Journal of Computational Chemistry最新文献

{"title":"Single- and Three-Photon Ionization of \u0000 \u0000 \u0000 \u0000 \u0000 N\u0000 \u0000 \u0000 2\u0000 \u0000 \u0000 \u0000 $$ {N}_2 $$\u0000 in Presence of Fano Resonances","authors":"Vinay Pramod Majety,&nbsp;Armin Scrinzi","doi":"10.1002/jcc.70067","DOIUrl":"https://doi.org/10.1002/jcc.70067","url":null,"abstract":"<p>We report single- and three-photon ionization cross-sections of the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>N</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {N}_2 $$</annotation>\u0000 </semantics></math> molecule in the region of the Hopfield series of doubly excited states. Results are obtained by solving the time-dependent Schrödinger equation in a hybrid basis combining neutral and ionic CI states with a fully numerical basis. Contributions to the spectrum during and after the interaction are obtained using the tSurff and iSurf methods. Calculations at arbitrary molecular orientation and details of the spectral calculation are presented. For single-photon ionization synchrotron data is reproduced. For three-photon ionization we find a pronounced change of resonance line shape when going from single- to three-photon transitions.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595131","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":"Unraveling Solvent and Substituent Effects in the Photodynamics of Light-Dependent Microtubule Inhibitors for Cancer Phototherapy","authors":"Amirhossein Bakhtiiari,&nbsp;Ruibin Liang","doi":"10.1002/jcc.70076","DOIUrl":"https://doi.org/10.1002/jcc.70076","url":null,"abstract":"<div>\u0000 \u0000 <p>In photopharmacology, molecular photoswitches enable light-controlled drug activities, offering precision in targeting biomolecular functions while minimizing side effects. Photostatins (PSTs) are photoswitchable analogs of combretastatin A-4 (CA4), designed to inhibit tubulin polymerization for cancer treatment. However, the influence of substituents and molecular environments on their photochemistry remains unclear. In this work, the <i>cis</i>-to-<i>trans</i> photodynamics of five PSTs (PST1 to PST5) in the vacuum and aqueous solution were simulated using the ab initio multiple spawning (AIMS) coupled with correlated multireference electronic structure calculations. Four distinct minima in the same conical intersection seam were discovered, serving as nonradiative decay channels. The aqueous environment slows photoisomerization and lowers its quantum yields and changes the structures near the conical intersection seam. Substituent position and electronegativity significantly impact the isomerization kinetics by altering energy gaps between MECIs and the S₁ state at the Franck-Condon region. These findings provide useful insights into designing next-generation phototherapeutics for cancer.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595129","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":"Ladderenes as Covalently Condensed Acetylene: A DFT Investigation of Gold(I)-Catalyzed Mechanism, Substituent Effects and Energy Storage Potential","authors":"Ramakrishnan Thushara,&nbsp;Cherumuttathu H. Suresh","doi":"10.1002/jcc.70078","DOIUrl":"https://doi.org/10.1002/jcc.70078","url":null,"abstract":"<div>\u0000 \u0000 <p>Ladderenes, unique polymers composed of fused cyclobutane rings, exhibit promising properties for energy storage applications, including reversible redox behavior and structural tunability. This density functional theory (DFT) study investigates the formation of ladderenes via gold(I)-catalyzed alkyne-alkene coupling reactions. Our calculations reveal a step-wise chain propagation mechanism where the alkene product of each step reacts with a ligand-gold-alkyne complex, leading to the sequential addition of cyclobutene units. We demonstrate that electron-withdrawing substituents on the alkynes, such as chlorine, facilitate the dissociation of the gold catalyst (PMe₃Au⁺) from the cyclobutene adduct, enhancing catalytic efficiency. Solvent effects are also shown to significantly influence the reaction energetics. This finding highlights the significant impact of alkyne substitution on the catalytic cycle. The inherent exothermicity of ladderene formation, coupled with their unique structural features, suggests their potential for storing energy in the form of “covalently condensed acetylene”.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595128","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":"Quantum Chemical and Trajectory Surface Hopping Molecular Dynamics Study of Iodine-Based BODIPY Photosensitizer","authors":"Mirza Wasif Baig,&nbsp;Marek Pederzoli,&nbsp;Mojmír Kývala,&nbsp;Jiří Pittner","doi":"10.1002/jcc.70026","DOIUrl":"https://doi.org/10.1002/jcc.70026","url":null,"abstract":"<p>A computational study of I-BODIPY (2-ethyl-4,4-difluoro-6,7-diiodo-1,3-dimethyl-4-bora-3a,4a-diaza-s-indacene) has been carried out to investigate its key photophysical properties as a potential triplet photosensitizer capable of generating singlet oxygen. Multireference CASPT2 and CASSCF methods have been used to calculate vertical excitation energies and spin–orbit couplings (SOCs), respectively, in a model (mono-iodinated BODIPY) molecule to assess the applicability of the single-reference second-order algebraic diagrammatic construction, ADC(2), method to this and similar molecules. Subsequently, time-dependent density functional theory (TD-DFT), possibly within the Tamm–Dancoff approximation (TDA), using several exchange-correlation functionals has been tested on I-BODIPY against ADC(2), both employing a basis set with a two-component pseudopotential on the iodine atoms. Finally, the magnitudes of SOC between excited electronic states of all types found have thoroughly been discussed using the Slater–Condon rules applied to an arbitrary one-electron one-center effective spin–orbit Hamiltonian. The geometry dependence of SOCs between the lowest-lying states has also been addressed. Based on these investigations, the TD-DFT/B3LYP and TD-DFT(TDA)/BHLYP approaches have been selected as the methods of choice for the subsequent nuclear ensemble approach absorption spectra simulations and mixed quantum-classical trajectory surface hopping (TSH) molecular dynamics (MD) simulations, respectively. Two bright states in the visible spectrum of I-BODIPY have been found, exhibiting a redshift of the main peak with respect to unsubstituted BODIPY caused by the iodine substituents. Excited-state MD simulations including both non-adiabatic effects and SOCs have been performed to investigate the relaxation processes in I-BODIPY after its photoexcitation to the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mtext>S</mtext>\u0000 <msub>\u0000 <mrow></mrow>\u0000 <mrow>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{S}}_1 $$</annotation>\u0000 </semantics></math> state. The TSH MD simulations revealed that intersystem crossings occur on a time scale comparable to internal conversions and that after an initial phase of triplet population growth a “saturation” is reached where the ratio of the net triplet to singlet populations is about 4:1. The calculated triplet quantum yield of 0.85 is in qualitative agreement with the previously reported experimental singlet oxygen generation yield of 0.99 <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mo>±</mo>\u0000 </mrow>\u0000 <annotation>$$ pm $$</annotation>\u0000 </semantics></math> 0.06.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595130","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":"Reversible Hydrogen Storage by Planar Hypercoordinate Hydrogen Clusters","authors":"Kangkan Sarmah,&nbsp;Ankur K. Guha","doi":"10.1002/jcc.70077","DOIUrl":"https://doi.org/10.1002/jcc.70077","url":null,"abstract":"<div>\u0000 \u0000 <p>Lithium-decorated planar hypercoordinate hydrogen clusters have been investigated as hydrogen storage materials by density functional theory. The topological study shows the molecular interaction of the hydrogen with each cluster. The gravimetric densities were found to be 50.3 and 46.4 for the planar tetra-and pentacoordinate hydrogen clusters. Born-Oppenheimer molecular dynamics (BOMD) simulation study reveals the reversibility of the adsorbed hydrogens at different temperatures. Our study revealed that the Lithium-decorated planar hypercoordinate clusters are promising candidates for reversible hydrogen storage.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581668","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":"Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening","authors":"Andreas Vitalis,&nbsp;David Parker,&nbsp;Fabian Radler,&nbsp;Pablo A. Vargas-Rosales,&nbsp;Yang Zhang,&nbsp;Jean-Rémy Marchand,&nbsp;Amedeo Caflisch","doi":"10.1002/jcc.70074","DOIUrl":"https://doi.org/10.1002/jcc.70074","url":null,"abstract":"<div>\u0000 \u0000 <p>We introduce a software package, ParaLig, that provides solutions for several workflows occurring repeatedly in computational drug discovery: parameterization of small molecules with partial charges and free energies of solvation, generation of conformers, virtual chemical reactions, creating combinatorial libraries, and molecule editing tasks. Throughout, we emphasize the maintenance/creation of 3D coordinates and better interoperability. The latter is achieved by stable embedding of meta-information into output files and by improving the mutual compatibility of molecular representations (e.g., aromaticity perception). ParaLig wraps around core functionalities provided by a variety of existing software: the two popular cheminformatics packages OpenBabel and RDKit, and the general force field providers CGenFF and AmberTools. Our workflows emphasize scalable bulk processing of large libraries of molecules, and we provide an MPI-based wrapper to simplify deployment to high-performance computing resources. Along with salient descriptions of the methods, we benchmark performance both in terms of throughput and in terms of the quality of some of the results.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 7","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565206","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 Molecular Energies of Small Organic Molecules With Multi-Fidelity Methods","authors":"Vivin Vinod,&nbsp;Dongyu Lyu,&nbsp;Marcel Ruth,&nbsp;Peter R. Schreiner,&nbsp;Ulrich Kleinekathöfer,&nbsp;Peter Zaspel","doi":"10.1002/jcc.70056","DOIUrl":"https://doi.org/10.1002/jcc.70056","url":null,"abstract":"<p>Multi-fidelity methods in machine learning (ML) have seen increasing usage for the prediction of quantum chemical properties. These methods, such as <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>Δ</mi>\u0000 </mrow>\u0000 <annotation>$$ Delta $$</annotation>\u0000 </semantics></math>-ML and Multifidelity Machine Learning (MFML), have been shown to significantly reduce the computational cost of generating training data. This work implements and analyzes several multi-fidelity methods including <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>Δ</mi>\u0000 </mrow>\u0000 <annotation>$$ Delta $$</annotation>\u0000 </semantics></math>-ML and MFML for the prediction of electronic molecular energies at DLPNO-CCSD(T) level, that is, at the level of coupled cluster theory including single and double excitations and perturbative triples corrections. The models for small organic molecules are evaluated not only on the basis of accuracy of prediction, but also on efficiency in terms of the time-cost of generating training data. In addition, the models are evaluated for the prediction of energies for molecules sampled from a public dataset, in particular for atmospherically relevant molecules, isomeric compounds, and highly conjugated complex molecules.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70056","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143535901","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":"Not Just Another Crystal Field Software","authors":"Letizia Fiorucci,&nbsp;Enrico Ravera","doi":"10.1002/jcc.70063","DOIUrl":"10.1002/jcc.70063","url":null,"abstract":"<p>This manuscript presents NJA-CFS, a Python-based comprehensive toolkit for crystal field/ligand field calculations. NJA-CFS is designed to perform simulations of electronic structure properties, including the magnetic ones, for transition metals and lanthanoid complexes, giving access to several CF/LF parametrization schemes, from point-charge model and AOM to AILFT parameters, putting great effort in the implementation of routines for CF parameters manipulation and rotation. NJA-CFS was designed to meet the needs of both first-time users of crystal field theory and those who require a high degree of flexibility in the choice of crystal field parameters formalisms. In this manuscript, we present the theoretical foundations of the program routines and the comparison of NJA-CFS calculation results either to experimental data or ab initio computations, proving the advantages that access to multiple CFPs formalism can bring in. We also present intuitive applications of the NJA-CFS routines to didactically valuable examples, like the projection of CF/LF splitting on real d- and f- orbitals and the calculations of Tanabe–Sugano diagrams for arbitrary symmetries and with the inclusion of spin-orbit coupling.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532689","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":"Optical Properties and Tautomerism of 2-Carbamido-1,3-Indandione in Ground and Excited States","authors":"Venelin Enchev,&nbsp;Tsvetan Zahariev,&nbsp;Nina Stoyanova,&nbsp;Ivan Angelov,&nbsp;Ivelina Georgieva","doi":"10.1002/jcc.70041","DOIUrl":"https://doi.org/10.1002/jcc.70041","url":null,"abstract":"<div>\u0000 \u0000 <p>2-Carbamido-1,3-indanedione (CAID) is a fluorescent compound, existing in two tautomeric forms: <b>A</b> and <b>B</b>. Spectroscopic features of CAID suggest that the tautomeric equilibrium is possible both in ground and excited state. To further elucidate this, measurements of UV–Vis absorption and fluorescence spectra were recorded in various solvents. The ground and low-lying excited states of CAID are modeled at SOS-MP2/ADC(2) computational level. The two tautomers <b>A</b> and <b>B</b> coexist in ground state with the amount of <b>A</b> amounting to 90% and a dynamic equilibrium is established. However, in all excited states the tautomer <b>B</b> is more stable and its amount is almost 100%. Along with fluorescence from the first excited state of both tautomers, a rare case of breaking Kasha's rule—fluorescence from the third excited state of the two tautomers—has been observed. A scheme is proposed to explain the photophysical processes and photoreactions of CAID in ethanol solution.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143533295","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":"Dual-Branch Graph Neural Network for Predicting Molecular Odors and Discovering the Relationship Between Functional Groups and Odors","authors":"Yongquan Jiang,&nbsp;Xin Xie,&nbsp;Yan Yang,&nbsp;Yuerui Liu,&nbsp;Kuanping Gong,&nbsp;Tianrui Li","doi":"10.1002/jcc.70069","DOIUrl":"https://doi.org/10.1002/jcc.70069","url":null,"abstract":"<div>\u0000 \u0000 <p>Prediction of molecular odors is crucial for synthetic chemistry and the perfume industry. This paper presents a dual-branch graph neural network model for predicting molecular odors, named ScentGraphX, which combines transfer learning with graph attention mechanisms to address limitations of existing models. The ScentGraphX model captures atomic, chemical bond, and structural features of molecules through a feature encoder and a subgraph encoder. Experimental results show that the ScentGraphX model exhibits superior performance on a dataset comprising 4967 molecules, accurately predicting multi-label odor descriptors of molecules. Comparative analysis demonstrates that the ScentGraphX model excels in precision, recall, <i>F</i>1, and AUCROC evaluation metrics, validating its effectiveness in the field of molecular odor prediction. Moreover, interpretability analysis of the model reveals the impact of various chemical functional groups on odor characteristics, and ablation studies confirm the indispensability of each module in ScentGraphX.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490053","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}