Journal of Computational Chemistry最新文献

{"title":"Hydride and halide abstraction reactions behind the enhanced basicity of Be and Mg clusters with nitrogen bases","authors":"Manuel Yáñez,&nbsp;Otilia Mó,&nbsp;M. Merced Montero-Campillo,&nbsp;Ibon Alkorta,&nbsp;José Elguero","doi":"10.1002/jcc.27509","DOIUrl":"10.1002/jcc.27509","url":null,"abstract":"<p>In this study, we investigate the protonation effects on the structure, relative stability and basicity of complexes formed by the interaction of monomers and dimers of BeX₂ and MgX₂ (X = H, F) with NH₃, CH₂NH, HCN, and NC₅H₅ bases. Calculations were performed using the M06-2X/aug-cc-pVTZ formalism, along with QTAIM, ELF and NCI methods for electron density analysis and MBIE and LMO-EDA energy decomposition analyses for interaction enthalpies. The protonation of the MH₂– and M₂H₄–Base complexes occurs at the negatively charged hydrogen atoms of the MH₂ and M₂H₄ moieties through typical hydride abstraction reactions, while protonation at the N atom of the base is systematically less exothermic. The preference for the hydride transfer mechanism is directly associated with the significant exothermicity of H₂ formation through the interaction between H⁻ and H⁺, and the high hydride donor ability of these complexes. The basicity of both, MH₂ and M₂H₄ compounds increases enormously upon association with the corresponding bases, with the increase exceeding 40 orders of magnitude in terms of ionization constants. Due to the smaller exothermicity of HF formation, the basicity of fluorides is lower than that of hydrides. In Be complexes, the protonation at the N atom of the base dominates over the fluoride abstraction mechanism. However, for the Mg complexes the fluoride abstraction mechanism is energetically the most favorable process, reflecting the greater facility of Mg complexes to lose F⁻.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27509","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329121","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":"Theoretical study on the luminescent and reaction mechanism of dansyl-based fluorescence probe for detecting hydrogen sulfide","authors":"Huixue Li,&nbsp;Yvhua Wang,&nbsp;Sujuan Pan,&nbsp;Changqing Wang,&nbsp;Yanzhi Liu,&nbsp;Kun Yuan,&nbsp;Lingling Lv,&nbsp;Zhifeng Li","doi":"10.1002/jcc.27506","DOIUrl":"10.1002/jcc.27506","url":null,"abstract":"<p>The photophysical and photochemical properties of the sulfonyl azide-based fluorescent probe DNS–Az and its reduction product DNS by hydrogen sulfide (H₂S) have been investigated theoretically. The calculated results indicated the first excited states of DNS–Az was dark state (oscillator strength less than 0.03) and DNS was bright state (oscillator strength more than 0.1), which determined the predicted radiative rate <i>k</i>_r of DNS–Az was much smaller than that of DNS, meanwhile, due to more larger reorganization energy of DNS–Az, its predicted internal conversion rate <i>k</i>_ic was four times larger than that of DNS; moreover, owing to the effect of heavy atom from sulfur atom in DNS–Az, its predicted intersystem crossing rate <i>k</i>_isc was seven times larger than that of DNS, thus the calculated fluorescence quantum yield of DNS–Az was only 2.16% and that of DNS was more than 77.2%, the above factors is the basis for DNS–Az molecule to function as a fluorescent probe. Regarding both DNS-Az and DNS molecules, their maximum Huang-Rhys factors, which are less than unity, signify the reliability of 0–0 transitions between their <i>S</i>₀ and <i>S</i>₁ electronic states. In addition, for DNS, our simulated emission peak of the 0–0 transition is 515 nm, a value that exhibits enhanced accuracy and coherence when compared to the experimental datum of 528 nm. The reaction mechanism of DNS-Az generating DNS by H₂S has been investigated too, according to the potential energy profile, we found that the fluorescent probe firstly protonated, then this organic ion broke down into DNS with the aid of a proton.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142324880","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":"Development of a machine learning-based target-specific scoring function for structure-based binding affinity prediction for human dihydroorotate dehydrogenase inhibitors","authors":"Jinhui Meng, Li Zhang, Zhe He, Mengfeng Hu, Jinhan Liu, Wenzhuo Bao, Qifeng Tian, Huawei Feng, Hongsheng Liu","doi":"10.1002/jcc.27510","DOIUrl":"https://doi.org/10.1002/jcc.27510","url":null,"abstract":"Human dihydroorotate dehydrogenase (hDHODH) is a flavin mononucleotide-dependent enzyme that can limit de novo pyrimidine synthesis, making it a therapeutic target for diseases such as autoimmune disorders and cancer. In this study, using the docking structures of complexes generated by AutoDock Vina, we integrate interaction features and ligand features, and employ support vector regression to develop a target-specific scoring function for hDHODH (TSSF-hDHODH). The Pearson correlation coefficient values of TSSF-hDHODH in the cross-validation and external validation are 0.86 and 0.74, respectively, both of which are far superior to those of classic scoring function AutoDock Vina and random forest (RF) based generic scoring function RF-Score. TSSF-hDHODH is further used for the virtual screening of potential inhibitors in the FDA-Approved &amp; Pharmacopeia Drug Library. In conjunction with the results from molecular dynamics simulations, crizotinib is identified as a candidate for subsequent structural optimization. This study can be useful for the discovery of hDHODH inhibitors and the development of scoring functions for additional targets.","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"30 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321880","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":"Facile heterolytic bond splitting of molecular chlorine upon reactions with Lewis bases: Comparison with ICl and I2","authors":"Anna V. Pomogaeva,&nbsp;Anna S. Lisovenko,&nbsp;Alexey Y. Timoshkin","doi":"10.1002/jcc.27507","DOIUrl":"10.1002/jcc.27507","url":null,"abstract":"<p>Formation of molecular complexes and subsequent heterolytic halogen-halogen bond splitting upon reactions of molecular Cl₂ with nitrogen-containing Lewis bases (LB) are computationally studied at M06-2X/def2-TZVPD and for selected compounds at CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz levels of theory. Obtained results are compared with data for ICl and I₂ molecules. Reaction pathways indicate, that in case of Cl₂∙LB complexes the activation energies for the heterolytic Cl-Cl bond splitting are lower than the activation energies of the homolytic splitting of Cl₂ molecule into chlorine radicals. The heterolytic halogen splitting of molecular complexes of X₂∙Py with formation of [XPy₂]⁺…<span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>X</mi>\u0000 <mn>3</mn>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math> contact ion pairs in the gas phase is slightly endothermic in case of Cl₂ and I₂, but slightly exothermic in the case of ICl. Formation of {[ClPy₂]⁺…<span></span><math>\u0000 <mrow>\u0000 <msubsup>\u0000 <mi>Cl</mi>\u0000 <mn>3</mn>\u0000 <mo>−</mo>\u0000 </msubsup>\u0000 </mrow></math>}₂ dimers makes the overall process exothermic. Taking into account that polar solvents favor ionic species, generation of donor-stabilized Cl⁺ in the presence of the Lewis bases is expected to be favorable. Thus, in polar solvents the oxidation pathway via donor-stabilized Cl⁺ species is viable alternative to the homolytic Cl-Cl bond breaking.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276744","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":"Modeling the effect of substituents on the electronically excited states of indole derivatives","authors":"Jordan Howe,&nbsp;Salsabil Abou-Hatab,&nbsp;Spiridoula Matsika","doi":"10.1002/jcc.27502","DOIUrl":"10.1002/jcc.27502","url":null,"abstract":"<p>A proper understanding of excited state properties of indole derivatives can lead to rational design of efficient fluorescent probes. The optically active <span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>L</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mi>a</mi>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math> and <span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>L</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mi>b</mi>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math> excited states of a series of substituted indoles, where a substituent was placed on position four, were calculated using equation of motion coupled cluster and time dependent density functional theory. The results indicate that most substituted indoles have a brighter second excited state corresponding to experimental absorption maxima, but a few with electron withdrawing substituents absorb more on the first excited state. Absorption on the first excited state may increase their fluorescence quantum yield, making them better probes. Electronic structure methods were found to predict the energies of the systems with electron withdrawing substituents more accurately than those with electron donating substituents. The excited states of both states correlated well with electrophilicity, similar to the experimental trends for the absorption maxima. Overall, these computational studies indicate that theory can be used to predict excited state properties of substituted indoles, when the substituent is an electron withdrawing group.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247221","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":"Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess","authors":"Yi Sun","doi":"10.1002/jcc.27504","DOIUrl":"10.1002/jcc.27504","url":null,"abstract":"<p>We demonstrate that combining a shifted clustering algorithm with a fast-marching-based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)-string combined approach), significantly reduces the number of iterations required for MEP convergence. This approach saves substantial time compared to using linear interpolation (LI) for the initial guess. Our method offers a viable solution for obtaining an effective initial guess of the MEP when an approximate or converged FEL is available. This work highlights the potential of applying FMT-based approaches to extract the MEP in chemical reactions.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"46 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27504","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237228","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":"An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies","authors":"Alexander S. Ryzhako,&nbsp;Anna A. Tuma,&nbsp;Arseniy A. Otlyotov,&nbsp;Yury Minenkov","doi":"10.1002/jcc.27471","DOIUrl":"10.1002/jcc.27471","url":null,"abstract":"<p>An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)_<i>n</i> conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFN<i>n</i>-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid – harmonic oscillator approximations reaching 10 kcal mol⁻¹.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"3004-3016"},"PeriodicalIF":3.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236699","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":"Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum-chemical calculations","authors":"Roberto López,&nbsp;Dimas Suárez","doi":"10.1002/jcc.27503","DOIUrl":"10.1002/jcc.27503","url":null,"abstract":"<p>Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein, we collect the most relevant mechanistic proposals from the recent literature and organize them into a single reaction network. All the transition structures (TSs) and intermediates are characterized using highly accurate ab initio methods and the possible reaction pathways are assessed in terms of the Gibbs energies of the TSs and intermediates with respect to β-glucopyranose, selecting a 2D ideal-gas standard state at 773 K to represent the pyrolysis conditions. Several pathways can lead to the formation of both HMF and FF passing through rate-determining TSs that have <i>ΔG</i>^‡ values of ~49–50 kcal/mol. Both water-assisted mechanisms and nonspecific environmental effects have a minor impact on the Gibbs energy profiles. We find that the HMF → FF + CH₂O fragmentation has a small <i>Δ</i>_rxn<i>G</i> value and an accessible <i>ΔG</i>^‡ barrier. Our computational results, which are in consonance with the kinetic parameters derived from lumped models, the results of isotopic labeling experiments and the reported HMF/FF molecular ratios, could be useful for modeling studies including on nonequilibrium kinetic effects that may render more information about product yields and the relevance of the various pathways.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2991-3003"},"PeriodicalIF":3.4,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27503","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161147","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":"A computational mechanistic study on the formation of aryl sulfonyl fluorides via Bi(III) redox-neutral catalysis and further rational design","authors":"Zhaoyin Zhang,&nbsp;Qin Ma,&nbsp;Xing Yang,&nbsp;Shuqi Zhang,&nbsp;Kai Guo,&nbsp;Lili Zhao","doi":"10.1002/jcc.27501","DOIUrl":"10.1002/jcc.27501","url":null,"abstract":"<p>Sulfonyl fluorides hold significant importance as highly valued intermediates in chemical biology due to their optimal balance of biocompatibility with both aqueous stability and protein reactivity. The Cornella group introduced a one-pot strategy for synthesizing aryl sulfonyl fluorides via Bi(III) redox-neutral catalysis, which facilitates the transmetallation and direct insertion of SO₂ into the Bi<span></span>C(sp²) bond giving the aryl sulfonyl fluorides. We report herein a comprehensive computational investigation of the redox-neutral Bi(III) catalytic mechanism, disclose the critical role of the Bi(III) catalyst and base (i.e., K₃PO₄), and uncover the origin of SO₂ insertion into the Bi(III)<span></span>C(sp²) bond. The entire catalysis can be characterized via three stages: (i) transmetallation generating the Bi(III)-phenyl intermediate <b>IM3</b> facilitated by K₃PO₄. (ii) SO₂ insertion into <b>IM3</b> leading to the formation of Bi(III)-OSOAr intermediate <b>IM5</b>. (iii) <b>IM5</b> undergoes S(IV)-oxidation yielding the aryl sulfonyl fluoride product <b>4</b> and liberating the Bi(III) catalyst for the next catalytic cycle. Each stage is kinetically and thermodynamically feasible. Moreover, we explored other some small molecules (NO₂, CO₂, H₂O, N₂O, etc.) insertion reactions mediated by the Bi(III)-complex, and found that NO₂ insertions could be easily achieved due to the low insertion barriers (i.e., 17.5 kcal/mol). Based on the detailed mechanistic study, we further rationally designed additional Bi(III) and Sb(III) catalysts, and found that some of which exhibit promising potential for experimental realization due to their low barriers (&lt;16.4 kcal/mol). In this regard, our study contributes significantly to enhancing current Bi(III)-catalytic systems and paving the way for novel Bi(III)-catalyzed aryl sulfonyl fluoride formation reactions.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2979-2990"},"PeriodicalIF":3.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142138798","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":"Equation-of-motion orbital-optimized coupled-cluster doubles method with the density-fitting approximation: An efficient implementation","authors":"Aslı Ünal,&nbsp;Uğur Bozkaya","doi":"10.1002/jcc.27495","DOIUrl":"10.1002/jcc.27495","url":null,"abstract":"<p>Orbital-optimized coupled-cluster methods are very helpful for theoretical predictions of the molecular properties of challenging chemical systems, such as excited states. In this research, an efficient implementation of the equation-of-motion orbital-optimized coupled-cluster doubles method with the density-fitting (DF) approach, denoted by DF-EOM-OCCD, is presented. The computational cost of the DF-EOM-OCCD method for excitation energies is compared with that of the conventional EOM-OCCD method. Our results demonstrate that DF-EOM-OCCD excitation energies are dramatically accelerated compared to EOM-OCCD. There are almost 17-fold reductions for the <span></span><math>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>C</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>5</mn>\u0000 </mrow>\u0000 </msub>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>H</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>12</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow></math> molecule in an aug-cc-pVTZ basis set with the RHF reference. This dramatic performance improvement comes from the reduced cost of integral transformation with the DF approach and the efficient evaluation of the particle-particle ladder (PPL) term, which is the most expensive term to evaluate. Further, our results show that the DF-EOM-OCCD approach is very helpful for the computation of excitation energies in open-shell molecular systems. Overall, we conclude that our new DF-EOM-OCCD implementation is very promising for the study of excited states in large-sized challenging chemical systems.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"45 32","pages":"2969-2978"},"PeriodicalIF":3.4,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.27495","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131394","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}