Journal of Computational Chemistry最新文献

{"title":"Qcforever2: Advanced Automation of Quantum Chemistry Computations","authors":"Masato Sumita, Kei Terayama, Shoichi Ishida, Kensuke Suga, Shohei Saito, Koji Tsuda","doi":"10.1002/jcc.70017","DOIUrl":"https://doi.org/10.1002/jcc.70017","url":null,"abstract":"QCforever is a wrapper designed to automatically and simultaneously calculate various physical quantities using quantum chemical (QC) calculation software for blackbox optimization in chemical space. We have updated it to QCforever2 to search the conformation and optimize density functional parameters for a more accurate and reliable evaluation of an input molecule. In blackbox optimization, QCforever2 can work as compactly arranged surrogate models for costly chemical experiments. QCforever2 is the future of QC calculations and would be a good companion for chemical laboratories, providing more reliable search and exploitation in the chemical space.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"48 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Insights Into Corrosion Inhibition Mechanism: Dissociation of Imidazole on Iron Surface","authors":"Weina Zhao, Chang Shen, Anil Kumar Tummanapelli, Ming Wah Wong","doi":"10.1002/jcc.70047","DOIUrl":"https://doi.org/10.1002/jcc.70047","url":null,"abstract":"Corrosion inhibitors are widely used to mitigate safety risks and economic losses in engineering, yet post-adsorption processes remain underexplored. In this study, we employed density functional theory calculations with a periodic model to investigate the dissociation mechanisms of imidazole on the Fe(100) surface. Imidazole was found to adsorb optimally in a parallel orientation, with an adsorption energy of −0.88 eV. We explored two dissociation pathways: C<span></span>H and N<span></span>H bond cleavages and found C<span></span>H dissociation having a lower activation barrier of 0.46 eV. Intriguingly, an alternative indirect route C<span></span>H dissociation pathway involving a tilted intermediate state was found to be competitive. Both indirect and direct C<span></span>H dissociation pathways are energetically more favorable than N<span></span>H cleavage. Molecular dynamics simulations reveal that indirect C<span></span>H dissociation occurs rapidly. This study proposes an alternative protective mechanism involving dissociated imidazole inhibitors, offering new insights for corrosion inhibitor design.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"13 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Degree and Origin of the Cooperativity of the Chalcogen (Ch···N) and Dihydrogen (H···H) Bonds in Some Triad Systems","authors":"Aboulfazl Soufi, Sadegh Salehzadeh","doi":"10.1002/jcc.70022","DOIUrl":"https://doi.org/10.1002/jcc.70022","url":null,"abstract":"The strength and cooperative energy of chalcogen and dihydrogen bonds in some ABC triad systems of the types XHTe…NCH…HY (X = F, Cl, Br, I, H; Y = Li, Na, BeH, MgH) and FHCh…NCH…HNa (Ch = Te, Se, S) were computed and compared at several levels of theory. All resulting data showed that the strengths of chalcogen (Te…N) and dihydrogen (H…H) bonds increase in the order of H &lt; I &lt; Br &lt; Cl &lt; F, and Be &lt; Mg &lt; Li &lt; Na, respectively. Then, the comparison of data for the FHTe…NCH…HY, FHSe…NCH…HNa, and FHS…NCH…HNa triads indicated that the interaction, stabilization, and cooperativity energies decrease in the order of Te &gt; Se &gt; S. The data show that in all cases the chalcogen and dihydrogen bonds change the bond dissociation energies (BDEs) and interaction energies (IEs) of each other by the same quantitative value. However, the relative impact of the above bonds on BDEs and IEs of each other depends on the relative strength of these bonds. Finally, the nature of both dihydrogen and chalcogen bonds and the origin of the cooperativity of bonds were evaluated by NBO and energy decomposition analysis (EDA) analyses.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"114 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Some Challenges of Diffused Interfaces in Implicit-Solvent Models","authors":"Mauricio Guerrero-Montero, Michał Bosy, Christopher D. Cooper","doi":"10.1002/jcc.70036","DOIUrl":"https://doi.org/10.1002/jcc.70036","url":null,"abstract":"The standard Poisson-Boltzmann (PB) model for molecular electrostatics assumes a sharp variation of the permittivity and salt concentration along the solute-solvent interface. The discontinuous field parameters are not only difficult numerically, but also are not a realistic physical picture, as it forces the dielectric constant and ionic strength of bulk in the near-solute region. An alternative to alleviate some of these issues is to represent the molecular surface as a diffuse interface, however, this also presents challenges. In this work we analyzed the impact of the shape of the interfacial variation of the field parameters in solvation and binding energy. However we used a hyperbolic tangent function &lt;span data-altimg=\"/cms/asset/0c43901d-4a85-445f-99f3-79c33851a640/jcc70036-math-0001.png\"&gt;&lt;/span&gt;&lt;mjx-container ctxtmenu_counter=\"7\" ctxtmenu_oldtabindex=\"1\" jax=\"CHTML\" role=\"application\" sre-explorer- style=\"font-size: 103%; position: relative;\" tabindex=\"0\"&gt;&lt;mjx-math aria-hidden=\"true\" location=\"graphic/jcc70036-math-0001.png\"&gt;&lt;mjx-semantics&gt;&lt;mjx-mrow&gt;&lt;mjx-mrow data-semantic-children=\"11\" data-semantic-content=\"12,13\" data-semantic- data-semantic-role=\"leftright\" data-semantic-speech=\"left parenthesis hyperbolic tangent left parenthesis k Subscript p Baseline x right parenthesis right parenthesis\" data-semantic-type=\"fenced\"&gt;&lt;mjx-mo data-semantic-added=\"true\" data-semantic- data-semantic-operator=\"fenced\" data-semantic-parent=\"14\" data-semantic-role=\"open\" data-semantic-type=\"fence\" style=\"margin-left: 0.056em; margin-right: 0.056em;\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mo&gt;&lt;mjx-mrow data-semantic-children=\"0,9\" data-semantic-content=\"10,0\" data-semantic- data-semantic-parent=\"14\" data-semantic-role=\"prefix function\" data-semantic-type=\"appl\"&gt;&lt;mjx-mi data-semantic-font=\"normal\" data-semantic- data-semantic-operator=\"appl\" data-semantic-parent=\"11\" data-semantic-role=\"prefix function\" data-semantic-type=\"function\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mi&gt;&lt;mjx-mo data-semantic-added=\"true\" data-semantic- data-semantic-operator=\"appl\" data-semantic-parent=\"11\" data-semantic-role=\"application\" data-semantic-type=\"punctuation\" style=\"margin-left: 0.056em; margin-right: 0.056em;\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mo&gt;&lt;mjx-mrow data-semantic-children=\"6\" data-semantic-content=\"7,8\" data-semantic- data-semantic-parent=\"11\" data-semantic-role=\"leftright\" data-semantic-type=\"fenced\"&gt;&lt;mjx-mo data-semantic-added=\"true\" data-semantic- data-semantic-operator=\"fenced\" data-semantic-parent=\"9\" data-semantic-role=\"open\" data-semantic-type=\"fence\" style=\"margin-left: 0.056em; margin-right: 0.056em;\"&gt;&lt;mjx-c&gt;&lt;/mjx-c&gt;&lt;/mjx-mo&gt;&lt;mjx-mrow data-semantic-annotation=\"clearspeak:unit\" data-semantic-children=\"3,4\" data-semantic-content=\"5\" data-semantic- data-semantic-parent=\"9\" data-semantic-role=\"implicit\" data-semantic-type=\"infixop\"&gt;&lt;mjx-msub data-semantic-children=\"1,2\" data-semantic- data-semantic-parent=\"6\" data-semantic-role=\"latinletter\" data-semantic-type=\"sub","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"38 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Highly Correlated, Multireference Study of the Lowest Lying Singlet and Triplet States of the Four Thiophene Diradicals","authors":"Joshua Pandian, Khanh Vu, Jules Tshishimbi Muya, Anna Parker, Christine Mae F. Ancajas, Diomedes Saldana-Greco, Tabitha Yewer, Carol Parish","doi":"10.1002/jcc.70044","DOIUrl":"https://doi.org/10.1002/jcc.70044","url":null,"abstract":"The energies and geometries of the lowest lying singlet and triplet states of the four diradicals formed by removing two H atoms from thiophene have been characterized. We utilized the highly correlated, multireference methods configuration interaction with single and double excitations with and without the Pople correction for size-extensivity (MR-CISD+Q and MR-CISD) and averaged quadratic coupled cluster theory (MR-AQCC). CAS (8,7) and CAS (10,8) active spaces involving σ, σ*, π, and π* orbitals were employed along with the cc-pVDZ and cc-pVTZ basis sets. The larger active space included the two electrons in the nonbonding sp² hybrid orbital on sulfur. We find that all didehydro isomers exist as planar, stable ground state singlets. The singlet-triplet (S-T) adiabatic gaps range from 15 to 25 kcal/mol while the vertical splittings are 21–35 kcal/mol. The 2,3 isomer has the lowest absolute ground state singlet energy and the largest adiabatic and vertical S-T splitting. The ground states of the 2,3-, and 2,5-didehydrothiophene isomers are predicted to exhibit the smallest and largest diradical character, respectively, based on their electronic structures, spin densities and bonding analysis. To our knowledge, no experimental excitation energies of any of the didehydrothiophene isomers are available, and our computed MR-AQCC/cc-pVTZ data are believed to be among the most accurate computed results. This extensive study shows a competitive performance between MR-AQCC and MR-CISD+Q.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"57 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simplified Multireference Coupled-Cluster Methods: Hybrid Approaches With Averaged Coupled Pair Theories","authors":"Alexander Waigum, Sarah Suchaneck, Andreas Köhn","doi":"10.1002/jcc.70020","DOIUrl":"https://doi.org/10.1002/jcc.70020","url":null,"abstract":"We define an approximation to the internally contracted multireference coupled-cluster method with single and double excitations by a hybrid approach. The rationale is to treat the external pair energy contributions by the coupled-cluster method, which provides accurate results for a large part of the correlation energy while being tractable as the involved pair cluster operators commute. For the internal and semi-internal contributions, for which the coupled-cluster part becomes involved due to non-commuting operators, a linearized approach based on the coupled-electron pair approximation (CEPA) is used. For the latter, the CEPA(0) method, the averaged coupled pair functional (ACPF), the averaged quadratic coupled-cluster (AQCC) method, and the averaged CEPA method are tested. We test the methods concerning size consistency, potential energy curves for C₂, N₂, CN, and O₃ and for the singlet-triplet splitting of ortho-, meta-, and para-benzynes. Our results show that AQCC provides the most accurate results and stable performance. The main drawback of the method is that it shows small violations of size consistency.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"14 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mfgnn: Multi-Scale Feature-Attentive Graph Neural Networks for Molecular Property Prediction","authors":"Weiting Ye, Jingcheng Li, Xianfa Cai","doi":"10.1002/jcc.70011","DOIUrl":"https://doi.org/10.1002/jcc.70011","url":null,"abstract":"In the realm of artificial intelligence-driven drug discovery (AIDD), accurately predicting the influence of molecular structures on their properties is a critical research focus. While deep learning models based on graph neural networks (GNNs) have made significant advancements in this area, prior studies have primarily concentrated on molecule-level representations, often neglecting the impact of functional group structures and the potential relationships between fragments on molecular property predictions. To address this gap, we introduce the multi-scale feature attention graph neural network (MfGNN), which enhances traditional atom-based molecular graph representations by incorporating fragment-level representations derived from chemically synthesizable BRICS fragments. MfGNN not only effectively captures both the structural information of molecules and the features of functional groups but also pays special attention to the potential relationships between fragments, exploring how they collectively influence molecular properties. This model integrates two core mechanisms: a graph attention mechanism that captures embeddings of molecules and functional groups, and a feature extraction module that systematically processes BRICS fragment-level features to uncover relationships among the fragments. Our comprehensive experiments demonstrate that MfGNN outperforms leading machine learning and deep learning models, achieving state-of-the-art performance in 8 out of 11 learning tasks across various domains, including physical chemistry, biophysics, physiology, and toxicology. Furthermore, ablation studies reveal that the integration of multi-scale feature information and the feature extraction module enhances the richness of molecular features, thereby improving the model's predictive capabilities.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"3 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142992401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tuning Aromaticity, Stability and Radicaloid Character of Periacenes by Chemical BN Doping","authors":"Luan G. F. dos Santos, Julio C. V. Chagas, Luiz F. A. Ferrão, Adelia J. A. Aquino, Reed Nieman, Hans Lischka, Francisco B. C. Machado","doi":"10.1002/jcc.70039","DOIUrl":"https://doi.org/10.1002/jcc.70039","url":null,"abstract":"In this work, the stability, aromaticity and radical character of pristine and eleven BN-doped armchair 5 and zigzag 5, 6, and 7 periacenes, were chosen for studying the effect of different doping schemes to stabilize the periacene, and to direct the open-shell density into specific regions of the PAH sheets. Ab initio multireference methods and different DFT functionals were used to analyze the singlet triplet (S<span></span>T) energy. Moreover, a range of descriptors were used to characterize the open-shell character and aromaticity of the different doped structures. The overall results provide a good overview of the efficiency of the different doping topologies. In general, because of the closed-shell character of the borazine doping units, the role of the doping is to reduce the strong open-shell character of the pristine periacenes. Substitutions along the zigzag edges has a significant effect while doping along the armchair edges is not significant.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"14 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142991618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaled and Weighted Laplacian Matrices as Functional Descriptors for GPCR Ligands","authors":"Guillermo Goode-Romero, Laura Dominguez","doi":"10.1002/jcc.70015","DOIUrl":"https://doi.org/10.1002/jcc.70015","url":null,"abstract":"The G protein-coupled receptor (GPCR) pharmacology accounts for a significant field in research, clinical studies, and therapeutics. Computer-aided drug discovery is an evolving suite of techniques and methodologies that facilitate accelerated progress in drug discovery and repositioning. However, the structure–activity relationships of molecules targeting GPCRs are highly challenging in many cases since slight structural modifications can lead to drastic changes in biological functionality. Numerous molecular descriptors have been described, many of which successfully characterize the structural and physicochemical features of drug sets. Nonetheless, elucidating the structure–functionality relationships over extensive sets of drugs with multiple structural variations and known biological activity remains challenging in various biological systems. This work presents novel topological descriptors using Laplacian matrices, weighted, and scaled by atomic mass and partial charges. We tested these descriptors on three sets of GPCR ligands: muscarinic, β-adrenergic, and δ-opioid receptor ligands, evaluating their potential as functional descriptors of these receptors.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"33 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Suitability of Available Interatomic Potentials for Sn to Model Its 2D Allotropes","authors":"Marcin Maździarz","doi":"10.1002/jcc.70032","DOIUrl":"https://doi.org/10.1002/jcc.70032","url":null,"abstract":"The suitability of a range of interatomic potentials for elemental tin was evaluated in order to identify an appropriate potential for modeling the stanene (2D tin) allotropes. Structural and mechanical features of the flat (F), low-buckled (LB), high-buckled (HB), full dumbbell (FD), trigonal dumbbell (TD), honeycomb dumbbell (HD), and large honeycomb dumbbell (LHD) monolayer tin (stanene) phases, were gained by means of the density functional theory (DFT) and molecular statics (MS) calculations with ten different Tersoff, modified embedded atom method (MEAM), and machine-learning-based (ML-IAP) interatomic potentials. A systematic quantitative comparison and discussion of the results is reported.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"89 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}