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ORCIDJournal of Computational Chemistry, Volume 44
Volume 44, Number 1, January 2023
Cover Image
- Sai Manoj N. V. T. Gorantla, Harsha S. Karnamkkott, Selvakumar Arumugam, Sangita Mondal, Kartik Chandra Mondal
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Cover Image. i
Research Articles
- Kodai Kanemaru, Yoshihiro Watanabe, Norio Yoshida, Haruyuki Nakano:
Solvent effects in four-component relativistic electronic structure theory based on the reference interaction-site model. 5-14 - Shizhi Dong, Yanshuai Li, Hongyu Hu, Ruichuan Li, Bing Yan, Xing Zhang, Zeliang Wang, Jinyu Zhang, Lin Guo:
Effect of ZrS2 load single/dual-atom catalysts on the hydrogen evolution reaction: A first-principles study. 15-26 - Pablo Ramos-Sánchez, Jeremy N. Harvey, José A. Gámez:
An automated method for graph-based chemical space exploration and transition state finding. 27-42 - Sai Manoj N. V. T. Gorantla, Harsha S. Karnamkkott, Selvakumar Arumugam, Sangita Mondal, Kartik Chandra Mondal:
Stability and bonding of carbon(0)-iron-N2 complexes relevant to nitrogenase co-factor: EDA-NOCV analyses. 43-60
Volume 44, Number 2, January 2023
Research Articles
- Fabien Pascale, Klaus Doll, Francesco Silvio Gentile, Roberto Dovesi:
How deeply are core electrons perturbed when valence electrons are spin polarized? The case study of transition metal compounds. 65-75 - Dzvenymyra Yarish, Sofiya Garkot, Oleksandr O. Grygorenko, Dmytro S. Radchenko, Yurii S. Moroz, Oleksandr Gurbych:
Advancing molecular graphs with descriptors for the prediction of chemical reaction yields. 76-92 - Takao Tsuneda, Hiroki Sumitomo, Masatoshi Hasebe, Takuro Tsutsumi, Tetsuya Taketsugu:
Reactive orbital energy theory serving a theoretical foundation for the electronic theory of organic chemistry. 93-104 - Ambre Blanc, Antonio Monari, Jean Christophe Tremblay:
A posteriori localization of many-body excited states through simultaneous diagonalization. 105-116
Volume 44, Number 3, January 2023
Research Articles
- Hongmin Li, Yangyu Zhou, Guanjun Wang, Xiaoqing Zeng, Mingfei Zhou:
Formation and infrared spectroscopic characterization of carbon suboxide complexes TM-η1-C3O2 and the inserted ketenylidene complexes OCTMCCO (TM=Cu, Ag, Au) in solid neon. 129-137 - Dan Fan, Juan Du, Jing-Shuang Dang, Changwei Wang, Yirong Mo:
The strength and selectivity of perfluorinated nano-hoops and buckybowls for anion binding and the nature of anion-π interactions. 138-148 - Manuel Schmitt, Ingo Krossing:
Terminal end-on coordination of dinitrogen versus isoelectronic CO: A comparison using the charge displacement analysis. 149-158 - Manuel Yáñez, Filiberto Ortíz-Chi, Gabriel Merino, Ibon Alkorta:
Dismantlement of ammonia upon interaction with Ben (n ≤ 10) clusters. 159-167 - Pavel Rublev, Nikolay V. Tkachenko, Alexander I. Boldyrev:
Overlapping electron density and the global delocalization of π-aromatic fragments as the reason of conductivity of the biphenylene network. 168-178 - Jan-Niclas Luy, Pascal Henkel, Daniel Grigjanis, Jannis Jung, Doreen Mollenhauer, Ralf Tonner-Zech:
Bonding character of intermediates in on-surface Ullmann reactions revealed with energy decomposition analysis. 179-189 - Jun-Bo Lu, Xue-Lian Jiang, Jia-Qi Wang, Han-Shi Hu, W. H. Eugen Schwarz, Jun Li:
On the highest oxidation states of the actinoids in AnO4 molecules (An = Ac - Cm): A DMRG-CASSCF study. 190-198 - Sebastian Anila, Cherumuttathu H. Suresh:
Fulleride-metal η5 sandwich and multi-decker sandwich complexes: A DFT prediction. 199-208
Software Note
- Felipe S. S. Schneider, Giovanni F. Caramori:
Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions. 209-217
Research Articles
- Anna V. Pomogaeva, Anna S. Lisovenko, Artem S. Zavgorodnii, Alexey Y. Timoshkin:
Lewis acid stabilized group 13-15 element analogs of ethylene. 218-228 - Julia Kohn, Markus Bursch, Andreas Hansen, Stefan Grimme:
Computational study of ground-state properties of μ2-bridged group 14 porphyrinic sandwich complexes. 229-239 - Rui Yu, Gai-ru Yan, Yu-Qian Liu, Zhong-hua Cui:
Two-layer molecular rotors: A zinc dimer rotating over planar hypercoordinate motifs. 240-247 - Armando A. Morin-Martinez, Jessica Arcudia, Ximena Zarate, Miguel Eduardo Cifuentes-Quintal, Gabriel Merino:
The quest for a bidirectional auxetic, elastic, and enhanced fracture toughness material: Revisiting the mechanical properties of the BeH2 monolayers. 248-255 - D. Sravanakumar Perumalla, Sagar Ghorai, Tanmoy Pal, Drahomír Hnyk, Josef Holub, Eluvathingal D. Jemmis:
Rearrangement of dicarboranyl methyl cation to icosahedral C3B9H12+: An ab initio dynamics view. 256-260 - Subodh Khire, Shridhar R. Gadre:
Development and testing of an algorithm for efficient MP2/CCSD(T) energy estimation of molecular clusters with the 2-body approach. 261-267 - Enric Sabater, Miquel Solà, Pedro Salvador, Diego M. Andrada:
Cage-size effects on the encapsulation of P2 by fullerenes. 268-277
Review Article
- Ranita Pal, Pratim Kumar Chattaraj:
Electrophilicity index revisited. 278-297
Research Articles
- Moritz Schneider, Guntram Rauhut:
Quantum chemical rovibrational analysis of aminoborane and its isotopologues. 298-306 - Sergei F. Vyboishchikov:
A quick solvation energy estimator based on electronegativity equalization. 307-318 - Lukas Raßpe-Lange, Alexander Hoffmann, Christoph Udo Gertig, Joshua Heck, Kai Leonhard, Sonja Herres-Pawlis:
Geometrical benchmarking and analysis of redox potentials of copper(I/II) guanidine-quinoline complexes: Comparison of semi-empirical tight-binding and DFT methods and the challenge of describing the entatic state (part III). 319-328 - Rabindranath Lo, Anna Masínová, Maximilián Lamanec, Dana Nachtigallova, Pavel Hobza:
The unusual stability of H-bonded complexes in solvent caused by greater solvation energy of complex compared to those of isolated fragments. 329-333 - Josef Tomecek, Cen Li, Georg Schreckenbach:
Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands. 334-345 - Gurudutt Dubey, Tejender Singh, Prasad V. Bharatam:
The importance of four-membered NHCs in stabilizing Breslow intermediates on benzoin condensation pathway. 346-354 - Derek R. Langstieh, Richard H. Duncan Lyngdoh, Robert Bruce King, Henry F. Schaefer III:
Lantern-type dinickel complexes: An exploration of possibilities for nickel-nickel bonding with bridging bidentate ligands. 355-366 - Saikiran Kotaru, Sven Kähler, Maristella Alessio, Anna I. Krylov:
Magnetic exchange interactions in binuclear and tetranuclear iron(III) complexes described by spin-flip DFT and Heisenberg effective Hamiltonians. 367-380
Software Note
- Frank Neese:
The SHARK integral generation and digestion system. 381-396
Research Articles
- Lewis R. Thomas-Hargreaves, Yu-Qian Liu, Zhongma Cui, Sudip Pan, Magnus R. Buchner:
Bonding situations in tricoordinated beryllium phenyl complexes. 397-405 - Róbert Izsák, Christoph Riplinger, Nick S. Blunt, Bernardo de Souza, Nicole Holzmann, Ophelia Crawford, Joan Camps, Frank Neese, Patrick Schopf:
Quantum computing in pharma: A multilayer embedding approach for near future applications. 406-421 - Puthan Veetil Muhasina, Pattiyil Parameswaran:
σ versus π-radical: Tuning the electronic nature of neutral carbon (I) compounds with three non-bonding electrons. 422-431 - Yenamareddy Bhargav Kumar, Anwesh Pandey, Nandan Kumar, G. Narahari Sastry:
Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study. 432-441 - Paul Geerlings, Frank De Proft:
External fields in conceptual density functional theory. 442-455 - Jonas Weiser, Jingjing Cui, Rian D. Dewhurst, Holger Braunschweig, Bernd Engels, Felipe Fantuzzi:
Structure and bonding of proximity-enforced main-group dimers stabilized by a rigid naphthyridine diimine ligand. 456-467 - Ursula Rastetter, Axel Jacobi von Wangelin, Carmen Herrmann:
Redox-active ligands as a challenge for electronic structure methods. 468-479 - Congcong Zhang, Han Bai, Junyuan Hu, Kai Guo, Lili Zhao:
Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis. 480-488
Volume 44, Number 4, February 2023
Research Articles
- Xiaobo Sun, Thomas Hansen, Jordi Poater, Trevor A. Hamlin, Friedrich Matthias Bickelhaupt:
Rational design of iron catalysts for C-X bond activation. 495-505 - Steven M. Maley, Graham R. Lief, Richard M. Buck, Orson L. Sydora, Qing Yang, Steven M. Bischof, Daniel H. Ess:
Density functional theory and CCSD(T) evaluation of ionization potentials, redox potentials, and bond energies related to zirconocene polymerization catalysts. 506-515 - Gustavo Cárdenas, Jesús Lucia-Tamudo, Henar Mateo-delaFuente, Vito F. Palmisano, Nuria Anguita-Ortiz, Lorena Ruano, Álvaro Pérez-Barcia, Sergio Díaz-Tendero, Marcos Mandado, Juan J. Nogueira:
MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations. 516-533 - Daiki Fukuhara, Masataka Yamauchi, Satoru G. Itoh, Hisashi Okumura:
Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency. 534-545 - Kentaro Kido, Masashi Kaneko:
Conformation, hydration, and ligand exchange process of ruthenium nitrosyl complexes in aqueous solution: Free-energy calculations by a combination of molecular-orbital theories and different solvent models. 546-558 - Mütesir Temel, Omer Tayfuroglu, Abdulkadir Kocak:
The performance of ANI-ML potentials for ligand-n(H2O) interaction energies and estimation of hydration free energies from end-point MD simulations. 559-569 - Timothé R. L. Melin, Preston Harell, Betoul Ali, Narasimhan Loganathan, Angela K. Wilson:
Thermochemistry of per- and polyfluoroalkyl substances. 570-580 - Delong Ma, Song Ma, Yunfeng Li, Jianyong Yuan, Jionghao He, Shuangliang Zhao:
Reactivities of silane coupling agents in the silica/rubber composites: Theoretical insights into the relationships between energy barriers and electronic characteristics. 581-593 - Seonghan Kim, Yi Liu, Matthew Ziarnik, Sangjae Seo, Yiwei Cao, X. Frank Zhang, Wonpil Im:
Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. 594-601 - Adam K. Sieradzan, Jordi Sans-Duñó, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczynski, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo:
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. 602-625
Software Note
- Javier Cerezo, Fabrizio Santoro:
FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation. 626-643
Research Articles
- Lakhya Jyoti Mazumder, Rohan Sharma, Farnaz Yashmin, Pankaz Kumar Sharma:
Beryllium bonding with noble gas atoms. 644-655
Volume 44, Number 5, February 2023
Research Articles
- Yuki Mitsuta, Toshio Asada:
Curvature-weighted nudged elastic band method using the Riemann curvature. 662-669 - Thanachon Somnarin, Pacharaporn Krawmanee, Matthew Paul Gleeson, Duangkamol Gleeson:
Computational investigation of the radical-mediated mechanism of formation of difluoro methyl oxindoles: Elucidation of the reaction selectivity and yields. 670-676 - Xiao-Lei Li, Chao-Ming Li, Jia-Yi Zhu, Zhan Zhou, Qiang Hao, Chang-Sheng Wang:
A scheme for rapid evaluation of the intermolecular three-body polarization effect in water clusters. 677-686 - Yury Minenkov, Luigi Cavallo, Kirk A. Peterson:
Influence of the complete basis set approximation, tight weighted-core, and diffuse functions on the DLPNO-CCSD(T1) atomization energies of neutral H,C,O-compounds. 687-696 - Taewon David Kim, Michael Richer, Gabriela Sánchez-Díaz, Ramón Alain Miranda-Quintana, Toon Verstraelen, Farnaz Heidar-Zadeh, Paul W. Ayers:
Fanpy: A python library for prototyping multideterminant methods in ab initio quantum chemistry. 697-709
Software Note
- Oskar Weser, Björn Hein-Janke, Ricardo A. Mata:
Automated handling of complex chemical structures in Z-matrix coordinates - The chemcoord library. 710-726
Volume 44, Number 6, March 2023
Research Articles
- Gunnar Schmitz, Bastian Schnieder:
Adaptive regularized Gaussian process regression for application in the context of hydrogen adsorption on graphene sheets. 732-744 - Raphael F. Ligório, José L. Rodrigues, Anna Krawczuk, Leonardo H. R. Dos Santos:
A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium. 745-754 - Bruno D. Milanez, Gustavo M. dos Santos, Max Pinheiro Jr, Leonardo T. Ueno, Luiz F. A. Ferrão, Adélia J. A. Aquino, Hans Lischka, Francisco B. C. Machado:
Structural stability and the low-lying singlet and triplet states of BN-n-acenes, n = 1-7. 755-765 - Sota Hayashi, Naoki Uemura, Masayuki Uranagase, Shuji Ogata:
Pressure-assisted decomposition of tricresyl phosphate on amorphous FeO using hybrid quantum-classical simulations. 766-776 - Katerina Fatková, Radim Cajzl, Jaroslav V. Burda:
The vertical excitation energies and a lifetime of the two lowest singlet excited states of the conjugated polyenes from C2 to C22: Ab initio, DFT, and semiclassical MNDO-MD simulations. 777-787 - Marian D. Brodney, Gregory A. Bakken, Christopher R. Butler, Jacquelyn L. Klug-McLeod, Robert Owen, Shao-Tien Sng:
Integrated design environment: A multi-use platform for design idea capture, evaluation, and tracking in medicinal chemistry. 788-800
Volume 44, Number 7, 2023
Research Articles
- Yingfeng Zhang, Jian Zhao:
A density fitting scheme for the fast evaluation of molecular electrostatic potential. 806-813 - Maicon Pierre Lourenço, Jirí Hostas, Lizandra Barrios Herrera, Patrizia Calaminici, Andreas M. Köster, Alain Tchagang, Dennis R. Salahub:
GAMaterial - A genetic-algorithm software for material design and discovery. 814-823 - Shinya Nakamura, Tatsuo Akaki, Keiji Nishiwaki, Midori Nakatani, Yuji Kawase, Yuki Takahashi, Isao Nakanishi:
System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study. 824-831 - Justin K. Kirkland, Sophia K. Johnson, Konstantinos D. Vogiatzis:
Computational investigation of functionalized carbenes on dinitrogen activation. 832-842 - Sebastian Schwan, Andreas J. Achazi, Ferdinand Ziese, Peter R. Schreiner, Kerstin Volz, Stefanie Dehnen, Simone Sanna, Doreen Mollenhauer:
Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions. 843-856 - Ikuo Kurisaki, Seiya Tanaka, Ichiro Mori, Toshihito Umegaki, Yoshiharu Mori, Shigenori Tanaka:
Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape. 857-868
Volume 44, Number 8, 2023
Research Articles
- Priya Dey, Parbati Biswas:
Aggregation propensities of proteins with varying degrees of disorder. 874-886 - Md. Jaish Uddin, Hasina Akhter, Urmi Chowdhury, Jannatul Mawah, Sanzida Tul Karim, Mohammad Jomel, Md. Sirajul Islam, Mohammad Raqibul Islam, Latifa Afrin Bhuiyan Onin, Md. Ackas Ali, Faiyaz Md. Efaz, Mohammad A. Halim:
Large scale peptide screening against main protease of SARS CoV-2. 887-901 - Cong Pan:
A formula and numerical study on Ewald 1D summation. 902-911 - Okke Melse, Iris Antes, Ville R. I. Kaila, Martin Zacharias:
Benchmarking biomolecular force field-based Zn2+ for mono- and bimetallic ligand binding sites. 912-926 - Youhyun Nam, Songyi Lee, Rakwoo Chang:
Structure and stability of polydiacetylene membrane systems: Molecular dynamics simulation studies. 927-934 - Nicole M. Roussey, Alex Dickson:
Quality over quantity: Sampling high probability rare events with the weighted ensemble algorithm. 935-947
Volume 44, Number 9, 2023
Research Articles
- Alexey V. Ignatchenko, Jacob P. Willower:
Schwarz P-surface via isolated sp2 carbon heptagons: Design and properties. 954-961 - Sara Sadat Karachi, Kiamars Eskandari:
Bonding in the high spin lithium clusters: Non-nuclear attractors play a crucial role. 962-968 - Bozhu Chen, Xin Xu:
Discriminating and understanding molecular crystal polymorphism. 969-979
Software Note
- Kota Hanasaki, Zulfikhar A. Ali, Min Choi, Mauro Del Ben, Bryan M. Wong:
Implementation of real-time TDDFT for periodic systems in the open-source PySCF software package. 980-987
Research Articles
- Richard L. Zschau, Martin Zacharias:
Mechanism of β-hairpin formation in AzoChignolin and Chignolin. 988-1001 - Song-Ho Chong, Sihyun Ham:
Evolutionary conservation of amino acids contributing to the protein folding transition state. 1002-1009
Back Cover
- Sara Sadat Karachi, Kiamars Eskandari:
Back Cover. C4
Volume 44, Number 10, 2023
Research Articles
- Jurica Novak, Prateek Pathak, Maria A. Grishina, Vladimir A. Potemkin:
The design of compounds with desirable properties - The anti-HIV case study. 1016-1030 - Masatake Sugita, Fumio Hirata:
Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin mode analysis. 1031-1039 - João P. C. S. Felix, Krys E. A. Batista, Wesley O. Morais, Glaucio R. Nagurniak, Renato Pereira Orenha, Celso R. C. Rêgo, Diego Guedes-Sobrinho, Renato L. T. Parreira, Mateus Meneghetti Ferrer, Maurício J. Piotrowski:
Molecular adsorption on coinage metal subnanoclusters: A DFT+D3 investigation. 1040-1051 - Linda S. Reitz, Peter C. Müller, David Schnieders, Richard Dronskowski, Woon Ih Choi, Won-Joon Son, Inkook Jang, Dae Sin Kim:
On the atomistic origin of the polymorphism and the dielectric physical properties of beryllium oxide. 1052-1063 - Aaron Kramer, Ruth Pachter, Julia W. P. Hsu, William G. Vandenberghe:
The effect of solvent on determining highest occupied molecular orbital energies of semiconducting organic molecules: Insight from a combined computational approach. 1064-1072 - Cercis Morera-Boado, Margarita Isabel Bernal-Uruchurtu:
Interaction energy of Cl2 and Br2 with H2O: Exchange, dispersion and density the crucial ingredients. 1073-1087
Volume 44, Number 11, 2023
Research Articles
- Timothée O'Donnell, Frédéric Cazals:
Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry. 1094-1104 - Dmitrij Rappoport, Samuel Bekoe, Luke Nambi Mohanam, Scott Le, Naje' George, Ziyue Shen, Filipp Furche:
Libkrylov: A modular open-source software library for extremely large on-the-fly matrix computations. 1105-1118 - Harry W. Nash, Robert A. Shaw, John Grant Hill:
Correlation consistent auxiliary basis sets in density fitting Hartree-Fock: The atoms sodium through argon revisited. 1119-1128 - Mahroof Kalathingal, Young Min Rhee:
Molecular mechanism of binding between a therapeutic RNA aptamer and its protein target VEGF: A molecular dynamics study. 1129-1137 - Athanasios Koliogiorgos, Tomás Polcar, Bohuslav Rezek:
Energy transfer between Si nanocrystals and protoporphyrin molecules as a function of distance, orientation and size. 1138-1147 - Nobuki Inoue, Takahito Nakajima:
Realistic nuclear charge distribution model function for analytic nuclear attraction integrals in Gaussian basis functions. 1148-1157
Volume 44, Number 12, 2023
Research Articles
- Prasanta Bandyopadhyay, Mainak Sadhukhan:
Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators. 1164-1173 - Yingjin Ma, ZhiYing Li, Xin Chen, Bowen Ding, Ning Li, Teng Lu, Baohua Zhang, Bingbing Suo, Zhong Jin:
Machine-learning assisted scheduling optimization and its application in quantum chemical calculations. 1174-1188 - Maxim A. Maltsev, Svetlana A. Aksenova, Igor V. Morozov, Yury Minenkov, Evgenia L. Osina:
Ab initio calculations of the interaction potentials and thermodynamic functions for ArN and ArN+. 1189-1198 - Daniel Salgado-Blanco, Diana S. M. Flores-Saldaña, Fabiola Jaimes-Miranda, Florentino López-Urías:
Electronic and magnetic properties of TATA-DNA sequence driven by chemical functionalization. 1199-1207 - Chafia Sobhi, Lynda Merzoud, Souad Bouasla, Abdelmalek Khorief Nacereddine, Christophe Morell, Henry Chermette:
Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3, 3, 3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory. 1208-1220
Software Note
- Marina Macchiagodena, Marco Pagliai, Piero Procacci:
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes. 1221-1230
Volume 44, Number 13, 2023
RESEARCH ARTICLES
- Timothée O'Donnell, Viraj Agashe, Frédéric Cazals:
Geometric constraints within tripeptides and the existence of tripeptide reconstructions. 1236-1249 - Dan Krog, Martin Bødker Enghoff, Christoph Köhn:
A Monte Carlo approach to study the effect of ions on the nucleation of sulfuric acid-water clusters. 1250-1262 - Aleksandar Lazaric, Viren Pattni, Kaprao Fuegner, Arieh Ben-Naim, Matthias Heyden:
Solvation free energy arithmetic for small organic molecules. 1263-1277 - Jessica N. McCutcheon, D. Allen Clabo Jr.:
An atoms-in-molecules characterization of the nature of the OO bond in peroxides and nitroxide dimers. 1278-1290 - Chao Wang, Lin Chen, Wanxia Tang, Bing Zhao, Ruige Wang:
Molecular basis of RNA recognition by TBP of HIV-1 from multiple molecular dynamics simulations and energy predictions. 1291-1299 - Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang:
Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method. 1300-1311
SHORT COMMUNICATION
- Arslan R. Shaimardanov, Dmitry A. Shulga, Vladimir A. Palyulin:
On hidden anisotropy of formally charged fragments. 1312-1315
SOFTWARE NOTE
- Zhaoxuan Xie, Yinxuan Song, Fangwen Peng, Jianhao Li, Yifan Cheng, Lingzhi Zhang, Yingjin Ma, Yingqi Tian, Zhen Luo, Haibo Ma:
Kylin 1.0: An ab-initio density matrix renormalization group quantum chemistry program. 1316-1328
Volume 44, Number 14, 2023
REVIEW ARTICLE
- Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang:
Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. 1334-1346
RESEARCH ARTICLES
- Adrian L. Usler, Dennis Kemp, Alexander Bonkowski, Roger A. De Souza:
A general expression for the statistical error in a diffusion coefficient obtained from a solid-state molecular-dynamics simulation. 1347-1359 - Seho Lee, Chaok Seok, Hahnbeom Park:
Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design. 1360-1368 - Changsoo Lee, Jinsol Yang, Sohee Kwon, Chaok Seok:
GalaxyDock2-HEME: Protein-ligand docking for heme proteins. 1369-1380 - Dóra Vörös, Sebastian Mai:
Excited states of ortho-nitrobenzaldehyde as a challenging case for single- and multi-reference electronic structure theory. 1381-1394 - Luis Octavio de Araujo, Celso R. C. Rêgo, Wolfgang Wenzel, Danilo N. Silveira, Maurício J. Piotrowski, Fernando P. Sabino, Yohanes Pramudya, Diego Guedes-Sobrinho:
How cation nature controls the bandgap and bulk Rashba splitting of halide perovskites. 1395-1403
Volume 44, Number 15, 2023
RESEARCH ARTICLES
- Xiao-Ling Guan, Rui Sun, Bo Jin, Caixia Yuan, Yan-Bo Wu:
3-D molecular stars with covalent axial bonding. 1410-1417 - Leopold Maximilian Seidler, Joachim Laun, Thomas Bredow:
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence quality of the lanthanides La-Lu for solid-state calculations. 1418-1425 - Emna Rahali, Mohamed Oussama Zouaghi, Javier Fernández Sanz, Noureddine Raouafi, Youssef Arfaoui:
σ-Hole intermolecular interactions between carbon oxides and dihalogens: Ab-initio investigations. 1426-1436 - Jinyoung Byun, Srivithya Vellampatti, Prathit Chatterjee, Sun Ha Hwang, Byoung Choul Kim, Juyong Lee:
Characterization of the role of Kunitz-type protease inhibitor domain in dimerization of amyloid precursor protein. 1437-1445 - Sukanta Mondal, Gourhari Jana, Hemant Kumar Srivastava, Garikapati Narahari Sastry, Pratim Kumar Chattaraj:
Structure and stability of the sH binary hydrate cavity and host-guest versus guest-guest interactions therein: A DFT approach. 1446-1453 - Jakub Brzeski:
Aluminabenzene-based Lewis superacids and weakly coordinating anions. 1454-1463
Volume 44, Number 16, 2023
RESEARCH ARTICLES
- Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo:
Long-time scale simulations of virus-like particles from three human-norovirus strains. 1470-1483 - Pouria Nourian, Andrew J. Peters:
Implementation of probe rheology simulation technique in atomistically detailed molecular dynamics simulations. 1484-1492 - Sharath Belenahalli Shekarappa, Shivananda Kandagalla, Julian Lee:
Development of machine learning models based on molecular fingerprints for selection of small molecule inhibitors against JAK2 protein. 1493-1504 - Hilaire Chevreau, Julien Pilmé:
Promising insights in parallel grid-based algorithms for quantum chemical topology. 1505-1516 - Francesco Ferdinando Summa, Riccardo Zanasi, Paolo Lazzeretti:
On the computation of frequency-dependent molecular magnetizabilities via dynamical charge and current electron densities. 1517-1530
Volume 44, Number 17, 2023
SOFTWARE NOTE
- Siqin Cao, Michael L. Kalin, Xuhui Huang:
EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. 1536-1549
RESEARCH ARTICLES
- Mambatta Haritha, Cherumuttathu H. Suresh:
Hydrogen bonds of OCNH motif in rings in drugs: A molecular electrostatic potential analysis. 1550-1559 - Bhavana Panthi, Saheb Dutta, Amalendu Chandra:
All-atom simulations of the trimeric spike protein of SARS-CoV-2 in aqueous medium: Nature of interactions, conformational stability and free energy diagrams for conformational transition of the protein. 1560-1577 - Gabriel I. Pagola, Patricio F. Provasi, Marta B. Ferraro, Paolo Lazzeretti:
On the axial chirality of leucoindigo. 1578-1586 - Álvaro Valdés, Adriana Cabrera-Ramírez, Rita Prosmiti:
Confining CO2 inside sI clathrate-hydrates: The impact of the CO2-water interaction on quantized dynamics. 1587-1598
Volume 44, Number 18, 2023
RESEARCH ARTICLE
- Hirokazu Mishima, Yukihiro Itoh, Takashi Kurohara, Takayoshi Suzuki, Naoya Asada, Ken-ichi Kusakabe, Yuko Okamoto:
Origin of the kinetic HDAC2-selectivity of an HDAC inhibitor. 1604-1609
SOFTWARE NOTE
- Bruno César Feltes, Éderson Sales Moreira Pinto, Arthur Tonietto Mangini, Márcio Dorn:
NIAS-Server 2.0: A versatile complementary tool for structural biology studies. 1610-1623
RESEARCH ARTICLES
- Mohmmad Faizan, Ravinder Pawar:
Alanine boronic acid functionalized UiO-66 MOF as a nanoreactor for the conversion of CO2 into formic acid. 1624-1633 - Johannes R. Vornweg, Mario Wolter, Christoph R. Jacob:
A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions. 1634-1644 - Sneha Parambath, Vishnu Thannimangalath, Pattiyil Parameswaran:
Dative quadruple bonds between d10 transition metals and beryllium in BeM(PMe3)2 and BeM(CO)2 (M = Ni, Pd, and Pt) complexes: Transition metal fragments as six-electron donor and two-electron acceptor. 1645-1652
Volume 44, Number 19, 2023
RESEARCH ARTICLES
- J. Alfredo Freites, Mohab N. Louis, Douglas J. Tobias:
Insights into the solubility of γ D-crystallin from multiscale atomistic simulations. 1658-1666 - Kai Wang:
Cr2Gen- (n = 15-20) clusters with two Cr atoms exhibited antiferromagnetic coupling. 1667-1672 - Sujit Das, Kavita Devi, Sonam Suthar, Kartik Chandra Mondal:
Bonding and stability of elusive silaboryne (SiB) and germaboryne (GeB) with donor base ligands. 1673-1689 - Samah Al-Qaisi, Abdelazim M. Mebed, Muhammad Mushtaq, D. P. Rai, Tahani A. Alrebdi, Rais Ahmad Sheikh, Habib Rached, R. Ahmed, Muhammad Faizan, S. Bouzgarrou, Muhammad Anjum Javed:
A theoretical investigation of the lead-free double perovskites halides Rb2XCl6 (X = Se, Ti) for optoelectronic and thermoelectric applications. 1690-1703 - Luca Gerhards, Claus Nielsen, Daniel R. Kattnig, P. J. Hore, Ilia A. Solov'yov:
Modeling spin relaxation in complex radical systems using MolSpin. 1704-1714
Volume 44, Number 20, 2023
RESEARCH ARTICLES
- Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell Jr.:
GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. 1719-1732 - Farnaz Yashmin, Lakhya Jyoti Mazumder, Rohan Sharma, Pankaz Kumar Sharma:
Coordination of noble gases by alkali-metal-like superatom cation Be3B+. 1733-1739 - Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita:
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. 1740-1749
SOFTWARE NOTE
- Corentin Lefebvre, Jacques Klein, H. Khartabil, Jean-Charles Boisson, Eric Hénon:
IGMPlot: A program to identify, characterize, and quantify molecular interactions. 1750-1766
Volume 44, Number 21, 2023
RESEARCH ARTICLES
- Denis S. Tikhonov:
Metadynamics simulations with Bohmian-style bias potential. 1771-1775 - Hui Lu, Alireza Azizi, Xiao Peng Mi, Wenjing Yu, Yuting Peng, Tianlv Xu, Herbert Früchtl, Tanja Van Mourik, Steven R. Kirk, Samantha Jenkins:
Scoring molecular wires subject to an ultrafast laser pulse for molecular electronic devices. 1776-1785 - Pooja, Ravinder Pawar:
Origin of structure and stability of M@C18 (M = Cu, Ag, and Au) complexes with D9h point group. 1786-1794 - Robert J. Cordina, Beccy Smith, Tell Tuttle:
Triacylglyceride melting point determination using coarse-grained molecular dynamics. 1795-1801
Volume 44, Number 22, 2023
FRONT COVER
- Mincong Wu, Jun Liao, Zirui Shu, Changjun Chen:
Front Cover. C1
RESEARCH ARTICLES
- Arseniy A. Otlyotov, Yury Minenkov:
Gas-phase thermochemistry of noncovalent ligand-alkali metal ion clusters: An impact of low frequencies. 1807-1816 - Elena O. Levina, Vladimir G. Tsirelson:
DFT potentials from a chemical perspective: Anatomy of electron (de)localization in molecules and crystals. 1817-1835
SOFTWARE NOTES
- Payam Kelich, Huanhuan Zhao, Jose R. Orona, Lela Vukovic:
BinderSpace: A package for sequence space analyses for datasets of affinity-selected oligonucleotides and peptide-based molecules. 1836-1844 - Mincong Wu, Jun Liao, Zirui Shu, Changjun Chen:
Enhanced sampling in explicit solvent by deep learning module in FSATOOL. 1845-1856
Volume 44, Number 23, 2023
RESEARCH ARTICLES
- Mini Bharati Ahirwar, Milind M. Deshmukh:
Fragments-in-fragments method for efficient and reliable estimates of individual hydrogen bond energies in large molecular clusters. 1861-1874 - Malak Azmat Ali, Aboud Ahmed Awadh Bahajjaj, Samah Al-Qaisi, Mika A. Sillanpää, Afzal Khan, Xiaoyu Wang:
Structural, electronic, magnetic and thermoelectric properties of Tl2NbX6 (X = Cl, Br) variant perovskites calculated via density functional theory. 1875-1883 - Yuki Mitsuta, Toshio Asada:
Nudged elastic stiffness band method: A method to solve kinks problems of reaction paths. 1884-1897 - Vishal Kumar Porwal, Antoine Carof, Francesca Ingrosso:
Hydration effects on the vibrational properties of carboxylates: From continuum models to QM/MM simulations. 1898-1911
Volume 44, Number 24, 2023
RESEARCH ARTICLES
- Yufeng Wu, Jiajie Kang, Wei Gao, Mingshu Bi, Dongcheng Yang, Runlai Ji, Qingwei Meng, Cunfei Ma:
A DFT and kinetic study: Is it possible to prepare epoxides without catalysts using the in-situ generated peroxy radicals or peroxides by one-step method? 1917-1927 - Ivan N. Dobrovolskiy, Victor V. Kostjukov:
TD-DFT study of BIPS spiropyran: Effects of functionals and high-polarity solvent on CspiroO bond dissociation and recovery. 1928-1940 - Ali Ghiami-Shomami, Christof Hättig:
Performance of the COSMO solvation model for photoacidity and basicity in water. 1941-1955 - Umar Lucio Rezende, Leonardo A. De Souza, Jadson Cláudio Belchior:
An approach based on genetic algorithms and machine learning coupled for studying alloy and molecular clusters by optimizing quantum energy surfaces. 1956-1969
Volume 44, Number 25, 2023
RESEARCH ARTICLES
- Myung Keun Cho, Song-Ho Chong, Sihyun Ham, Seokmin Shin:
Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins. 1976-1985 - Jennifer Anders, Henrik Wiedenhaupt, Florian Kreuter, Ralf Tonner-Zech, Beate Paulus:
Chemical bonding of HF, HCl, and H 2 O onto YF 3 surfaces: Quantification by first principles. 1986-1997 - Alireza Tehrani, James S. M. Anderson, Debajit Chakraborty, Juan I. Rodriguez-Hernandez, David C. Thompson, Toon Verstraelen, Paul W. Ayers, Farnaz Heidar-Zadeh:
An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions. 1998-2015 - Giacomo Saielli:
Computational NMR spectroscopy of 205Tl. 2016-2029
SOFTWARE NOTE
- Arkadeep Sarkar, Lucia Sessa, Francesco Marrafino, Stefano Piotto:
GUIDE: A GUI for automated quantum chemistry calculations. 2030-2036
Volume 44, Number 26, 2023
RESEARCH ARTICLES
- Zilin Song, Ye Ding, Jing Huang:
Constant advance replicas method for locating minimum energy paths and transition states. 2042-2057 - Hsing-Yin Chen, Yu-Fen Lin:
DFT study on the catalytic decomposition of hydrogen peroxide by iron complexes of nitrilotriacetate. 2058-2072 - Nobuki Inoue, Takahito Nakajima:
Analytical quadrature method using recurrence formulas for two-electron integrals of frequency-dependent Breit interaction. 2073-2085 - Wanli You, Yuandao Chen:
Exploring the inhibition mechanism of SARS-CoV-2 main protease by ebselen: A molecular docking, molecular dynamics simulation and DFT approach. 2086-2095
SOFTWARE NOTE
- Joanna M. Zarnecka, Katarzyna H. Kaminska:
FRAGMENTISE: A user-friendly, cross-platform tool to create and analyze comprehensive small-molecule fragment databases. 2096-2102
Volume 44, Number 27, 2023
RESEARCH ARTICLES
- Celine Nieuwland, Pascal Vermeeren, Friedrich Matthias Bickelhaupt, Célia Fonseca Guerra:
Understanding chemistry with the symmetry-decomposed Voronoi deformation density charge analysis. 2108-2119 - Hagen Neugebauer, Benedikt Bädorf, Sebastian Ehlert, Andreas Hansen, Stefan Grimme:
High-throughput screening of spin states for transition metal complexes with spin-polarized extended tight-binding methods. 2120-2129 - Walid Taouali, Kamel Alimi, Asma Sindhoo Nangraj, Mark E. Casida:
Density-functional theory (DFT) and time-dependent DFT study of the chemical and physical origins of key photoproperties of end-group derivatives of a nonfullerene acceptor molecule for bulk heterojunction organic solar cells. 2130-2148 - Silvia Di Grande, Mihaly Kállay, Vincenzo Barone:
Accurate thermochemistry at affordable cost by means of an improved version of the JunChS-F12 model chemistry. 2149-2157
LETTER TO THE EDITOR
- Yu-Chen Wang, Shishi Feng, WanZhen Liang, Yi Zhao:
Comment on "A posteriori localization of many-body excited states through simultaneous diagonalization". 2158-2159
Volume 44, Number 28, 2023
RESEARCH ARTICLES
- Shitanshu Bajpai, Brian K. Petkov, Muchen Tong, Charlles R. A. Abreu, Nisanth N. Nair, Mark E. Tuckerman:
An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package. 2166-2183 - Sonam Suthar, Kartik Chandra Mondal:
Open shell versus closed shell bonding interaction in cyclopropane derivatives: EDA-NOCV analyses. 2184-2211 - Mirsada Cehic, Ivana Niksic-Franjic:
Reactions of a hydrogen atom with haloacetates in aqueous solutions: Computational evidence for proton-coupled electron transfer and competing mechanisms. 2212-2222 - Hao Tian, Sian Xiao, Xi Jiang, Peng Tao:
PASSerRank: Prediction of allosteric sites with learning to rank. 2223-2229
SOFTWARE NOTE
- Guang Chen:
polyGraft 1.0: A program for molecular structure and topology generation of polymer-grafted hybrid nanostructures. 2230-2239
Volume 44, Number 29, 2023
RESEARCH ARTICLES
- Roiney Beal, Danillo Valverde, Paulo Fernando Bruno Gonçalvez, Antonio Carlos Borin:
Photophysics of tzAdenine and tzGuanine fluorescent nucleobases embedded into DNA and RNA. 2246-2255 - Gabriel Monteiro-de-Castro, Itamar Borges Jr.:
A Hammett's analysis of the substituent effect in functionalized diketopyrrolopyrrole (DPP) systems: Optoelectronic properties and intramolecular charge transfer effects. 2256-2273 - Jan Bode, Gabriele Raabe:
Molecular dynamics studies of the solubility behavior of carbon dioxide (CO2), difluoromethane (R-32), 1-chloro-3,3,3-trifluoropropene (R-1233zd(E)) and 2,3,3,3-tetrafluoro-1-propene (R-1234yf) in pentaerythritol tetra(2-ethylhexanoate) (PEB8), pentaerythritol tetrabutyrate (PEC4) and pentaerythritol tetraoctanoate (PEC8). 2274-2283 - Yu-Sheng Xu, Dong Die, Ben-Xia Zheng:
Growth pattern and electronic and magnetic properties of Cr-doped silver clusters. 2284-2293
REVIEW ARTICLE
- Qianqian Deng, Jun Zhu:
Adaptive σ aromaticity in the rhenacyclopropene rings. 2294-2301
Volume 44, Number 30, 2023
RESEARCH ARTICLES
- Lorenzo Briccolani-Bandini, Éric Brémond, Marco Pagliai, Gianni Cardini, Ilaria Ciofini, Carlo Adamo:
Concerted versus stepwise proton transfer reactions in the [2, 2′-bipyridyl]-3-3′-diol molecule: A static and dynamic ab-initio investigation. 2308-2318 - Permono Adi Putro, Aditya Wibawa Sakti, Faozan Ahmad, Hiromi Nakai, Husin Alatas:
Quantum mechanical assessment on the optical properties of capsanthin conformers. 2319-2331 - Jimin Park, InSuk Joung, Keehyoung Joo, Jooyoung Lee:
Application of conformational space annealing to the protein structure modeling using cryo-EM maps. 2332-2346 - Zhipeng Ke, Jingwei Weng, Xin Xu:
Calculating 13C NMR chemical shifts of large molecules using the eXtended ONIOM method at high accuracy with a low cost. 2347-2357 - Luis López-Sosa, Patrizia Calaminici, Andreas M. Köster:
Cartesian constraints in QM/MM optimizations. 2358-2368
Volume 44, Number 31, 2023
RESEARCH ARTICLES
- Mihkel Ugandi, Michael Roemelt:
A configuration-based heatbath-CI for spin-adapted multireference electronic structure calculations with large active spaces. 2374-2390 - Masatoshi Hasebe, Takuro Tsutsumi, Tetsuya Taketsugu, Takao Tsuneda:
Total and orbital density-based analyses of molecules revealing long-range interaction regions. 2391-2403 - M. Ilk Capar, A. Cetin, Alexandre V. Zakharov:
Water/organic liquid interface properties with amine, carboxyl, thiol, and methyl terminal groups as seen from MD simulations. 2404-2413 - Umut Ozuguzel, Adélia J. A. Aquino, Reed Nieman, Shelley D. Minteer, Carol Korzeniewski:
Resonance Raman spectra and excited state properties of methyl viologen and its radical cation from time-dependent density functional theory. 2414-2423 - Itamar Borges Jr., Roberta M. P. O. Guimarães, Gabriel Monteiro-de-Castro, Nathália M. P. Rosa, Reed Nieman, Hans Lischka, Adélia J. A. Aquino:
A comprehensive analysis of charge transfer effects on donor-pyrene (bridge)-acceptor systems using different substituents. 2424-2436
Volume 44, Number 32, 2023
RESEARCH ARTICLES
- Samah Al-Qaisi, Habib Rached, Tahani A. Alrebdi, S. Bouzgarrou, Debidatta Behera, Sanat Kumar Mukherjee, Mohamed Khuili, Mohamed Adam, Ajay Singh Verma, Mohammed Ezzeldien:
Study of mechanical, optical, and thermoelectric characteristics of Ba2XMoO6 (X = Zn, Cd) double perovskite for energy harvesting. 2442-2452 - Dinara N. Sagatova, Pavel N. Gavryushkin, Nursultan E. Sagatov, Maksim V. Banaev:
Crystal structures and P-T phase diagrams of SrC 2 O 5 and BaC 2 O 5. 2453-2460 - Matthias Haasler, Toni M. Maier, Martin Kaupp:
Toward a correct treatment of core properties with local hybrid functionals. 2461-2477 - Eriosvaldo Florentino Gusmão, Roberto Luiz Andrade Haiduke:
Relativistic adapted Gaussian basis sets free of variational prolapse of small and medium size for cesium through radon. 2478-2485 - Manjinder Kour, Attila Táborosi, Eric S. Boyd, Robert K. Szilagyi:
Development of molecular cluster models to probe pyrite surface reactivity. 2486-2500
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