Journal of Computational Chemistry, Volume 42

Volume 42, Number 1, January 2021

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  Shuichi Ebisawa, Takuro Tsutsumi, Tetsuya Taketsugu:
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Full Papers

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  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
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  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
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  Shuichi Ebisawa, Takuro Tsutsumi, Tetsuya Taketsugu:
  Geometric analysis of anharmonic downward distortion following paths. 27-39
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  Seyed Abdolreza Sadjadi, Chérif F. Matta, Ian P. Hamilton:
  Bonding and metastability for Group 12 dications. 40-49
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  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
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  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

Full Papers

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  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
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  Wen-Jie Wei, Per E. M. Siegbahn:
  The active E4 structure of nitrogenase studied with different DFT functionals. 81-85
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  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
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  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
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  Son Tung Ngo:
  Estimating the ligand-binding affinity via λ-dependent umbrella sampling simulations. 117-123
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  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

Full Papers

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  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
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  Milica Feldt, Alex Brown:
  Assessment of local coupled cluster methods for excited states of BODIPY/Aza-BODIPY families. 144-155
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  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
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  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
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  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
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  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

Full Papers

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  Nityananda Sahu, Jeremy O. Richardson, Robert Berger:
  Instanton calculations of tunneling splittings in chiral molecules. 210-221
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  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
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  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
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  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
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  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

Full Papers

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  Mosavverul Hassan, Evangelos A. Coutsias:
  Protein secondary structure motifs: A kinematic construction. 271-292
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  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
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  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
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  Rubén Laplaza, Carlos Cárdenas, Patrick Chaquin, Julia Contreras-Garcia, Paul W. Ayers:
  Orbital energies and nuclear forces in DFT: Interpretation and validation. 334-343
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  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

Software News and Updates

• 
  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

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  Bartosz Blasiak, Joanna D. Bednarska, Marta Choluj, Robert W. Góra, Wojciech Bartkowiak:
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Full Papers

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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

Software News and Updates

• 
  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

Full Papers

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  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 MMˊ 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

Letter to the Editor

• 
  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

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  Shoichi Tanimoto, Koichi Tamura, Shigehiko Hayashi, Norio Yoshida, Haruyuki Nakano:
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Letter to the Editor

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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

Full Papers

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  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

Software News and Updates

• 
  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

Full Papers

• 
  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

Software News and Updates

• 
  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

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  Lucas de Azevedo Santos, Teodorico C. Ramalho, Trevor A. Hamlin, Friedrich Matthias Bickelhaupt:
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Full Papers

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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

Full Papers

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  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

Full Papers

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  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

Full Papers

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  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

Software News and Updates

• 
  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 A. 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

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  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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Full Papers

• 
  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 CH stretching band in polycyclic aromatic hydrocarbons. 1018-1027

Software News and Updates

• 
  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

Full Papers

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  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

Software Notes

• 
  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

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  Sai Manoj N. V. T. Gorantla, Pattiyil Parameswaran, Kartik Chandra Mondal:
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Full Papers

• 
  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

Full Papers

• 
  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

Full Papers

• 
  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

Software note

• 
  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

Letters to the Editor

• 
  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

Full Papers

• 
  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

Software Note

• 
  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

Full Papers

• 
  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

Software note

• 
  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

Full Papers

• 
  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

Software note

• 
  Santiago Alonso-Gil:
  MonteCarbo: A software to generate and dock multifunctionalized ring molecules. 1526-1534

Volume 42, Number 22, August 2021

Full Papers

• 
  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

Software note

• 
  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

Full Papers

• 
  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

Full Papers

• 
  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

Software Notes

• 
  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

Cover Image

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  Tomomi Kondo, Takehiko Sasaki, Motoyuki Shiga:
  Cover Image. i

Full Papers

• 
  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

Full Papers

• 
  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

Cover Image

• 
  Zhen Chao, Dexuan Xie:
  Cover Image. i

Full Papers

• 
  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

Full Papers

• 
  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

Software Notes

• 
  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

Cover Image

• 
  Sara Tortorella, Emanuele Carosati, Giulia Sorbi, Giovanni Bocci, Simon Cross, Gabriele Cruciani, Loriano Storchi:
  Cover Image. i

Full Papers

• 
  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

Software note

• 
  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

Cover Image

• 
  Yuxia Mao, Shiliang Li, Bojie Gong, Luhua Lai, Gaoqi He, Honglin Li:
  Cover Image. i

Full Papers

• 
  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

Software note

• 
  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

Full Papers

• 
  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

Full Papers

• 
  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

Software Notes

• 
  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