Journal of Theoretical and Computational Chemistry最新文献

{"title":"Influence of Iodine Merz–Singh–Kollman Radius on the Calculated Charges and Hydration Free Energies of Iodinated Molecules","authors":"Andreia Fortuna, Pedro M. S. Suzano, Miguel Machuqueiro, Paulo J. Costa","doi":"10.1142/s2737416523500722","DOIUrl":"https://doi.org/10.1142/s2737416523500722","url":null,"abstract":"<p>Empirical force field methods typically rely on point charges to describe the electrostatic interactions, which is problematic when anisotropy needs to be considered, as in the case of the electrostatic potential of covalently bound halogens that possess a positive site, termed <span><math altimg=\"eq-00001.gif\" display=\"inline\" overflow=\"scroll\"><mi>σ</mi></math></span><span></span>-hole, surrounded by a large negative belt. To address this, an off-center point charge (extra point, EP) is usually placed at a given distance from the halogen to emulate the <span><math altimg=\"eq-00002.gif\" display=\"inline\" overflow=\"scroll\"><mi>σ</mi></math></span><span></span>-hole and commonly used implementations are based on the restrained electrostatic potential (RESP) procedure to fit atomic charges, being one of the most used charge models. In this context, no specific Merz–Singh–Kollman (MK) radius for iodine is available in the literature, which is an essential parameter in the RESP fitting procedure. In this work, we explored the impact of the iodine MK radius on the obtained RESP charges for a set of 12 iodinated molecules. We verified that the relative root mean square (RRMS) values obtained with and without an EP kept decreasing with increasing radii for most compounds, thus impairing optimization using such a procedure. Nevertheless, the use of an iodine MK radius lower than 2 Å is not advisable since the RRMS kept decreasing considerably until this value was reached. Moreover, the performance of three iodine MK radii was studied with the estimation of the free energy of hydration (<span><math altimg=\"eq-00003.gif\" display=\"inline\" overflow=\"scroll\"><mi mathvariant=\"normal\">Δ</mi><msub><mrow><mi>G</mi></mrow><mrow><mi mathvariant=\"normal\">hyd</mi></mrow></msub></math></span><span></span>) values using alchemical free energy calculations, which are particularly sensitive to the charges used. Despite the usage of different radii not leading to remarkable differences, our results indicate that using a value of 2.70 Å leads to lower mean absolute errors (MAE) and root mean squared error (RMSE) values when comparing the calculated with the experimental <span><math altimg=\"eq-00004.gif\" display=\"inline\" overflow=\"scroll\"><mi mathvariant=\"normal\">Δ</mi><msub><mrow><mi>G</mi></mrow><mrow><mi mathvariant=\"normal\">hyd</mi></mrow></msub></math></span><span></span> values.</p>","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"104 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140173145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical Studies on OH−+NH2Cl Reaction: Nucleophilic Substitution at Neutral Nitrogen","authors":"Rui Li, Xu Liu, Boxue Pang, Hui Li, Yang Wu","doi":"10.1142/s2737416523500102","DOIUrl":"https://doi.org/10.1142/s2737416523500102","url":null,"abstract":"<p>The S_N2 and proton transfer (PT) pathways for <span><math altimg=\"eq-00003.gif\" display=\"inline\" overflow=\"scroll\"><msup><mrow><mstyle><mtext mathvariant=\"normal\">OH</mtext></mstyle></mrow><mrow><mo>−</mo></mrow></msup><mo>+</mo><msub><mrow><mstyle><mtext mathvariant=\"normal\">NH</mtext></mstyle></mrow><mrow><mn>2</mn></mrow></msub></math></span><span></span>Cl reaction are represented by employing various electronic structure computations. Both back-side S_N2 and PT channels are exothermic and stationary points of PESs are below the reactant asymptote. Overall, the PES is similar to the C-centered S_N2 reactions. Conversely, ion-dipole complex was not found for <span><math altimg=\"eq-00004.gif\" display=\"inline\" overflow=\"scroll\"><msup><mrow><mstyle><mtext mathvariant=\"normal\">OH</mtext></mstyle></mrow><mrow><mo>−</mo></mrow></msup><mo>+</mo><msub><mrow><mstyle><mtext mathvariant=\"normal\">NH</mtext></mstyle></mrow><mrow><mn>2</mn></mrow></msub></math></span><span></span>Cl system. The N–HOH/NH–Cl hydrogen bond characterizes on either side of the reaction barrier of nitrogen complexes. Moreover, a halogen-bonded complex (HO⁻–ClNH₂) and two types of H-bond complexes (HONH₂–Cl⁻ and Cl⁻–HONH₂) were described, predicting an important role in dynamics. The PT pathway may be the major channel in the title system, which is contradictory to <span><math altimg=\"eq-00005.gif\" display=\"inline\" overflow=\"scroll\"><msup><mrow><mstyle><mtext mathvariant=\"normal\">OH</mtext></mstyle></mrow><mrow><mo>−</mo></mrow></msup><mo>+</mo><msub><mrow><mstyle><mtext mathvariant=\"normal\">CH</mtext></mstyle></mrow><mrow><mn>3</mn></mrow></msub></math></span><span></span>Cl and <span><math altimg=\"eq-00006.gif\" display=\"inline\" overflow=\"scroll\"><msup><mrow><mstyle><mtext mathvariant=\"normal\">F</mtext></mstyle></mrow><mrow><mo>−</mo></mrow></msup><mo>+</mo><msub><mrow><mstyle><mtext mathvariant=\"normal\">NH</mtext></mstyle></mrow><mrow><mn>2</mn></mrow></msub></math></span><span></span>Cl reactions. Here, MP2, B3LYP and CAM-B3LYP methods show overall excellent consistency with CCSD(T)/CBS energies and are recommended to carry out dynamics simulations.</p>","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"228 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138529326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated in Silico–in Vitro Rational Design of Osteogenic Peptides derived from the Armpit Epitope of Human Bone Morphogenetic Proteins","authors":"Fangguo Li, Xi Zhang, Yandong Lu, Lei Chen, Jie Sun","doi":"10.1142/s2737416523500072","DOIUrl":"https://doi.org/10.1142/s2737416523500072","url":null,"abstract":"<p>Bone morphogenetic proteins (BMPs) are multi-functional growth factors that initiate, promote and maintain cartilage and bone morphogenesis, differentiation and regeneration in both the developing embryo and adult. The proteins have a conformational <i>wrist</i> epitope and a linear <i>knuckle</i> epitope responsible for, respectively, type-I and type-II receptor binding, as well as a hybrid <i>armpit</i> epitope targeted by natural BMP antagonists. In this study, the recognition and interaction between human BMPs and their pan-antagonist Crossveinless was investigated systematically at molecular level. It is revealed that the <i>armpit</i> epitope shares a roughly common region over different BMPs, which consists of a loop segment and a turn segment that are sequentially discontinuous but spatially vicinal on these BMP protein surfaces. Turn segment is the primary binding site that can be bound effectively by Crossveinless using a tightly packed mode. The segment was further extended at its two termini to cover a complete double-stranded sheet of BMPs, which was then split from the interfacial context of BMP–Crossveinless complexes to derive a series of osteogenic peptides; they exhibit moderate intrinsic disorder in free state, but can be constrained into a native-like conformation by stapling a disulfide bridge across two strands of the sheet. The disulfide bridge was rationally designed and optimized to avoid disrupting the native interaction of BMP sheet peptides with the active pocket of Crossveinless. Biophysical assays substantiated that the binding affinities of resulting cyclic peptides were improved by 2–6-fold relative to their linear counterpart upon the stapling, in which the cyclic peptide Bmp7-<i>sb</i>1 (S[CLYFDDNSNVILC]K) derived from the double-stranded sheet region of BMP7 <i>armpit</i> epitope was determined to have the highest affinity to Crossveinless in all tested samples. These rationally designed epitope-derived peptides can be used as osteogenic agents to activate the human BMP signaling by competitively targeting their natural antagonist.</p>","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138529327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Properties and Functionalization of Graphene - A Computational Chemistry Approach","authors":"","doi":"10.1016/c2018-0-04557-0","DOIUrl":"https://doi.org/10.1016/c2018-0-04557-0","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79058233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Modeling of the Sensitivities of Energetic Materials","authors":"","doi":"10.1016/c2019-0-04335-x","DOIUrl":"https://doi.org/10.1016/c2019-0-04335-x","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"69 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83984470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Crystalline States of Organic Compounds","authors":"","doi":"10.1016/c2020-0-00257-4","DOIUrl":"https://doi.org/10.1016/c2020-0-00257-4","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78613119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The dynamic simulation of aggregate chemical systems: Use and misuse of long lists of numbers","authors":"A. Gavezzotti","doi":"10.1016/b978-0-12-823747-2.00008-1","DOIUrl":"https://doi.org/10.1016/b978-0-12-823747-2.00008-1","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87011816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Series Page","authors":"","doi":"10.1016/b978-0-12-823747-2.09990-x","DOIUrl":"https://doi.org/10.1016/b978-0-12-823747-2.09990-x","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"157 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75756708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electron densities and chemical bonding: Old and new ideas","authors":"A. Gavezzotti","doi":"10.1016/b978-0-12-823747-2.00011-1","DOIUrl":"https://doi.org/10.1016/b978-0-12-823747-2.00011-1","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78720480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The intermolecular chemical bond: Physical facts and geometric fiction","authors":"A. Gavezzotti","doi":"10.1016/b978-0-12-823747-2.00002-0","DOIUrl":"https://doi.org/10.1016/b978-0-12-823747-2.00002-0","url":null,"abstract":"","PeriodicalId":17388,"journal":{"name":"Journal of Theoretical and Computational Chemistry","volume":"31 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83583551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}