Journal of Computational Chemistry最新文献

{"title":"Clarification of Some Bonding Concepts: Virial Theorem, Electron Pair Repulsion, and Rotational Barriers","authors":"W. H. Eugen Schwarz,&nbsp;Gernot Frenking,&nbsp;Sudip Pan","doi":"10.1002/jcc.70085","DOIUrl":"https://doi.org/10.1002/jcc.70085","url":null,"abstract":"<p>The molecular <i>virial theorem</i> relates kinetic and potential energies (<i>T</i> &amp; <i>V</i>) to total energy and forces (<i>E</i> &amp; <i>R</i>·∂<i>E</i>/∂<i>R</i>); it is a useful tool for analyzing the data, but does not provide clues on the origin of the stability of the “bonded” state. A strict conceptual distinction between cause and effect is recommended. Depending on the physical relationships, the induced change of one variable of the system leads to a resulting change of another variable; relaxation or response of the system can either moderate this change (in the sense of Le Chatelier's principle), enhance it, or even reverse it. Such unexpected, paradoxical behavior is common in reality and in daily life. As two examples of conceptual mix-up in molecular chemistry, we discuss details of the origin of the steric pair-pair repulsion and of the internal rotation barrier in ethane.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717034","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":"Is It Worth Running the Hartree-Fock Calculations With Localized Molecular Orbitals Within the Framework of Variational Coupled Cluster Singles Theory?","authors":"Ján Šimunek,&nbsp;Jozef Noga","doi":"10.1002/jcc.70075","DOIUrl":"https://doi.org/10.1002/jcc.70075","url":null,"abstract":"<div>\u0000 \u0000 <p>Some years ago, we proved that Variational Coupled Cluster Singles (VCCS) theory can be effectively used to solve the independent particle model, which gave rise to a diagonalization-free self-consistent-field approach. The resulting formulation enables a solution with “a priori” localized orbitals. In the current contribution, we have explored this still unexplored possibility. Starting molecular orbitals were either localized using the Pipek-Mezey procedure or via an incomplete Cholesky decomposition of the density matrix. The Hartree-Fock solution was obtained within a VCCS iterative procedure, with the starting localized molecular orbitals used for the creation of the reference and the singly excited determinants. The same localized basis was kept in each iteration. For a series of medium-sized molecules, we have investigated the convergence behavior of the iterative procedure together with the sparsity of the single-excitation amplitude vector and the corresponding density matrix expressed in the localized basis.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699039","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":"Impact of Structure on Excitation Energies and S1-T1 Energy Gaps of Asymmetrical Systems of Interest for Inverted Singlet-Triplet Gaps","authors":"Gideon Odonkor,&nbsp;Samuel O. Odoh","doi":"10.1002/jcc.70090","DOIUrl":"https://doi.org/10.1002/jcc.70090","url":null,"abstract":"<div>\u0000 \u0000 <p>Computational investigations of Inverted Singlet-Triplet (INVEST) emitters often rely on ADC(2) and TD-DFT excitation energies (EEs) obtained with the vertical approximation. Here, we first considered several cyclazine derivatives and examine the sensitivity of vertical EEs (VEEs) as well as singlet-triplet gaps, ΔE_S1T1 gaps, to the level at which the ground state (S₀) structure was optimized. For cyclazine, VEEs and vertical gaps from ADC(2) or TD-DFT are spread over a narrow range (&lt; 0.064 eV) whether the S₀ structure is optimized with various DFT, CCSD, and RI-MP2 methods. However, for asymmetric cyclazines, depending on the protocol for optimizing S₀ structures, not only are VEEs spread over a substantially wider range (up to 0.75 eV) but so are vertical ΔE_S1T1 gaps (up to 0.30 eV), leading to cases where, with different S₀ structures, one obtains positive vertical ΔE_S1T1 gaps or significantly negative gaps. We relate this behavior to the introduction of significant asymmetry and bond-length variations in the cyclazine derivatives, formed by ligand functionalization or modification of the cyclazine core. On a more positive note, adiabatic EEs (AEEs) and adiabatic ΔE_S1T1 gaps display significantly lower sensitivity (7–30× less) to the geometry optimization protocols than their vertical analogs. Crucially, for cyclazine, the M06-HF functional with 100% non-local exchange provides the closest S₀ geometry to available CCSD(T) data. We show that this effect exists also for other frameworks (e.g., azulene, pentaazaphenalene, and non-alternant polycyclic hydrocarbons) that have been considered for the INVEST property, with VEEs spread over a broader range of up to 1.19 eV and vertical ΔE_S1T1 gaps over a range of 0.62 eV. For INVEST emitters, it is therefore extremely important to judiciously choose the computational protocol for optimizing ground state geometries, in computing VEEs and vertical ΔE_S1T1 gaps.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699041","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":"Study of the Photoinduced Charge Injection in the Reaction Intermediate of the Dehydrogenation of Formic Acid on Palladium","authors":"L. Biancorosso,&nbsp;E. Coccia","doi":"10.1002/jcc.70087","DOIUrl":"https://doi.org/10.1002/jcc.70087","url":null,"abstract":"<p>The production rate of hydrogen from formic acid on palladium is enhanced in the presence of an Au nanorod by irradiating the system at its plasmon frequency. Taking inspiration from this, we study here the effect of the shape of the Pd cluster (from Pd(111)) on the photoinduced charge injection into the HCOO moiety and adsorbed H, which are the reaction intermediates of the dehydrogenation of formic acid, upon irradiation with a pulse with a carrier frequency equal to the plasmon resonance of a (not included) Au nanorod. We simulate the electron/hole dynamics at frozen nuclei by propagating the time-dependent Schrödinger equation in the space of time-dependent density-functional-theory pseudo-eigenstates in the tight-binding approximation. We have taken into account a cluster with two layers of Pd and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>3</mn>\u0000 <mo>×</mo>\u0000 <mn>3</mn>\u0000 </mrow>\u0000 <annotation>$$ 3times 3 $$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>4</mn>\u0000 <mo>×</mo>\u0000 <mn>4</mn>\u0000 </mrow>\u0000 <annotation>$$ 4times 4 $$</annotation>\u0000 </semantics></math> atoms per layer (2L3 and 2L4, respectively) or with three layers and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mn>3</mn>\u0000 <mo>×</mo>\u0000 <mn>3</mn>\u0000 </mrow>\u0000 <annotation>$$ 3times 3 $$</annotation>\u0000 </semantics></math> atoms per layer (3L3). For all the systems, a net negative charge on HCOO has been found, according to a photoinduced direct charge-transfer mechanism. For 3L3, an indirect charge-transfer mechanism, occurring after 50 fs and inducing a hole injection into HCOO, has also been found. Moreover, we also used a tailored pulse to populate the antibonding molecular orbital localized on the C-H bond for 3L3.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70087","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699040","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":"On the Meaning of De-Excitations in Time-Dependent Density Functional Theory Computations","authors":"Felix Plasser","doi":"10.1002/jcc.70072","DOIUrl":"https://doi.org/10.1002/jcc.70072","url":null,"abstract":"<p>De-excitations play a prominent role within the mathematical formalism of time-dependent density functional theory (TDDFT) and other excited-state response methods. However, their physical meaning remains largely unexplored and poorly understood. It is the purpose of this work to shed new light on this issue. The main thesis developed here is that de-excitations are not a peculiarity of TDDFT but that they are a more fundamental property of the underlying wave functions reflecting how electrons are excited between partially occupied orbitals. The paraquinodimethane (pQDM) molecule is chosen as a convenient model system whose open-shell character can be modulated via twisting of its methylene groups. Using the one-electron transition density matrix as a rigorous basis for our analysis, we highlight qualitative and quantitative parallels in the way that de-excitations are reflected in multireference wave function and TDDFT computations. As a physically observable consequence, we highlight a lowering of the transition dipole moment that derives from destructive interference between the excitation and de-excitation contributions. In summary, we hope that this work will shed new light on formal and practical aspects regarding the application of TDDFT to excited-state computations, especially of diradicaloid systems.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689662","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":"Molecular Dynamics-Assisted Interaction Between HABT and PI3K Enzyme: Exploring Metastable States for Promising Cancer Diagnosis Applications","authors":"Rodrigo Mancini Santos,&nbsp;Teodorico Castro Ramalho","doi":"10.1002/jcc.70080","DOIUrl":"https://doi.org/10.1002/jcc.70080","url":null,"abstract":"<p>Local nonequilibrium approach has been used for many purposes when dealing with biological systems. Not only for unraveling important features of cancer development, a disease that affects the lives of many people worldwide, but also to understand drug–target interactions in a more real scenario, which can help to combat this disease. Therefore, aiming to contribute to new strategies against cancer, the present work used this approach to investigate the spectroscopy of 2-(2′-hydroxy-4′-aminophenyl)benzothiazole (HABT) when interacting with the PI3K enzyme, a widely associated target for the mentioned illness. The study consisted of evaluating the Excited State Intramolecular Proton Transfer (ESIPT) performance of HABT, in spectroscopic terms, when interacting with the PI3K enzyme in a local nonequilibrium regime. This scenario could be considered by investigating the metastable states of HABT in this system. From this, it was possible to observe that the ESIPT performance of HABT considerably differs when comparing the solution and protein environments, where 63% have appropriate geometry in the protein environment, against 97% in the aqueous environment. Thus, from an entirely theoretical methodology, the present work provides insights when modeling biological systems and contributes significantly to a better comprehension of promising probes for cancer diagnosis.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70080","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689848","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 Mechanism of Nitrite Reductase","authors":"Per E. M. Siegbahn","doi":"10.1002/jcc.70088","DOIUrl":"https://doi.org/10.1002/jcc.70088","url":null,"abstract":"<p>Cytochrome c nitrite reductase (CcNiR) activates nitrite and produces ammonia. It is one of several enzymes that use a redox-active cofactor to perform its reaction. In this case, the cofactor has a heme with a lysine as the proximal ligand and a charged nearby arginine. The role of a tyrosine, which is also close, has been less clear. There are also four bis-histidine-ligated hemes involved in the electron transfers. CcNiR has been studied before, using essentially the same methods as here. However, the mechanism is very complicated, involving six reductions, and quite different results for the mechanism have been obtained here. For example, the tyrosine has here been found to be redox active in the final step when ammonia is produced. Also, the arginine has here been found to stay protonated throughout the mechanism, which is different from what was found in the previous study. The present results are in very good agreement with experimental findings and are, therefore, another case where the methodology has been shown to work very well. Previous examples include Photosystem II and Nitrogenase, normally considered to be the most important enzymes in nature for the development of life.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689846","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":"Foreword to the Special Issue for Hans Lischka","authors":"Adelia J. A. Aquino,&nbsp;Mario Barbatti,&nbsp;Peter G. Szalay,&nbsp;Gernot Frenking","doi":"10.1002/jcc.70089","DOIUrl":"https://doi.org/10.1002/jcc.70089","url":null,"abstract":"","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689847","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":"Physical Significance of Descriptors to Predict the Band Center of High-Entropy Nanoalloys","authors":"Yusuke Nanba,&nbsp;Michihisa Koyama","doi":"10.1002/jcc.70086","DOIUrl":"10.1002/jcc.70086","url":null,"abstract":"<div>\u0000 \u0000 <p>The band center of <i>d</i> orbitals (<i>d</i>-band center) has been widely used as an effective descriptor for analyzing material properties. However, in high-entropy nanoalloys, the diverse atomic environments present challenges in systematically exploring all possible combinations. Due to computational resource limitations, generating a sufficient number of samples is infeasible. Consequently, the <i>d</i>-band center should be treated as a response variable in machine-learning models. We calculated the <i>d</i>-band center for individual atoms and applied supervised learning techniques to identify key factors influencing its behavior. While several factors were identified, their physical significance in predicting <i>d</i>-band centers remained unclear. To address this issue, we incorporated various interatomic distance terms as descriptors, along with element-based coordination numbers (ECN). The resulting model closely resembled the overlap integral of the Slater-type orbital, and the regression coefficients of the ECN exhibited sensitivity to the effective principal quantum number and nuclear charge. Understanding the physical significance of these descriptors is crucial for improving property predictions and facilitating data collection on novel materials.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672753","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":"Prediction of Activation Energies of Organic Molecules With at Most Seven Non-Hydrogen Atoms Using Quantum-Chemically Assisted ML","authors":"K. G. Kalamatianos,&nbsp;Olga N. Flenga","doi":"10.1002/jcc.70083","DOIUrl":"10.1002/jcc.70083","url":null,"abstract":"<div>\u0000 \u0000 <p>In this study, a hybrid machine learning (ML) approach is presented for accurately predicting activation energies (<i>E</i>_a) of gas-phase elementary reactions involving organic compounds with up to seven non-hydrogen atoms. Given the importance of activation energies in reaction studies and modeling, ML composite models were created that effectively integrate molecular descriptors with semi-empirical and single energy density functional theory (DFT) calculations. The dataset, containing 300 randomly selected elementary gas-phase reactions, was assembled using accurate DFT (ωB97X-D3/def2-TZVP) values for activation energies <i>E</i>_a from a database alongside semi-empirical computations. For accurate predictions, this approach required the inclusion of both physical organic and geometric/empirical descriptors in the training procedure. The best two ML models demonstrated efficient <i>E</i>_a prediction capability, achieving a mean absolute error (MAE) of 1.314 kcal mol⁻¹ and <i>R</i>² of 0.992 (Model 3) and (MAE) of 1.949 kcal mol⁻¹ and <i>R</i>² of 0.979 (Model 2) in validation tests. Notably, this performance approaches the threshold of “chemical accuracy” of 1 kcal mol⁻¹. Model's 3 robustness was tested across the reaction types present in the dataset, demonstrating its ability in properly predicting activation energies, which is critical for the study and optimization of chemical processes.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661055","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}