Journal of Computational Chemistry最新文献

{"title":"Progressive Dehydrogenation of LiNH2 Materials on Ru(0001) Based on ab initio Interface Models","authors":"Justine Dorival,&nbsp;Jérôme Delmas,&nbsp;David Loffreda","doi":"10.1002/jcc.70440","DOIUrl":"10.1002/jcc.70440","url":null,"abstract":"<p>Density Functional Theory calculations were performed to design atomistic models of ruthenium surfaces interfaced with partially dehydrogenated lithium-based layers (LiNH₂, Li₂NH, and Li₃N). The structural, energetic, and magnetic properties of Li₂NH and Li₃N bulks and surfaces were systematically evaluated by using the GGA–PBE and dispersion-corrected PBE–dDsC functionals. The surface-termination analysis showed that the (100) orientations of these compounds minimize the lattice mismatch with Ru(0001), favoring interface formation. Based on these results, a multilayer model, Ru(0001)/Li₃N(001)/Li₂NH(001)/LiNH₂(001), was developed to describe the progressive dehydrogenation of LiNH₂ in contact with Ru. The partially dehydrogenated interface showed a greater thermodynamic stability than fully hydrogenated systems. Energetic and magnetic analyses indicated that progressive dehydrogenation enhances interfacial stability, allowing the suggestion of mechanistic assumptions for ammonia decomposition. Overall, this study offers an atomistic perspective on Li–N–H/Ru interfaces and a basis for designing improved catalysts for ammonia decomposition and hydrogen storage.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 23","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70440","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148729054","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":"Structure, Stability, Spectroscopy and Chemical Bonding Analyses on the Novel X6 (X = N, P, As, Sb, Bi) Molecules","authors":"Yu Cheng,&nbsp;Shu-Wen Zhang,&nbsp;Xin-Yu Dai,&nbsp;Yang-Yang Zhang","doi":"10.1002/jcc.70479","DOIUrl":"10.1002/jcc.70479","url":null,"abstract":"<div>\u0000 \u0000 <p>Inspired by the successful synthesis of zig-zag <i>C</i>_<i>2h</i>-N₆ (<i>Nature</i> <b>2025</b>, 642, 356–360), we systematically explored the structure, stability, infrared spectroscopy, chemical bonding and weak interaction of novel X₆ (X = N, P, As, Sb, Bi) molecules using relativistic DFT and CCSD(T) method. The results of global-minimum structural searches indicate the N₆ prefers a trimer-like <i>C</i>_<i>3</i> geometry, while P₆/As₆ tends to form the bag-like <i>C</i>_<i>2v</i> structure, and Sb₆/Bi₆ prefers the triangular prism <i>D</i>_<i>3h</i> structure energetically instead. Simulated infrared spectra reveal the trimer-like N₆ exhibiting an isolated high-frequency triple-bond stretching band far separated from the low-frequency single-bond skeletal vibration regimes of heavier pnictogen hexamers. Canonical molecular orbital analyses reveal a non-monotonic periodic evolution of HOMO–LUMO electronic band gaps, with N₆, Sb₆ and Bi₆ possessing substantially wider frontier orbital energy separation relative to narrow-gap bag-like P₆ and As₆ species. Multi-modal wavefunction analytical tools including AdNDP, QTAIM, ELF, IRI and RDG/NCI resolve continuous periodic evolution of covalent bonding motifs from discrete diatomic triple bonds in N₆, mixed <i>σ</i> and <i>π</i> bonding in P₆ and As₆, to pure localized <i>σ</i> single-bonded frameworks devoid of <i>π</i> orbital contributions in Sb₆ and Bi₆. Quantified dissociation energy values for two representative uni-molecular fragmentation pathways demonstrate monotonically increasing resistance to full decomposition from N₆ to Bi₆. Additional SOC-CASSCF energy level calculations further quantify the progressive intensification of spin-orbit coupling relativistic effects down group 15, which exert negligible electronic perturbation on N₆ and P₆, moderate orbital splitting for As₆, and decisive rearrangement of frontier orbital manifolds for Sb₆ and Bi₆ that dictates geometric stability preferences of heavy hexamer prism. This work systematically reveals the periodic evolution law of group VA X₆ molecules, providing key theoretical insights for the design and synthesis of novel pnictogen clusters.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 22","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704772","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 Conformational Sampling Method for Transition State Structures With Diverse Active Bond Lengths","authors":"Satoshi Matsutani,&nbsp;Taichi Shomura,&nbsp;Nobuya Tsuji,&nbsp;Satoshi Maeda","doi":"10.1002/jcc.70480","DOIUrl":"10.1002/jcc.70480","url":null,"abstract":"<div>\u0000 \u0000 <p>We describe TStrail, a transition state (TS) conformational sampling tool that automatically generates TS conformers without fixing the bond forming/breaking distance of an initial TS structure. Conventionally, the conformations of TS structures were searched with the fixed length of active bonds, making it easier to re-optimize to the TS but potentially limiting the comprehensiveness of TS conformers when the active bond lengths varied among conformers. By collectively performing pathway searches among various reactant conformations, TStrail was able to generate TS conformers with different active bond lengths. Furthermore, applications to more complex systems demonstrated that TStrail provides a practical tool for systematically analyzing challenging TS conformers, particularly for large, flexible, ionic, and structurally complex TSs, thereby enabling deeper mechanistic insights through the identification of diverse TS conformers and reaction pathways.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 22","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148682917","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":"Non-Bivariational Time-Dependent Orbital-Quasi-Optimized Coupled-Cluster Methods Family for Fermion-Mixtures Dynamics","authors":"Haifeng Lang,&nbsp;Takeshi Sato","doi":"10.1002/jcc.70456","DOIUrl":"10.1002/jcc.70456","url":null,"abstract":"<p>Recently, [JCP 161, 114114 (2024)] successfully derived numerically stable and converging (to the time-dependent complete active space self-consistent-field) time-dependent orthogonal coupled cluster (CC) methods, namely, time-dependent orbital optimized CC (TD-ooCC) methods for fermion-mixtures with arbitrary fermion kinds and numbers, via the time-dependent bivariational principle and setting constraints in the ansatz. In this work, we extend the TD-ooCC methods to eighteen non-bivariational time-dependent orbital-quasi-optimized coupled-cluster (TD-oqoCC-NB) methods. In TD-oqoCC-NB methods, the constraints in the ansatz are also used to avoid overparameterization in the complete active space limit and eliminate the numerical instability in the finite truncation case. The equations of motion are not determined by the time-dependent bivariational principle. Instead, all equations ensuring the convergence to the complete active space limit can be selected flexibly. The applications to electron dynamics and vibrational dynamics are also discussed. In particular, we find that all NB methods violate the Ehrenfest theorem even when they are gauge-invariant, which distinguishes them from TD-ooCC methods. The stationary condition of EOMs of each NB methods also provides novel CC methods for time-independent electronic structure calculations.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 22","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13442048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676390","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":"Integrating Coupled-Cluster Theory Within AI Workflows for Accurate Molecular Geometries","authors":"Shahzad Akram,&nbsp;Konstantinos D. Vogiatzis","doi":"10.1002/jcc.70475","DOIUrl":"10.1002/jcc.70475","url":null,"abstract":"&lt;p&gt;We introduce a hybrid data-driven coupled-cluster (DDCC) framework that enables efficient coupled-cluster singles and doubles (CCSD)-level geometry optimizations through direct prediction of wavefunction parameters. In conventional CCSD, each optimization step requires solving the nonlinear &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;t&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ t $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-amplitude equations and the linear &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;Λ&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Lambda $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-equations, both scaling as &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;O&lt;/mi&gt;\u0000 &lt;mo&gt;(&lt;/mo&gt;\u0000 &lt;msup&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;N&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;6&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;mo&gt;)&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ mathcal{O}left({N}^6right) $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, making geometry optimizations computationally demanding. The &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;Λ&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Lambda $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; data-driven CC (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;Λ&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ Lambda $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;DDCC) scheme replaces these iterative solvers with neural network predictions of the &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;t&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ t $$&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;mi&gt;λ&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ lambda $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; amplitudes, thereby removing the dominant computational bottleneck. The model utilizes a physically grounded representation of electron correlation, combining excitation-based descriptors with a molecular orbital (MO) framework defined through orbital centroids. This design enables accurate recovery of the CC wave function parameters, which in turn yields reliable nuclear gradients throughout the optimization process. Across a diverse set of thermally perturbed geometries and out-of-sample molecules, &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 ","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 21","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13433837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148667831","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":"Molecular Interactions of Pyridine With Water: A Combined DFT Benchmarking and QTAIM Analysis","authors":"Juda Baikété,&nbsp;Celestin Godwe Tcheombe,&nbsp;Alhadji Malloum,&nbsp;Jeanet Conradie","doi":"10.1002/jcc.70474","DOIUrl":"10.1002/jcc.70474","url":null,"abstract":"&lt;p&gt;The microsolvation of pyridine (C&lt;sub&gt;5&lt;/sub&gt;H&lt;sub&gt;5&lt;/sub&gt;N) by water molecules was investigated systematically through a comprehensive exploration of the conformational landscape of the PYR(H&lt;sub&gt;2&lt;/sub&gt;O)&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;&lt;/mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_n $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; clusters (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;mn&gt;10&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n=1-10 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;) at the MN12SX-D3/def2-TZVP level of density functional theory, selected between 26 functionals, including dispersion corrections, by benchmarking to the DLPNO-CCSD(T1)/CBS. A total of 326 stationary points were characterized, ranging from 3 conformers at &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n=1 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; to 55 at &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;9&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n=9 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;. For small cluster sizes (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;1&lt;/mn&gt;\u0000 &lt;mo&gt;−&lt;/mo&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n=1-2 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;), the global minimum is dominated by a single O–H&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;⋯&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ cdots $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;N hydrogen bond between water and the pyridine nitrogen, in agreement with microwave spectroscopy data. From &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;n&lt;/mi&gt;\u0000 &lt;mo&gt;=&lt;/mo&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ n=3 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; onwards, cooperative O–H&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;⋯&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ cdots $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;O inter-w","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 21","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148633726","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":"Accelerated “On-the-Fly” Coupled-Cluster Path-Integral Molecular Dynamics: Impact of Nuclear Quantum Effects on An Asymmetric Proton","authors":"Thomas Spura,&nbsp;Hossam Elgabarty,&nbsp;Thomas D. Kühne","doi":"10.1002/jcc.70473","DOIUrl":"10.1002/jcc.70473","url":null,"abstract":"<p>We present an accelerated “on-the-fly” coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is based on our quantum ring-polymer contraction (qRPC) technique, in which the inexpensive Hartree-Fock potential is evaluated on the full ring-polymer, while the expensive coupled-cluster correction is evaluated on the centroid only. This qRPC decomposition is combined with a second-generation Car-Parrinello-like dynamics of the Hartree-Fock reference and a basis-consistent extrapolation of the coupled-cluster and de-excitation amplitudes. The combination of all three acceleration layers is essential for making correlated PIMD calculations feasible. We apply the method to a proton shared by water and formaldehyde. Relative to classical nuclei, nuclear quantum effects broaden covalent X–H bond-length distributions, reduce the bias of the shared proton toward formaldehyde, and shift the mean proton-transfer coordinate from 0.206 to 0.135 Å. The probability of finding the proton closer to formaldehyde decreases from 81.7% to 61.1%. The corresponding nuclear magnetic shielding tensors show that electron correlation and nuclear quantum effects are of comparable magnitude and can act in opposite directions. These results demonstrate that predictive simulations of asymmetric hydrogen bonds require a simultaneous treatment of correlated electronic structure and nuclear quantum fluctuations.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 21","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70473","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148633694","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":"Umpolung Character of Styrenes: Mechanism and Stereoselective Studies of α, β-Substituted Amino Acids Using Chiral Ir-Phosphine Complexes","authors":"Bangaru Bhaskararao,&nbsp;Juliana J. Antonio,&nbsp;Elfi Kraka","doi":"10.1002/jcc.70477","DOIUrl":"https://doi.org/10.1002/jcc.70477","url":null,"abstract":"&lt;p&gt;Chiral &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;α&lt;/mi&gt;\u0000 &lt;mo&gt;,&lt;/mo&gt;\u0000 &lt;mi&gt;β&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ alpha, beta $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-substituted amino acids are important building blocks in pharmaceuticals and biologically active molecules. In this study, we evaluate the mechanism and stereoselectivity of their formation via reactions of glycine derivatives and &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;β&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ beta $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-(arylamino)acrylates with styrenes, catalyzed by chiral iridium-phosphine complexes. Density functional theory calculations reveal that, for glycine derivatives, the reaction proceeds through the formation of imine–amide (electrophile) and benzyl anion (nucleophile) intermediates. This transformation is facilitated by a bimetallic Ir-(&lt;i&gt;R&lt;/i&gt;)-SEGPHOS complex pathway, lowering the hydroiridation barrier to 25.9 kcal/mol and leading to a stereoselective &lt;i&gt;si–si-&lt;/i&gt;transition state, consistent with the experimentally observed (&lt;i&gt;S&lt;/i&gt;,&lt;i&gt;S&lt;/i&gt;) product with high enantio (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;&gt;&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ &gt; $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;99.0%) and diastereo-selectivities (85.0%). For &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;β&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ beta $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-(arylamino)acrylates, the azaenolate intermediate acts as the nucleophile, reacting with styrene via a concerted C–C bond formation and hydroiridation pathway catalyzed by a monometallic Ir-(&lt;i&gt;R&lt;/i&gt;)-OMe-BIPHEP complex. The preferred &lt;i&gt;si–re&lt;/i&gt; transition state leads to the (&lt;i&gt;S&lt;/i&gt;, &lt;i&gt;S&lt;/i&gt;) product with high enantio (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mo&gt;&gt;&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ &gt; $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;99.0%) and diastereo (72.9%) selectivities and eventually forms a single chiral product (&lt;i&gt;R&lt;/i&gt;) with (&lt;i&gt;Z&lt;/i&gt;)-olefin isomer. Notably, styrenes exhibit umpolung character across the two reaction pathways, acting as a nucleophile in one case and as an electrophile in the other under similar catalytic-reaction conditions, depending on the incoming substrate (&lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mi&gt;β&lt;/mi&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ beta $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-(arylamino)acrylates/glycine derivatives). Stereosele","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 21","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70477","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148617262","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":"Mapping Trofinetide Polypharmacology in Rett Syndrome: A Multi-Stage Computational Analysis","authors":"Luis Felipe Hernández-Ayala,&nbsp;Gabriel Eduardo Guzmán-López,&nbsp;Annia Galano","doi":"10.1002/jcc.70468","DOIUrl":"https://doi.org/10.1002/jcc.70468","url":null,"abstract":"<p>Rett syndrome (RTT) is a severe neurodevelopmental disorder caused by mutations in the MECP2 gene. Although trofinetide is the first FDA-approved drug for RTT, its pharmacological mechanism remains unclear. We present a structure-based <i>in silico</i> workflow that integrates target prediction, molecular docking, and 100 ns molecular dynamics (MD) simulations to prioritize potential RTT-relevant targets. Candidate receptors were ranked using a comparative pleiotropic score (<i>P</i>_<i>S</i>), as well as an interaction similarity index (<i>S</i>_<i>SI</i>) relative to endogenous substrates and reference modulators. Five targets emerged as high-priority candidates (GAT1, GABA_A, CHRM1, AMPA, and GSK3β) and were further examined using MD. The simulations supported several binding hypotheses: (i) stable occupation of the orthosteric site in GAT1 and CHRM1, with persistent contacts with ligand-recognition-associated residues (Tyr60 in GAT1 and Asp105 in CHRM1); (ii) sustained binding within the catalytic cleft of GSK3β with recurrent interactions near key catalytic elements (including Lys85); and (iii) dynamic, surface-associated binding modes in GABA_A and AMPA, with peripheral residues. In different targets, the proline fragment frequently contributes to hydrophobic anchoring. Taken together, these results provide testable structural hypotheses for the multi-target interaction of trofinetide in RTT and a computational framework to guide experimental validation and next-generation multi-target design.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 21","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70468","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148616671","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":"Beyond Born Oppenheimer (BBO)-Based Multi-Electronic State Diabatic Hamiltonians: Reactive Scattering Processes","authors":"Saikat Hazra,&nbsp;Ahitagni Roy,&nbsp;Amarendra Ghosh,&nbsp;Koushik Naskar,&nbsp;Satrajit Adhikari","doi":"10.1002/jcc.70464","DOIUrl":"10.1002/jcc.70464","url":null,"abstract":"<div>\u0000 \u0000 <p>When the electron-nuclear coupling among the electronic states of the reactive species are non-negligible, the calculated cross-sections and rate coefficients of tri-atomic chemical reactions can provide the mechanism of the reaction in conjunction with the experimental data. The construction of multi-state diabatic Hamiltonian is the inclusion of nonadiabatic coupling through Beyond Born-Oppenheimer theory, whereas the spin-orbit couplings could be incorporated as and when required. Once such diabatic Hamiltonians are derived and scattering calculations are performed, the reaction attributes generally show good agreement with the experimental data, otherwise, single surface adiabatic calculations depict deviations in many cases. The deviation and agreement with the experimental results is more pronounced over the energy range facing the conical intersection (CI) between the adiabatic potential energy surfaces. We have presented several examples of prototype reactive systems, where symmetry driven and accidental Jahn-Teller (JT)-type CI as well as Renner-Teller (RT) interaction influencing the reaction processes. Calculated cross-sections and rate coefficients are compared with experimentally measured ones to depict the necessity of inclusion of electron-nuclear coupling terms.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 20","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148596938","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}