Journal of Computational Chemistry最新文献

{"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}

{"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,&nbsp;Sadegh Salehzadeh","doi":"10.1002/jcc.70022","DOIUrl":"10.1002/jcc.70022","url":null,"abstract":"<div>\u0000 \u0000 <p>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.</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":"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,&nbsp;Michał Bosy,&nbsp;Christopher D. Cooper","doi":"10.1002/jcc.70036","DOIUrl":"10.1002/jcc.70036","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;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&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;tanh&lt;/mi&gt;\u0000 &lt;mfenced&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;k&lt;/mi&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mi&gt;x&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/mfenced&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ left(tanh left({k}_pxright)right) $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; to couple the internal and external regions, our analysis is valid for other definitions. Our methodology, restricted to the linear PB, was based on a coupled finite element (FEM) and boundary element (BEM) scheme that allowed us to have a special treatment of the permittivity and ionic strength in a bounded FEM region near the interface, while maintaining BEM elsewhere. Our results suggest that the shape of the function (represented by &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;k&lt;/mi&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {k}_p $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) has a large impact on solvation and binding energy. We saw that high values of &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;k&lt;/mi&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {k}_p $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; induce a high gradient on the interface, to the limit of recovering the sharp jump when &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;k&lt;/mi&gt;\u0000 &lt;mi&gt;p&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;mo&gt;→&lt;/mo&gt;\u0000 &lt;mo&gt;∞&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {k}_pto infty $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, presenting a numeric","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"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}