Theoretical and Computational Chemistry

Last Month

Dispersion Corrected r2SCAN Based Global Hybrid Functionals: r2SCANh, r2SCAN0, and r2SCAN50

Markus Bursch, Hagen Neugebauer, Sebastian Ehlert, Stefan Grimme

129

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Theoretical and Computational Chemistry

Advantages and Limitations of Hydrogen Peroxide for Direct Oxidation of Methane to Methanol at Mono-Copper Active Sites in Cu-Exchanged Zeolites

Lu Cheng, Xuning Chen, P. Hu, Xiaoming Cao

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Theoretical and Computational Chemistry

ANN-based Drug-isolate-fold-change model predicting the resistance profiles of HIV-1 protease inhibitors

Huseyin Tunc, Serdar Durdagi, Murat Sari, Seyfullah Kotil

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Catalysis

High-entropy oxides for the oxygen evolution reaction

Katrine Svane, Jan Rossmeisl

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Theoretical and Computational Chemistry

Reaction SPL - extension of a public document markup standard to chemical reactions

Gunther Schadow, Yulia Borodina, Victorien Delannée, Wolf-Dietrich Ihlenfeldt, Alexander Godfrey, Marc Nicklaus

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Physical Chemistry

Local order in AgAuCuPdPt high entropy alloy surfaces

Henrik Kristoffersen, Jan Rossmeisl

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Nanoscience

HADOKEN: An Open-Source Software Package for Predicting Electron Confinement Effects in Various Nanowire Geometries and Configurations

Cameron Chevalier, Bryan Wong

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Organic Chemistry

Topological reference systems

OHMAE TAKAYUKI OHMAE

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Organic Chemistry

A Theoretical Study of Tridentenes

OHMAE TAKAYUKI OHMAE

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Physical Chemistry

Ion mobility studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes

Alexander Schäfer, Violeta Vetsova, Erik Schneider, Manfred Kappes, Michael Seitz, Lena Daumann, Patrick Weis

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Materials Chemistry

Performance of GFN1-xTB for periodic optimization of Metal Organic Frameworks

Maryam Nurhuda, Carole Perry, Matthew Addicoat

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Theoretical and Computational Chemistry

N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study

Alen T Mathew, Anurag TK Baidya, Bhanuranjan Das, Rajnish Kumar

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Theoretical and Computational Chemistry

O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems

Pier Paolo Poier, Louis Lagardère, Jean-Philip Piquemal

141

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Theoretical and Computational Chemistry

Efficient CPU and GPU implementations of multicenter integrals over long-range operators using Cartesian Gaussian functions

Alexander Humeniuk, William Glover

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Biological and Medicinal Chemistry

An explainable multi-parameter optimization approach for de novo drug design against proteins from central nervous system

Navneet Bung, Sowmya Ramaswamy Krishnan, Arijit Roy

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Theoretical and Computational Chemistry

Scalable Constant pH Molecular Dynamics in GROMACS

Noora Aho, Pavel Buslaev, Anton Jansen, Paul Bauer, Gerrit Groenhof, Berk Hess

271

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Biological and Medicinal Chemistry

An Interpretable Machine Learning model for Selectivity of Small Molecules against Homologous Protein Family

Sarveswara Rao Vangala, Navneet Bung, Sowmya Ramaswamy Krishnan, Arijit Roy

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Theoretical and Computational Chemistry

Poisoning density functional theory with benchmark sets of difficult systems

Tim Gould, Stephen Dale

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Materials Chemistry

Elucidating the germanium distribution in ITQ-13 zeolites by density functional theory

Michael Fischer, Carlos Bornes, Luís Mafra, João Rocha

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Catalysis

The Ir–OOOO–Ir Transition State and the Mechanism of the Oxygen Evolution Reaction on IrO2(110)

Tobias Binninger, Marie-Liesse Doublet

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Physical Chemistry

Effects of fluoride salt addition to the physico-chemical properties of the MgCl2-NaCl-KCl heat transfer fluid : a molecular dynamics study

Weiguang Zhou, Yanping Zhang, Mathieu Salanne

110

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Chemical Engineering and Industrial Chemistry

Hybridizing organic chemistry and synthetic biology reaction networks for optimizing synthesis routes

Chonghuan Zhang, Alexei Lapkin

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Organic Chemistry

The Effect of Chemical Representation on Active Machine Learning Towards Closed-Loop Optimization

Alexander Pomberger, Antonio Pedrina McCarthy, Ahmad Khan, Simon Sung, Connor Taylor, Matthew Gaunt, Lucy Colwell, David Walz, Alexei Lapkin

280

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Biological and Medicinal Chemistry

Are Vanadium Intermediates Suitable Mimics in Non-Heme Iron Enzymes? An Electronic Structure Analysis

Vyshnavi Vennelakanti, Rimsha Mehmood, Heather Kulik

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Theoretical and Computational Chemistry

Assessing the Interplay Between Functional-Driven and Density-Driven Errors in DFT Models of Water

Etienne Palos, Eleftherios Lambros, Steven Swee, Jie Hu, Saswata Dasgupta, Francesco Paesani

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Biological and Medicinal Chemistry

Tuaimenal A, a meroterpene from the Irish deep-sea soft coral <i>Drifa</i> sp., displays antiviral and antiproliferative bioactivity.

Nicole E. Avalon, Jordan Nafie, Tracess Smalley, Carolina De Marco Verissimo, Sarah G. Dietrick, Ryan M. Young, Luke C. Warrensford, Amanda R. Pittman, Fiona L. Kearns, Jennifer M. Binning, John P. Dalton, Mark P. Johnson, H. Lee Woodcock, A. Louise Allcock, Bill J. Baker

312

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Theoretical and Computational Chemistry

A Physical Expression of Electrons in Density Functional Theory

Stefano Racioppi, Phalgun Lolur, Per Hyldgaard, Martin Rahm

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Materials Chemistry

Augmented Magnetic Response and Spin-Transfer in Copper Corrole/Graphene Hybrids - A DFT Study

Kerry Wrighton-Araneda, Diego Cortés-Arriagada, Paulina Dreyse, Simon Pascal, Gabriel Canard, Luis Sanhueza

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Inorganic Chemistry

From simple to complex crystal chemistry in the RE−Au−Tt systems (RE = La, Ce, Pr, Nd, Ho; Tt = Ge, Sn, Pb)

Sogol Lotfi, Roy Arrieta, Gordon Peterson, Pablo Delgado, Jakoah Brgoch

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Catalysis

The Role of Homoaromaticity in the Tropylium-Catalyzed Carboxylic Acid O-H Insertion with Diazoesters

Anakuthil Anoop, Venkataraman Ganesh

188

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Theoretical and Computational Chemistry

Spin Purification in Full-CI Quantum Monte Carlo via a First-Order Penalty Approach

Giovanni Li Manni, Oskar Weser, Niklas Liebermann, Daniel Kats, Ali Alavi

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Physical Chemistry

Manifestation of Energy and Entropy of Particles in a Box

Mohsen Farshad

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Biological and Medicinal Chemistry

Evaluating the use of absolute binding free energy in the fragment optimization process.

Irfan Alibay, Aniket Mangakar, Daniel Seeliger, Philip Biggin

568

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Theoretical and Computational Chemistry

Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches

Jesús Lucia-Tamudo, Gustavo Cárdenas, Nuria Anguita-Ortiz, Sergio Díaz-Tendero, Juan J. Nogueira

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Theoretical and Computational Chemistry

Predictive stochastic analysis of massive filter-based electrochemical reaction networks

Daniel Barter, Evan Walter Clark Spotte-Smith, Nikita S. Redkar, Shyam Dwaraknath, Kristin A. Persson, Samuel M. Blau

424

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Physical Chemistry

Heavy-Atom Tunneling in the Covalent/Dative Bond Complexation of Cyclo[18]carbon–piperidine

Ashim Nandi, Gershom (Jan M.L.) Martin

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Theoretical and Computational Chemistry

Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space

Revisiting the Role of Charge Transfer and Local Excitations in Thermally Activated Delayed Fluorescence

Leonardo Evaristo de Sousa, Piotr de Silva

165

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Materials Chemistry

Protonation-Induced Charge Transfer and Polaron Formation in Organic Semiconductors Doped by Lewis Acids

Fabian Bauch, Chuanding Dong, Stefan Schumacher

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Physical Chemistry

Improving machine learning performance on small chemical reaction data with unsupervised contrastive pretraining

Mingjian Wen, Samuel M. Blau, Xiaowei Xie, Shyam Dwaraknath, Kristin A. Persson

549

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Nanoscience

Temperature and curvature-dependent thermal interface conductance between nanoscale-gold and water from molecular simulation

Blake Wilson, Steven Nielsen, Jaona Randrianalisoa, Zhenpeng Qin

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Theoretical and Computational Chemistry

Machine learned calibrations to high-throughput molecular excited state calculations

Shomik Verma, Miguel Rivera, David O. Scanlon, Aron Walsh

157

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Theoretical and Computational Chemistry

AutoSolvate: A Toolkit for Automating Quantum Chemistry Design and Discovery of Solvated Molecules

Eugen Hruska, Ariel Gale, Xiao Huang, Fang Liu

237

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Theoretical and Computational Chemistry

Water Interaction with Fe2NiP Schreibersite (110) Surface: a Quantum Mechanical Atomistic Perspective

Stefano Pantaleone, Marta Corno, Albert Rimola, Nadia Balucani, Piero Ugliengo

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Catalysis

Predicting Ruthenium Catalysed Hydrogenation of Esters using Machine Learning

Challenger Mishra, Niklas von Wolff, Abhinav Tripathi, Eric Brémond, Annika Preiss, Amit Kumar

135

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Theoretical and Computational Chemistry

Virtual-Ligand-Assisted Screening Strategy to Discover Enabling Ligands for Transition Metal Catalysis

Wataru Matsuoka, Yu Harabuchi, Satoshi Maeda

195

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Theoretical and Computational Chemistry

Small Gold-Thiolate Clusters Au3(SMe)3: Benchmarking of Density Functionals and Bonding Analysis

Maya Khatun, Sayan Paul, Saikat Roy, Subhasis Dey, Anakuthil Anoop

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Theoretical and Computational Chemistry

Persistence Diagrams to Visualise Damage to Biological Networks

Matthew Bailey, Mark Wilson

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Theoretical and Computational Chemistry

A simple predictor of interface orientation of mesogenic fluids and its implications for organic semiconductors

Belinda Boehm, David Huang

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Theoretical and Computational Chemistry

Single excitation energies obtained from the ensemble HOMO-LUMO gap: exact results and approximations

Tim Gould, Zahed Hashimi, Leeor Kronik, Stephen Dale

119

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Organic Chemistry

Diastereoselective Indole-Dearomative Cope Rearrangements by Compounding Minor Driving Forces.

Subhadip De, Breanna Tomiczek, Yinuo Yang, Kenneth Ko, Ion Ghivirga, Adrian Roitberg, Alexander Grenning

335

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Energy

Machine Learning as a Tool for Specific Capacity Prediction of Prospective Potassium Battery Electrodes

Souvik Manna, Diptendu Roy, Sandeep Das, Biswarup Pathak

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Materials Science

Electronic Structure and Magnetism of Pristine, Defected, and Strained Ti2N MXene

Yogendra Limbu, Gopi Chandra Kaphle, Alok Lal Karn, Niraj Kumar Shah, Durga Paudyal

346

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Theoretical and Computational Chemistry

Prediction of Protein pKa with Representation Learning

Hatice Gokcan, Olexandr Isayev

511

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Theoretical and Computational Chemistry

Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification

Felix Brandt, Christoph Jacob

151

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Theoretical and Computational Chemistry

The Oriented and Flux-Weighted Current Density Stagnation Graph of LiH

Raphael J F Berger, Maria Dimitrova

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Theoretical and Computational Chemistry

Identification of Enzymatic Active Sites with Unsupervised Language Modeling

Loïc Kwate Dassi, Matteo Manica, Daniel Probst, Philippe Schwaller, Yves Gaetan Nana Teukam, Teodoro Laino

638

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Theoretical and Computational Chemistry

Static and Dynamic Statistical Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature With Path Integral Simulations at Ambient Temperature

Chenghan Li, Francesco Paesani, Gregory A. Voth

565

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Theoretical and Computational Chemistry

Quantum Mechanical Study of Protonation of Oxygen Ligands in the Laccase Active Site Based on X-Ray Structures of Subatomic Resolution

Sergei Gavryushov, Nikolay Kuzmich, Konstantin Polyakov

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Theoretical and Computational Chemistry

Bio-inspired Chemical Space Exploration of Terpenoids

tao zeng, B. Andes Hess, fan zhang, ruibo wu

133

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Theoretical and Computational Chemistry

Wild Type and Omicron SARS-CoV-2 Spike Receptor Binding Domains Bind Similarly to the Human ACE2 Receptor: An MM-GBSA Study

Camryn Carter, Justin Airas, Carol A. Parish

140

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Theoretical and Computational Chemistry

Kinetic Monte Carlo Modeling of Graphene Sheet Growth During CVD

Hironori Kondo

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Theoretical and Computational Chemistry

Prediction of Thermal Properties of Zeolites through Machine Learning

Maxime Ducamp, François-Xavier Coudert

126

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Theoretical and Computational Chemistry

Is [ReCl4(CN)2]2− a good Building Block for Single Molecule Magnets? A Theoretical Investigation.

Christoph van Wüllen, Eva M. V. Kessler

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Earth, Space, and Environmental Chemistry

Applicability Domain of Polyparameter Linear Free Energy Relationship Models for Predicting Equilibrium Partition Coefficients

Satoshi Endo

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Organic Chemistry

A Bond Bundle Case Study of Diels-Alder Catalysis Using Oriented Electric Fields

Timothy Wilson, Mark Eberhart

123

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Physical Chemistry

Must be the wave function single-valued? Ring vs. periodic boundary conditions, spinors and double rotations

Josep Planelles

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Theoretical and Computational Chemistry

A Hessian free method to prevent zero-point energy leakage in classical trajectory simulation

Saikat Mukherjee, Mario Barbatti

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Theoretical and Computational Chemistry

Novel ultra-hard hexacarbon allotropes from first principles

Samir F. Matar, Vladimir L. Solozhenko

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Theoretical and Computational Chemistry

Systematic Bottom-Up Molecular Coarse-Graining via Force Matching using Anisotropic Particles

David Huang, Huong Nguyen

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Theoretical and Computational Chemistry

Predicting the Redox Potentials of Phenazine Derivatives using DFT Assisted Machine Learning

Siddharth Ghule, Soumya Dash, Sayan Bagchi, Kavita Joshi, Kumar Vanka

434

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Theoretical and Computational Chemistry

Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics

Chenghan Li, Gregory A. Voth

252

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Theoretical and Computational Chemistry

Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy

Yunsie Chung, Florence H. Vermeire, Haoyang Wu, Pierre J. Walker, Michael H. Abraham, William H. Green

254

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Physical Chemistry

Synergistic effect of p-type and n-type dopants in semiconductors for efficient electrocatalytic water splitting

Tugce Kutlusoy, Spyridon Divanis, Riccardo Marina, Rebecca Pittkowski, Petr Krtil, Jan Rossmeisl

132

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Materials Science

Generative Design of Stable Semiconductor Materials Using Deep Learning And DFT

Edirisuriya Siriwardane, Yong Zhao, Indika Perera, Jianjun Hu

111

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Analytical Chemistry

Completely computational model setup for spectroscopic techniques: the ab initio molecular dynamics indirect hard modeling (AIMD-IHM) approach

Justus Wöhl, Wassja Kopp, Iryna Yevlakhovych, Leo Bahr, Hans-Jürgen Koß, Kai Leonhard

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Theoretical and Computational Chemistry

Modeling the Interplay of Conformational and Electronic Structure in Conjugated Polyelectrolytes

David Friday, Nicholas Jackson

117

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Earth, Space, and Environmental Chemistry

Molecular Modelling of Ionic Liquids: Force-Field Validation and Thermodynamic Perspective from Large-Scale Fast-Growth Solvation Free Energy Calculations

Zhaoxi Sun, Mao Wang, Qiaole He, Zhirong Liu

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Theoretical and Computational Chemistry

Ultrafast Proton Transfer Reaction in Phenol–(Ammonia)n Clusters: An Ab-Initio Molecular Dynamics Investigation.

Reman Kumar Singh, Rakesh Pant, G Naresh Patwari

120

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Theoretical and Computational Chemistry

JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields

Mehmet Cagri Kaymak, Ali Rahnamoun, Kurt A. O'Hearn, Adri C. T. van Duin, Kenneth M. Merz Jr., Hasan Metin Aktulga

752

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Theoretical and Computational Chemistry

PreSS/MD: Predictor of Skin Sensitization Caused by Chemicals Leaching from Medical Devices

Joyce Borba, Vinicius Alves, Rodolpho Braga, Daniel Korn, Nicole Kleinstreuer, Kevin Causey, Alexander Tropsha, Diego Rua, Eugene Muratov

112

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Theoretical and Computational Chemistry

The Synergetic and Multifaceted Nature of Carbon-Carbon Rotation Reveals the Origin of Stability for Bulky Alkane Dimers

Shubin Liu, Xinjie Wan, Xin He, Meng Li, Bin Wang, Chunying Rong

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Theoretical and Computational Chemistry

Towards a Density-Based Description of Chemical Bonds and Noncovalent Interactions with Pauli Energy

Shubin Liu, Shujing Zhong, Xin He, Siyuan Liu, Bin Wang, Tian Lu, Chunying Rong

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Theoretical and Computational Chemistry

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Gal Bouskila, Arie Landau, Idan Haritan, Nimrod Moiseyev, Debarati Bhattacharya

119

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Theoretical and Computational Chemistry

Inverse Molecular Design of Alkoxides and Phenoxides for Aqueous Direct Air Capture of CO2

Zisheng Zhang, Amanda L. Kummeth, Jenny Y. Yang, Anastassia N. Alexandrova

137

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Theoretical and Computational Chemistry

Computational Design of Stapled Peptide Inhibitor against SARS-CoV-2 Receptor Binding Domain

Asha Rani Choudhury, Atanu Maity, Sayantani Chakraborty, Rajarshi Chakrabarti

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Physical Chemistry

Shallow and deep trap states of solvated electrons in methanol and their formation, electronic excitation, and relaxation dynamics

Jinggang Lan, Yo-ichi Yamamoto, Toshinori Suzuki, Vladimir Rybkin

242

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Theoretical and Computational Chemistry

Quantum Dynamics of Water from Møller-Plesset Perturbation Theory via a Neural Network Potential

Jinggang Lan, David Wilkins, Vladimir Rybkin, Marcella Iannuzzi, Juerg Hutter

310

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Materials Chemistry

Modulating Electronic Properties of Dinitrosoarene Polymers

Lujo Matasović, Barbara Panić, Matej Bubaš, Hrvoj Vančik, Ivana Biljan, Igor Rončević

129

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Theoretical and Computational Chemistry

mwfn: A Strict, Concise and Extensible Format for Electronic Wavefunction Storage and Exchange

Superhydrophilicity of $\alpha$-Alumina Surfaces Results from Tight Binding of Interfacial Waters to Specific Aluminols

Ruiyu Wang, Richard C. Remsing, Michael L. Klein, Vincenzo Carnevale, Eric Borguet

113

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Biological and Medicinal Chemistry

Single-image super-resolution improvement of X-ray single-particle diffraction images using convolutional neural network

Atsushi Tokuhisa, Yoshinobu Akinaga, Kei Terayama, Yasushi Okuno

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Theoretical and Computational Chemistry

Hot atom chemistry: oxygen at stepped platinum surfaces

Axel Gross

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Catalysis

Alkali Cation Effect on CO2 Electroreduction to CO: A Local Colligative Property

Seung-Jae Shin, Hansol Choi, Stefan Ringe, Da Hye Won, Chang Hyuck Choi, Hyungjun Kim

552

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Biological and Medicinal Chemistry

In silico drug repurposing of anticancer drug 5-FU and analogues against SARS-CoV-2 main protease

Aristote Matondo, Washington Dendera, Bienfait K. Isamura, Koto-te-Nyiwa Ngbolua, Hilaire V.S. Mambo, Mayaliwa Muzomwe, Virima Mudogo

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Theoretical and Computational Chemistry

Methods to Calculate Electronic Excited-state Dynamics For Molecules on Large Metal Clusters with Many States: Ensuring Fast Overlap Calculations and a Robust Choice of Phase

Hsing-Ta Chen, Junhan Chen, Vale Cofer-Shabica, Zeyu Zhou, Vishikh Athavale, Gregory Medders, Joseph Subotnik, Zuxin Jin

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Theoretical and Computational Chemistry

Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost

Montgomery Gray, John Herbert

137

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Catalysis

Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: the Case of Formate Dehydrogenase

Azadeh Nazemi, Adam Steeves, Heather Kulik

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Polymer Science

Discovery of Innovative Polymers for Next-Generation Gas-Separation Membranes using Interpretable Machine Learning

Jason Yang, Lei Tao, Jinlong He, Jeffrey McCutcheon, Ying Li

325

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Organic Chemistry

Synthesis of Stilbenes Using Various Catalysts and Investigation of their Optical Properties

Pelin Ulukan, Saron Catak, Erdal Ertas

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Catalysis

Bayesian active learning of interatomic force field for molecular dynamics simulation of Pt/Ag(111)

Kai Xu, Lei Yan, Bingran You

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Theoretical and Computational Chemistry

Role of conical intersection seam topography in the chemiexcitation of 1,2-dioxetanes

Ignacio Fernández Galván, Anders Brakestad, Morgane Vacher

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Catalysis

Workflow for Biocatalytic Reaction Performance Prediction and Analysis

Hanna Clements, Autumn Flynn, Bryce Nicholls, Daria Grosheva, Todd Hyster, Matthew Sigman

554

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Theoretical and Computational Chemistry

Solvation structure and dynamics of Li and LiO2 and their transformation in non-aqueous organic electrolyte solvents from first-principles simulations

Behnaz Rahmani Didar, Axel Gross

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