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ORCIDJournal of Computational Chemistry, Volume 43
Volume 43, Number 1, January 2022
- Tina Mathea, Taras Petrenko, Guntram Rauhut
:
Advances in vibrational configuration interaction theory - part 2: Fast screening of the correlation space. 6-18
- Attila Á. Dékány, Gábor Czakó:
Benchmark ab initio proton affinity and gas-phase basicity of α-alanine based on coupled-cluster theory and statistical mechanics. 19-28 - Jorge I. Martínez-Araya, Rafael Islas:
Analysis in silico of chemical reactivity employing the local hyper-softness in some classic aromatic compounds, boron aromatic clusters and all-metal aromatic clusters. 29-42 - Danny K. Long, Wolfgang Bangerth, Derek R. Handwerk, Christopher B. Whitehead, Patrick D. Shipman, Richard G. Finke:
Estimating reaction parameters in mechanism-enabled population balance models of nanoparticle size distributions: A Bayesian inverse problem approach. 43-56 - Arash Mollahosseini, Shaghayegh Saadati, Amira Abdelrasoul:
Effects of mussel-inspired co-deposition of 2-hydroxymethyl methacrylate and poly (2-methoxyethyl acrylate) on the hydrophilicity and binding tendency of common hemodialysis membranes: Molecular dynamics simulations and molecular docking studies. 57-73
- Eric Alcaide, Stella Biderman, Amalio Telenti, M. Cyrus Maher:
MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates. 74-78
Volume 43, Number 2, January 2022
- Asja A. Kroeger, Amir Karton:
Cover Image. i
- Sai Lakshmana Vankayala, Luke C. Warrensford, Amanda R. Pittman, Benjamin C. Pollard, Fiona L. Kearns, Joseph D. Larkin, H. Lee Woodcock III:
CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. 84-95 - Asja A. Kroeger, Amir Karton:
Graphene-induced planarization of cyclooctatetraene derivatives. 96-105 - Zoe L. Seeger, Ekaterina I. Izgorodina:
A DLPNO-CCSD(T) benchmarking study of intermolecular interactions of ionic liquids. 106-120 - Regina Matveeva, Merete Falck Erichsen, Henrik Koch, Ida-Marie Høyvik:
The effect of midbond functions on interaction energies computed using MP2 and CCSD(T). 121-131 - Jirí Fukal, Milos Budesínský, Ondrej Páv, Petr Jurecka, Marie Zgarbová, Jakub Sebera, Vladimír Sychrovský:
The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA. 132-143
- Lihuan Yuan, Chengkun Wu, Xiaowei Guo, Canqun Yang:
ParaCopasi: A package for parallel biochemical simulation and analysis. 144-154
Volume 43, Number 3, January 2022
- T. Ngoc Han Pham, Trung Hai Nguyen, Nguyen Minh Tam, Thien Y. Vu, Nhat Truong Pham, Nguyen Truong Huy, Binh Khanh Mai, Nguyen Thanh Tung, Minh Quan Pham, Van V. Vu, Son Tung Ngo:
Improving ligand-ranking of AutoDock Vina by changing the empirical parameters. 160-169 - Enrico Benassi:
An inexpensive density functional theory-based protocol to predict accurate 19F-NMR chemical shifts. 170-183 - Fabien Pascale, Philippe D'Arco, Francesco Silvio Gentile, Roberto Dovesi:
Strategies for the optimization of the structure of crystalline compounds. 184-196 - Catrina Nguyen, Lauren M. Yearwood, Michelle E. McCully:
Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins. 197-205 - Zi Li, Yong Yang, Tianlv Xu, Herbert Früchtl, Tanja Van Mourik, Martin J. Paterson, Yasuteru Shigeta, Steven R. Kirk, Samantha Jenkins:
Next generation quantum theory of atoms in molecules for the design of emitters exhibiting thermally activated delayed fluorescence with laser irradiation. 206-214
- Zirui Shu, Mincong Wu, Jun Liao, Changjun Chen:
FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program. 215-224
Volume 43, Number 4, February 2022
- Ying Qian, Xuelian Li, Jian Wu, Aimin Zhou, Zhijian Xu, Qian Zhang:
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- Maurício J. Piotrowski, Renato Pereira Orenha, Renato L. T. Parreira, Diego Guedes-Sobrinho:
Assessment of the van der Waals, Hubbard U parameter and spin-orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters. 230-243 - Shanshan Xu, You Li, Donghan Wang, Chao Fang, Chengwei Luo, Jiankun Deng, LiHong Hu, Hui Li, Hongzhi Li:
Efficient prediction for high precision CO-N2 potential energy surface by stacking ensemble DNN. 244-254 - Ying Qian, Xuelian Li, Jian Wu, Aimin Zhou, Zhijian Xu, Qian Zhang:
Picture-word order compound protein interaction: Predicting compound-protein interaction using structural images of compounds. 255-264 - Kevin M. Lefrancois-Gagnon, Robert C. Mawhinney:
Toward universal substituent constants: Transferability of group descriptors from the quantum theory of atoms in molecules. 265-278 - Sergey A. Katsyuba, Tatiana P. Gerasimova, Sebastian Spicher, Fabian Bohle, Stefan Grimme:
Computer-aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution. 279-288 - Jing Dong, Lichao Peng, Xiaohui Yang, Zelin Zhang, Puyu Zhang:
XGBoost-based intelligence yield prediction and reaction factors analysis of amination reaction. 289-302
Volume 43, Number 5, February 2022
- Rohit Modee, Siddhartha Laghuvarapu, U. Deva Priyakumar:
Benchmark study on deep neural network potentials for small organic molecules. 308-318 - Steve Scheiner:
Maximal occupation by bases of π-hole bands surrounding linear molecules. 319-330 - Ali Abbasi, Sepideh Amjad-Iranagh, Bahram Dabir:
CellSys: An open-source tool for building initial structures for bio-membranes and drug-delivery systems. 331-339 - Jan Badorrek, Michael Walter:
Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds. 340-348 - Rodrigo Labiak, Carlile Lavor, Michael Souza:
Distance geometry and protein loop modeling. 349-358
- Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr., Wonpil Im:
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. 359-375
Volume 43, Number 6, March 2022
- Hector H. Corzo, Ali Abou Taka, Aurora Pribram-Jones, Hrant P. Hratchian:
Using projection operators with maximum overlap methods to simplify challenging self-consistent field optimization. 382-390 - German P. Barletta, Matias Barletta, Tadeo E. Saldaño, Sebastian Fernandez Alberti:
Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility. 391-401 - Xuening Li, Ying Li, Yuanyuan Sun, Lingpeng Meng, Yanli Zeng:
BF3-Catalyzed Mukaiyama aldol reaction of acetaldehyde with 2-siloxy-1-propene. 402-412 - Mitisha Jain, Uwe Gerstmann, Wolf Gero Schmidt, Hazem Aldahhak:
Adatom mediated adsorption of N-heterocyclic carbenes on Cu(111) and Au(111). 413-420 - Xuan Zhang, Yongtao Wang, Jia Yao, Haoran Li, Kenji Mochizuki:
A tiny charge-scaling in the OPLS-AA + L-OPLS force field delivers the realistic dynamics and structure of liquid primary alcohols. 421-430
- Yessica Gómez, Andrew M. Natale, James Lincoff, Charles W. Wolgemuth, John M. Rosenberg, Michael Grabe:
Taking the Monte-Carlo gamble: How not to buckle under the pressure! 431-434
Volume 43, Number 7, March 2022
- Runfeng Huang, Jiali Cai, Lei Yao, Yuna Bai, Kai Guo, Lili Zhao:
Mechanistic study of cobalt(I)-catalyzed asymmetric coupling of ethylene and enynes to functionalized cyclobutanes. 440-447 - Ctirad Cervinka:
Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory. 448-456 - Daria Tolstykh, Laurent Lemmens, Stijn De Baerdemacker, Dimitri Van Neck, Patrick Bultinck, Guillaume Acke:
Uncovering Clar's aromatic -sextet rule in the Hubbard model using Maximum Probability Domain Partitions. 457-464 - Yi-Liang Zhang, Fu-Li Wang, Ai-Min Ren:
Reliability of computed molecular structures. 465-476 - Mambatta Haritha, Cherumuttathu H. Suresh:
Hydration patterns of rings in drugs and relationship to lipophilicity: A DFT study. 477-490 - Jacek Koput:
Ground-state potential energy functions and vibration-rotation energy levels of beryllium lithium and its cation. 491-498
Volume 43, Number 8, March 2022
- Kristoffer T. Bæk, Kasper P. Kepp:
Data set and fitting dependencies when estimating protein mutant stability: Toward simple, balanced, and interpretable models. 504-518 - Irén Simkó, Kalyani Chordiya, Attila G. Császár, Mousumi Upadhyay Kahaly, Tamás Szidarovszky:
A quantum-chemical perspective on the laser-induced alignment and orientation dynamics of the CH3X (X = F, Cl, Br, I) molecules. 519-538 - Tian Lu, Qinxue Chen:
Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems. 539-555 - Mirzam Carreon-Gonzalez, Leonardo Muñoz-Rugeles, Annik Vivier Bunge, Juan Raúl Alvarez-Idaboy:
Chemical repair of damaged leucine and tryptophane by thiophenols at close to diffusion-controlled rates: Mechanisms and kinetics. 556-567 - Anh L. P. Nguyen, Ekaterina I. Izgorodina:
Behavior of counterpoise correction in many-body molecular clusters of organic compounds: Hartree-Fock interaction energy perspective. 568-576 - Ariadni Boziki, Pablo Baudin, Elisa Liberatore, Negar Ashari Astani, Ursula Rothlisberger:
A theoretical perspective of the ultrafast transient absorption dynamics of CsPbBr3. 577-582
Volume 43, Number 9, April 2022
- Sagarmoy Mandal, Ritama Kar, Tobias Klöffel, Bernd Meyer, Nisanth N. Nair:
Improving the scaling and performance of multiple time stepping-based molecular dynamics with hybrid density functionals. 588-597 - Agnieszka Brzyska, Krzysztof Wolinski:
Search for transition states with external forces. 598-610 - Jakub Brzeski:
The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes. 611-618 - Sreerama Rajasekhar, Soumyadip Das, Ramanathan Karuppasamy, Balamurali Musuvathi Motilal, Kaushik Chanda:
Identification of novel inhibitors for Prp protein of Mycobacterium tuberculosis by structure based drug design, and molecular dynamics simulations. 619-630 - Andrei V. Afonin, Danuta Rusinska-Roszak:
Guide to tuning the chalcone molecular properties based on the push-pull effect energy scale created via the molecular tailoring approach. 631-643
- Yan M. H. Gonçalves, Sadra Kashefolgheta, Marina P. Oliveira, Philippe H. Hünenberger, Bruno A. C. Horta:
Simultaneous parametrization of torsional and third-neighbor interaction terms in force-field development: The LLS-SC algorithm. 644-653
Volume 43, Number 10, April 2022
- Shubhadeep Nag, Yashonath Subramanian:
Separation of hydrocarbon mixture of neopentane and n-hexane using NaY zeolite: Large distinct diffusivity. 660-673 - Stefan D. Search, Christopher D. Cooper, Elwin van't Wout:
Towards optimal boundary integral formulations of the Poisson-Boltzmann equation for molecular electrostatics. 674-691 - Quentin Perron, Olivier Mirguet, Hamza Tajmouati, Adam Skiredj, Anne Rojas, Arnaud Gohier, Pierre Ducrot, Marie-Pierre Bourguignon, Patricia Sansilvestri-Morel, Nicolas Do Huu, Françoise Gellibert, Yann Gaston-Mathé:
Deep generative models for ligand-based de novo design applied to multi-parametric optimization. 692-703 - Yunzhi Li, Dong Wang, Fangjia Fu, Qiying Xia, Wei Li, Shuhua Li:
Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy-based fragmentation method. 704-716 - Diego Sorbelli, Paola Belanzoni, Leonardo Belpassi, Ji-Woong Lee, Gianluca Ciancaleoni:
An ETS-NOCV-based computational strategies for the characterization of concerted transition states involving CO2. 717-727 - Tymofii Yu. Nikolaienko, Oleksandr Gurbych, Maksym Druchok:
Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network. 728-739
Volume 43, Number 11, April 2022
- Hans Georg Gallmetzer, Thomas S. Hofer:
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches. 746-756 - Kavita Devi, Sai Manoj N. V. T. Gorantla, Kartik Chandra Mondal:
EDA-NOCV analysis of carbene-borylene bonded dinitrogen complexes for deeper bonding insight: A fair comparison with a metal-dinitrogen system. 757-777 - Dmitry V. Khakimov, Victor P. Zelenov, Tatyana S. Pivina:
Di- and trioxides of triazolotetrazine: Computational prediction of crystal structures and estimation of physicochemical characteristics. 778-784 - Miguel Gallegos, Aurora Costales, Ángel Martín Pendás:
A real space picture of the role of steric effects in SN2 reactions. 785-795 - Israel Fernández, Anurag Noonikara-Poyil, H. V. Rasika Dias:
Bonding situation in isolable silver(I) carbonyl complexes of the Scorpionates. 796-803 - Angel Sanchez-Gonzalez, Pierre Grenut, Adrià Gil:
Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. 804-821
Volume 43, Number 12, May 2022
- Dong Liu, Song Xu, Gerui Pei, Jianzhi Xu, Xintian Zhao, Chuncai Kong, Zhimao Yang, Tao Yang:
Geometries, electronic structures, and bonding properties of endohedral Group-14 Zintl clusters TM@E10 (TM = Fe, Co, Ni; E = Ge, Sn, Pb). 828-838 - Joachim Laun, Thomas Bredow:
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence with polarization quality of the fifth period for solid-state calculations. 839-846 - Sivakumar Prasanth Kumar, Nandan Y. Dixit, Chirag N. Patel, Rakesh M. Rawal, Himanshu A. Pandya:
PharmRF: A machine-learning scoring function to identify the best protein-ligand complexes for structure-based pharmacophore screening with high enrichments. 847-863 - Aneta Leskourová, Michal H. Kolár:
The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules. 864-869 - Samuel Bertolini, Timo Jacob:
Valence energy correction for electron reactive force field. 870-878
- Demian Riccardi, Zachary Trautt, Ala Bazyleva, Eugene Paulechka, Vladimir Diky, Joseph W. Magee, Andrei F. Kazakov, Scott A. Townsend, Chris D. Muzny:
Towards improved FAIRness of the ThermoML Archive. 879-887
Volume 43, Number 13, May 2022
- Prasenjit Das, Pratim Kumar Chattaraj:
CSiGaAl2-/0 and CGeGaAl2-/0 having planar tetracoordinate carbon atoms in their global minimum energy structures. 894-905 - Yuqing Xiong, Juan Zeng, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu:
Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process. 906-916 - Joyce K. Daré, Matheus P. Freitas:
Is conformation relevant for QSAR purposes? 2D Chemical representation in a 3D-QSAR perspective. 917-922 - Thorren Kirschbaum, Tristan Petit, Joachim Dzubiella, Annika Bande:
Effects of oxidative adsorbates and cluster formation on the electronic structure of nanodiamonds. 923-929
- Daniel R. Roe, Christina Bergonzo:
prepareforleap: An automated tool for fast PDB-to-parameter generation. 930-935
Volume 43, Number 14, May 2022
- Ioanna Gkogka, Nicholas M. Glykos:
Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor: Structure, dynamics, and comparison with the experimental data. 942-952 - Alexander V. Serdtsev, Nadezhda I. Medvedeva:
Electronic structure, sodium diffusion and redox potentials of low-symmetry NaMFe(MoO4)3 (M = Mg, Ni). 953-960 - Jemal Mohamed Ali, Ahmed Mustefa Mohammed, Yedilfana Setarge Mekonnen:
Mechanistic study on the coupling reaction of CO2 with propylene oxide catalyzed by (CH3)4PI·MgCl2. 961-971 - Mbah Bake Maraf, Adjieufack Abel Idrice, Manwal A. Mekoung Pélagie, Auguste Abouem A. Zintchem, Gouet Bebga, Lydia Rhyman, Mbouombouo Ndassa Ibrahim, Ponnadurai Ramasami:
Decoding the reaction mechanism of the cyclocondensation of ethyl acetate2-oxo-2-(4-oxo-4H-pyrido [1.2-a] pyrimidin-3-yl) polyazaheterocycle and ethylenediamine using bond evolution theory. 972-985 - Jacek Koput:
Ab initio characterization of the aluminum dimer in its X 3 Π u and A 3 ∑ g - electronic states. 986-993
Volume 43, Number 15, June 2022
- Elena O. Levina, Maria G. Khrenova, Andrey A. Astakhov, Vladimir G. Tsirelson:
Keto-enol tautomerism from the electron delocalization perspective. 1000-1010 - Niklas Sülzner, Julia Haberhauer, Christof Hättig, Arnim Hellweg:
Prediction of acid pKa values in the solvent acetone based on COSMO-RS. 1011-1022 - Jakob Kraus, Jens Kortus:
A theoretical investigation into gallic acid pyrolysis. 1023-1032 - Gyun-Tack Bae, Christine M. Aikens:
Time-dependent density functional theory study of the optical properties of tetrahedral aluminum nanoparticles. 1033-1041
- Pim N. H. Wassenaar, Emiel Rorije, Martina G. Vijver, Willie J. G. M. Peijnenburg:
ZZS similarity tool: The online tool for similarity screening to identify chemicals of potential concern. 1042-1052 - Daniel K. Gehlhaar, Brock A. Luty, Philip P. Cheung, Andy H. Litman, Robert M. Owen, Peter W. Rose:
The Pfizer Crystal Structure Database: An essential tool for structure-based design at Pfizer. 1053-1062
Volume 43, Number 16, June 2022
- Jesús Jara-Cortés, Chérif F. Matta, Jesús Hernández-Trujillo:
A fast approximate extension of the interacting quantum atoms energy decomposition to excited states. 1068-1078 - Bónis Barcza, Ádám B. Szirmai, Katalin J. Szántó, Attila Tajti, Péter G. Szalay:
Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles. 1079-1093 - Dmitri G. Fedorov:
Polarization energies in the fragment molecular orbital method. 1094-1103 - Kai Trepte, Johannes Voss:
Data-driven and constrained optimization of semi-local exchange and nonlocal correlation functionals for materials and surface chemistry. 1104-1112
- Marcelo Depólo Polêto, Justin A. Lemkul:
TUPÃ: Electric field analyses for molecular simulations. 1113-1119
- Miroslaw Jablonski:
Endo- and exohedral complexes of superphane with cations. 1120-1133
Volume 43, Number 17, June 2022
- Lyman Monroe, Daisuke Kihara:
Using steered molecular dynamic tension for assessing quality of computational protein structure models. 1140-1150 - Marcus Wieder, Markus Fleck, Benedict Braunsfeld, Stefan Boresch:
Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program. 1151-1160 - Dusan Cocic, Biljana Petrovic, Ralph Puchta, Marta Chrzanowska, Anna Katafias, Rudi van Eldik:
Investigation of water substitution at RuII complexes by conceptual density function theory approach. 1161-1175 - Roberto Cammi, Bo Chen:
The second derivative of the electronic energy with respect to the compression scaling factor in the XP-PCM model: Theory and applications to compression response functions of atoms. 1176-1185 - Abhinav Gupta, Shivani Verma, Ramsha Javed, Suraj Sudhakar, Saurabh Srivastava, Nisanth N. Nair:
Exploration of high dimensional free energy landscapes by a combination of temperature-accelerated sliced sampling and parallel biasing. 1186-1200
Volume 43, Number 18, July 2022
- Miroslaw Jablonski:
The physical nature of the ultrashort spike-ring interaction in iron maiden molecules. 1206-1220 - Agnieszka Kacka-Zych, Radomir Jasinski:
Mechanistic aspects of the synthesis of seven-membered internal nitronates via stepwise [4 + 3] cycloaddition involving conjugated nitroalkenes: Molecular Electron Density Theory computational study. 1221-1228 - Bryan A. Raubenolt, Steven W. Rick:
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing. 1229-1236 - Debabrata Pramanik, Aiswarya B. Pawar, Sudip Roy, Jayant K. Singh:
Mechanistic insights of key host proteins and potential repurposed inhibitors regulating SARS-CoV-2 pathway. 1237-1250 - Leighton Wilson, Robert Krasny, Tyler Luchko:
Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs. 1251-1270
Volume 43, Number 19, July 2022
- Kun Yuan, Meng-Yang Li, Yao-Xiao Zhao, Yanzhi Liu, Xiang Zhao:
Composition-selective full inclusion host-guest interaction of azobenzene-containing photoresponsive nanoring with fullerene C60. 1276-1285 - Hesam Arabzadeh, Chengwen Liu, Orlando Acevedo, Pengyu Y. Ren, Wei Yang, Thomas Albrecht-Schönzart:
Hydration of divalent lanthanides, Sm2+ and Eu2+: A molecular dynamics study with polarizable AMOEBA force field. 1286-1297 - Rodrigo D. Tosso, M. Natalia C. Zarycz, Ayelén Schiel, Luisa Goicoechea Moro, Héctor A. Baldoni, Emilio Angelina, Ricardo D. Enriz:
Evaluating the conformational space of the active site of D2 dopamine receptor. Scope and limitations of the standard dock