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ORCIDJournal of Computational Chemistry, Volume 45
Volume 45, Number 1, 2024
FRONT COVER
- Shweta Singh Chauhan, Anshika Gupta, Aashna Srivastava, Ramakrishnan Parthasarathi
:
Front Cover. C1
RESEARCH ARTICLES
- Rodrigo Báez-Grez, Ricardo Pino-Rios:
On the aromaticity and stability of benzynes in the ground and lowest-lying triplet excited states. 6-12 - Shweta Singh Chauhan, Anshika Gupta, Aashna Srivastava, Ramakrishnan Parthasarathi:
Discovering targeted inhibitors for Escherichia coli efflux pump fusion proteins using computational and structure-guided approaches. 13-24 - Jagdish Kumar Satyam, Sapan Mohan Saini:
Comprehensive investigation of electronic structure, phonon spectrum and thermoelectric performance of LuMSb (M = Ni, Pd, Pt) half Heusler compounds from first principles. 25-34 - João Ricardo Bueno de Morais Borba, Leonardo Pereira de Araújo, Marcia Paranho Veloso, Nelson José Freitas da Silveira:
Applying the bioisosterism strategy to obtain lead compounds against SARS-CoV-2 cysteine proteases: An in-silico approach. 35-46
SOFTWARE NOTE
- Trent E. Balius, Y. Stanley Tan, Mayukh Chakrabarti:
DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking. 47-63
Volume 45, Number 2, 2024
RESEARCH ARTICLES
- Aditya Ramesh Sachin, Gopinadhanpillai Gopakumar, Cherukuri Venkata Siva Brahmananda Rao, Sivaraman Nagarajan:
Exploring phosphoryl oxygen basicity in U(VI) complexation: A comparative study from trialkyl phosphate to phosphine oxide. 70-82 - Oleg Egorov, Michaël Rey, Dominika Viglaska, Andrei V. Nikitin:
Accurate ab initio potential energy surface, rovibrational energy levels and resonance interactions of triplet ( X ~ 3B1) methylene. 83-100 - Vasilii Korotenko, Hendrik Zipse:
The stability of oxygen-centered radicals and its response to hydrogen bonding interactions. 101-114 - Michal Novotný, Matús Dubecký, Frantisek Karlický:
Toward accurate modeling of structure and energetics of bulk hexagonal boron nitride. 115-121
SOFTWARE NOTE
- Moritz Buchhorn, Vera Krewald:
AOMadillo: A program for fitting angular overlap model parameters. 122-134
Volume 45, Number 3, 2024
RESEARCH ARTICLES
- Otilia Mó, Al Mokhtar Lamsabhi, Jean-Claude Guillemin, Manuel Yáñez:
Ionization, intrinsic basicity, and intrinsic acidity of unsaturated diols of astrochemical interest: 1,1- and 1,2-ethenediol: A theoretical survey. 140-149 - Xiao Peng Mi, Hui Lu, Tianlv Xu, Herbert Früchtl, Tanja Van Mourik, Martin J. Paterson, Steven R. Kirk, Samantha Jenkins:
Response of the mechanical and chiral character of ethane to ultra-fast laser pulses. 150-158 - Lina Liu, Zhihong Wei, Qiang Chen, Chaoren Shen, Tonghao Shen, Xinxin Tian, Si-Dian Li:
Benchmarking boron cluster calculations: Establishing reliable geometrical and energetic references for Bn (n = 1-4). 159-169 - Vlada V. Petrova, Anton V. Domnin, Yuri B. Porozov, Pavel O. Kuliaev, Yaroslav V. Solovev:
Implementation of machine learning protocols to predict the hydrolysis reaction properties of organophosphorus substrates using descriptors of electron density topology. 170-182 - Kimihiko Hirao, Takahito Nakajima, Bun Chan, Ho-Jin Lee:
The verification of delta SCF and Slater's transition state theory for the calculation of core ionization energy. 183-192
Volume 45, Number 4, 2024
RESEARCH ARTICLES
- M. A. Orekhov:
Correcting charge distribution in reduced Li-molecule pair for computational screening of battery solvents. 197-203 - Debashree Manna, Rabindranath Lo, Vijay Madhav Miriyala, Dana Nachtigallova, Zdenek Trávnícek, Pavel Hobza:
Impact of dielectric constant of solvent on the formation of transition metal-ammine complexes. 204-209 - Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega:
Tuning ultrafast time-evolution of photo-induced charge-transfer states: A real-time electronic dynamics study in substituted indenotetracene derivatives. 210-221
REVIEW ARTICLE
- Marinela Irimia, Jian Wang:
Self-consistent field method for open-shell systems within the density-matrix functional theory. 222-229
CORRECTION
- Correction to "Terminal end-on coordination of dinitrogen vs. isoelectronic CO: A comparison using the charge displacement analysis". 230-232
Volume 45, Number 5, 2024
RESEARCH ARTICLES
- Jie Wang, Gui-Chang Wang:
Mechanisms of CH4 activation over oxygen-preadsorbed transition metals by ReaxFF and AIMD simulations. 238-246 - Md Fulbabu Sk, Sunanda Samanta, Sayan Poddar, Parimal Kar:
Microsecond dynamics of H10N7 influenza neuraminidase reveals the plasticity of loop regions and drug resistance due to the R292K mutation. 247-263 - Diego López-Carballeira, Tomás Polcar:
High throughput selection of organic cathode materials. 264-273
SOFTWARE NOTE
- Mini Bharati Ahirwar, Subodh Khire, Shridhar R. Gadre, Milind M. Deshmukh:
Hydrogen bond energy estimation (H-BEE) in large molecular clusters: A Python program for quantum chemical investigations. 274-283
RESEARCH ARTICLE
- Rachid Boutiddar, Khalid Abbiche, Moulay Driss Mellaoui, Abdallah Imjjad, Mustapha Alahiane, Youssef Ait Albrimi, Khadija Marakchi, Muneerah Mogren Al-Mogren, Abdellatif El Hammadi, Majdi Hochlaf:
Insights into the mechanism of [3+2] cycloaddition reactions between N-benzyl fluoro nitrone and maleimides, its selectivity and solvent effects. 284-299
Volume 45, Number 6, 2024
RESEARCH ARTICLES
- Sheik Ahmed Ullah, Xin Yang, Benjamin Jones, Shan Zhao, Weihua Geng, Guo-Wei Wei:
Bridging Eulerian and Lagrangian Poisson-Boltzmann solvers by ESES. 306-320 - Shuai Wang, ChiYung Yam, Shuguang Chen, LiHong Hu, Liping Li, Faan-Fung Hung, Jiaqi Fan, Chi-Ming Che, Guanhua Chen:
Predictions of photophysical properties of phosphorescent platinum(II) complexes based on ensemble machine learning approach. 321-330 - ChenFei Sun, Qing Liu, Lingpeng Meng, Xiaoyan Li:
Small molecules (CO2, iPrNCO, and iPrNCNiPr) activation by the metallomimetics (μ-Hydrido) diborane anion: A DFT investigation on mechanism and chemoselectivity controlling. 331-340 - Motoji Sakai, Mitsunori Kaneshige, Koji Yasuda:
Learning organo-transition metal catalyzed reactions by graph neural networks. 341-351
SOFTWARE NOTE
- Freya Edholm, Aditya Nandy, Clorice R. Reinhardt, David W. Kastner, Heather J. Kulik:
Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. 352-361
Volume 45, Number 7, 2024
RESEARCH ARTICLES
- Toni Oestereich, Ralf Tonner-Zech, Julia Westermayr:
Decoding energy decomposition analysis: Machine-learned Insights on the impact of the density functional on the bonding analysis. 368-376 - Zakaria Bouchouireb, Steeve H. Thany, Jean-Yves Le Questel:
Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone. 377-391 - Nishattasnim Liza, Daniel J. Coe, Yuhui Lu, Enrique P. Blair:
Ab initio studies of counterion effects in molecular quantum-dot cellular automata. 392-404 - Thom H. Dunning, Lu T. Xu:
Electronic structure of Li1,2,3+,0,- and nature of the bonding in Li2,3+,0,-. 405-418 - Christoph Plett, Stefan Grimme, Andreas Hansen:
Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules. 419-429
Volume 45, Number 8, March 2024
RESEARCH ARTICLES
- Jing Wang, Sheng Chen, Qianmu Yuan, Jianwen Chen, Danping Li, Lei Wang, Yuedong Yang:
Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. 436-445 - Kai Wang, Ying Zhang, Chaoyong Wang, Jun Zhao, Le Liu, Jiaye Chen, Yarui Wang:
Discovery of a series of silicon-based ferrimagnets in CrMnSin (n = 4-20) clusters. 446-453 - Xunshan Liu, Zhen Liang, Zhetong Jin, Xu Zhang, Chengshuo Shen:
Enantiomerization of five-membered-heterocycle-embedded helicenes: A DFT study. 454-460 - Vilakkathala U. Krishnapriya, Cherumuttathu H. Suresh:
Unraveling pnicogen bonding cooperativity: Insights from molecular electrostatic potential analysis. 461-475 - Albert J. F. W. H. de S. Silva, Gessenildo Pereira Rodrigues, Elizete Ventura, Silmar Andrade do Monte:
Photodissociation and formation of an ion-pair in CH2FCl (HCFC-31). 476-486 - Wenjun Xu, Yanling Zhao, Jialu Chen, Zhongyu Wan, Dadong Yan, Xinghua Zhang, Ruiqin Zhang:
A Q-learning method based on coarse-to-fine potential energy surface for locating transition state and reaction pathway. 487-497 - Isseki Yu, Takaharu Mori, Daisuke Matsuoka, Donatas Surblys, Yuji Sugita:
SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. 498-505
Volume 45, Number 9, April 2024
FRONT COVER
- Satoi Wada, Takuro Tsutsumi, Kenichiro Saita, Tetsuya Taketsugu:
Front Cover. C1
RESEARCH ARTICLES
- Soohyung Park, Amy Rice, Wonpil Im, Richard W. Pastor:
Spontaneous curvature generation by peptides in asymmetric bilayers. 512-522 - Nobuki Inoue, Yoshihiro Watanabe, Haruyuki Nakano:
Generalized Foldy-Wouthuysen transformation for relativistic two-component methods: Systematic analysis of two-component Hamiltonians. 523-535 - Farnaz Yashmin, Rohan Sharma, Lakhya Jyoti Mazumder, Pankaz Kumar Sharma:
Noble gas dative bonding with coinage metal carbene complexes: A theoretical study. 536-545
SOFTWARE NOTE
- Sudarshan Vijay, Hendrik H. Heenen, Aayush R. Singh, Karen Chan, Johannes Voss:
Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models. 546-551
RESEARCH ARTICLES
- Satoi Wada, Takuro Tsutsumi, Kenichiro Saita, Tetsuya Taketsugu:
Ab initio molecular dynamics study of intersystem crossing dynamics for MH2 (M = Si, Ge, Sn, Pb) on spin-pure and spin-mixed potential energy surfaces. 552-562 - Abir Jendoubi, Youssef Arfaoui, Jérôme Palaudoux, Muneerah Mogren Al-Mogren, Majdi Hochlaf:
DFT mechanistic study of the chemical fixation of CO2 by aziridine derivatives. 563-573 - Marek Freindorf, Juliana J. Antonio, Elfi Kraka:
Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. 574-588
Volume 45, Number 10, April 2024
RESEARCH ARTICLES
- Luis López-Sosa, Patrizia Calaminici:
Cycloaddition reactions via "on water" protocol reactions: A density functional theory study. 595-609 - Yuna Bai, Anmei Xian, Xing Yang, Ming Zhou, Xuefei Zhao, Lili Zhao:
Mechanistic study of the Ni-catalyzed hydroalkylation of 1,3-dienes: The origins of regio- and enantioselectivities and a further rational design. 610-621 - Muhammad Sanwal Khan, Nasir Maha, Maira Riaz, Tahira Yasmin, Ahmad Irfan, Muhammad Asim Raza Basra:
Computational investigation of pyrazinamide drugs and its transition metal complexes using a DFT approach. 622-632
SOFTWARE NOTE
- Daniel R. Roe, Bernard R. Brooks:
MPI-parallelization of the grid inhomogeneous solvation theory calculation. 633-637
RESEARCH ARTICLES
- Xiaoliang Pan, Ryan Snyder, Jia-Ning Wang, Chance Lander, Carly Wickizer, Richard Van, Andrew Chesney, Yuanfei Xue, Yuezhi Mao, Ye Mei, Jingzhi Pu, Yihan Shao:
Training machine learning potentials for reactive systems: A Colab tutorial on basic models. 638-647 - Jie Zeng, Feiying You, Jun Zhu:
Screening seven-electron boron-centered radicals for dinitrogen activation. 648-654 - Isuru R. Ariyarathna:
Ground and excited electronic structures of electride and alkalide units: The cases of Metal-Tren, -Azacryptand, and -TriPip222 complexes. 655-662 - Eslam Dabbish, Stefano Scoditti, Mohammed N. I. Shehata, Ida Ritacco, Mahmoud A. A. Ibrahim, Tamer Shoeib, Emilia Sicilia:
Insights on cyclophosphamide metabolism and anticancer mechanism of action: A computational study. 663-670 - Hyunsik Kim, Jorge Alberto Morales:
Testing standard basis sets for direct ionizations: H+ + H at ELab = 0.1-100 keV. 671-682 - Fabien Pascale, Saber Gueddida, Klaus Doll, Roberto Dovesi:
Band gap, Jahn-Teller deformation, octahedra rotation in transition metal perovskites LaTiO 3. 683-694
Volume 45, Number 11, April 2023
RESEARCH ARTICLES
- Martin Mrovec, Peter M. W. Gill:
How delocalized are the polyacenes? 701-709 - Thorren Kirschbaum, Xiangfei Wang, Annika Bande:
Ground and excited state charge transfer at aqueous nanodiamonds. 710-718 - Pradip Si, Ajay Jayanth, Oliviero Andreussi:
Soft-sphere continuum solvation models for nonaqueous solvents. 719-737 - Takashi Yoshidome:
Four-dimensional imaging for cryo-electron microscopy experiments using molecular simulations and manifold learning. 738-751 - Ruirui Su, Xue He, Kendall N. Houk, Qianqian Lu, Fang Liu:
Periselectivity and ambimodal transition states in cycloadditions of tetrachloro-o-benzoquinone with 6,6-dimethylfulvene. 752-760 - Katja-Sophia Csizi, Markus Reiher:
Automated preparation of nanoscopic structures: Graph-based sequence analysis, mismatch detection, and pH-consistent protonation with uncertainty estimates. 761-776 - Cristina Puzzarini, Hexu Ye, Silvia Alessandrini:
Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization. 777-786 - Michal Bosy, Matthew W. Scroggs, Timo Betcke, Erik Burman, Christopher D. Cooper:
Coupling finite and boundary element methods to solve the Poisson-Boltzmann equation for electrostatics in molecular solvation. 787-797
SHORT COMMUNICATION
- Md Mostakim Meraz, Wenhong Yang, Weisheng Yang, Wen-Hua Sun:
Predicting the catalytic activities of transition metal (Cr, Fe, Co, Ni) complexes towards ethylene polymerization by machine learning. 798-803
RESEARCH ARTICLE
- Harsha S. Karnamkkott, Sujit Das, Totan Mondal, Kartik Chandra Mondal:
Small molecule activation by sila/germa boryne species. 804-819
Volume 45, Number 12, May 2024
RESEARCH ARTICLES
- Padmavathy Venkatakrishnan, Artem V. Kuklin, Rahul Suresh, Vijayakumar Subramaniam:
Superatom molecular orbital in C80. 827-833 - Raphaël Rullan, Pauline Colinet, Quentin Desdion, Stephan N. Steinmann, Tangui Le Bahers:
Modeling the polychromism of oxide minerals: The case of alexandrite and cordierite. 834-842 - Saad Tariq, Ayash O. Alrashdi, Areej Al Bahir, S. M. Sohail Gilani, Farida Hamioud, A. A. Mubarak, Afaq Ahmed, M. Musa Saad H.-E:
DFT insights into LaFeO3 with Mn substitution: A promising path to energy-efficient magneto-optical applications. 843-854 - Jin Zeng, Yue Qian:
Adaptive lambda schemes for efficient relative binding free energy calculation. 855-862 - Julio C. V. Chagas, Bruno D. Milanez, Vytor P. Oliveira, Max Pinheiro Jr, Luiz F. A. Ferrão, Adélia J. A. Aquino, Hans Lischka, Francisco B. C. Machado:
A multi-descriptor analysis of substituent effects on the structure and aromaticity of benzene derivatives: π-Conjugation versus charge effects. 863-877 - Ronit Sarangi, Kaushik D. Nanda, Anna I. Krylov:
Two- and one-photon absorption spectra of aqueous thiocyanate anion highlight the role of symmetry in the condensed phase. 878-885 - Roumaissa Khelifi, Nadjia Latelli, Zoulikha Charifi, Christophe Morell, Henry Chermette:
Predicting the activity of methoxyphenol derivatives antioxidants: II - Importance of the nature of the solvent on the mechanism, a DFT study. 886-897
SHORT COMMUNICATION
- Sota Matsuoka, Kota Sakakura, Yoshinobu Akinaga, Kazuki Akisawa, Koji Okuwaki, Hideo Doi, Yuji Mochizuki:
Enhancement of energy decomposition analysis in fragment molecular orbital calculations. 898-902
RESEARCH ARTICLES
- Anna V. Pomogaeva, Anna S. Lisovenko, Alexey Y. Timoshkin:
Structures and stability of I2 and ICl complexes with pyridine: Ab initio and DFT study. 903-914 - Jothi Balakrishnan, Pavithrakumar Muthukumar, David Stephen Arputharaj, Pitchumani Violet Mary Christopher, Selvaraju Karuppannan, Senthilkumar Kittusamy:
Theoretical investigations of the substituent effect on the opto-electronic properties of the linearly fused napthadithiophene-based molecules. 915-929
Volume 45, Number 13, May 2024
RESEARCH ARTICLES
- Andrij A. Rovenchak, Maksym Druchok:
Machine learning-assisted search for novel coagulants: When machine learning can be efficient even if data availability is low. 937-952 - Hathaichanok Chuntakaruk, Kajjana Boonpalit, Jiramet Kinchagawat, Fahsai Nakarin, Tanatorn Khotavivattana, Chanat Aonbangkhen, Yasuteru Shigeta, Kowit Hengphasatporn, Sarana Nutanong, Thanyada Rungrotmongkol, Supot Hannongbua:
Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. 953-968 - Mohammad Taha I. Ibrahim, Dunia Alatoom, Tibor Furtenbacher, Attila G. Császár, Sergei N. Yurchenko, Ala'a A. A. Azzam, Jonathan Tennyson:
MARVEL analysis of high-resolution rovibrational spectra of 13 C 16 O 2. 969-984 - Carson L. Tang, Alexander G. Heide, Alexandra D. Heide, Gary E. Douberly, Justin M. Turney, Henry F. Schaefer III:
Exploring the Tl 2 H 2 potential energy surface: A comparative analysis with group 13 systems and experiment. 985-994 - M. Rodríguez-Mayorga, P. Besalú-Sala, Ángel J. Pérez-Jiménez, Juan Carlos Sancho-García:
Application to nonlinear optical properties of the RSX-QIDH double-hybrid range-separated functional. 995-1001 - Lucas de Souza Silva, Guilherme Colherinhas, Wesley B. Cardoso:
Evaluating quantum entanglement generation in two-dimensional graphene systems through lithium ion interactions: A DFT-based study. 1002-1007 - Sangeeta Lakra, Sanat Kumar Mukherjee:
First principle studies on structural, elastic, electronic, optical, and thermoelectric properties of new perovskite TlTaO3: For renewable energy applications. 1008-1016 - Nisha Mehta, Jan M. L. Martin:
On the sensitivity of computed partial charges toward basis set and (exchange-)correlation treatment. 1017-1032 - Michael Filatov, Vladimir A. Mironov, Elfi Kraka:
Unraveling the effect of aromaticity for the dynamics of excited states of single benzene fluorophores. 1033-1045 - Daniil A. Shitov, Danil V. Krutin, Elena Yu. Tupikina:
Mutual influence of non-covalent interactions formed by imidazole: A systematic quantum-chemical study. 1046-1060
Volume 45, Number 14, May 2024
FRONT COVER
- Andreas J. Achazi, Xhesilda Fataj, Philip Rohland, Martin D. Hager, Ulrich S. Schubert, Doreen Mollenhauer:
Front Cover. C1
RESEARCH ARTICLES
- Fabien Pascale, Philippe D'Arco, Sébastien Lebègue, Roberto Dovesi:
Jahn-Teller distortion, octahedra rotations and orbital ordering in perovskites: KScF 3 as a model system. 1067-1077 - Ahmed Shaalan Alag, Péter G. Szalay, Attila Tajti:
Ab initio investigation of excited state charge transfer pathways in differently capped bithiophene cages. 1078-1086 - Jia-Ming Zhang, Huai-Qian Wang, Hui-Fang Li, Xun-Jie Mei, Jin-Kun Zeng, Lan-Xin Qin, Hao Zheng, Yong-Hang Zhang, Kai-Le Jiang, Bo Zhang, Wen-Hai Wu:
Aromatic and magnetic properties in a series of heavy rare earth-doped Ge6 cluster anions. 1087-1097 - Himangshu Mondal, Pratim Kumar Chattaraj:
CO2 reduction using aluminum hydride: Generation of in-situ frustrated Lewis pairs and small molecule activation therein. 1098-1111 - Andreas J. Achazi, Xhesilda Fataj, Philip Rohland, Martin D. Hager, Ulrich S. Schubert, Doreen Mollenhauer:
Development of a multi-step screening procedure for redox active molecules in organic radical polymer anodes and as redox flow anolytes. 1112-1129 - Filippo Bodo, Alessandro Erba, Elfi Kraka, Renaldo T. Moura Jr.:
Chemical bonding in Uranium-based materials: A local vibrational mode case study of Cs 2 UO 2 Cl 4 and UCl 4 crystals. 1130-1142 - Jas Kalayan, Ismaeel Ramzan, Christopher D. Williams, Richard A. Bryce, Neil A. Burton:
A neural network potential based on pairwise resolved atomic forces and energies. 1143-1151 - Yoshio Barrera, James S. M. Anderson:
Does the radical GPRI strongly depend on the population scheme? A comparative study to predict radical attack on unsaturated molecules with the radical general-purpose reactivity indicator. 1152-1159
REVIEW ARTICLE
- Manajit Das, Ankit Ghosh, Raghavan B. Sunoj:
Advances in machine learning with chemical language models in molecular property and reaction outcome predictions. 1160-1176
RESEARCH ARTICLE
- Bun Chan:
Limiting factors in the accuracy of DFT calculation for redox potentials. 1177-1186
Volume 45, Number 15, June 2024
RESEARCH ARTICLES
- Julio J. Valdés, Alain B. Tchagang:
Novel machine learning insights into the QM7b and QM9 quantum mechanics datasets. 1193-1214 - Laura Grazioli, Luca T. Schleicher, Stella Stopkowicz, Jürgen Gauss:
Theoretical prediction of closed-shell paramagnetism for scandium and yttrium hydride. 1215-1223 - Wouter Vervust, Daniel T. Zhang, An Ghysels, Sander Roet, Titus S. van Erp, Enrico Riccardi:
PyRETIS 3: Conquering rare and slow events without boundaries. 1224-1234 - Yulian T. Manchev, Paul L. A. Popelier:
FFLUX molecular simulations driven by atomic Gaussian process regression models. 1235-1246 - Andreas Heßelmann, Emmanuel Giner, Peter Reinhardt, Peter J. Knowles, Hans-Joachim Werner, Julien Toulouse:
A density-fitting implementation of the density-based basis-set correction method. 1247-1253 - Alessandra G. Ritacca, Mario Prejanò, Marta Erminia Alberto, Tiziana Marino, Marirosa Toscano, Nino Russo:
On the antibacterial photodynamic inactivation mechanism of Emodin and Dermocybin natural photosensitizers: A theoretical investigation. 1254-1260 - Mahdi Aarabi, Ankit Pandey, Bill Poirier:
"On-the-fly" Crystal : How to reliably and automatically characterize and construct potential energy surfaces. 1261-1278 - Josué Maya, Alhadji Malloum, Jean Jules Fifen, Zoubeida Dhaouadi, Henri Paul Ekobena Fouda, Jeanet Conradie:
Quantum cluster equilibrium theory applied to liquid ammonia. 1279-1288 - Maicon Pierre Lourenço, Jirí Hostas, Colin Bellinger, Alain Tchagang, Dennis R. Salahub:
Reinforcement learning for in silico determination of adsorbate - substrate structures. 1289-1302 - Gustavo A. Andolpho, Teodorico C. Ramalho:
Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme. 1303-1315
Volume 45, Number 16, June 2024
RESEARCH ARTICLES
- Wichien Sang-aroon, Marta Erminia Alberto, Marirosa Toscano, Nino Russo:
Chalcogen atom effect on the intersystem crossing kinetic constant of oxygen- and sulfur disubstituted heteroporphyrins. 1322-1328 - Mohamad Adil Iman Ishak, Tan Tiek Aun, Nadiah Sidek, Sharifah Mohamad, Khairulazhar Jumbri, Ninie Suhana Abdul Manan:
An enantioselective study of β-cyclodextrin and ionic liquid-β-cyclodextrin towards propranolol enantiomers by molecular dynamic simulations. 1329-1351 - Prajay Patel, Joseph Chung, Max Aksel Bowman, Inga Ulusoy, Angela K. Wilson:
Potential energy surfaces and dynamic properties via ab initio composite and density functional approaches. 1352-1363 - Mikhail Ivanov, Alexander P. Lyubartsev:
Development of a bottom-up coarse-grained model for interactions of lipids with TiO 2 nanoparticles. 1364-1379 - Carl Philipp Klemm, Till Frömling:
Machine learning assisted analysis of equivalent circuit usage in electrochemical impedance spectroscopy applications. 1380-1389 - Simon Ghysbrecht, Bettina G. Keller:
Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. 1390-1403 - Tomás Kuzela, Dmitrij Bondarev, Eva Kutálková, Zuzana Benková, Josef Hrncirík, Marek Ingr:
Study of absorption and emission spectra of substituted terthiophene compounds by methods of theoretical chemistry. 1404-1418 - Nitai P. Sahoo, Peter R. Franke, John F. Stanton:
On the performance of composite schemes in determining equilibrium molecular structures. 1419-1427
Volume 45, Number 17, June 2024
RESEARCH ARTICLES
- Sukanta Mondal:
β-D-Glucopyranose - silver+ (1:1) complex as a small gas molecule scavenger. 1434-1443 - Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys:
Resolving coupled pH titrations using alchemical free energy calculations. 1444-1455 - Lifan Jia, Yunxia Wang, Lulu Song, Ruirui Liu, Longgang Li, Jisheng Li, Yongquan Zhou, Jianmin Pan, Fayan Zhu:
Hydrolysis mechanism of the cyclohexaborate anion: Unraveling the intricacies. 1456-1469
SOFTWARE NOTE
- Yutaka Maruyama, Norio Yoshida:
RISMiCal: A software package to perform fast RISM/3D-RISM calculations. 1470-1482
RESEARCH ARTICLES
- Olga D'Anania, Eugenio Romano, Vincenzo Barone, Giovanni Talarico:
Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory. 1483-1492 - Sian Xiao, Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao:
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. 1493-1504
SOFTWARE NOTE
- Rian Koots, Yu Wang, Marjan Mirahmadi, Jesús Pérez-Ríos:
Py3BR: A software for computing atomic three-body recombination rates. 1505-1514
RESEARCH ARTICLE
- Yueyang Zhang, Gaofeng Hu, Xueting Gao, Zhuxia Zhang, Peng Cui:
Simulation study on functional group-modified Ni-MOF-74 for CH4/N2 adsorption separation. 1515-1524
Volume 45, Number 18, July 2024
RESEARCH ARTICLES
- Kevser Kübra Kirboga, Mesut Isik:
Explainable artificial intelligence in the design of selective carbonic anhydrase I-II inhibitors via molecular fingerprinting. 1530-1539 - Dmitri G. Fedorov:
Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method. 1540-1551 - Hieu Huynh, Khanh Le, Linh Vu, Trang Nguyen, Matthew Holcomb, Stefano Forli, Hung Phan:
Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms. 1552-1561 - Francesco Calcagno, Boris Maryasin, Marco Garavelli, Davide Avagliano, Ivan Rivalta:
Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM. 1562-1575 - Samah Al-Qaisi, Nazia Iram, Saidi Samah, Afaf Khadr Alqorashi, A. I. Aljameel, Tahani A. Alrebdi, Zeesham Abbas, S. Bouzgarrou, Md. Ferdous Rahman, Ajay Singh Verma:
Opto-electronic and thermophysical characteristics of A2TlAgF6 (A = Rb, Cs) for green technology applications. 1576-1586 - Zoi Salta, Oscar N. Ventura, Nadjib Rais, Nicola Tasinato, Vincenzo Barone:
A new chapter in the never ending story of cycloadditions: The puzzling case of SO2 and acetylene. 1587-1602 - ZhiYe Zhu, Xiaoqing Wei, WanZhen Liang:
A theoretical investigation of benzothiadiazole derivatives for high efficiency OLEDs. 1603-1613 - Luca Nanni:
Investigating proton tunneling dynamics in the time-dependent Schrödinger equation. 1614-1623
Volume 45, Number 19, July, 2024
RESEARCH ARTICLE
- Qingqing Yao, Kun Yuan, Mengyang Li, Yaoxiao Zhao, Yanzhi Liu, Xiang Zhao:
Synergistic regulation of chloride anion recognition using a triple-functional sites receptor with two different cationic effectors. 1630-1641
EDITORIAL
- Adélia J. A. Aquino, Hans Lischka, Gernot Frenking:
Foreword to the special issue for Elfi Kraka. 1642
RESEARCH ARTICLES
- Lizandra Barrios Herrera, Maicon Pierre Lourenço, Jirí Hostas, Patrizia Calaminici, Andreas M. Köster, Alain Tchagang, Dennis R. Salahub:
Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce4-xNixO8-x (x = 1, 2, 3). 1643-1656 - Pierpaolo D'Antoni, Daniele Toffoli, Giovanna Fronzoni, Mauro Stener, Luca Sementa, Alessandro Fortunelli:
Dichroism of plasmonic chiral nanoalloys by rational design. 1657-1666 - Amy C. Hancock, Erica Giudici, Lars Goerigk:
How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models. 1667-1681 - Atsushi Ishikawa:
Machine-learning descriptor search on the density of states profile of bimetallic alloy systems and comparison with the d-band center theory. 1682-1689 - Subash Arjunan, Joshua M. Sims, Carole Duboc, Pascale Maldivi, Anne Milet:
Investigating the interplay between charge transfer and CO2 insertion in the adsorption of a NiFe catalyst for CO2 electroreduction on a graphite support through DFT computational approaches. 1690-1696
Volume 45, Number 20, July 2024
RESEARCH ARTICLES
- Otilia Mó, M. Merced Montero-Campillo, Manuel Yáñez, Ibon Alkorta, José Elguero:
Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size. 1702-1715 - Guillaume Hoffmann, Frédéric Guégan, Vanessa Labet, Laurent Joubert, Henry Chermette, Christophe Morell, Vincent Tognetti:
Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns. 1716-1726 - Adam Vavrecka, Katerina Fatková, Jaroslav V. Burda:
Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data. 1727-1736 - Suen Wang, Xiaoyu Liu, Yang Zhang, Shasha Li, Xiangyan Bo, Lujun Wei, Wei Niu, Hong Wu, Yong Pu, Feng Li:
Modifying electronic and optical properties of violet phosphorus through variable fluorine coverage. 1737-1743 - Eduardo Adonay Ortiz-Vázquez, Fernando Montejo-Alvaro, Heriberto Cruz-Martínez, Patrizia Calaminici:
Theoretical study of PdNi and PdCu clusters embedded on graphene modified by monovacancy and nitrogen doping. 1744-1749 - Sasa Terek, Milan Milovanovic:
Ab initio multireference calculation of electronic spectra of the osmium complexes, [Os(bpy) 3 ] 2 + and [Os(phen) 3 ] 2 +. 1750-1761 - Peter E. G. F. Ibrahim, Fabio Zuccotto, Ulrich Zachariae, Ian H. Gilbert, Mike Bodkin:
Accurate prediction of dynamic protein-ligand binding using P-score ranking. 1762-1778
Volume 45, Number 21, August, 2024
Research Articles
- Johannes T. Margraf:
Neural graph distance embedding for molecular geometry generation. 1784-1790 - Pierre-François Loos, Denis Jacquemin:
A mountaineering strategy to excited states: Accurate vertical transition energies and benchmarks for substituted benzenes. 1791-1805 - Arslan R. Shaimardanov, Dmitry A. Shulga, Vladimir A. Palyulin:
Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function? 1806-1820 - Kamron Fazel, Nima Karimitari, Tanooj Shah, Christopher Sutton, Ravishankar Sundararaman:
Improving the reliability of machine learned potentials for modeling inhomogeneous liquids. 1821-1828
Review Article
- Johannes Voss:
Machine learning for accuracy in density functional approximations. 1829-1845
Research Articles
- Ruiqin Xu, Zhongming Jiang, Qin Yang, Julien Bloino, Malgorzata Biczysko:
Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. 1846-1869 - Yuya Nakajima, Takuto Ohmura, Junji Seino:
Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. 1870-1879
Volume 45, Number 22, August, 2024
Review Article
- Bhuvanesh Sridharan, Animesh Sinha, Jai Bardhan, Rohit Modee, Masahiro Ehara, U. Deva Priyakumar:
Deep reinforcement learning in chemistry: A review. 1886-1898
Research Article
- Mike Devereux, Eric D. Boittier, Markus Meuwly:
Systematic improvement of empirical energy functions in the era of machine learning. 1899-1913 - Bruna R. Ferreira, Francisco A. Martins, Matheus P. Freitas:
Expanding chalcogen bonds in thiophenes to interactions with halogens. 1914-1920
Review Article
- Russell J. Boyd:
The Nobel history of computational chemistry. A personal perspective. 1921-1935
Research Article
- Zhihao Deng, Chang Liu, Zhongwei Li, Yingsheng Zhang:
An efficient method by combining different basis sets and SAPT levels. 1936-1944 - Filip Cernatic, Emmanuel Fromager:
Extended N-centered ensemble density functional theory of double electronic excitations. 1945-1962
Volume 45, Number 23, September, 2024
Research Article
- Dávid P. Jelenfi, Attila Tajti, Péter G. Szalay:
Interpretation of molecular electron transport in ab initio many-electron framework incorporating zero-point nuclear motion effects. 1968-1979 - Muzammil Kabier, Nicola Gambacorta, Daniela Trisciuzzi, Sunil Kumar, Orazio Nicolotti, Bijo Mathew:
MzDOCK: A free ready-to-use GUI-based pipeline for molecular docking simulations. 1980-1986 - Nicolas Poirier, Jakob S. Kottmann, Alán Aspuru-Guzik, Luc Mongeau, Alireza Najafi-Yazdi:
Range-separated density functional theory using multiresolution analysis and quantum computing. 1987-2000 - Bundit Boonyarit, Nattawin Yamprasert, Pawit Kaewnuratchadasorn, Jiramet Kinchagawat, Chanatkran Prommin, Thanyada Rungrotmongkol, Sarana Nutanong:
GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. 2001-2023 - Hannah M. Baumann, David L. Mobley:
Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system. 2024-2033 - Pierraffaele Barretta, Stefano Scoditti, Daniele Belletto, Fortuna Ponte, Vincenzo Vigna, Gloria Mazzone, Emilia Sicilia:
Ruthenium complexes bearing nile red chromophore and one of its derivative: Theoretical evaluation of PDT-related properties. 2034-2041
Volume 45, Number 24, September, 2024
Research Article
- Fabien Pascale, Philippe D'Arco, Sami Mustapha, Roberto Dovesi:
t2g d orbital ordering patterns in KBF3 (B = Sc, Ti, Fe, Co) perovskites. 2048-2058 - Daniele Belletto, Vincenzo Vigna, Pierraffaele Barretta, Fortuna Ponte, Gloria Mazzone, Stefano Scoditti, Emilia Sicilia:
Computational assessment of the use of graphene-based nanosheets as PtII chemotherapeutics delivery systems. 2059-2070 - Aurélien Moncomble, Jean-Paul Cornard:
Orthogonal effect of exchange and correlation parameters in density functional theory to compute geometric and spectroscopic quantities. 2071-2079 - Bin-Bin Pei, Hongjuan Yang, Cai-Yue Gao, Yuan Man, Yonggang Yang, Si-Dian Li:
Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene. 2080-2090 - Anthony Scemama, Andreas Savin:
Exploring the role of mean-field potentials and short-range wave function behavior in the adiabatic connection. 2091-2097 - Ulviyya Askerova, Yusif Abdullayev, Namiq Shikhaliyev, Abel Maharramov, Valentine G. Nenajdenko, Jochen Autschbach:
Computational exploration of the copper(I)-catalyzed conversion of hydrazones to dihalogenated vinyldiazene derivatives. 2098-2103
Volume 45, Number 25, September, 2024
Editorial
- Éric Brémond, Ilaria Ciofini, Frédéric Labat, Vincent Tognetti:
Preface of Carlo Adamo's virtual special issue. 2110-2111
Research Article
- Kyohei Kawashima, Xu Lu, Yoichiro Kuninobu, Toshifumi Mori:
Mechanistic insights into the role of cyclodextrin in the regioselective radical CH trifluoromethylation of aromatic compounds. 2112-2118 - Kyle I. Williamson, Daniel J. C. Herr, Yirong Mo:
Mapping the correlations between bandgap, HOMO, and LUMO trends for meta substituted Zn-MOFs. 2119-2127 - Wei-Wei Wang, Tsunehiro Tanaka, Masahiro Ehara:
Theoretical study on the mechanism of alcohol photooxidation on Nb2O5 surface. 2128-2135
Software note
- Bin Gao:
Tinned: A symbolic library for response theory and high-order derivatives. 2136-2152
Research Article
- Asma Marzouk, Konstantinos D. Papavasileiou, Loukas D. Peristeras, Leendert Bezemer, Alexander P. van Bavel, Prathamesh M. Shenai, Ioannis G. Economou:
A systematic DFT study of structure and electronic properties of titanium dioxide. 2153-2166 - Antoine Salichon, Agustin Salcedo, Carine Michel, David Loffreda:
Theoretical study of structure sensitivity on ceria-supported single platinum atoms and its influence on carbon monoxide adsorption. 2167-2179
Volume 45, Number 26, October, 2024
Research Article
- Felix R. S. Purtscher, Thomas S. Hofer:
Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures. 2186-2197 - Gennaro Vincenzo Sannino, Adriana Pecoraro, Paola Delli Veneri, Michele Pavone, Ana Belén Muñoz-García:
Effective prediction of SnO2 conduction band edge potential: The key role of surface oxygen vacancies. 2198-2203 - Kenji Sugisaki, Tatsuya Nakano, Yuji Mochizuki:
Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme. 2204-2213 - Orlando Crescenzi, Giuseppe Graziano:
The interaction of thiocyanate with peptides - A computational study. 2214-2231 - Nghia Nguyen Thi Minh, Carolin König:
The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines. 2232-2241
Software note
- Enric Petrus, Jordi Buils, Diego Garay-Ruiz, Mireia Segado-Centellas, Carles Bo:
POMSimulator: An open-source tool for predicting the aqueous speciation and self-assembly mechanisms of polyoxometalates. 2242-2250
Research Article
- Lam H. Nguyen, Thanh N. Truong:
Nature of partial sigma bond. 2251-2264
Volume 45, Number 27, October, 2024
Research Article
- Vincent Tognetti, Laurent Joubert:
Exchange-correlation effects in interatomic energies for pure density functionals and their application to the molecular energy prediction. 2270-2283 - Aurore E. F. Denjean, Jordan Rio, Ilaria Ciofini, Marie-Eve L. Perrin, Pierre-Adrien Payard:
Computed versus experimental energy barriers in solution: Influence of the type of the density functional approximation. 2284-2293 - Shaoze Zhang, De-en Jiang, Nan Zhou, Jiaxing Tang, Keyu Zhang, Yin Li, Junxian Hu, Changjun Peng, Honglai Liu, Bin Yang, Yaochun Yao:
Ionic liquids intercalation in titanium carbide MXenes: A first-principles investigation. 2294-2307
Software note
- Thijs Stuyver:
TS-tools: Rapid and automated localization of transition states based on a textual reaction SMILES input. 2308-2317
Research Article
- Kai Wang, Jun Zhao, Junji Guo, Shanbao Chen, Yapeng Zhao, Jiaye Chen, Yarui Wang, Le Liu, Chaoyong Wang, Zhiqing Liu:
Magnetic properties of CrMnGen (n = 3-20) clusters. 2318-2324 - Patrick Chaquin, Franck Fuster, Alexis Markovits:
How the addition of atomic hydrogen to a multiple bond can be catalyzed by water molecules. 2325-2332
Software note
- Walter Filgueira de Azevedo Jr., Rodrigo Quiroga, Marcos Ariel Villarreal, Nelson José Freitas da Silveira, Gabriela Bitencourt-Ferreira, Amauri Duarte da Silva, Martina Veit-Acosta, Patricia Rufino Oliveira, Marco Tutone, Nadezhda Yu. Biziukova, Vladimir Poroikov, Olga A. Tarasova, Stéphanie Baud:
SAnDReS 2.0: Development of machine-learning models to explore the scoring function space. 2333-2346
Volume 45, Number 28, October 2024
Research Article
- Francesco Muniz-Miranda, Alfonso Pedone, Maria Cristina Menziani:
Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study. 2352-2359 - Kanishka Singh, Ka Hei Lee, Daniel Peláez, Annika Bande:
Accelerating wavepacket propagation with machine learning. 2360-2373
Review Article
- Hugo Petitjean, Aude Giard, Jean-Pierre Flament, Catherine Berthomieu, Dorothée Berthomieu:
Fast vibrational analysis of molecular systems. 2374-2382
Research Article
- Linlin Jia, Éric Brémond, Larissa Zaida, Benoit Gaüzère, Vincent Tognetti, Laurent Joubert:
Predicting redox potentials by graph-based machine learning methods. 2383-2396 - F. Pakzad, K. Eskandari:
Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis. 2397-2408 - Govindan Subramanian, Kanika Manchanda, Yirong Mo, Rohit Y. Sathe, Prasad V. Bharatam:
Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside. 2409-2423
Volume 45, Number 29, November 2024
Letter to the Editor
- Gernot Frenking:
Foreword to the special issue on machine learning/artificial intelligence. 2430
Research Article
- Nathanael J. King, Ian D. LeBlanc, Alex Brown:
A variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules. 2431-2445 - Emran Masoumifeshani, Tatiana Korona:
Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules. 2446-2464 - Robert Fox, Joaquin Klug, Damien Thompson, Anthony Reilly:
Computational predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models. 2465-2475 - Md. Tarekuzzaman, Mohammad Hasin Ishraq, Md. Atikur Rahman, Ahmad Irfan, Md. Zillur Rahman, Mist. Shamima Akter, Sumaya Abedin, M. A. Rayhan, Md. Rasheduzzaman, M. Moazzam Hossen, Md. Zahid Hasan:
A systematic first-principles investigation of the structural, electronic, mechanical, optical, and thermodynamic properties of Half-Heusler ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) for spintronics and optoelectronics applications. 2476-2500 - Cristina Puzzarini, Silvia Alessandrini:
Carbamic acid and its dimer: A computational study. 2501-2512
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