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Journal of Computational Chemistry, Volume 42
Volume 42, Number 1, January 2021
- Shuichi Ebisawa, Takuro Tsutsumi, Tetsuya Taketsugu
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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 - 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
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Geometric analysis of anharmonic downward distortion following paths. 27-39 - Seyed Abdolreza Sadjadi
, Chérif F. Matta
, Ian P. Hamilton
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Bonding and metastability for Group 12 dications. 40-49 - Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman-Konieczna, Katarzyna Stapor
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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
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Structure, stability and bonding of the leapfrog B240, ±1, ±2. 72-80 - Wen-Jie Wei
, Per E. M. Siegbahn
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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
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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
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On the many-body nature of intramolecular forces in FFLUX and its implications. 107-116 - Son Tung Ngo
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Estimating the ligand-binding affinity via λ-dependent umbrella sampling simulations. 117-123 - Lily Arrué
, Ricardo Pino-Rios
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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
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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
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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
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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
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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
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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
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Instanton calculations of tunneling splittings in chiral molecules. 210-221 - Simone L. Waite, Amir Karton
, Bun Chan
, Alister J. Page
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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
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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
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Prediction of lattice energy of benzene crystals: A robust theoretical approach. 248-260 - Subhamoy Mahajan
, Tian Tang
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Comment on "Martini force field for protonated polyethyleneimine". 261-263
Volume 42, Number 5, February 2021
- Mosavverul Hassan
, Evangelos A. Coutsias
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Protein secondary structure motifs: A kinematic construction. 271-292 - Michael Edmund Beck
, Christoph Riplinger
, Frank Neese, Giovanni Bistoni
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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
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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
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Orbital energies and nuclear forces in DFT: Interpretation and validation. 334-343 - Karinna Mendanha, Richard Costa Prado, Leonardo Bruno Assis Oliveira, Guilherme Colherinhas
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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
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Accelerating atomistic simulations of proteins using multiscale enhanced sampling with independent tempering. 358-364
- Rebecca L. M. Gieseking
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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
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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
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Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials. 398-411 - Yang Wang
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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
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PyVisA: Visualization and Analysis of path sampling trajectories. 435-446
- Sergio Martí
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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
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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
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Revisiting the effect of f-functions in predicting the right reaction mechanism for hypervalent iodine reagents. 470-474 - Martin Sulka
, Matús Dubecký
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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
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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
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A diagonalization-free optimization algorithm for solving Kohn-Sham equations of closed-shell molecules. 492-504 - Dae-Hwan Ahn
, Jong-Won Song
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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
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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
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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
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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
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Rational design of the nickel-borane complex for efficient hydrogenation of styrene. 545-551 - Shoichi Tanimoto
, Koichi Tamura
, Shigehiko Hayashi
, Norio Yoshida
, Haruyuki Nakano
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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
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Estimations of FH···X hydrogen bond energies from IR intensities: Iogansen's rule revisited. 564-571
- Fabian Schuhmann
, Vasili Korol, Ilia A. Solov'yov
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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
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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
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Energy-based automatic determination of buffer region in the divide-and-conquer second-order Møller-Plesset perturbation theory. 620-629
- Kai Trepte
, Sebastian Schwalbe
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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
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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
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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
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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
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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
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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
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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
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To the fast calculation of the solvation free energy. Combining expanded ensembles with L2MC. 787-792 - Marvin Hoffmann
, Andreas Dreuw
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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
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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
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Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces. 827-839 - Johanna Klein
, Paul Fleurat-Lessard
, Julien Pilmé
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New insights in chemical reactivity from quantum chemical topology. 840-854 - Vicente Ramm, Jehanzeb H. Chaudhry
, Christopher D. Cooper
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Efficient mesh refinement for the Poisson-Boltzmann equation with boundary elements. 855-869 - Elena O. Levina
, Maria G. Khrenova
, Vladimir G. Tsirelson
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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
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Judicious design functionalized 3D-COF to enhance CO2 adsorption and separation. 888-896 - Yudibeth Sixto-López
, Marlet Martínez-Archundia
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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
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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
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Developing a variation of 3D-QSAR/MD method in drug design. 917-929
- Vivien Walter
, Céline Ruscher
, Olivier Benzerara
, Fabrice Thalmann
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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
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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
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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
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ClassicalGSG: Prediction of logP using classical molecular force fields and geometric scattering for graphs. 1006-1017 - Hugo Geindre
, Abdul-Rahman Allouche
, Daniel Peláez
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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
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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
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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
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A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. 1088-1094
- Florian Flachsenberg
, Matthias Rarey
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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
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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
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Quadruple chemical bonding in the diatomic anions TcN-, RuC-, RhB-, and PdBe-. 1126-1137 - Adyasa Priyadarsini, Bhabani S. Mallik
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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
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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
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Fast non-iterative calculation of solvation energies for water and non-aqueous solvents. 1184-1194 - Agnieszka Kacka-Zych
, Radomir Jasinski
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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
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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
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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
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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
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The best density functional theory functional for the prediction of 1H and 13C chemical shifts of protonated alkylpyrroles. 1248-1262