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ORCIDJournal of Computational Chemistry, Volume 42
Volume 42, Number 1, January 2021
- Shuichi Ebisawa, Takuro Tsutsumi, Tetsuya Taketsugu
:
Cover Image. i
- Zhenghao Wu, Andreas Kalogirou, Antonio De Nicola, Giuseppe Milano, Florian Müller-Plathe:
Atomistic hybrid particle-field molecular dynamics combined with slip-springs: Restoring entangled dynamics to simulations of polymer melts. 6-18 - Hiromitsu Shimoyama, Yasushige Yonezawa:
Atomistic detailed free-energy landscape of intrinsically disordered protein studied by multi-scale divide-and-conquer molecular dynamics simulation. 19-26 - Shuichi Ebisawa, Takuro Tsutsumi, Tetsuya Taketsugu:
Geometric analysis of anharmonic downward distortion following paths. 27-39 - Seyed Abdolreza Sadjadi, Chérif F. Matta, Ian P. Hamilton:
Bonding and metastability for Group 12 dications. 40-49 - Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman-Konieczna, Katarzyna Stapor:
ProteinUnet - An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures. 50-59 - Roxana M. del Castillo, Estrella Ramos, Ana Martínez:
Interaction of graphene with antipsychotic drugs: Is there any charge transfer process? 60-65
Volume 42, Number 2, January 2021
- Jules Tshishimbi Muya, Bienfait Kabuyaya Isamura, Issofa Patouossa, Minh Tho Nguyen, Arnout Ceulemans:
Structure, stability and bonding of the leapfrog B240, ±1, ±2. 72-80 - Wen-Jie Wei, Per E. M. Siegbahn:
The active E4 structure of nitrogenase studied with different DFT functionals. 81-85 - Karolina Kwapien, Laurent Gavara, Jean-Denis Docquier, Dorothée Berthomieu, Jean-François Hernandez, Nohad Gresh:
Intermolecular interactions of the extended recognition site of VIM-2 metallo-β-lactamase with 1, 2, 4-triazole-3-thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio QC. 86-106 - Anton Konovalov, Benjamin C. B. Symons, Paul L. A. Popelier:
On the many-body nature of intramolecular forces in FFLUX and its implications. 107-116 - Son Tung Ngo:
Estimating the ligand-binding affinity via λ-dependent umbrella sampling simulations. 117-123 - Lily Arrué, Ricardo Pino-Rios:
On the stability and chemical bond of noble gas halide cations NgX+ (Ng = He - Rn; X = F - I). 124-129
Volume 42, Number 3, January 2021
- Motomichi Tashiro, Yutaka Imamura, Michio Katouda:
De novo generation of optically active small organic molecules using Monte Carlo tree search combined with recurrent neural network. 136-143 - Milica Feldt, Alex Brown:
Assessment of local coupled cluster methods for excited states of BODIPY/Aza-BODIPY families. 144-155 - Tomomi Kondo, Takehiko Sasaki, Sergi Ruiz-Barragan, Jordi Ribas-Ariño, Motoyuki Shiga:
Refined metadynamics through canonical sampling using time-invariant bias potential: A study of polyalcohol dehydration in hot acidic solutions. 156-165 - Satoru Iuchi, Nobuaki Koga:
A model electronic Hamiltonian to describe low-lying d-d and metal-to-ligand charge-transfer excited states of [Fe(bpy)3]2+. 166-179 - Prathap Kumar Jharapla, Subrata Mondal, Ganapathy Vaitheeswaran:
Comparative DFT study of vibrational, electronic, and optical properties of energetic alkali metal salts based on nitrogen-rich 5-aminotetrazole. 180-191 - Koichi Ohno, Naoki Kishimoto, Takeaki Iwamoto, Hiroko Satoh, Hiromasa Watanabe:
High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H5C2NO2. 192-204
Volume 42, Number 4, February 2021
- Nityananda Sahu, Jeremy O. Richardson, Robert Berger:
Instanton calculations of tunneling splittings in chiral molecules. 210-221 - Simone L. Waite, Amir Karton, Bun Chan, Alister J. Page:
Thermochemical stabilities of giant fullerenes using density functional tight binding theory and isodesmic-type reactions. 222-230 - Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita:
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems. 231-241 - Robert A. Evarestov, Andrej I. Panin, Yuri S. Tverjanovich:
Argentophillic interactions in argentum chalcogenides: First principles calculations and topological analysis of electron density. 242-247 - Anh L. P. Nguyen, Thomas G. Mason, Benny D. Freeman, Ekaterina I. Izgorodina:
Prediction of lattice energy of benzene crystals: A robust theoretical approach. 248-260 - Subhamoy Mahajan, Tian Tang:
Comment on "Martini force field for protonated polyethyleneimine". 261-263
Volume 42, Number 5, February 2021
- Mosavverul Hassan, Evangelos A. Coutsias:
Protein secondary structure motifs: A kinematic construction. 271-292 - Michael Edmund Beck, Christoph Riplinger, Frank Neese, Giovanni Bistoni:
Unraveling individual host-guest interactions in molecular recognition from first principles quantum mechanics: Insights into the nature of nicotinic acetylcholine receptor agonist binding. 293-302 - Marc Jäger, Rolf Schäfer:
Variation of the optical properties with size and composition of small, isolated CdxSey+ clusters. 303-309 - San Kiong Lai, Chong Chiat Lim:
Neutral gold clusters studied by the isothermal Brownian-type molecular dynamics and metadynamics molecular dynamics simulations. 310-325 - Tom Speelman, Ana V. Cunha, R. K. Kathir, Remco W. A. Havenith:
Electronic couplings for singlet fission: Orbital choice and extrapolation to the complete basis set limit. 326-333 - Rubén Laplaza, Carlos Cárdenas, Patrick Chaquin, Julia Contreras-Garcia, Paul W. Ayers:
Orbital energies and nuclear forces in DFT: Interpretation and validation. 334-343 - Karinna Mendanha, Richard Costa Prado, Leonardo Bruno Assis Oliveira, Guilherme Colherinhas:
Molecular dynamic simulations, GIAO-NMR and TD-DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution. 344-357 - Xiaorong Liu, Xiping Gong, Jianhan Chen:
Accelerating atomistic simulations of proteins using multiscale enhanced sampling with independent tempering. 358-364
- Rebecca L. M. Gieseking:
A new release of MOPAC incorporating the INDO/S semiempirical model with CI excited states. 365-378 - Jianfu Chen, Menglei Jia, Peijun Hu, Haifeng Wang:
CATKINAS: A large-scale catalytic microkinetic analysis software for mechanism auto-analysis and catalyst screening. 379-391
Volume 42, Number 6, March 2021
- Bartosz Blasiak, Joanna D. Bednarska, Marta Choluj, Robert W. Góra, Wojciech Bartkowiak:
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- Bartosz Blasiak, Joanna D. Bednarska, Marta Choluj, Robert W. Góra, Wojciech Bartkowiak:
Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials. 398-411 - Yang Wang:
Superposition of waves or densities: Which is the nature of chemical resonance? 412-417 - Maria Pechlaner, Andreas P. Dorta, Zhixiong Lin, Victor H. Rusu, Wilfred F. van Gunsteren:
A method to apply bond-angle constraints in molecular dynamics simulations. 418-434 - Ola Aarøen, Henrik Kiær, Enrico Riccardi:
PyVisA: Visualization and Analysis of path sampling trajectories. 435-446
- Sergio Martí:
QMCube (QM3): An all-purpose suite for multiscale QM/MM calculations. 447-457 - Toon Verstraelen, William Adams, Leila Pujal, Alireza Tehrani, Braden D. Kelly, Luis Macaya, Fanwang Meng, Michael Richer, Raymundo Hernández-Esparza, Xiaotian Derrick Yang, Matthew Chan, Taewon David Kim, Maarten Cools-Ceuppens, Valerii Chuiko, Esteban Vöhringer-Martinez, Paul W. Ayers, Farnaz Heidar-Zadeh:
IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files. 458-464
Volume 42, Number 7, March 2021
- Tian-yu Sun, Kai Chen, Huakang Zhou, Tingting You, Penggang Yin, Xiao Wang:
Revisiting the effect of f-functions in predicting the right reaction mechanism for hypervalent iodine reagents. 470-474 - Martin Sulka, Matús Dubecký:
Fragmentation of natural orbital occupation numbers-based diagnostic of differential multireference character in complexes with hydrogen bonds. 475-483 - Na Zhang, Jinhui Mi, Suhong Huo, Lingpeng Meng, Xiaoyan Li:
Computational prediction on the catalytic activity of heterobimetallic complex featuring MMˊ triple bond in acetylene cyclotrimerization: Mechanistic study. 484-491 - Martin Mrovec, J. A. Berger:
A diagonalization-free optimization algorithm for solving Kohn-Sham equations of closed-shell molecules. 492-504 - Dae-Hwan Ahn, Jong-Won Song:
Assessment of long-range corrected density functional theory on the absorption and vibrationally resolved fluorescence spectrum of carbon nanobelts. 505-515
- Sadisha Nanayakkara, Yunwen Tao, Elfi Kraka:
Comment on "Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory". 516-521
Volume 42, Number 8, March 2021
- Shoichi Tanimoto, Koichi Tamura, Shigehiko Hayashi, Norio Yoshida, Haruyuki Nakano:
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- Marcos Casanova-Páez, Lars Goerigk:
Global double hybrids do not work for charge transfer: A comment on "Double hybrids and time-dependent density functional theory: An implementation and benchmark on charge transfer excited states". 528-533
- Jiri Brabec, Jan Brandejs, Karol Kowalski, Sotiris S. Xantheas, Örs Legeza, Libor Veis:
Massively parallel quantum chemical density matrix renormalization group method. 534-544 - Lei Zhang, Qin Zhu, Liuzhou Gao, Linlin Yang, Wei Li, Shuhua Li, Jun Zhu, Wei Wang, Guixiang Zeng:
Rational design of the nickel-borane complex for efficient hydrogenation of styrene. 545-551 - Shoichi Tanimoto, Koichi Tamura, Shigehiko Hayashi, Norio Yoshida, Haruyuki Nakano:
A computational method to simulate global conformational changes of proteins induced by cosolvent. 552-563 - Elena Yu. Tupikina, Peter M. Tolstoy, Anna A. Titova, Mikhail A. Kostin, Gleb S. Denisov:
Estimations of FH···X hydrogen bond energies from IR intensities: Iogansen's rule revisited. 564-571
- Fabian Schuhmann, Vasili Korol, Ilia A. Solov'yov:
Introducing Pep McConst - A user-friendly peptide modeler for biophysical applications. 572-580
Volume 42, Number 9, April 2021
- Arnaldo Rapallo, Roberto Gaspari, Gianvito Grasso, Andrea Danani:
Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations. 586-599 - John T. Bedford, Jennifer Poutsma, Norou Diawara, Lesley H. Greene:
The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. 600-607 - Stefano Scoditti, Vincenzo Vigna, Eslam Dabbish, Emilia Sicilia:
Iodido equatorial ligands influence on the mechanism of action of Pt(IV) and Pt(II) anti-cancer complexes: A DFT computational study. 608-619 - Toshikazu Fujimori, Masato Kobayashi, Tetsuya Taketsugu:
Energy-based automatic determination of buffer region in the divide-and-conquer second-order Møller-Plesset perturbation theory. 620-629
- Kai Trepte, Sebastian Schwalbe:
porE: A code for deterministic and systematic analyses of porosities. 630-643 - Francesco Segatta, Artur Nenov, Daniel R. Nascimento, Niranjan Govind, Shaul Mukamel, Marco Garavelli:
iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software. 644-659
Volume 42, Number 10, April 2021
- Lucas de Azevedo Santos, Teodorico C. Ramalho, Trevor A. Hamlin, Friedrich Matthias Bickelhaupt:
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- Ananya Gangopadhyay, Simon Winberg, Kevin J. Naidoo:
Anisotropic numerical potentials for coarse-grained modeling from high-speed multidimensional lookup table and interpolation algorithms. 666-675 - Fernando Jiménez-Grávalos, Miguel Gallegos, Ángel Martín Pendás, Alexander S. Novikov:
Challenging the electrostatic σ-hole picture of halogen bonding using minimal models and the interacting quantum atoms approach. 676-687 - Lucas de Azevedo Santos, Teodorico C. Ramalho, Trevor A. Hamlin, Friedrich Matthias Bickelhaupt:
Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. 688-698 - Ehsan Rahmatizad KhajePasha, Stefan Goedecker, S. Alireza Ghasemi:
New strontium titanate polymorphs under high pressure. 699-705 - Thomas G. Bates, Jurgens Hendrik de Lange, Ignacy Cukrowski:
The CH···HC interaction in biphenyl is a delocalized, molecular-wide and entirely non-classical interaction: Results from FALDI analysis. 706-718 - Vikrant Tripathy, Arjun Saha, Krishnan Raghavachari:
Electrostatically embedded molecules-in-molecules approach and its application to molecular clusters. 719-734
Volume 42, Number 11, April 2021
- Grzegorz Matyszczak, Krzysztof Zberecki:
Application of artificial neural network and global optimization techniques for high throughput modeling of the crystal structure of stannites and kesterites. 740-745 - Maksym Druchok, Dzvenymyra Yarish, Oleksandr Gurbych, Mykola Maksymenko:
Toward efficient generation, correction, and properties control of unique drug-like structures. 746-760 - Christopher Robertson, Scott Habershon:
Simple position and orientation preconditioning scheme for minimum energy path calculations. 761-770 - Yongna Yuan, Shaowei Fu, Dongxu Huo, Wei Su, Ruisheng Zhang, Jiaxuan Wei:
Multipolar electrostatics for hairpin and pseudoknots in RNA: Improving the accuracy of force field potential energy function. 771-786 - Alexei M. Nikitin, Vladislava Milchevskaya, Alexander Lyubartsev:
To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC. 787-792 - Marvin Hoffmann, Andreas Dreuw:
Deciphering excited state properties utilizing algebraic diagrammatic construction schemes of decreasing order. 793-800
Volume 42, Number 12, May 2021
- Alexander Platonenko, Francesco Silvio Gentile, Fabien Pascale, Philippe D'Arco, Roberto Dovesi:
Interstitial carbon defects in silicon. A quantum mechanical characterization through the infrared and Raman spectra. 806-817 - Sebastián Adolfo Cuesta, Luis Rincón, Fernando Javier Torres, Vladimir Rodriguez, José Ramón Mora:
A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack. 818-826 - Jan-Niclas Luy, Mahlet Molla, Lisa Pecher, Ralf Tonner:
Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces. 827-839 - Johanna Klein, Paul Fleurat-Lessard, Julien Pilmé:
New insights in chemical reactivity from quantum chemical topology. 840-854 - Vicente Ramm, Jehanzeb H. Chaudhry, Christopher D. Cooper:
Efficient mesh refinement for the Poisson-Boltzmann equation with boundary elements. 855-869 - Elena O. Levina, Maria G. Khrenova, Vladimir G. Tsirelson:
The explicit role of electron exchange in the hydrogen bonded molecular complexes. 870-882
Volume 42, Number 13, May 2021
- Fang Yuan, Zhifang Yang, Xiaoying Zhang, Cuiyan Tong, Godefroid Gahungu, Wenliang Li, Jingping Zhang:
Judicious design functionalized 3D-COF to enhance CO2 adsorption and separation. 888-896 - Yudibeth Sixto-López, Marlet Martínez-Archundia:
Drug repositioning to target NSP15 protein on SARS-CoV-2 as possible COVID-19 treatment. 897-907 - Shaojie Shen, Xinyue Jing, Xueying Zhang, Xiaoyan Li, Yanli Zeng:
The competition and cooperativity of hydrogen/halogen bond and π-hole bond involving the heteronuclear ethylene analogues. 908-916 - Hamed Haghshenas, Bita Kaviani, Monireh Firouzeh, Hossein Tavakol:
Developing a variation of 3D-QSAR/MD method in drug design. 917-929
- Vivien Walter, Céline Ruscher, Olivier Benzerara, Fabrice Thalmann:
MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes. 930-943 - Nikolai Andreadi, Artem Mitrofanov, Artem Eliseev, Petr Matveev, Stepan Kalmykov, Vladimir Petrov:
PyRad: A software shell for simulating radiolysis with Qball package. 944-950
Volume 42, Number 14, May 2021
- Éric Brémond, Alistar Ottochian, Ángel J. Pérez-Jiménez, Ilaria Ciofini, Giovanni Scalmani, Michael J. Frisch, Juan Carlos Sancho-García, Carlo Adamo:
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- Junichi Higo, Hajime Takashima, Yoshifumi Fukunishi, Atsushi Yoshimori:
Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions. 956-969 - Éric Brémond, Alistar Ottochian, Ángel J. Pérez-Jiménez, Ilaria Ciofini, Giovanni Scalmani, Michael J. Frisch, Juan Carlos Sancho-García, Carlo Adamo:
Assessing challenging intra- and inter-molecular charge-transfer excitations energies with double-hybrid density functionals. 970-981 - Vijay Gopal Chilkuri, Frank Neese:
Comparison of many-particle representations for selected-CI I: A tree based approach. 982-1005 - Nazanin Donyapour, Matthew J. Hirn, Alex Dickson:
ClassicalGSG: Prediction of logP using classical molecular force fields and geometric scattering for graphs. 1006-1017 - Hugo Geindre, Abdul-Rahman Allouche, Daniel Peláez:
Non long-range corrected density functionals incorrectly describe the intensity of the CH stretching band in polycyclic aromatic hydrocarbons. 1018-1027
- Jean-Marc Crowet, Sébastien Buchoux, Nicolas Belloy, Catherine Sarazin, Laurence Lins, Manuel Dauchez:
LIMONADA: A database dedicated to the simulation of biological membranes. 1028-1033
Volume 42, Number 15, June 2021
- Martyna Maszota-Zieleniak, Mateusz Marcisz, Malgorzata M. Kogut, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov:
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. 1040-1053 - Bernardino Tirri, Gloria Mazzone, Alistar Ottochian, Jérôme Gomar, Umberto Raucci, Carlo Adamo, Ilaria Ciofini:
A combined Monte Carlo/DFT approach to simulate UV-vis spectra of molecules and aggregates: Merocyanine dyes as a case study. 1054-1063 - Joachim Laun, Thomas Bredow:
BSSE-corrected consistent Gaussian basis sets of triple-zeta valence with polarization quality of the sixth period for solid-state calculations. 1064-1072 - Yoshimichi Andoh, Shin'ichi Ichikawa, Tatsuya Sakashita, Noriyuki Yoshii, Susumu Okazaki:
Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations. 1073-1087 - Ryan L. Hayes, Charles L. Brooks III:
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. 1088-1094
- Florian Flachsenberg, Matthias Rarey:
LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. 1095-1100
Volume 42, Number 16, June 2021
- Sai Manoj N. V. T. Gorantla, Pattiyil Parameswaran, Kartik Chandra Mondal:
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- Zaki S. Safi, Nuha Wazzan:
Benchmark calculations of proton affinity and gas-phase basicity using multilevel (G4 and G3B3), B3LYP and MP2 computational methods of para-substituted benzaldehyde compounds. 1106-1117 - Jorge I. Martínez-Araya, Christophe Morell:
The density polarization reveals directions of electron displacements due to the substituent effect: Analysis performed on a metal-organic Mo-Oxo catalyst. 1118-1125 - Demeter Tzeli:
Quadruple chemical bonding in the diatomic anions TcN-, RuC-, RhB-, and PdBe-. 1126-1137 - Adyasa Priyadarsini, Bhabani S. Mallik:
Comparative first principles-based molecular dynamics study of catalytic mechanism and reaction energetics of water oxidation reaction on 2D-surface. 1138-1149 - Raúl Palmeiro, Obis Castaño:
[10]annulene: Electrocyclization mechanisms. 1150-1158 - Sai Manoj N. V. T. Gorantla, Pattiyil Parameswaran, Kartik Chandra Mondal:
Stabilization of group 14 elements E = C, Si, Ge by hetero-bileptic ligands cAAC, MCOn with push-pull mechanism. 1159-1177
Volume 42, Number 17, June 2021
- Sergei F. Vyboishchikov, Alexander A. Voityuk:
Fast non-iterative calculation of solvation energies for water and non-aqueous solvents. 1184-1194 - Agnieszka Kacka-Zych, Radomir Jasinski:
Understanding the molecular mechanism of γ-elimination of nitrous acid in the framework of the molecular electron density theory. 1195-1203 - Xiangyu Jia, Hu Ge, Ye Mei:
Free energy change estimation: The Divide and Conquer MBAR method. 1204-1211 - Davide Luise, Liam Wilbraham, Frédéric Labat, Ilaria Ciofini:
Modeling UV-Vis spectra of low dimensional materials using electrostatic embedding: The case of CdSe. 1212-1224 - Gabriela Dias-da-Silva, Rodrigo L. O. R. Cunha, Mauricio D. Coutinho-Neto:
Equilibrium between tri- and tetra-coordinate chalcogenuranes is critical for cysteine protease inhibition. 1225-1235 - Pirouz Kiani, Elaine S. Dodsworth, A. B. P. Lever, William J. Pietro:
Modeling ligand electrochemical parameters by repulsion-corrected eigenvalues. 1236-1242
Volume 42, Number 18, July 2021
- Sarah L. V. Zahn, Ole Hammerich, Poul Erik Hansen, Stephan P. A. Sauer:
The best density functional theory functional for the prediction of 1H and 13C chemical shifts of protonated alkylpyrroles. 1248-1262 - Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren:
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. 1263-1282 - Pascal Henkel, Doreen Mollenhauer:
Uncertainty of exchange-correlation functionals in density functional theory calculations for lithium-based solid electrolytes on the case study of lithium phosphorus oxynitride. 1283-1295 - Abdelmalek Khorief Nacereddine, Lynda Merzoud, Christophe Morell, Henry Chermette:
A computational investigation of the selectivity and mechanism of the Lewis acid catalyzed oxa-Diels-Alder cycloaddition of substituted diene with benzaldehyde. 1296-1311 - Mohammadreza Eidi, Mohsen Vafaee, Hamed Koochaki Kelardeh, Alexandra Landsman:
High-order harmonic generation by static coherent states method in single-electron atomic and molecular systems. 1312-1320
- Ryan S. DeFever, Ray A. Matsumoto, Alexander W. Dowling, Peter T. Cummings, Edward J. Maginn:
MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software. 1321-1331
Volume 42, Number 19, July 2021
- Frank Weinhold, Eric D. Glendening:
Comment on "Superposition of Waves or Densities: Which Is the Nature of Chemical Resonance?" [J. Comput. Chem. 2021 , 42, 412-417]. 1338-1340 - Yang Wang:
Response to comment on "Superposition of waves or densities: Which is the nature of chemical resonance?". 1341-1343
- Hieu C. Dong, Thi H. Ho, Thu M. Nguyen, Yoshiyuki Kawazoe, Hung M. Le:
Dissociation of hydrogen peroxide in water and methanol through a biased molecular dynamics investigation. 1344-1353 - Samaneh Hokmi, Sadegh Salehzadeh, Yasin Gholiee:
The comparison of structure, nature of bond, and electronic transitions in [M(η5-Cp)(η5-C60Me5)] (M = Fe2+, Ru2+, Os2+) hybrids and corresponding metallocenes; a theoretical study. 1354-1363 - Lynda Merzoud, Frédéric Guégan, Henry Chermette, Christophe Morell:
Understanding the intermolecular Diels-Alder cycloaddition promotion: Activation strain model/energy decomposition analysis model and conceptual density functional theory viewpoints. 1364-1372
- Samarjeet Prasad, Andrew C. Simmonett, Rubén Meana-Pañeda, Bernard R. Brooks:
The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. 1373-1383
Volume 42, Number 20, July 2021
- Bastien Casier, Mauricio Chagas da Silva, Michael Badawi, Fabien Pascale, Tomás Bucko, Sébastien Lebègue, Dario Rocca:
Hybrid localized graph kernel for machine learning energy-related properties of molecules and solids. 1390-1401 - Nils Schieschke, Beatrix M. Bold, Philipp M. Dohmen, Daniel Wehl, Marvin Hoffmann, Andreas Dreuw, Marcus Elstner, Sebastian Höfener:
Geometry dependence of excitonic couplings and the consequences for configuration-space sampling. 1402-1418 - Anders Hutcheson, Alexander Christian Paul, Rolf Heilemann Myhre, Henrik Koch, Ida-Marie Høyvik:
Describing ground and excited state potential energy surfaces for molecular photoswitches using coupled cluster models. 1419-1429 - Nohad Gresh, David Perahia:
Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules - Preliminary validations of a polarizable potential by ab initio quantum chemistry. 1430-1446 - Sora Ishioka, Itsuki Miyazato, Lauren Takahashi, Thanh Nhat Nguyen, Toshiaki Taniike, Keisuke Takahashi:
Unveiling gas-phase oxidative coupling of methane via data analysis. 1447-1451
- Nicola Chirico, Alessandro Sangion, Paola Gramatica, Linda Bertato, Ilaria Casartelli, Ester Papa:
QSARINS-Chem standalone version: A new platform-independent software to profile chemicals for physico-chemical properties, fate, and toxicity. 1452-1460
Volume 42, Number 21, August 2021
- Agustina Arroyuelo, Jorge A. Vila, Osvaldo A. Martin:
Exploring the quality of protein structural models from a Bayesian perspective. 1466-1474 - Jingjing Shao, Beate Paulus, Jean Christophe Tremblay:
Local current analysis on defective zigzag graphene nanoribbons devices for biosensor material applications. 1475-1485 - Musen Li, Jeffrey R. Reimers, Michael J. Ford, Rika Kobayashi, Roger D. Amos:
Accurate prediction of the properties of materials using the CAM-B3LYP density functional. 1486-1497 - Andreì L. Tchougréeff, Evgeny Plekhanov, Richard Dronskowski:
Solid-state quantum chemistry with ΘΦ (ThetaPhi): Spin-liquids, superconductors, and magnetic superstructures made computationally available. 1498-1513 - Shaojun Gui, Ling Jiang, Zhi-Feng Liu:
Evolution of the linker in microhydrated hydrogen dinitrate anions: From H+ to H5O2+. 1514-1525
- Santiago Alonso-Gil:
MonteCarbo: A software to generate and dock multifunctionalized ring molecules. 1526-1534
Volume 42, Number 22, August 2021
- Éderson Sales Moreira Pinto, Bruno César Feltes, Conrado Pedebos, Márcio Dorn:
Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies. 1540-1551 - Leighton Wilson, Robert Krasny:
Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver. 1552-1560 - Marwa A. Saleh, Mohamed A. ElBadry, Rogy R. Ezz Eldin:
Novel 6-hydroxyquinolinone derivatives: Design, synthesis, antimicrobial evaluation, in silico study and toxicity profiling. 1561-1578 - Emilia A. Lubecka, Adam Liwo:
ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons. 1579-1589 - Amir Karton, Peter R. Spackman:
Evaluation of density functional theory for a large and diverse set of organic and inorganic equilibrium structures. 1590-1601
- Hubert Okadome Valencia, Busheng Wang, Gilles Frapper, Andrew L. Rohl:
New developments in the GDIS simulation package: Integration of VASP and USPEX. 1602-1626
Volume 42, Number 23, September 2021
- Rasmus Andersson, Fabian Årén, Alejandro A. Franco, Patrik Johansson:
CHAMPION: Chalmers hierarchical atomic, molecular, polymeric and ionic analysis toolkit. 1632-1642 - Patrice Koehl, Henri Orland, Marc Delarue:
Parameterizing elastic network models to capture the dynamics of proteins. 1643-1661 - Kaho Nakatani, Masahiro Higashi, Ryoichi Fukuda, Hirofumi Sato:
An analysis of valence electronic structure from a viewpoint of resonance theory: Tautomerization of formamide and diazadiboretidine. 1662-1669 - Han Sun, Wei Chen, Lin Chen, Wenqing Zheng:
Exploring the molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43 using molecular dynamics simulation and free energy calculation. 1670-1680 - Tatiana Gomez, Patricio Fuentealba, Andrés Robles-Navarro, Carlos Cárdenas:
Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule. 1681-1688 - Tuanan C. Lourenço, Mahsa Ebadi, Matthew J. Panzer, Daniel Brandell, Luciano T. Costa:
A molecular dynamics study of a fully zwitterionic copolymer/ionic liquid-based electrolyte: Li+ transport mechanisms and ionic interactions. 1689-1703
Volume 42, Number 24, September 2021
- Vikas Khatri, Harender S. Dhattarwal, Hemant K. Kashyap, Gurmeet Singh:
First-principles based theoretical investigation of impact of polyolefin structure on photooxidation behavior. 1710-1719 - Hideo Doi, Kazuaki Z. Takahashi, Takeshi Aoyagi:
Searching for local order parameters to classify water structures at triple points. 1720-1727 - Moumita Dutta, Hemant Kumar Srivastava, Akshai Kumar:
Rational design of pincer-nickel complexes for catalytic cyanomethylation of benzaldehyde: A systematic DFT study. 1728-1735 - Sreerama Rajasekhar, Ramanathan Karuppasamy, Kaushik Chanda:
Exploration of potential inhibitors for tuberculosis via structure-based drug design, molecular docking, and molecular dynamics simulation studies. 1736-1749
- Anthony J. Schaefer, Victoria M. Ingman, Steven E. Wheeler:
SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems. 1750-1754 - In Seong Lee, Jong-Kwon Ha, Daeho Han, Tae In Kim, Sung Wook Moon, Seung Kyu Min:
PyUNIxMD: A Python-based excited state molecular dynamics package. 1755-1766
Volume 42, Number 25, September 2021
- Tomomi Kondo, Takehiko Sasaki, Motoyuki Shiga:
Cover Image. i
- Gabriel I. Pagola, Marta B. Ferraro, Patricio F. Provasi, Stefano Pelloni, Paolo Lazzeretti:
Physical achirality in geometrically chiral rotamers of hydrazine and boranylborane molecules. 1772-1782 - Tomomi Kondo, Takehiko Sasaki, Motoyuki Shiga:
The mechanism of sorbitol dehydration in hot acidic solutions. 1783-1791 - Anna V. Pomogaeva, Alexey Y. Timoshkin:
Influence of the solvent on the Lewis acidity of antimony pentahalides and group 13 Lewis acids toward acetonitrile and pyridine. 1792-1802 - Bruna Clara De Simone, Marta Erminia Alberto, Nino Russo, Marirosa Toscano:
Photophysical properties of heavy atom containing tetrasulfonyl phthalocyanines as possible photosensitizers in photodynamic therapy. 1803-1808 - Nicolas Frazee, Blake Mertz:
Intramolecular interactions play key role in stabilization of pHLIP at acidic conditions. 1809-1816 - Taiji Nakamura, Tamotsu Uchiyama, Takako Kudo:
Comparison of group 14 elements in sp3 and sp2 environment by fragment structure energy analysis. 1817-1825
Volume 42, Number 26, October 2021
- Svetoslav Nakov, Ekaterina Sobakinskaya, Thomas Renger, Johannes Kraus:
ARGOS: An adaptive refinement goal-oriented solver for the linearized Poisson-Boltzmann equation. 1832-1860 - Surjeet Verma, Chirag N. Patel, Muktesh Chandra:
Identification of novel inhibitors of SARS-CoV-2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation. 1861-1872 - Ahmed M. Mkadmh, Zaki S. Safi, Adnan A. Elkhaldy, Richard J. Staples, Savas Kaya, Goncagül Serdaroglu:
Synthesis, identification, density functional and Hirshfeld surface studies of 2, 2′-disulfanediylbis(tetrahydro-4H-cyclopenta[d][1, 3, 2]dioxaphosphole-2-sulfide). 1873-1884 - Jan Paul Menzel, Martijn Kloppenburg, Jelena Belic, Huub J. M. de Groot, Lucas Visscher, Francesco Buda:
Efficient workflow for the investigation of the catalytic cycle of water oxidation catalysts: Combining GFN-xTB and density functional theory. 1885-1894 - Milan Milovanovic:
Small lithium-chloride clusters: Superalkalis, superhalogens, supersalts and nanocrystals. 1895-1904 - Mohamad Toutounji:
Excited state distribution function for probing Herzberg-Teller vibronic coupling using linear optical response theory: Application to glassy pheophytin a. 1905-1913
Volume 42, Number 27, October 2021
- Zhen Chao, Dexuan Xie:
Cover Image. i
- Zhifeng Ma, Naoki Nakatani, Masahiko Hada:
Insights into the electronic structure and mechanism of norcarane hydroxylation by OxoMn(V) porphyrin complexes: A density functional theory study. 1920-1928 - Zhen Chao, Dexuan Xie:
An improved Poisson-Nernst-Planck ion channel model and numerical studies on effects of boundary conditions, membrane charges, and bulk concentrations. 1929-1943 - Akhil S. Nair, Anakuthil Anoop, Rajeev Ahuja, Biswarup Pathak:
Role of atomicity in the oxygen reduction reaction activity of platinum sub nanometer clusters: A global optimization study. 1944-1958 - Miquel Garcia-Ratés, Ute Becker, Frank Neese:
Implicit solvation in domain based pair natural orbital coupled cluster (DLPNO-CCSD) theory. 1959-1973 - Chloe Ramos, Jeremiah Muehlbrad, Benjamin G. Janesko:
Density functionals with full nonlocal exchange, nonlocal rung-3.5 correlation, and D3 dispersion: Combined accuracy for general main-group thermochemistry, kinetics, and noncovalent interactions. 1974-1981 - Moumita Kar, Atish Ghosh, Ritabrata Sarkar, Sougata Pal, Pranab Sarkar:
Arene and functionalized arene based two dimensional organic-inorganic hybrid perovskites for photovoltaic applications. 1982-1990
Volume 42, Number 28, October 2021
- Asit Pal, Subhendu Pal, Shivani Verma, Motoyuki Shiga, Nisanth N. Nair:
Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes. 1996-2003 - Kristopher Brown, Yasheng Maimaiti, Kai Trepte, Thomas Bligaard, Johannes Voss:
MCML: Combining physical constraints with experimental data for a multi-purpose meta-generalized gradient approximation. 2004-2013 - Valerii V. Karpov, Aleksandra M. Puzyk, Peter M. Tolstoy, Elena Yu. Tupikina:
Hydration of selenolate moiety: Ab initio investigation of properties of O-H⋯Se(-) hydrogen bonds in CH3Se(-)⋯(H2O)n clusters. 2014-2023 - Feng Li, Weibo Han, Zhi Cao, Shilei Ji, Haiyun Wang, Lixia Wang, Hong Wu, Yuping Zhu, Yong Pu:
Two novel semiconducting B2CO monolayers with high carrier mobilities. 2024-2030
- Jacob A. Parkman, Caleb A. Barksdale, David J. Michaelis:
CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations. 2031-2035 - Emilio Martínez-Núñez, George L. Barnes, David R. Glowacki, Sabine Kopec, Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez-Fernández, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces, Saulo A. Vázquez:
AutoMeKin2021: An open-source program for automated reaction discovery. 2036-2048
Volume 42, Number 29, November 2021
- Sara Tortorella, Emanuele Carosati, Giulia Sorbi, Giovanni Bocci, Simon Cross, Gabriele Cruciani, Loriano Storchi:
Cover Image. i
- Mateusz Kogut, Zhou Gong, Chun Tang, Adam Liwo:
Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. 2054-2067 - Sara Tortorella, Emanuele Carosati, Giulia Sorbi, Giovanni Bocci, Simon Cross, Gabriele Cruciani, Loriano Storchi:
Combining machine learning and quantum mechanics yields more chemically aware molecular descriptors for medicinal chemistry applications. 2068-2078 - Miroslaw Jablonski, Tadeusz M. Krygowski:
Dependence of the substituent energy on the level of theory. 2079-2088 - Yixiang X. Cao, Mathew D. Halls, Tati Reddy Vadicherla, Richard A. Friesner:
Pseudospectral implementations of long-range corrected density functional theory. 2089-2102 - Barbara Bankiewicz, Stephan Kupfer, Piotr Matczak:
Tuning the metal-ligand bond in the σ-complexes of stannylenes and azabenzenes. 2103-2115
- Krishnamohan G. Prasanna, Rahul Sunil, Kapil Gupta, Seung-Cheol Lee:
DJMol: An open-source modeling platform for computational chemistry and materials science with a Python interpreter. 2116-2129
Volume 42, Number 30, November 2021
- Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li:
Cover Image. i
- Kazushi Fujimoto, Tetsuro Nagai, Tsuyoshi Yamaguchi:
Momentum removal to obtain the position-dependent diffusion constant in constrained molecular dynamics simulation. 2136-2144 - Pham Vu Nhat, Nguyen Thanh Si, Vitaly G. Kiselev, Minh Tho Nguyen:
Another look at energetically quasi-degenerate structures of the gold cluster Au27q with q = 1, 0, -1. 2145-2153 - Victor García, David Zorrilla, Manuel Fernández, Jesús Sánchez-Márquez:
Property-oriented basis sets for computation of atomization energies. 2154-2162 - Kanami Sugiyama, Kenichiro Saita, Satoshi Maeda:
A reaction route network for methanol decomposition on a Pt(111) surface. 2163-2169 - Wallace K. B. Chan, Debarati DasGupta, Heather A. Carlson, John R. Traynor:
Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4. 2170-2180
- Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li:
ePharmer: An integrated and graphical software for pharmacophore-based virtual screening. 2181-2195
Volume 42, Number 31, December 2021
- Jidong Zhang, Wei Guo:
The role of electric field on decomposition of CL-20/HMX cocrystal: A reactive molecular dynamics study. 2202-2212 - Jinyang Xi, Liangliang Zheng, Shenghao Wang, Jiong Yang, Wenqing Zhang:
Temperature-dependent structural fluctuation and its effect on the electronic structure and charge transport in hybrid perovskite CH3NH3PbI3. 2213-2220 - Xiaokun Zhang, James T. Kindt:
Free energy of micellization of dodecyl phosphocholine (DPC) from molecular simulation: Hybrid PEACH-BAR method. 2221-2232 - Anji Babu Kapakayala, Nisanth N. Nair:
Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics. 2233-2240 - Diego López-Carballeira, Tomás Polcar:
A new protocol for the identification of singlet fission sensitizers through computational screening. 2241-2249 - Yves-Henri Sanejouand:
Normal-mode driven exploration of protein domain motions. 2250-2257
Volume 42, Number 32, December 2021
- Gunnar Schmitz, Özlem Yönder, Bastian Schnieder, Rochus Schmid, Christof Hättig:
An automatized workflow from molecular dynamic simulation to quantum chemical methods to identify elementary reactions and compute reaction constants. 2264-2282 - Faiyaz Md. Efaz, Shafiqul Islam, Shafi Ahmad Talukder, Shaila Akter, Md. Zakaria Tashrif, Md. Ackas Ali, Md. Abu Sufian, Md. Rimon Parves, Md. Jahirul Islam, Mohammad A. Halim:
Repurposing fusion inhibitor peptide against SARS-CoV-2. 2283-2293 - Abdallah Ammar, Lorenzo Ugo Ancarani, Arnaud Leclerc:
A complex Gaussian approach to molecular photoionization. 2294-2305 - Ridha Ben Said, Riadh Hanachi, Seyfeddine Rahali, Mohammed A. M. Alkhalifah, Faisal Alresheedi, Bahoueddine Tangour, Majdi Hochlaf:
Evaluation of a new series of pyrazole derivatives as a potent epidermal growth factor receptor inhibitory activity: QSAR modeling using quantum-chemical descriptors. 2306-2320 - Tina Mathea, Guntram Rauhut:
Advances in vibrational configuration interaction theory - part 1: Efficient calculation of vibrational angular momentum terms. 2321-2333 - Yuwen Bai, Bayaer Buren, Zijiang Yang, Boyi Zhou, Maodu Chen:
Feshbach resonances in D + HD(v = 1, j = 0) reaction at low collision energies. 2334-2340
- Zhen Tang, Yanlin Song, Shu Zhang, Wei Wang, Yuan Xu, Di Wu, Wei Wu, Peifeng Su:
XEDA, a fast and multipurpose energy decomposition analysis program. 2341-2351 - Ilya V. Popov, Timofei S. Kushnir, Andreì L. Tchougréeff:
Local perturbations of periodic systems. Chemisorption and point defects by GoGreenGo. 2352-2368
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