augmentation. The analysis showed that true-like data augmentation was necessary since the prevailing non-binding augmented data shifted the overall predictions, increasing the false negative ratio for active compounds. Involving additional true-like data augmentation along with negative data augmentation improved the model performance significantly. The series of processes to get insight from the results can guide the research direction of developing DL-based DTI prediction methods.

TAILORING ORGANIC MOLECULES FOR SINGLET FISSION USING PHOSPHORUS SUBSTITUTION AND FUKUI FUNCTION AS AN INDICATOR

Christina Mariam Mathew*^,+, Ann Varghese*, Sunish K Sugunan* and Vibin Ipe Thomas*

*Department of Chemistry, CMS College, Kottayam, Kerala, India

+ Department of Chemistry, Baselius College, Kottayam, Kerala, India

Singlet fission is a photophysical process proposed to surpass the Schokley-Quessier limit associated with photovoltaics. As only a few molecules exhibit efficient singlet fission, tailoring organic molecules with desirable photophysical properties is essential in solar energy research. Tuning of energy levels to satisfy energetic requirements for exhibiting singlet fission can be achieved by heteroatom substitution, core substitution, and sidechain engineering. We investigated the feasibility of singlet fission in a set of linearly fused oligoacene (anthracene, tetracene, pentacene) and a chrysene derivative (anthanthrene) doped with phosphorus atom (replacement of a -CH group in the carbon skeleton with phosphorus atom) by assessing the energies of excited singlet and triplet states, diradical character, and the Fukui function at the doping sites. A TDDFT-based rapid computational approach were utilized for designing singlet fission chromophores. The computational analysis reveals a correlation between the atom-specific chemical reactivity parameter, Fukui function with diradical characters, and vertical triplet and singlet excitation energies. The diradical character and Fukui function exhibited a  linear correlation on phosphorus substitution. Our findings enable one to utilize the Fukui function as an indicator for screening the diradical character in heteroatom-doped polyaromatic hydrocarbons. It entitles one to quickly asses the doping criteria to develop design rules for SF molecules at reasonable computational time and cost.

REFERENCES

1. Christina Mariam Mathew, Ann Varghese, Sunish K Sugunan, Vibin Ipe Thomas., Phys. Chem. A.,2022, 126, 10, 1579–1590
2. Casanova.,Chem. Rev., 2018, 118, 15, 7164–7207

Theoretical studies combining quantum mechanical calculations and reaction kinetics simulations

– Application to some amidation reactions –

Adsorption and release of oxygen molecules on iron porphyrin complexes

Mr. Kentaro NAKAMURA (Primary author)

Email: (Will be shown in the real poster)

Faculty of Systems Engineering, Wakayama University, Wakayama, Japan

Prof. Hideo YAMAKADO (Co-author, Presenting)

Email: (Will be shown in the real poster)

Faculty of Systems Engineering, Wakayama University, Wakayama, Japan

Graduate School of Systems Engineering, Wakayama University, Wakayama, Japan

What Happens at Surfaces and Grain Boundaries of Halide Perovskites: Insights from Reactive Molecular Dynamics Simulations of CsPbI₃

Mike Pols^1,*, Adri C.T. van Duin², Sofía Calero¹ and Shuxia Tao¹

¹ Molecular Simulation & Modelling, Department of Applied Physics, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands

² Department of Mechanical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States

Contact: (Will be shown in the real poster)

The commercialization of perovskite solar cells is hindered by the poor long-term stability of the metal halide perovskite (MHP) light-absorbing layer. Solution processing, the common fabrication method for MHPs, produces polycrystalline films with a wide variety of defects, such as point defects, surfaces, and grain boundaries. Although the optoelectronic effects of such defects have been widely studied, the evaluation of their impact on the long-term stability remains challenging. In particular, an understanding of the dynamics of degradation reactions at the atomistic scale is lacking.

In this poster, I will explain our recent advances in understanding the effects of defects in the form of surfaces, surface defects, and grain boundaries, on the stability of the CsPbI₃ halide perovskite. Using reactive force field (ReaxFF) molecular dynamics simulations, we establish a stability trend for a variety of surfaces, which correlates well with the occurrence of these surfaces in experiments. Moreover, we find that perovskite surfaces degrade by progressively changing the local geometry of PbI_x octahedra from corner- to edge- to face-sharing. Importantly, we find that Pb dangling bonds and the lack of steric hindrance of I species are two crucial factors that induce degradation reactions. Finally, we show that the stability of these surfaces can be modulated by adjusting their atomistic details, either by creating additional point defects or merging them to form grain boundaries. While generally additional defects, particularly upon clustering, have a negative impact on the material stability, some grain boundaries have a stabilizing effect, primarily because of additional steric hindrance.

Fluorescent of Organoboron complexes bearing base Schiff: photophysical characterization and DFT studies

C–N Bond Forming Radical Rebound Is the Enantioselectivity-Determining Step in P411-Catalyzed Enantioselective C(sp³)–H Amination: A Combined Computational and Experimental Investigation

Binh Khanh Mai^a, Natalia M. Neris^b, Yang Yang^b*, and Peng Liu^a*

^a Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States

^b Department of Chemistry and Biochemistry and Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, California 93106, United States

Engineered metalloenzymes represent promising catalysts for stereoselective C–H functionalization reactions. Recently, P450 enzymes were evolved to allow for new-to-nature intramolecular C(sp³)–H amination reactions via a nitrene transfer mechanism, giving rise to diamine derivatives with excellent enantiocontrol. To shed light on the origin of enantioselectivity, a combined computational and experimental study was carried out. Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations were performed to investigate the activation energies and enantioselectivities of both the hydrogen atom transfer (HAT) and the subsequent C–N bond forming radical rebound steps. Contrary to previously hypothesized enantioinduction mechanisms, our calculations show that the radical rebound step is enantioselectivity-determining, whereas the preceding HAT step is only moderately stereoselective. Furthermore, the selectivity in the initial HAT is ablated by rapid conformational change of the radical intermediate prior to C–N bond formation. This finding is corroborated by our experimental study using a set of enantiomerically pure, monodeuterated substrates. Furthermore, classical and ab initio molecular dynamics (MD) simulations were carried out to investigate the conformational flexibility of the carbon-centered radical intermediate. This key radical species undergoes a facile conformational change in the enzyme active site from the pro-(R) to the pro-(S) configuration, whereas the radical rebound is slower due to spin-state change and ring strain of the cyclization process, thereby allowing for stereoablative C–N bond formation. Together, these studies revealed an underappreciated enantioinduction mechanism for biocatalytic C(sp³)–H functionalizations involving radical intermediates, opening up new avenues for the development of challenging asymmetric C(sp³)–H functionalizations.

SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than Wild Type: Evidence from Molecular Dynamics Simulation

Hoang Linh Nguyen^1,2,3†, Nguyen Quoc Thai^1,4, Phuong H. Nguyen⁵ and Mai Suan Li^6,*

¹Life Science Lab, Institute for Computational Science and Technology, Quang Trung

Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam

²Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam

³Vietnam National University, Ho Chi Minh City 700000, Vietnam

⁴Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap,

Vietnam

⁵CNRS, Universit ́e de Paris, UPR9080, Laboratoire de Biochimie Th ́eorique, Paris,France ; Institut de Biologie Physico-Chimique, FondationEdmond de Rothschild, PSLResearch University, Paris, France

⁶Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668, Warsaw, Poland

†Current address: Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam

*Email: (Will be shown in the real poster)

The emergence of the variant of concern  Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aggravates the covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of  the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. We showed that Omicron binds to human cells more strongly than WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R and Q498R mutations in RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and  heterogeneous models of glycans coating the viral RBD and the peptidyl domain (PD) of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have little effect on the binding affinity of WT RBD to hACE2.

Keywords: Omicron variant, COVID-19, SARS-CoV-2, glycans, spike protein, human angiotensin-converting enzyme 2, receptor binding domain, peptidyl domain, MM-PBSA, binding free energy

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