Journal of Computational Chemistry最新文献

{"title":"Projector-Based Quantum Embedding Study of Iron Complexes","authors":"Jonathan M. Waldrop,&nbsp;Ajay Panyala,&nbsp;Daniel Mejia-Rodriguez,&nbsp;Theresa L. Windus,&nbsp;Niranjan Govind","doi":"10.1002/jcc.70043","DOIUrl":"10.1002/jcc.70043","url":null,"abstract":"<div>\u0000 \u0000 <p>Projection-based embedding theory (PBET) is used to calculate and assess the challenging spin-crossover energies for a selection of small Fe-containing systems by embedding the metal center into the frozen potential of the ligands. MP2, CCSD, and CCSD(T) are embedded in potentials from the SCAN and r²SCAN functionals and compared with the canonical values for the constituent methods and previously reported reference values. Considering the PBET calculations as a correction for the underlying DFT, the embedding calculations are able to provided improvement for most cases. In some cases, the PBET methods are able to compensate for limitations in the wave function methods and produce results similar to more rigorous calculations from the literature. For the systems with spin-crossover energies near zero, the current methodology fails to provide consistent improvement. The isolated recalculation of the electronic structure around the metal center when embedded into a DFT treatment of the ligand field shows promise as a pragmatic and lower cost treatment compared to the canonical treatment of the whole system of the difficult class of spin-crossover complexes.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056387","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":"PSSKB: A Web Application to Study Protein Structures","authors":"Denis V. Petrovskiy,&nbsp;Kirill S. Nikolsky,&nbsp;Liudmila I. Kulikova,&nbsp;Vladimir R. Rudnev,&nbsp;Tatiana V. Butkova,&nbsp;Kristina A. Malsagova,&nbsp;Valeriya I. Nakhod,&nbsp;Arthur T. Kopylov,&nbsp;Anna L. Kaysheva","doi":"10.1002/jcc.70046","DOIUrl":"10.1002/jcc.70046","url":null,"abstract":"<div>\u0000 \u0000 <p>The proteins expressed during the cell cycle determine cell function and ensure signaling pathway activation in response to environmental influences. Developments in structural biology, biophysics, and bioinformatics provide information on the structure and function of particular proteins including that on the structural changes in proteins due to post-translational modification (PTM) and amino acid substitutions (AAS), which is essential for understanding protein function and life cycle. These are PTMs and AASs that often modulate the function and alter the stability and localization of a protein in a cell. PSSKB is a platform that integrates all necessary tools for modeling the five common natural modifications and all canonical AASs in proteins. The available tools are not limited to the local database, so the user can select a protein from Uniprot ID or PDB ID. The result will be a three-dimensional (3D) representation of the modified structure, as well as an analysis of the changes in the performance of the intact and modified structures after energy minimization compared with the original structure, which not only makes it possible to evaluate AAS/PTM influence of on a protein's characteristics but also to use the 3D model for further studies. Additionally, PSSKB enables the user to search, align, overlay, and determine the exact coordinates of protein structure fragments. The search results are a set of structural motifs similar to the query and ranked by statistical significance. The platform is fully functional and publicly available at https://psskb.org/. No registration is required to access the platform. A tutorial video can be found at https://psskb.org/page/about. Services provided on the platform are based on previously developed and published software. SCPacker applied for PTM Modeling and AAS services available at GitHub (https://github.com/protdb/SCPacker). SaFoldNet applied for a Similar Search service is also available at GitHub (https://github.com/protdb/ABBNet).</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055437","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":"Mechanism of the Non-Kasha Fluorescence in Pyrene","authors":"Sourav Majumdar,&nbsp;Robin Grotjahn,&nbsp;Ahmadreza Rajabi,&nbsp;Bibo Feng,&nbsp;Luke Nambi Mohanam,&nbsp;Gabriel S. Phun,&nbsp;Nicolas Lutfi,&nbsp;Mohammad Khan,&nbsp;Dmitrij Rappoport,&nbsp;Filipp Furche","doi":"10.1002/jcc.70040","DOIUrl":"10.1002/jcc.70040","url":null,"abstract":"<div>\u0000 \u0000 <p>The high-energy shoulder in the gas-phase fluorescence emission spectrum of pyrene is a well-known example of non-Kasha emission. We comparatively assess two approaches, vibronic perturbation theory and nonadiabatic dynamics, in their ability to predict and explain the gas-phase fluorescence spectrum of pyrene. While both methods qualitatively capture the non-Kasha emission, they differ in their computational requirements, accuracy, and physical interpretation. Vibronic perturbation theory and nonadiabatic dynamics are complementary and can be combined in a two-step approach to non-Kasha fluorescence.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055011","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":"Theoretical Study on Adsorption of Halogenated Benzenes on Montmorillonites Modified With M(I)/M(II) Cations","authors":"Daniel Tunega,&nbsp;Martin H. Gerzabek,&nbsp;Leonard Böhm","doi":"10.1002/jcc.70042","DOIUrl":"10.1002/jcc.70042","url":null,"abstract":"<p>Halogenated benzenes (HBs) are hydrophobic organic chemicals belonging to persistent organic pollutants. Owing to their persistence, they represent a serious problem in environmental contamination, specifically of soils and sediments. One of the most important physical processes determining the fate of HBs in soils is adsorption to main soil components such as soil organic matter and soil minerals. Smectites, layered clay minerals of the 2:1 type, are common minerals in clay-rich soils, of which montmorillonite (Mt) is a typical representative. This work focuses on a systematic modeling study of the adsorption mechanism of selected HBs interacting with the basal (001) surface, which is the dominant surface of Mt particles. The HB···Mt interactions were studied by means of a quantum chemical approach based on the density functional theory method. HBs were represented by five molecules, particularly C₆F₆, C₆Cl₃F₃, C₆Cl₆, C₆Br₃Cl₃, and C₆Br₆. In mixed HBs (C₆Cl₃F₃ and C₆Br₃Cl₃) Cl atoms are in 1,3,5 or rather 2,4,6 positions. The effect of a different cation type on adsorption was investigated for M⁺/M²⁺-Mt models with cations from alkali group (M⁺: Li, K, Na, Rb, Cs) and alkaline earth metal group (M²⁺: Mg, Ca, Sr., Ba). The calculations were also performed on the gas phase HB···M⁺/M²⁺ complexes for comparison. Adsorption energies and distances of the main HB molecular plane from the Mt surface were calculated as a measure of the adsorption strength. The results showed that the strongest HB adsorption is for the Na⁺-Mt and Ca²⁺-Mt surfaces. The strongest affinity was observed for hexabromobenzene, while the weakest adsorption was found for hexafluorobenzene. The decomposition of the adsorption energy showed that its dominant component is dispersion energy and less important is the cation-π interaction. The calculated adsorption energies showed a good correlation with experimentally determined log <i>K</i>_d values.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decision Trees for the Recognition of Metal-Centered Chirality in Coordination Complexes","authors":"Gabriel H. L. Munguba,&nbsp;Mateus F. da Silva,&nbsp;Frederico T. Silva,&nbsp;Gabriel A. Urquiza-Carvalho,&nbsp;Alfredo M. Simas","doi":"10.1002/jcc.70025","DOIUrl":"10.1002/jcc.70025","url":null,"abstract":"<div>\u0000 \u0000 <p>While established guidelines exist for chirality in tetrahedral molecules, there is a notable absence of clear rules for recognizing metal-centered chirality in higher-coordination complexes. We develop decision trees to assess the likelihood of chirality-at-metal in coordination complexes with coordination numbers 4–9 with mono and bidentate ligands. Using binary decision rules based on shape, ligand type, and quantity, the trees classify complexes as chiral or achiral. The theoretical formalism employs stereoisomer enumeration via Pólya's theorem, assuming ideal geometries and <i>cis</i> coordination of bidentate ligands. Additionally, analysis of over 2700 crystallographic structures reveals a high prevalence of metal-centered chirality, especially in complexes with higher coordination numbers. These powerful yet easy-to-use decision trees provide chemists with deeper insights into the stereochemistry of metal coordination complexes and with effective tools to identify and understand this often-overlooked stereochemical property and its impact on molecular interactions and crystal packing.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044550","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":"Hybrid Unsupervised/Supervised Machine Learning for Identifying Molecular Structural Fingerprints From Ensemble Property","authors":"Arpan Choudhury,&nbsp;Debashree Ghosh","doi":"10.1002/jcc.70038","DOIUrl":"10.1002/jcc.70038","url":null,"abstract":"<div>\u0000 \u0000 <p>The ensemble properties of a system are obtained by averaging over the properties calculated for the various configurations it can have at a finite temperature and thus cannot be captured by a single molecular structure. Such ensemble properties are often important in material discovery. In designing new materials, the goal is to predict those ensemble structures that display a tailored property. However, mapping this average property to multiple structures introduces ambiguities and unreliable convergence in supervised machine learning. This presents a major obstacle in designing new materials. Here, we introduce a hybrid unsupervised/supervised learning method and demonstrate how to predict the structural parameters defining the conformers of a heterogeneous system, melanin, from its ensemble-averaged spectra. This also shows a new way to identify different structural fingerprints responsible for an ensemble-averaged superposition spectrum.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044789","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":"Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome","authors":"Andrea Nedělníková,&nbsp;Petr Stadlbauer,&nbsp;Michal Otyepka,&nbsp;Petra Kührová,&nbsp;Markéta Paloncýová","doi":"10.1002/jcc.70035","DOIUrl":"10.1002/jcc.70035","url":null,"abstract":"<p>Doxorubicin (DOX) is a widely used chemotherapeutic agent known for intercalating into DNA. However, the exact modes of DOX interactions with various DNA structures remain unclear. Using molecular dynamics (MD) simulations, we explored DOX interactions with DNA duplexes (dsDNA), G-quadruplex, and nucleosome. DOX predominantly stacks on terminal bases of dsDNA and occasionally binds into its minor groove. In the G-quadruplex, DOX stacks on planar tetrads but does not spontaneously intercalate into these structures. Potential of mean force calculations indicate that while intercalation is the most energetically favorable interaction mode for DOX in dsDNA, the process requires overcoming a significant energy barrier. In contrast, DOX spontaneously intercalates into bent nucleosomal DNA, due to the increased torsional stress. This preferential intercalation of DOX into regions with higher torsional stress provides new insights into its mechanism of action and underscores the importance of DNA tertiary and quaternary structures in therapies utilizing DNA intercalation.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Achieving Pressure Consistency in Mechanochemical Simulations of Chemical Reactions Under Pressure","authors":"Jonas Bentrup,&nbsp;Rahel Weiß,&nbsp;Felix Zeller,&nbsp;Tim Neudecker","doi":"10.1002/jcc.70024","DOIUrl":"10.1002/jcc.70024","url":null,"abstract":"<p>The eXtended Hydrostatic Compression Force Field (X-HCFF) is a mechanochemical approach in which a cavity is used to exert hydrostatic pressure on a target system. The cavity used in this method is set up to represent the van der Waals (VDW) surface of the system by joining spheres sized according to the respective atomic VDW radii. The size of this surface can be varied via a scaling factor, and it can be shown that the compression forces exerted in X-HCFF in its current implementation depend on this factor. To address this dependency, we have developed a rescaling formalism for the applied forces, allowing us to drastically reduce the dependency of the compression forces on the chosen scaling factor. Independency from the scaling factor is important, as the scaling of the VDW spheres is often used to ensure an overlap of cavities in supramolecular complexes, which is necessary for the simulation of chemical reactions. Our rescaling formalism reduces the empiricism of the X-HCFF approach and boosts its applicability in the field of computational high-pressure chemistry.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Qcforever2: Advanced Automation of Quantum Chemistry Computations","authors":"Masato Sumita,&nbsp;Kei Terayama,&nbsp;Shoichi Ishida,&nbsp;Kensuke Suga,&nbsp;Shohei Saito,&nbsp;Koji Tsuda","doi":"10.1002/jcc.70017","DOIUrl":"10.1002/jcc.70017","url":null,"abstract":"<div>\u0000 \u0000 <p>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.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"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,&nbsp;Chang Shen,&nbsp;Anil Kumar Tummanapelli,&nbsp;Ming Wah Wong","doi":"10.1002/jcc.70047","DOIUrl":"10.1002/jcc.70047","url":null,"abstract":"<p>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.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70047","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}