Journal of Computational Chemistry最新文献_第10页

Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures 探索结构和能量调整 QM/MM 链接键的适用范围 III：以层状碳结构为例，对固态系统进行 QM/MM MD 模拟。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-25 DOI: 10.1002/jcc.27428

Felix R. S. Purtscher, Thomas S. Hofer

{"title":"Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures","authors":"Felix R. S. Purtscher, Thomas S. Hofer","doi":"10.1002/jcc.27428","DOIUrl":"10.1002/jcc.27428","url":null,"abstract":"The previously introduced workflow to achieve an energetically and structurally optimized description of frontier bonds in quantum mechanical/molecular mechanics (QM/MM)-type applications was extended into the regime of computational material sciences at the example of a layered carbon model systems. Optimized QM/MM link bond parameters at HSEsol/6-311G(d,p) and self-consistent density functional tight binding (SCC-DFTB) were derived for graphitic systems, enabling detailed investigation of specific structure motifs occurring in graphene-derived structures <math>\u0000 <mrow>\u0000 <mi>v</mi>\u0000 <mi>i</mi>\u0000 <mi>a</mi>\u0000 </mrow></math> quantum-chemical calculations. Exemplary molecular dynamics (MD) simulations in the isochoric-isothermic (NVT) ensemble were carried out to study the intercalation of lithium and the properties of the Stone–Thrower–Wales defect. The diffusivity of lithium as well as hydrogen and proton adsorption on a defective graphene surface served as additional example. The results of the QM/MM MD simulations provide detailed insight into the applicability of the employed link-bond strategy when studying intercalation and adsorption properties of graphitic materials.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 26","pages":"2186-2197"},"PeriodicalIF":3.4,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27428","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141097119","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}

引用次数: 0

A systematic DFT study of structure and electronic properties of titanium dioxide 对二氧化钛的结构和电子特性进行系统的 DFT 研究。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-24 DOI: 10.1002/jcc.27376

Asma Marzouk, Konstantinos D. Papavasileiou, Loukas D. Peristeras, Leendert Bezemer, Alexander P. van Bavel, Prathamesh M. Shenai, Ioannis G. Economou

{"title":"A systematic DFT study of structure and electronic properties of titanium dioxide","authors":"Asma Marzouk, Konstantinos D. Papavasileiou, Loukas D. Peristeras, Leendert Bezemer, Alexander P. van Bavel, Prathamesh M. Shenai, Ioannis G. Economou","doi":"10.1002/jcc.27376","DOIUrl":"10.1002/jcc.27376","url":null,"abstract":"DFT functionals are of paramount importance for an accurate electronic and structural description of transition metal systems. In this work, a systematic analysis using some well-known and commonly used DFT functionals is performed. A comparison of the structural and energetic parameters calculated with the available experimental data is made in order to find the adequate functional for an accurate description of the TiO2 bulk and surface of both anatase and rutile structures. In the absence of experimental data on the surface energy, the theoretical predictions obtained using the high-accuracy HSE06 functional were used as a reference to compare against the surface energy values calculated with the other DFT functionals. A clear improvement in the electronic description of both anatase and rutile was observed by introducing the Hubbard U correction term to PBE, PW91, and OptPBE functionals. The OptPBE-U4 functional was found to offer a good compromise between accurately describing the structural and electronic properties of titania.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 25","pages":"2153-2166"},"PeriodicalIF":3.4,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27376","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141086330","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}

引用次数: 0

Tinned: A symbolic library for response theory and high-order derivatives Tinned：用于响应理论和高阶导数的符号库。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-23 DOI: 10.1002/jcc.27437

Bin Gao

引用次数: 0

Mechanistic insights into the role of cyclodextrin in the regioselective radical CH trifluoromethylation of aromatic compounds 环糊精在芳香族化合物的区域选择性自由基 CH 三氟甲基化反应中的作用的机理启示

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-17 DOI: 10.1002/jcc.27430

Kyohei Kawashima, Xu Lu, Yoichiro Kuninobu, Toshifumi Mori

引用次数: 0

Theoretical study on the mechanism of alcohol photooxidation on Nb2O5 surface Nb2O5 表面酒精光氧化机理的理论研究

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-17 DOI: 10.1002/jcc.27435

Wei-Wei Wang, Tsunehiro Tanaka, Masahiro Ehara

{"title":"Theoretical study on the mechanism of alcohol photooxidation on Nb2O5 surface","authors":"Wei-Wei Wang, Tsunehiro Tanaka, Masahiro Ehara","doi":"10.1002/jcc.27435","DOIUrl":"10.1002/jcc.27435","url":null,"abstract":"Theoretical modeling of the solid-state photocatalysis is one of the important issues as various useful photocatalysts have been developed to date. In this work, we investigated the mechanism of the alcohol photooxidation on niobium oxide (Nb2O5) which was experimentally developed, using the density functional theory (DFT)/time-dependent (TD)DFT calculations based on the cluster model. The alcohol adsorption and the first hydrogen transfer from hydroxy group to surface occur in the ground state, while the second hydrogen transfer from CH proceeds in the excited states during the photoirradiation of UV or visible light. The spin crossing was identified and the low-lying triplet states were solved for the reaction pathway. The photoabsorption in the visible light region was characterized as the charge transfer transition from O 2p of alcohol to Nb 4d of the Nb2O5 surface. The spin density and the natural population analysis indicated the generation of spin density in the moiety of carbonyl compound and its dissipation to the interface of the surface, which partly explains the electron paramagnetic resonance measurement. It was confirmed that the rate determining step is the desorption of carbonyl compound and water molecule in agreement with the experimental rate equation analysis. The present findings with the theoretical modeling will provide useful information for the further studies of the solid-state photocatalysis.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 25","pages":"2128-2135"},"PeriodicalIF":3.4,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27435","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954626","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}

引用次数: 0

Computational exploration of the copper(I)-catalyzed conversion of hydrazones to dihalogenated vinyldiazene derivatives 铜(I)催化的酰肼向二卤化乙烯基二氮烯衍生物转化的计算探索

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-17 DOI: 10.1002/jcc.27433

Ulviyya Askerova, Yusif Abdullayev, Namiq Shikhaliyev, Abel Maharramov, Valentine G. Nenajdenko, Jochen Autschbach

{"title":"Computational exploration of the copper(I)-catalyzed conversion of hydrazones to dihalogenated vinyldiazene derivatives","authors":"Ulviyya Askerova, Yusif Abdullayev, Namiq Shikhaliyev, Abel Maharramov, Valentine G. Nenajdenko, Jochen Autschbach","doi":"10.1002/jcc.27433","DOIUrl":"10.1002/jcc.27433","url":null,"abstract":"This computational study explores the copper (I) chloride catalyzed synthesis of (E)-1-(2,2-dichloro-1-phenylvinyl)-2-phenyldiazene (2Cl-VD) from readily available hydrazone derivative and carbon tetrachloride (CCl4). 2Cl-VD has been extensively utilized to synthesize variety of heterocyclic organic compounds in mild conditions. The present computational investigations primarily focus on understanding the role of copper (I) and N1,N1,N2,N2-tetramethylethane-1,2-diamine (TMEDA) in this reaction, TMEDA often being considered a proton scavenger by experimentalists. Considering TMEDA as a ligand significantly alters the energy barrier. In fact, it is only 8.3 kcal/mol higher compared to the ligand-free (LF) route for the removal of a chlorine atom to form the radical ·CCl3 but the following steps are almost barrierless. This intermediate then participates in attacking the electrophilic carbon in the hydrazone. Crucially, the study reveals that the overall potential energy surface is thermodynamically favorable, and the theoretical turnover frequency (TOF) value is higher in the case of Cu(I)-TMEDA complex catalyzed pathway.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 24","pages":"2098-2103"},"PeriodicalIF":3.4,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954648","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}

引用次数: 0

Mapping the correlations between bandgap, HOMO, and LUMO trends for meta substituted Zn-MOFs 绘制元取代 Zn-MOF 的带隙、HOMO 和 LUMO 趋势之间的关联图

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-17 DOI: 10.1002/jcc.27432

Kyle I. Williamson, Daniel J. C. Herr, Yirong Mo

{"title":"Mapping the correlations between bandgap, HOMO, and LUMO trends for meta substituted Zn-MOFs","authors":"Kyle I. Williamson, Daniel J. C. Herr, Yirong Mo","doi":"10.1002/jcc.27432","DOIUrl":"10.1002/jcc.27432","url":null,"abstract":"Bandgap is a key property that determines electrical and optical properties in materials. Modulating the bandgap thus is critical in developing novel materials particularly semiconductors with improved features. This study examines the bandgap, highest occupied molecular orbital (HOMO), and lowest unoccupied molecular orbital (LUMO) energy level trends in a metal organic framework, metal–organic framework 5 (MOF-5), as a function of Hammett substituent effect (with the constant σm in the meta-position of the benzene ring) and solvent dielectric effect (with the constant ε). Specifically, experimental design and response surface methodologies helped to assess the significance of trends and correlations between these molecular properties with σm and ε. While the HOMO and LUMO decrease with increasing σm, the LUMO exhibits greater sensitivity to the substituent's electron withdrawing capability. The relative difference in these trends helps to explain why the bandgap tends to decrease with increasing σm.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 25","pages":"2119-2127"},"PeriodicalIF":3.4,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27432","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140953885","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}

引用次数: 0

Exploring the role of mean-field potentials and short-range wave function behavior in the adiabatic connection 探索均场势能和短程波函数行为在绝热连接中的作用。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-15 DOI: 10.1002/jcc.27378

Anthony Scemama, Andreas Savin

{"title":"Exploring the role of mean-field potentials and short-range wave function behavior in the adiabatic connection","authors":"Anthony Scemama, Andreas Savin","doi":"10.1002/jcc.27378","DOIUrl":"10.1002/jcc.27378","url":null,"abstract":"In this article, we explore the construction of Hamiltonians with long-range interactions and their corrections using the short-range behavior of the wave function. A key aspect of our investigation is the examination of the one-particle potential, kept constant in our previous work, and the effects of its optimization on the adiabatic connection. Our methodology involves the use of a parameter-dependent potential dependent on a single parameter to facilitate practical computations. We analyze the energy errors and densities in a two-electron system (harmonium) under various conditions, employing different confinement potentials and interaction parameters. The study reveals that while the mean-field potential improves the expectation value of the physical Hamiltonian, it does not necessarily improve the energy of the system within the bounds of chemical accuracy. We also delve into the impact of density variations in adiabatic connections, challenging the common assumption that a mean field improves results. Our findings indicate that as long as energy errors remain within chemical accuracy, the mean field does not significantly outperform a bare potential. This observation is attributed to the effectiveness of corrections based on the short-range behavior of the wave function, a universal characteristic that diminishes the distinction between using a mean field or not.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 24","pages":"2091-2097"},"PeriodicalIF":3.4,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140943470","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}

引用次数: 0

Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene 取代对分子流动性的限制：1,10-二氰基丁戊烯的案例研究。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-14 DOI: 10.1002/jcc.27379

Bin-Bin Pei, Hongjuan Yang, Cai-Yue Gao, Yuan Man, Yonggang Yang, Si-Dian Li

{"title":"Restriction on molecular fluxionality by substitution: A case study for the 1,10-dicyanobullvalene","authors":"Bin-Bin Pei, Hongjuan Yang, Cai-Yue Gao, Yuan Man, Yonggang Yang, Si-Dian Li","doi":"10.1002/jcc.27379","DOIUrl":"10.1002/jcc.27379","url":null,"abstract":"We show herein that 1,10-dicyano substitution restricts the paragon fluxionality of bullvalene to just 14 isomers which isomerize along a single cycle. The restricted fluxionality of 1,10-dicyanobullvalene (DCB) is investigated by means of: (i) Bonding analyses of the isomer structures using the adaptive natural density partitioning (AdNDP). (ii) Quantum dynamical simulations of the isomerizations along the cyclic intrinsic reaction coordinate of the potential energy surface (PES). The PES possesses 14 equivalent potential wells supporting 14 isomers which are separated by 14 equivalent potential barriers supporting 14 transition states. Accordingly, at low temperatures, DCB appears as a hindered molecular rotor, without any delocalization of the wavefunction in the 14 potential wells, without any nuclear spin isomers, and with completely negligible tunneling. These results are compared and found to differ from those for molecular boron rotors. (iii) Born-Oppenheimer molecular dynamics (BOMD) simulations of thermally activated isomerizations. (iv) Calculations of the rate constants in the frame of transition state theory (TST) with reasonable agreement achieved with the BOMD results. (v) Simulations of the equilibration dynamics using rate equations for the isomerizations with TST rate coefficients. Accordingly, in the long-time limit, isomerizations of the 14 isomers, each with Cs symmetry, approach the “14 Cs → C7v” thermally averaged structure. This is a superposition of the 14 equally populated isomer structures with an overall C7v symmetry. By extrapolation, the results for DCB yield working hypotheses for so far un-explored properties e.g. for the equilibration dynamics of C10H10.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 24","pages":"2080-2090"},"PeriodicalIF":3.4,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140915310","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}

引用次数: 0

Computational assessment of the use of graphene-based nanosheets as PtII chemotherapeutics delivery systems 将石墨烯基纳米片用作 PtII 化疗药物输送系统的计算评估。

IF 3.4 3区化学

Journal of Computational Chemistry Pub Date : 2024-05-13 DOI: 10.1002/jcc.27394

Daniele Belletto, Vincenzo Vigna, Pierraffaele Barretta, Fortuna Ponte, Gloria Mazzone, Stefano Scoditti, Emilia Sicilia

{"title":"Computational assessment of the use of graphene-based nanosheets as PtII chemotherapeutics delivery systems","authors":"Daniele Belletto, Vincenzo Vigna, Pierraffaele Barretta, Fortuna Ponte, Gloria Mazzone, Stefano Scoditti, Emilia Sicilia","doi":"10.1002/jcc.27394","DOIUrl":"10.1002/jcc.27394","url":null,"abstract":"Graphene is the newest form of elemental carbon and it is becoming rapidly a potential candidate in the framework of nano-bio research. Many reports confirm the successful use of graphene-based materials as carriers of anticancer drugs having relatively high loading capacities compared with other nanocarriers. Here, the outcomes of a systematic study of the adsorption behavior of FDA approved PtII drugs cisplatin, oxaliplatin, and carboplatin on surface models of pristine, holey, and nitrogen-doped holey graphene are reported. DFT investigations in water solvent have been carried out considering several initial orientations of the drugs with respect to the surfaces. Adsorption free energies, calculated including basis set superposition error (BSSE) corrections, result to be significantly negative for many of the drug@carrier adducts indicating that tested layers could be used as potential carriers for the delivery of anticancer PtII drugs. The reduced density gradient (RDG) analysis allows to show that many kinds of non-covalent interactions, including canonical H-bond, are responsible for the stabilization of the formed adducts.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 24","pages":"2059-2070"},"PeriodicalIF":3.4,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140915309","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}

引用次数: 0