Journal of Computational Chemistry最新文献

{"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}

{"title":"A Highly Correlated, Multireference Study of the Lowest Lying Singlet and Triplet States of the Four Thiophene Diradicals","authors":"Joshua Pandian,&nbsp;Khanh Vu,&nbsp;Jules Tshishimbi Muya,&nbsp;Anna Parker,&nbsp;Christine Mae F. Ancajas,&nbsp;Diomedes Saldana-Greco,&nbsp;Tabitha Yewer,&nbsp;Carol Parish","doi":"10.1002/jcc.70044","DOIUrl":"10.1002/jcc.70044","url":null,"abstract":"<p>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.</p>","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":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70044","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":"OA","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,&nbsp;Sarah Suchaneck,&nbsp;Andreas Köhn","doi":"10.1002/jcc.70020","DOIUrl":"10.1002/jcc.70020","url":null,"abstract":"<p>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.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 3","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70020","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}