Journal of Computational Chemistry最新文献

{"title":"Carbamic acid and its dimer: A computational study","authors":"Cristina Puzzarini,&nbsp;Silvia Alessandrini","doi":"10.1002/jcc.27442","DOIUrl":"10.1002/jcc.27442","url":null,"abstract":"<p>A recent work by Marks et al. on the formation of carbamic acid in NH<span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mo> </mo>\u0000 <mrow>\u0000 <mn>3</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math>-CO<span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mo> </mo>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math> interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2501-2512"},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544213","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":"Comparative study of the photocatalytic activity of g-C3N4/MN4 (M = Mn, Fe, Co) for water splitting reaction: A theoretical study","authors":"Dhilshada. V. N,&nbsp;Sabyasachi Sen,&nbsp;Mausumi Chattopadhyaya","doi":"10.1002/jcc.27464","DOIUrl":"10.1002/jcc.27464","url":null,"abstract":"<p>In this study, nanocomposites of g-C₃N₄/MN₄ (where M is Mn, Fe and Co) have been designed using advanced density functional theory (DFT) calculations. A comprehensive analysis was conducted on the geometry, electronic, optical properties, work function, charge transfer interaction and adhesion energy of the g-C₃N₄/MN₄ heterostructures and concluded that g-C₃N₄/FeN₄ and g-C₃N₄/CoN₄ heterojunctions exhibit higher photocatalytic performance than individual units. The better photocatalytic activity can be attributed mainly by two facts; (i) the visible light absorption of both g-C₃N₄/FeN₄ and g-C₃N₄/CoN₄ interfaces are higher compared to its isolated analogs and (ii) a significant enhancement of band gap energy in g-C₃N₄/FeN₄ and g-C₃N₄/CoN₄ heterostructures limited the electron–hole recombination significantly. The potential of the g-C₃N₄/MN₄ heterojunctions as a photocatalyst for the water splitting reaction was assessed by examining its band alignment for water splitting reaction. Importantly, while the electronic and magnetic properties of MN₄ systems were studied, this is the first example of inclusion of MN₄ on graphene-based material (g-C₃N₄) for studying the photocatalytic activity. The state of the art DFT calculations emphasis that g-C₃N₄/FeN₄ and g-C₃N₄/CoN₄ heterojunctions are half metallic photocatalysts, which is limited till date.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 30","pages":"2518-2529"},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544214","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 systematic first-principles investigation of the structural, electronic, mechanical, optical, and thermodynamic properties of Half-Heusler ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) for spintronics and optoelectronics applications","authors":"Md. Tarekuzzaman,&nbsp;Mohammad Hasin Ishraq,&nbsp;Md. Atikur Rahman,&nbsp;Ahmad Irfan,&nbsp;Md. Zillur Rahman,&nbsp;Mist. Shamima Akter,&nbsp;Sumaya Abedin,&nbsp;M. A. Rayhan,&nbsp;Md. Rasheduzzaman,&nbsp;M. Moazzam Hossen,&nbsp;Md. Zahid Hasan","doi":"10.1002/jcc.27455","DOIUrl":"10.1002/jcc.27455","url":null,"abstract":"<p>This paper is the first to look at the structural, electronic, mechanical, optical, and thermodynamic properties of the ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) half-Heusler (HH) using DFT based first principles method. The lattice parameters that we have calculated are very similar to those obtained in prior investigations with theoretical and experimental data. The positive phonon dispersion curve confirm the dynamical stability of ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn). The electronic band structure and DOS confirmed that the studied materials ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) are direct band gap semiconductors. The investigation also determined significant constants, including dielectric function, absorption, conductivity, reflectivity, refractive index, and loss function. These optical observations unveiled our compounds potential utilization in various electronic and optoelectronic device applications. The elastic constants were used to fulfill the Born criteria, confirming the mechanical stability and ductility of the solids ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn). The calculated elastic modulus revealed that our studied compounds are elastically anisotropic. Moreover, ANiX (ASc, Ti, Y, Zr, Hf; XBi, Sn) has a very low minimum thermal conductivity (<i>K</i>_min), and a low Debye temperature (<i>θ</i>_D), which indicating their appropriateness for utilization in thermal barrier coating (TBC) applications. The Helmholtz free energy (<i>F</i>), internal energy (<i>E</i>), entropy (<i>S</i>), and specific heat capacity (<i>Cv</i>) are determined by calculations derived from the phonon density of states.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2476-2500"},"PeriodicalIF":3.4,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544136","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 predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models","authors":"Robert Fox,&nbsp;Joaquin Klug,&nbsp;Damien Thompson,&nbsp;Anthony Reilly","doi":"10.1002/jcc.27454","DOIUrl":"10.1002/jcc.27454","url":null,"abstract":"<p>Cocrystals are assemblies of more than one type of molecule stabilized through noncovalent interactions. They are promising materials for improved drug formulation in which the stability, solubility, or biocompatibility of the active pharmaceutical ingredient (API) is improved by including a coformer. In this work, a range of density functional theory (DFT) and density functional tight binding (DFTB) models are systematically compared for their ability to predict the lattice enthalpy of a broad range of existing pharmaceutically relevant cocrystals. These range from cocrystals containing model compounds 4,4′-bipyridine and oxalic acid to those with the well benchmarked APIs of aspirin and paracetamol, all tested with a large set of alternative coformers. For simple cocrystals, there is a general consensus in lattice enthalpy calculated by the different DFT models. For the cocrystals with API coformers the cocrystals, enthalpy predictions depend strongly on the DFT model. The significantly lighter DFTB models predict unrealistic values of lattice enthalpy even for simple cocrystals.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2465-2475"},"PeriodicalIF":3.4,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27454","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490150","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":"Intermolecular interaction energies with AROFRAG–A systematic approach for fragmentation of aromatic molecules","authors":"Emran Masoumifeshani,&nbsp;Tatiana Korona","doi":"10.1002/jcc.27429","DOIUrl":"10.1002/jcc.27429","url":null,"abstract":"<p>Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2446-2464"},"PeriodicalIF":3.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464658","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 variant on the CREST iMTD algorithm for noncovalent clusters of flexible molecules","authors":"Nathanael J. King,&nbsp;Ian D. LeBlanc,&nbsp;Alex Brown","doi":"10.1002/jcc.27458","DOIUrl":"10.1002/jcc.27458","url":null,"abstract":"<p>Conformational ensemble generation and the search for the global minimum conformation are important problems in computational chemistry. In this work, a variant on the conformer-rotamer ensemble sampling tool (CREST) iterative metadynamics (iMTD) algorithm designed for determining structural ensembles and energetics of noncovalent clusters of flexible molecules is presented. We term this new algorithm a low-energy diversity-enhanced variant on CREST, or LEDE-CREST. As with CREST, the energies are evaluated using the semiempirical GFN2-xTB extended tight binding approach. The utility of the algorithm is highlighted by generating ensembles for a variety of noncovalent clusters of flexible or rigid monomers using both CREST and LEDE-CREST.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2431-2445"},"PeriodicalIF":3.4,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27458","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464053","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":"Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside","authors":"Govindan Subramanian,&nbsp;Kanika Manchanda,&nbsp;Yirong Mo,&nbsp;Rohit Y. Sathe,&nbsp;Prasad V. Bharatam","doi":"10.1002/jcc.27451","DOIUrl":"10.1002/jcc.27451","url":null,"abstract":"<p>This study focuses on the systematic exploration of the emodepside conformations bound to monovalent K⁺ ion using quantum mechanical density functional theory (DFT) calculations at the M06-2X/6-31+G(d,p) level of theory. Nine conformers of emodepside and their complexes with K⁺ ion were characterized as stationary points on the potential energy surface. The conformational isomers were examined for their 3D structures, bonding, energetics, and interactions with the cation. A cavitand-like structure (<b>CC</b>) is identified to be the energetically most stable arrangement. To arrive at a better understanding of the K⁺ ion binding, calculations were initially performed on complexes formed by the K⁺ and Na⁺ ions with model ligands (methyl ester and N,N-dimethyl acetamide). Both the natural bond orbital (NBO) method and the block-localized wavefunction (BLW) energy decomposition approach was employed to assess the bonding and energetic contributions stabilizing the ion-bound model complexes. Finally, the solvent effect was evaluated through complete geometry optimizations and energy minimizations for the model ion-ligand complexes and the emodepside-K⁺ bound complexes using an implicit solvent model mimicking water and DMSO.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 28","pages":"2409-2423"},"PeriodicalIF":3.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27451","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454183","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 on machine learning/artificial intelligence","authors":"Gernot Frenking","doi":"10.1002/jcc.27460","DOIUrl":"10.1002/jcc.27460","url":null,"abstract":"","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 29","pages":"2430"},"PeriodicalIF":3.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141454182","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":"Predicting redox potentials by graph-based machine learning methods","authors":"Linlin Jia,&nbsp;Éric Brémond,&nbsp;Larissa Zaida,&nbsp;Benoit Gaüzère,&nbsp;Vincent Tognetti,&nbsp;Laurent Joubert","doi":"10.1002/jcc.27380","DOIUrl":"10.1002/jcc.27380","url":null,"abstract":"<p>The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoretical chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic compounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol<span></span><math>\u0000 <mrow>\u0000 <msup>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 </msup>\u0000 </mrow></math> for reduction and 7.2 kcal mol<span></span><math>\u0000 <mrow>\u0000 <msup>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 </msup>\u0000 </mrow></math> for oxidation potentials, which paves a way toward efficient <i>in silico</i> design of new electrochemical systems.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 28","pages":"2383-2396"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27380","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445071","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":"Exploring the influence of metal cations on individual hydrogen bonds in Watson–Crick guanine–cytosine DNA base pair: An interacting quantum atoms analysis","authors":"F. Pakzad,&nbsp;K. Eskandari","doi":"10.1002/jcc.27441","DOIUrl":"10.1002/jcc.27441","url":null,"abstract":"<p>This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson–Crick guanine–cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mⁿ⁺–GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H<span></span><math>\u0000 <mrow>\u0000 <mi>⋯</mi>\u0000 </mrow></math>D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H<span></span><math>\u0000 <mrow>\u0000 <mi>⋯</mi>\u0000 </mrow></math>D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by <b><i>a</i></b>) and reinforcing the other (<b><i>b</i></b> and <b><i>c</i></b>) interactions. Notably, the interaction <b><i>a</i></b>, the strongest H<span></span><math>\u0000 <mrow>\u0000 <mi>⋯</mi>\u0000 </mrow></math>D interaction in the GC base pair, becomes the weakest in the M^<i>n</i>+–GC complexes. A broader perspective on the stability of GC and M^<i>n</i>+–GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and M^<i>n</i>+–GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and M^<i>n</i>+–GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 28","pages":"2397-2408"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445080","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}