Journal of Computational Chemistry最新文献

{"title":"CCPE: A Tool to Quickly Extract, Format, and Present the Outputs From Gaussian and VEDA Computational Chemistry Programs","authors":"Mehmet Bozuyla,&nbsp;Alpaslan Bayrakdar,&nbsp;Yusuf Sert,&nbsp;Hasan Huseyin Kart,&nbsp;Sevgi Ozdemir Kart,&nbsp;Prasath Manivannan,&nbsp;Mehmet Hakkı Alma","doi":"10.1002/jcc.70098","DOIUrl":"https://doi.org/10.1002/jcc.70098","url":null,"abstract":"<div>\u0000 \u0000 <p>The analysis and interpretation of theoretical results remain significant challenges for researchers in computational chemistry, particularly when working with molecules containing a large number of atoms. The manual selection, organization, and interpretation of desired parameters from output files generated by computational tools can be error-prone, tedious, and time-intensive, often taking days to complete. This study introduces the Computational Chemistry Parameter (CCPE), providing extraction, formatting, and presentation of the computational data obtained from Gaussian and VEDA programs. By integrating outputs from the widely used GAUSSIAN and VEDA programs, CCPE provides an efficient, user-friendly solution for extracting and organizing key data such as vibrational modes, frequency assignments, optimization parameters, and molecular orbital data. This tool significantly reduces the time required for these tasks from several days to a matter of minutes, while minimizing the likelihood of errors. The CCPE software, developed using the C# programming language, emphasizes reliability and adaptability, offering researchers a practical means of handling complex computational data. Through its ability to generate publication-ready outputs in widely accepted formats, CCPE aims to enhance productivity and data accuracy, presenting a transformative step in the field of computational chemistry.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 9","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761970","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 Probing of Schleyer's Hyperconjugative Aromaticity in a Novel Designed Anion Acceptor","authors":"Lawen Mohammed Rasul,&nbsp;Morteza Rouhani,&nbsp;Zohreh Mirjafary","doi":"10.1002/jcc.70084","DOIUrl":"https://doi.org/10.1002/jcc.70084","url":null,"abstract":"<div>\u0000 \u0000 <p>Quantum chemical simulations were utilized to investigate the nature of the bonding of N³⁻, P³⁻, As³⁻, O²⁻, S²⁻, Se²⁻, F⁻, Cl⁻, and Br⁻ anions with the designed anion receptor cyclopenta-2,4-diene-1,1-diylbis(borane) abbreviated as CPDB and consecutive hyperconjugative aromaticity in its cyclopentadiene ring. Various analytical tools, including quantum theory of atoms in molecules (QTAIM), Electron Localization function (ELF), and reduced density gradient (RDG) were employed to explore the interaction between the selected anions and the CPDB structure. Moreover, the changes in the bond lengths (∆BL), harmonic oscillator model of aromaticity (HOMA), and localized orbital locator purely contributed by π-orbitals (LOL-π) analyses were performed to study the hyperconjugative aromaticity upon anion accepting. The findings indicate that the anions are connected to the CPDB structure through the electron deficiency of the B atoms and can induce the aromaticity via Schleyer's hyperconjugative aromaticity to the CPBD's ring. The nature of the interactions and hyperconjugative aromaticity effect of each anion is discussed in detail.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 9","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761995","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":"Intricate Spin-Vibronic Dynamics and Excited-State Intramolecular Thiol Proton Transfer in Dithiotropolone","authors":"Anshuman Bera,&nbsp;Sivaranjana Reddy Vennapusa","doi":"10.1002/jcc.70094","DOIUrl":"https://doi.org/10.1002/jcc.70094","url":null,"abstract":"<div>\u0000 \u0000 <p>We perform a computational investigation to unravel the mechanisms of intramolecular thiol proton transfer and triplet formation in dithiotropolone. The S₁ and S₂ states are dipole-forbidden, whereas S₃ and S₄ are dipole-allowed states in this molecule. Upon initiating the nuclear wavepacket on S₃, this molecule exhibits simultaneous S₃ to S₂/S₁ internal conversion and S₃-T₄ intersystem crossing. Further simulations reveal that the molecule shows ultrafast internal conversion in the triplet manifold, similar to its singlet dynamics. Apart from these decay processes in the Franck-Condon region, this molecule can display thiol proton transfer via multiple singlet states due to low barrier energies along the reaction coordinate. The S₁-T₄ and S₃-T₅/T₆ crossings upon the S-H coordinate's elongation illustrate that the molecule can also show the triplet formation outside the Franck-Condon region.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741447","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":"UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study","authors":"Mercedes Kukulka,&nbsp;Barbara Pem,&nbsp;Katarina Vazdar,&nbsp;Lukasz Cwiklik,&nbsp;Mario Vazdar","doi":"10.1002/jcc.70096","DOIUrl":"https://doi.org/10.1002/jcc.70096","url":null,"abstract":"<p>This study explores the structural and electronic factors affecting the absorption spectra of 5-carboxy-tetramethylrhodamine (TAMRA) in water, a widely used fluorophore in imaging and molecular labeling in biophysical studies. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we examine TAMRA UV absorption spectra together with TAMRA-labeled peptides (Arg₉, Arg₄, Lys₉). We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by ~100 nm, resulting in the maximum at ca. 450 nm instead of the experimental value of ca. 550 nm. However, incorporating MD simulation snapshots of TAMRA in water, the UV maximum peak shifts and is in close agreement with the experimental results due to the rotation of TAMRA N(CH₃)₂ groups, effectively captured in MD simulations. The method is used to estimate the UV absorption spectra of TAMRA-labeled peptides, matching experimental values.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741446","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":"DFT Insights Into the Structural, Stability, Elastic, and Optoelectronic Characteristics of Na2LiZF6 (Z = Ir and Rh) Double Perovskites for Sustainable Energy","authors":"Adil Es-Smairi,&nbsp;Samah Al-Qaisi,&nbsp;N. Sfina,&nbsp;Abderrazak Boutramine,&nbsp;Hamad Rahman Jappor,&nbsp;Hind Saeed Alzahrani,&nbsp;Amani H. Alfaifi,&nbsp;Habib Rached,&nbsp;Ajay Singh Verma,&nbsp;Marouane Archi,&nbsp;Md. Ferdous Rahman","doi":"10.1002/jcc.70097","DOIUrl":"https://doi.org/10.1002/jcc.70097","url":null,"abstract":"<div>\u0000 \u0000 <p>Halide perovskites have gained significant attention due to their tunable bandgaps and environmentally friendly properties, making them strong candidates for advanced optoelectronic applications. In this study, we employed the FP-LAPW method to explore the structural, electronic, and optical properties of Na₂LiZF₆ (Z = Ir and Rh). Our findings confirm the stability of the cubic phase through a Goldschmidt tolerance factor of 0.99 and negative formation energies of −3.34 Ry for Na₂LiIrF₆ and −3.22 Ry for Na₂LiRhF₆. Additionally, phonon dispersion analysis verifies their dynamic stability. Mechanical analysis indicates that these materials are structurally robust, with bulk moduli of 84.21 and 80.48 GPa, while their ductile nature is supported by Pugh's ratios of 2.21 and 2.41, respectively. From an electronic perspective, both compounds exhibit indirect bandgaps of 4.05 and 3.98 eV, making them suitable for UV applications. Optical studies further reveal strong UV absorption, with static dielectric constants of 1.42 and 1.50, along with refractive indices (<i>n</i>(0)) of 1.19 and 1.22. These characteristics make Na₂LiZF₆ (Z = Ir and Rh) promising candidates for next-generation UV photodetectors and light-emitting devices.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 8","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741454","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":"Editorial Note","authors":"Gernot Frenking","doi":"10.1002/jcc.70068","DOIUrl":"https://doi.org/10.1002/jcc.70068","url":null,"abstract":"","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726914","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":"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":"On the Origin of the Rotational Barrier in Ethane","authors":"Volker Staemmler,&nbsp;Robert Franke","doi":"10.1002/jcc.70014","DOIUrl":"https://doi.org/10.1002/jcc.70014","url":null,"abstract":"<div>\u0000 \u0000 <p>The origin of rotational barriers around C<span></span>C single bonds is still vividly discussed and often referred to concepts like steric repulsion or hyperconjugation. In 1990, a paper was published in which the physical causes for the rotational barrier in ethane, that is, the well-known finding that the potential energy in the eclipsed form is slightly higher than in the staggered form, appears as a consequence of a lowering of the nuclear-electron attraction and not as a greater electronic repulsion in the eclipsed form. Surprisingly, this finding has practically not found its way neither into the textbook literature nor into the scientific discourse. Here we will show, by a careful analysis of the components to the total energy and their dependence on the geometry of the molecule, that the kinetic energy of the electrons and the virial theorem play the decisive role. This is very similar to their role for the origin of the chemical bond.</p>\u0000 </div>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726915","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":"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}