Journal of Computational Chemistry最新文献

{"title":"Charge-Derived Polarization Fingerprints from Charge-Aware Molecular Dynamics: A Descriptor Framework for \u0000 \u0000 \u0000 \u0000 \u0000 BaTiO\u0000 \u0000 \u0000 3\u0000 \u0000 \u0000 \u0000 $$ {mathrm{BaTiO}}_3 $$","authors":"Junais Habeeb Mokkath","doi":"10.1002/jcc.70516","DOIUrl":"https://doi.org/10.1002/jcc.70516","url":null,"abstract":"<div>\u0000 \u0000 <p>Charge-aware molecular dynamics provides access to dynamically evolving effective atomic charges alongside conventional structural quantities. Here, we introduce a charge-derived polarization fingerprint framework for characterizing local polarization-active environments in <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>BaTiO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>3</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{BaTiO}}_3 $$</annotation>\u0000 </semantics></math> using trajectories generated with a charge-aware neuroevolution potential (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>q</mi>\u0000 </mrow>\u0000 <annotation>$$ q $$</annotation>\u0000 </semantics></math>-NEP). Local <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>TiO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>6</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{TiO}}_6 $$</annotation>\u0000 </semantics></math> environments are described using structural quantities, including Ti off-centering and Ti–O bond asymmetry, together with charge-derived descriptors such as the local <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mtext>TiO</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>6</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{TiO}}_6 $$</annotation>\u0000 </semantics></math> dipole magnitude, charge asymmetry, and oxygen-charge fluctuations. Correlation analysis, density mapping, event-aligned trajectory analysis, and principal component analysis reveal coupled variations of structural and charge-derived descriptors across the sampled local environments. In particular, oxygen-charge fluctuations and local dipole magnitudes provide charge-response signatures that complement geometric descriptors in distinguishing transient polarization-active configurations. Independent <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mtext>r</mtext>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msup>\u0000 <mtext>SCAN</mtext>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{r}}^2mathrm{SCAN} $$</annotation>\u0000 </seman","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 26","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149084204","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":"CAML-RNA: Commutative Algebra Machine Learning for RNA–Ligand Binding Affinity Prediction","authors":"Stalin Arulsamy,&nbsp;Yashwanth Krishna,&nbsp;Rajesh Kumar,&nbsp;Vanktesh Kumar","doi":"10.1002/jcc.70511","DOIUrl":"https://doi.org/10.1002/jcc.70511","url":null,"abstract":"<div>\u0000 \u0000 <p>We introduce commutative algebra machine learning for RNA (CAML-RNA), a framework that combines bipartite persistent homology (PH) and persistent Stanley–Reisner theory (PSRT) for predicting RNA–small-molecule binding affinities. RNA–ligand interactions are represented as bipartite atom-pair point clouds, enabling element-specific (ES, 36 pairs, 4 RNA × 9 ligand elements) and category-specific (CS, 36 pairs, 4 RNA structural categories × 9 ligand elements) Vietoris–Rips filtrations that extract <i>β</i>₀ and <i>β</i>₁ Betti curves (PH features, 3888-dim combined), supplemented by persistent <i>f</i>-vectors and <i>h</i>-vectors from a true bipartite distance filtration (PSRT features, 3744-dim, following Suwayyid and Wei). Applied to a curated benchmark of 143 RNA–ligand complexes spanning seven structurally distinct subtypes, CAML-RNA achieves Pearson's <i>R</i> = 0.7283 (RMSE = 1.08 <i>pK</i>_d units) under leave-one-out cross-validation and <i>R</i> = 0.6255 under nested 10-fold cross-validation (Supporting Information), outperforming AffiGrapher (<i>R</i> = 0.498), RLaffinity (<i>R</i> = 0.559), and RLASIF (<i>R</i> = 0.666, all LOO-CV). A subtype-aware feature selection strategy achieves <i>R</i> = 0.940 for aptamers and <i>R</i> = 0.771 for the riboswitch family.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 26","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149084203","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":"Application of the String Method to Determine the Ambimodal Nature of Transition States in Bifurcation Reactions","authors":"Keita Yamaki,&nbsp;Hayato Yamada,&nbsp;Daichi Okamoto,&nbsp;Shoto Nakagawa,&nbsp;Toshiyuki Takayanagi","doi":"10.1002/jcc.70517","DOIUrl":"10.1002/jcc.70517","url":null,"abstract":"<p>Recent quantum chemical studies have revealed that a wide range of organic reactions exhibit post-transition-state bifurcation (PTSB), in which a single transition state (TS) leads directly to two or more distinct products along barrierless downhill pathways. Such TSs are commonly referred to as ambimodal TSs. In contrast, conventional intrinsic reaction coordinate (IRC) calculations typically connect the TS to only one of the possible products and therefore fail to identify alternative non-IRC products. To assess the ambimodal character of TSs in PTSB reactions, we analyzed relaxed pathways connecting a TS directly to a non-IRC product using the double-ended string method. Application of this approach to a total of 33 reaction systems, including pericyclic reactions (among them two trifurcation systems) and non-pericyclic reactions, enabled unambiguous classification of TS-product connections as either a static downhill connection or a static small-barrier connection, depending on whether an energy maximum exists below the TS. The proposed method provides a practical and robust tool for the static topological analysis of PTSB reactions and serves as an effective complement to on-the-fly dynamical trajectory simulations.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13620280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149072929","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":"Linearly Expanded Azulenes in the \u0000 \u0000 \u0000 \u0000 \u0000 S\u0000 \u0000 \u0000 0\u0000 \u0000 \u0000 \u0000 $$ {mathrm{S}}_0 $$\u0000 , \u0000 \u0000 \u0000 \u0000 \u0000 T\u0000 \u0000 \u0000 1\u0000 \u0000 \u0000 \u0000 $$ {mathrm{T}}_1 $$\u0000 , and \u0000 \u0000 \u0000 \u0000 \u0000 Qu\u0000 \u0000 \u0000 1\u0000 \u0000 \u0000 \u0000 $$ {mathrm{Qu}}_1 $$\u0000 States: A Unified View of Electronic Structure and Aromaticity","authors":"Pallavi Sarkar,&nbsp;Itay Almog,&nbsp;Renana Gershoni-Poranne","doi":"10.1002/jcc.70504","DOIUrl":"10.1002/jcc.70504","url":null,"abstract":"&lt;p&gt;Linearly expanded azulenes (LEAs) are isomers of polyacenes (PAs) in which the two terminal benzene rings are replaced by a five- and seven-membered ring, respectively. Despite this seemingly minor structural perturbation, LEAs exhibit electronic behavior fundamentally distinct from their PA counterparts. Herein, we systematically investigate the electronic structure and magnetic aromaticity of a series of LEAs in their &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;S&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;0&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{S}}_0 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;T&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{T}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, and &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;Qu&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{Qu}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; states. We find that LEAs begin to exhibit biradical character at smaller molecular sizes than the corresponding PAs, driven by preferential localization of unpaired electrons on the terminal rings, which allows for the formation of a migrating Clar sextet in the central benzenoid chain and results in a distinctive pattern of paratropic terminal domains and diatropic central domains. This same preference causes the two families to show opposite locations of unpaired electrons in &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;T&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {mathrm{T}}_1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;. In &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mtext&gt;Qu&lt;/mtext&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149068733","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":"Hybrid QM/QM Study of Electronic d–d Spectra of Trivalent Transition Metal Oxides","authors":"Ilya Popov,&nbsp;Andrei L. Tchougréeff,&nbsp;Elena Besley","doi":"10.1002/jcc.70485","DOIUrl":"10.1002/jcc.70485","url":null,"abstract":"<div>\u0000 \u0000 <p>Transition metal oxides have been traditionally studied in theoretical chemistry and solid-state physics as they reflect the complexity of the electronic structure of materials with open <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>d</mi>\u0000 </mrow>\u0000 <annotation>$$ d $$</annotation>\u0000 </semantics></math>-shells. The complex electronic structure stems from the presence of strong correlations of both static and dynamical nature which are characteristic of open shell <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>d</mi>\u0000 </mrow>\u0000 <annotation>$$ d $$</annotation>\u0000 </semantics></math>-electrons. Systematic and computationally efficient account for correlation effects in transition metal compounds is a key challenge in theoretical chemistry. Hybrid electronic structure methods represent a promising way to address this problem. In this work, we apply a hybrid QM/QM method—periodic Effective Hamiltonian of Crystal Field (pEHCF)—to study multiplet structure of open <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>d</mi>\u0000 </mrow>\u0000 <annotation>$$ d $$</annotation>\u0000 </semantics></math>-shells in a series of trivalent and mixed-valence oxides: <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>α</mi>\u0000 </mrow>\u0000 <annotation>$$ alpha $$</annotation>\u0000 </semantics></math>-Fe₂O₃, <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>α</mi>\u0000 </mrow>\u0000 <annotation>$$ alpha $$</annotation>\u0000 </semantics></math>-Mn₂O₃, Cr₂O₃ and Co₃O₄. The calculated energies of the excited <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>d</mi>\u0000 </mrow>\u0000 <annotation>$$ d $$</annotation>\u0000 </semantics></math>-multiplets are compared with available experimental optical spectroscopy data. Our calculations clarify the interpretation of spectroscopic lines observed in experiments for two challenging systems: Fe₂O₃ and Co₃O₄. Furthermore, we assess the overall performance of pEHCF for transition metal oxides and place our results in a more general context by comparing them with previous studies that used different electronic structure methods.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035729","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":"Effect of Al Location and Ga Species in ZSM-5 on Adsorption of Soluble Coke","authors":"Jinping Liu,&nbsp;Hongyan Liu,&nbsp;Lixia Ling,&nbsp;Caiping Ma,&nbsp;Riguang Zhang,&nbsp;Yang Zhang,&nbsp;Maohong Fan,&nbsp;Baojun Wang","doi":"10.1002/jcc.70515","DOIUrl":"10.1002/jcc.70515","url":null,"abstract":"<div>\u0000 \u0000 <p>During the methanol-to-hydrocarbons process catalyzed by H-ZSM-5, coke deposition occurs and can severely hinder the reaction. The effect of Al location and Ga species in ZSM-5 on the adsorption of soluble coke was investigated using density functional theory calculations with the ONIOM method. The results show that soluble coke is adsorbed more stably when Al is situated at straight channels and channel intersections than that in the sinusoidal channel. For Ga species, Ga(OH)²⁺, GaO⁺ and GaH²⁺ are found to readily adsorb soluble coke compared with GaH₂⁺, GaH(OH)⁺, and Ga⁺. Further analysis reveals that the acid strength of Ga species does not exhibit a linear correlation with the adsorption energy of soluble coke. Apart from pyrene that fails to be stably adsorbed, the charge variation of Ga species shows an inverted-volcano-shaped correlation with the adsorption energies of aromatics. Our work provides theoretical references and data support for the design of anti-coking zeolite catalysts and the precise regulation of active sites.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029293","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":"Partial Atomic Charges, Dipole Moments and Electrostatic Potentials","authors":"Jorge Vega Martín,&nbsp;Daniel G. Trabada,&nbsp;Diego Soler-Polo,&nbsp;C. Roldán-Piñero,&nbsp;Jesús I. Mendieta-Moreno,&nbsp;José Ortega","doi":"10.1002/jcc.70496","DOIUrl":"10.1002/jcc.70496","url":null,"abstract":"<p>Partial atomic charges are indispensable tools in chemistry, materials science, and atomic-scale modeling of materials, yet they are not uniquely defined. In this work, we introduce a new charge-assignment model—the Dipole-Projected Overlap Density (DPOD) charges—and assess it systematically against several other schemes: Mulliken (M), Löwdin (L), electrostatic-potential-fitted (ESP), Weighted Löwdin (WL), also introduced here, and Mulliken-Dipole (MD) on which DPOD builds. Using Kohn–Sham DFT electron densities for a diverse test set of 37 molecules, we evaluate the ability of each scheme to: (i) reproduce the molecular dipole moment, (ii) accurately describe the electrostatic potential in regions relevant for intermolecular interactions, and (iii) yield chemically meaningful and transferable charge distributions. The DPOD model, which incorporates both monopole and bond-directed dipolar contributions from overlap densities and distributes intra-atomic dipoles locally, is shown to reproduce the molecular dipole moment by construction while providing a robust and chemically consistent description of atomic charges. Across the entire test set, DPOD and ESP charges are the only methods that consistently yield accurate dipole moments; however, ESP charges often suffer from weakly determined fits leading to chemically unreasonable values, particularly in hydrocarbons. DPOD charges, in contrast, remain stable across chemical environments and achieve good electrostatic-potential description. Surprisingly, WL charges, which are related to Natural Population Analysis, also display reasonably good electrostatic-potential performance despite poor dipole-moment accuracy. Overall, our results demonstrate that the DPOD scheme combines strong physical grounding, excellent dipole-moment reproduction, good electrostatic-potential accuracy, and chemical interpretability, making it a promising and reliable option for atomistic simulations, force-field parameterization, and studies requiring chemically meaningful partial atomic charges.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13594691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149014863","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":"Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations","authors":"Sofiya B. Bettencourt,&nbsp;Wonmuk Hwang","doi":"10.1002/jcc.70499","DOIUrl":"10.1002/jcc.70499","url":null,"abstract":"<p>Protein conformational motion depends on geometric and chemical constraints in side-chain packing. Thermal forces and incomplete packing produce “breathing” motions that allow internal rearrangement. Packing dynamics therefore inform protein allostery, conformational change, and folding. While Voronoi tessellation is a promising approach to this end, its application to proteins has been mainly focused on static structures. Here, the Voro++ library is adopted to investigate time-dependent amino acid packing in molecular dynamics trajectories of a titin immunoglobulin domain at 300 and 400 K. Tracking per-residue Voronoi volume changes and reorganization of neighbor faces in the Voronoi lattice reveals residue-level volume shifts and the corresponding timing of localized protein swelling. Side-chain motion into and out of the protein core can also be monitored by mapping neighbor switching. This framework is applicable to detecting delicate changes preceding protein conformational transition or unfolding, and analyzing protein–protein interface reorganization or surface hydration.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13594690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149014884","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":"In Silico Design of Amino Acid-Functionalized Materials for the Capture of Neonicotinoids","authors":"Joana R. C. Santos,&nbsp;Paulo E. Abreu,&nbsp;Jorge M. C. Marques","doi":"10.1002/jcc.70502","DOIUrl":"10.1002/jcc.70502","url":null,"abstract":"<div>\u0000 \u0000 <p>We used a computational methodology to guide the design of bio-inspired materials for the adsorption of neonicotinoids. The study resorts to a multi-stage protocol, previously proposed for imidacloprid, to select key amino acids for incorporation into chitosan to enhance the adsorption of thiacloprid, acetamiprid, clothianidin, and <i>S</i>- and <i>R</i>-dinotefuran enantiomers. Molecular dynamics (MD) simulations of the protein–pesticide complexes were used to identify relevant amino acids of the <i>Aplysia californica</i> acetylcholine-binding protein (<i>Ac</i>-AChBP). Among these amino acids, the final selection was based on the electronic-structure calculations of pesticide–residue interactions. Tryptophan (Trp), tyrosine (Tyr), isoleucine (Ile) and cysteine (Cys) emerged as promising candidates to functionalize chitosan, while phenylalanine (Phe) was also considered for comparison. The efficiency of functionalized chitosan models for adsorbing each pesticide was evaluated against non-functionalized analogues through MD simulations. The functionalization of chitosan with aromatic amino acids, and especially Trp, significantly enhances the adsorption of neonicotinoids in water media.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149014892","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":"Optimized M-SHAKE Constraint Implementations for GPU-Accelerated Molecular Dynamics: Balancing Precision and Performance Across Architectures","authors":"Jaewoon Jung,&nbsp;Diego Ugarte La Torre,&nbsp;Chigusa Kobayashi,&nbsp;Katsuhisa Ozaki,&nbsp;Yuji Sugita","doi":"10.1002/jcc.70492","DOIUrl":"https://doi.org/10.1002/jcc.70492","url":null,"abstract":"<p>In molecular dynamics (MD) simulations, enforcing holonomic constraints on specific interatomic distances is crucial to extend the integration time step while maintaining numerical stability. While double-precision arithmetic has traditionally been used to ensure numerical accuracy, there is a growing demand for single- and mixed-precision calculations as GPU-accelerated MD simulations become increasingly widespread. In this study, we present improvements to the constraint solvers through an analytical treatment for bonds involving a single hydrogen atom (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>X</mi>\u0000 <msub>\u0000 <mi>H</mi>\u0000 <mn>1</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ X{H}_1 $$</annotation>\u0000 </semantics></math> groups). For more complex groups with multiple hydrogens (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>X</mi>\u0000 <msub>\u0000 <mi>H</mi>\u0000 <mn>2</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ X{H}_2 $$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>X</mi>\u0000 <msub>\u0000 <mi>H</mi>\u0000 <mn>3</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ X{H}_3 $$</annotation>\u0000 </semantics></math>), we introduce two precision-level implementation strategies: (1) a mixed-precision approach, where variables are generally described in single-precision while temporary coordinate updates are handled in double-precision and (2) a pairwise arithmetic approach, where temporary coordinate variables are represented as pairs of single-precision values to reduce rounding errors. These implementation strategies reduce velocity-update errors compared with schemes using single precision for all variables. Energy drift analysis in microcanonical simulations confirms that these strategies maintain accuracy comparable to full double-precision implementations. Performance benchmarks on GPUs with limited FP64 throughput (RTX 3080 and A6000 Ada) show that our proposed implementation strategies substantially reduce runtime compared with full double-precision calculations. Conversely, on architectures with balanced FP32 and FP64 performance, such as CPUs or H100 GPUs, full double-precision arithmetic remains the preferred choice for the constraint kernels evaluated in this study. Overall, these findings demonstrate that the proposed strategies provide an effective balance between numerical accuracy and computational performance on GPUs with limited FP64 throughput.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 25","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70492","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148981467","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}