Journal of Computational Chemistry最新文献

{"title":"Computational Insights Into g-C3N4-Based Heterojunctions for Photocatalytic Water Splitting Reaction","authors":"Dhilshada V. N., Neeraj Ramachandran, Mausumi Chattopadhyaya","doi":"10.1002/jcc.70437","DOIUrl":"10.1002/jcc.70437","url":null,"abstract":"<div>\u0000 \u0000 <p>The growing demand for sustainable hydrogen production has intensified research into photocatalytic water splitting driven by solar energy. Graphitic carbon nitride (g-C<sub>3</sub>N<sub>4</sub>), a metal-free polymeric semiconductor with visible-light activity, tunable electronic structure, low cost, and environmental compatibility, has emerged as a promising photocatalyst. Nevertheless, pristine g-C<sub>3</sub>N<sub>4</sub> is limited by insufficient visible-light absorption, sluggish charge transport, rapid electron–hole recombination, and low surface reactivity. Heterojunction engineering has therefore become a key strategy to overcome these intrinsic limitations and enhance photocatalytic efficiency. Distinct from conventional experimental or performance-oriented reviews, this work presents a computationally driven and methodology-oriented review that explicitly addresses how to model g-C<sub>3</sub>N<sub>4</sub>-based heterojunction photocatalysts using density functional theory (DFT). Rather than merely summarizing reported efficiencies, this review provides a step-by-step conceptual and practical framework that enables readers to rationally construct, analyze, and optimize heterojunction photocatalysts at the atomic scale. The review begins with the structural and electronic fundamentals of g-C<sub>3</sub>N<sub>4</sub>, followed by a mechanistic overview of photocatalytic water splitting, including light absorption, charge generation, interfacial charge separation, and surface redox reactions. Various heterojunction architectures: Type I, Type II, Z-scheme, S-scheme, p–n junctions, Schottky interfaces, and multicomponent systems are systematically discussed, with particular emphasis on interfacial charge-transfer mechanisms revealed by first-principles calculations. A key contribution of this review is the consolidation of DFT-based modeling protocols and descriptors essential for evaluating and enhancing photocatalytic performance. These include structural stability (lattice mismatch, phonon dispersion, and ab initio molecular dynamics), electronic properties (band structure, density of states, and band-edge alignment), charge-transfer characteristics (work function, charge density difference, planar-averaged charge density, and Bader charge analysis), optical properties (absorption spectra, dielectric function, optical band gap, and solar-to-hydrogen efficiency), and carrier transport descriptors (effective mass and carrier mobility). In addition, DFT-based reaction pathway analysis is discussed to elucidate hydrogen and oxygen evolution mechanisms at heterojunction interfaces. Importantly, this review highlights computational strategies to enhance photocatalytic activity, including strain engineering, external electric fields, defect and dopant engineering, and interface optimization, providing clear guidance on how these approaches can be implemented and interpreted within a DFT framework. Challenges relate","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 16","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148209507","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":"Computational Investigation of GNMT-Catalyzed Methyl Transfer Reaction: Integrating MD, QM, and ML Approaches","authors":"Jonathan Epih,&nbsp;Anjali Arya,&nbsp;Saghar Gomrok,&nbsp;Qianyi Cheng","doi":"10.1002/jcc.70434","DOIUrl":"10.1002/jcc.70434","url":null,"abstract":"<div>\u0000 \u0000 <p>The glycine N-methyltransferase (GNMT) reaction was examined using an integrated workflow combining molecular dynamics (MD), quantum mechanical (QM) cluster calculations, and machine learning (ML) analysis. Instead of relying on a single crystal-like conformation, multiple MD simulations were used to sample diverse reactant (SAM + glycine bound to GNMT) and product (SAH + sarcosine bound to GNMT) state geometries for QM cluster modeling. Across more than 150 QM-cluster models constructed by the Residue Interaction Network ResidUe Selector (RINRUS) from selected MD frames with and without explicit waters, the computed activation and reaction free energies span broad ranges (7 to 25 kcal mol⁻¹ and −36 to +3 kcal mol⁻¹), demonstrating a strong dependence on the initial MD conformation. Product-state consistently yields lower reaction barriers, while explicit water introduces only small shifts in energetics and preserves the relative ordering among frames. The two-coordinate potential energy surface (PES) offers only limited insight and cannot fully account for the observed energetic variability. These QM-cluster models were further analyzed using machine-learning methods to identify structural descriptors that correlate with the observed energy variations and provide insight into their structural origin. ML models trained on multiple feature representations show that the donor–methyl–acceptor distances are the most informative and yield the strongest predictive accuracy, while higher dimensional solvent- or residue-based features contribute comparatively little. Overall, the results highlight the importance of conformational sampling for reliable QM-cluster energetics and point toward more expressive structure-to-property representations for analyzing enzymatic reactions.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 16","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148196488","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":"Jahn–Teller Distortions in Pseudo-Octahedral Low-Spin Ni(III) Complexes With O,O or N,N Bidentate Ligands: A DFT Study","authors":"Jeanet Conradie","doi":"10.1002/jcc.70399","DOIUrl":"https://doi.org/10.1002/jcc.70399","url":null,"abstract":"&lt;p&gt;The Jahn–Teller (JT) effect plays a central role in determining the structure and electronic properties of open-shell transition-metal complexes, yet its reliable theoretical description remains sensitive to the choice of density functional, basis set, and molecular model. In close analogy to the well-established behavior of d&lt;sup&gt;9&lt;/sup&gt; Cu(II) systems, low-spin d&lt;sup&gt;7&lt;/sup&gt; Ni(III) complexes exhibit an E ⊗ e vibronic instability that gives rise to a multidimensional (“Mexican hat”) potential energy surface and dynamic Jahn–Teller behavior. In this work, we present a systematic density functional theory investigation of the Jahn–Teller effect in a series of seven pseudo-octahedral Ni(III) complexes bearing bidentate ligands with O,O or N,N donor atoms, of varying size and rigidity. Geometry optimizations initiated from both axially elongated and compressed starting structures were performed under symmetry constraints to map the Jahn–Teller potential energy surface. At the TPSSh/def2-TZVP level, optimizations from elongated and compressed starting points identify elongated structures as minima and compressed structures as first-order saddle points. The presence of multiple symmetry-equivalent elongated minima and low barriers between them is consistent with a dynamically averaged Jahn–Teller distortion rather than a purely static one. The resulting axial–equatorial bond length differences (Δ&lt;i&gt;R&lt;/i&gt; ≈ 0.16–0.23 Å) and Jahn–Teller stabilization energies (Δ&lt;i&gt;E&lt;/i&gt;&lt;sub&gt;JT&lt;/sub&gt; ≈ 0.02–0.04 eV) indicate a moderate but systematic preference for axial elongation across the ligand series. Frontier molecular orbital and spin density analyses reveal that the distortion is driven by lifting of the &lt;i&gt;e&lt;/i&gt;&lt;sub&gt;g&lt;/sub&gt; orbital degeneracy in the low-spin d&lt;sup&gt;7&lt;/sup&gt; configuration, with axial elongation stabilizing the predominantly Ni-centered &lt;span&gt;&lt;/span&gt;&lt;math&gt;\u0000 &lt;semantics&gt;\u0000 &lt;mrow&gt;\u0000 &lt;msub&gt;\u0000 &lt;mi&gt;d&lt;/mi&gt;\u0000 &lt;msup&gt;\u0000 &lt;mi&gt;z&lt;/mi&gt;\u0000 &lt;mn&gt;2&lt;/mn&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {d}_{z^2} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-based HOMO. Comparative calculations using PW6B95-D3, M06, B3LYP, and OLYP functionals, as well as alternative triple-ζ and double-ζ (def2-SVP) basis sets, confirm that the qualitative Jahn–Teller behavior and ligand-dependent trends are robust, while quantitative differences emphasize the importance of hybrid meta-GGA and dispersion-corrected approaches. Continuum solvation calculations (water, acetonitrile, and dichloromethane) demonstrate that solvent effects do not alter the qualitative Jahn–Teller distortion pattern or energetic ordering. In addition, simplified ligand models are shown to reliably reproduce the essential features of the Jahn–Teller distortion when the immediate coordination e","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 16","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.70399","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174614","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":"Generalized Turnstile Rotation: Formulation, Visualization, Workflow Implementation, and Application for Modeling Polytopal Rearrangements","authors":"Yunwen Tao,&nbsp;Xianlong Wang,&nbsp;Wenli Zou,&nbsp;Elfi Kraka","doi":"10.1002/jcc.70432","DOIUrl":"https://doi.org/10.1002/jcc.70432","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 &lt;p&gt;Turnstile rotation is a well-known polytopal rearrangement mechanism in coordination compounds, yet its computational description is often hindered by the challenges of conventional internal coordinates to represent such collective, large-amplitude motions. In this work, we present a mathematical formulation for generalized &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;/mrow&gt;\u0000 &lt;annotation&gt;$$ N $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;-arm turnstile rotation, a dedicated PyMOL plugin (gTA) for intuitive structure visualization and a command-line utility (gTA-cli) for structure manipulation. On this basis, we develop a practical computational workflow that combines turnstile rotation-driven relaxed scans with two downstream routes to locate the transition states. The generality of the approach is demonstrated through five chemically diverse case studies, ranging from classical rearrangements in SF&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;mn&gt;4&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_4 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, IF&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;mn&gt;7&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_7 $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt;, and [Co(en)&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;mn&gt;3&lt;/mn&gt;\u0000 &lt;/msub&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}_3 $$&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;msup&gt;\u0000 &lt;mrow&gt;&lt;/mrow&gt;\u0000 &lt;mrow&gt;\u0000 &lt;mn&gt;3&lt;/mn&gt;\u0000 &lt;mo&gt;+&lt;/mo&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;/msup&gt;\u0000 &lt;/mrow&gt;\u0000 &lt;annotation&gt;$$ {}^{3+} $$&lt;/annotation&gt;\u0000 &lt;/semantics&gt;&lt;/math&gt; to previously unexplored fluxional processes in bismuth and nickel complexes. In all cases, the method enables the identification of transition states associated with pronounced polytopal rearrangements that are difficult to access using standard coordinate schemes. These results establish generalized turnstile rotation as a fundamental molecular motion and highlight its potential as a broadly applicable strategy for studying fluxionality and dynamic stereochemistry in coordination chemistry. The PyMOL plugin gTA and the Python utility gTA-cli with the associated relaxed scan workflows are open-source and freely available on Github at https://github.com/smutao/gTA-plugin and https://github.com/smu","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 16","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148174615","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":"Seeking a Direct Optimization Method Using Distance Geometry Space for Molecular Orientation","authors":"Kanami Sugiyama,&nbsp;Masatoshi Okada,&nbsp;Hirofumi Sato,&nbsp;Masahiro Higashi","doi":"10.1002/jcc.70409","DOIUrl":"10.1002/jcc.70409","url":null,"abstract":"<div>\u0000 \u0000 <p>We report a direct method to determine the relative configuration of two molecules using distance geometry, in which the structure is expressed as a set of distances between atoms. In the calculation, the gradient and bordered Hessian with inequality and equality constraints, based on the Cayley-Menger determinant for embedding the structure in three-dimensional space, are evaluated by introducing slack variables. The developed method is then applied to three molecular systems: <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>H</mi>\u0000 <mn>2</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{H}}_2 $$</annotation>\u0000 </semantics></math>O with <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mi>Li</mi>\u0000 <mo>+</mo>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{Li}}^{+} $$</annotation>\u0000 </semantics></math>, HF dimer, and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>NH</mi>\u0000 <mn>3</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{NH}}_3 $$</annotation>\u0000 </semantics></math> with <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msup>\u0000 <mi>Na</mi>\u0000 <mo>+</mo>\u0000 </msup>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{Na}}^{+} $$</annotation>\u0000 </semantics></math>. The present approach could be related to a straightforward route to explore the entire potential-energy landscape for a small molecular system described with simple analytical functions.</p>\u0000 </div>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 15","pages":""},"PeriodicalIF":4.8,"publicationDate":"2026-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148147644","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":"Collective Interactions in Ion Pairs.","authors":"Jorge Gonzalo, Julen Munárriz, Angel Martín Pendás, Jorge Echeverría","doi":"10.1002/jcc.70408","DOIUrl":"https://doi.org/10.1002/jcc.70408","url":null,"abstract":"<p><p>Collective interactions represent a recently proposed bonding mode in which stabilization arises not from a localized two-center bond but from the distributed exchange-correlation effects between a central site and several surrounding atoms, whereas the interaction between the central atom and the metal is destabilizing. While this phenomenon has been demonstrated in certain organometallic complexes, its possible existence in predominantly ionic systems remains unexplored. Here, we present a comprehensive study on a family of ion pairs of general formula M[AX₄] (M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺; A = B, Fe Co, Zn, Cd; X = -CH₃, -CO, -CCH, -OCH₃, -Cl) aimed at determining whether collective interactions can arise in systems conventionally described as ionic. Through a combination of penetration index analysis and Interacting Quantum Atoms (IQA) decomposition, we quantify the contributions of Coulombic and exchange-correlation terms to the total interaction energy. The calculated exchange-correlation interaction collectivity indices (ICI_XC) reveal that alkali metal-tetramethylborate ion pairs and several transition metal tetrahedral anions exhibit distinctly collective behavior, particularly when complexes possess electron-rich or polarizable ligands (-CCH, -OCH₃, -Cl). In contrast, carbonyl-containing systems display larger ICI_XC values, consistent with a classical noncollective bonding scheme. These results demonstrate that collective interactions can indeed manifest in ionic environments, extending the scope of the concept beyond covalent or organometallic frameworks and offering new insights into the fundamental nature of ion pairing and electronic delocalization.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 14","pages":"e70408"},"PeriodicalIF":4.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148040582","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":"Assessment of Solvation Models for Quantum Chemistry Calculations through A-Value Determination and Conformational Equilibrium Analysis of Difluorocyclohexanes as Benchmark Systems.","authors":"Ken-Ichi Yamada, Tsubasa Inokuma","doi":"10.1002/jcc.70386","DOIUrl":"10.1002/jcc.70386","url":null,"abstract":"<p><p>To provide a guide for selecting appropriate calculation methods for conformational analyses of organic molecules with explicit consideration of solvation effects, the A-values of twenty-two substituents were computed with solvation corrections across multiple solvation models. In addition, conformational equilibrium analyses of 1,4- and 1,2-trans-difluorocyclohexanes were performed as complementary benchmark systems, and a comprehensive evaluation was achieved through integration of both datasets. Comparison with reported experimental data furnished a robust benchmark for identifying the optimal combination of solvation models and theoretical levels for energy calculation and geometry optimization.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 14","pages":"e70386"},"PeriodicalIF":4.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147985987","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":"A Virtual Model for Describing Organophosphorus Reactivity: Validation and Application to Virtual Molecule-Assisted Optimization.","authors":"Takayuki Furukawa, Ren Yamada, Satoshi Maeda, Wataru Matsuoka","doi":"10.1002/jcc.70396","DOIUrl":"10.1002/jcc.70396","url":null,"abstract":"<p><p>Optimizing reagent and catalyst molecules remains a fundamental yet resource-intensive task in organic chemistry, which our group previously streamlined by developing the \"virtual ligand strategy.\" This in silico optimization framework approximates the electronic and steric effects of phosphine ligands using a mathematical model that enables rational-design principles to be extracted by numerically optimizing the corresponding parameters. Herein, this concept is extended and a new model that accounts for the reactivities of phosphines as reagents or organocatalysts is developed. The model reproduces substituent effects using distinct electronic and steric parameters and successfully captures changes in the valence state and coordination number of the phosphorus center that occur during a reaction. This approximation accurately reproduces the reactivities and structural features of real phosphines, with the Wittig reaction as a representative example. Furthermore, numerically optimizing the model parameters facilitates designing phosphines that minimize the activation barriers associated with the catalytic Staudinger amidation reaction.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 14","pages":"e70396"},"PeriodicalIF":4.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147986000","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":"PES-trotter: A Cross-Platform Open-Source Application for the Analysis of Molecular Processes on 3D Potential-Energy Landscapes.","authors":"Erwan Privat, Ajay Mohan Singh Rawat, Bernardo Ballotta, Antonino Polimeno, Sergio Rampino","doi":"10.1002/jcc.70397","DOIUrl":"10.1002/jcc.70397","url":null,"abstract":"<p><p>We present PES-trotter, a cross-platform application for the exploration and analysis of 3D potential-energy landscapes generated from multi-dimensional potential-energy surfaces (PESs) of molecular systems. Inspired by the main ideas behind the previously released software AVATAR (Martino et al., Journal of Computational Chemistry 41 (2020): 1310-1323) relying on virtual-reality technology and third-party commercial software, PES-trotter is based on the open-source game engine Godot and related open-source assets, and introduces radically new important features for the navigation and topological analysis of the PES, among which the possibility of (1) navigating in walk, fly or free-mouse mode, (2) plotting energy profiles from custom curvilinear paths, (3) computing critical points and minimum-energy paths, and (4) playing back dynamical trajectories in first-person ride or spectator mode. Designed to match high portability and adaptability, PES-trotter can be run either as a stand-alone application on Windows, Linux, Android and macOS operating systems or in the window of a simple web browser on devices as widespread as mobile phones. In the article, the main features of PES-trotter are thoroughly described through two illustrative applications (the conformational analysis of a functionalized glycine and the analysis of classical trajectories for the H + LiH⁺ <math> <semantics><mrow><mo>→</mo></mrow> <annotation>$$ to $$</annotation></semantics> </math> H₂ + Li⁺ reactive process) highlighting the versatilty of PES-trotter as an innovative and accessible tool supporting chemical research and education.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 14","pages":"e70397"},"PeriodicalIF":4.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012808","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":"Computational Design of Zinc Single-Atom Catalysts in Lantern Organic Framework.","authors":"Lam H Nguyen, Thanh N Truong","doi":"10.1002/jcc.70404","DOIUrl":"10.1002/jcc.70404","url":null,"abstract":"<p><p>The design of the metal-support interface is fundamental to the performance of single-atom catalysts (SACs). Here, we present a comprehensive computational study by using Density Functional Theory (B3LYP-D3/LANL2DZ for zinc atoms and 6-31+G(d) for other nonmetal atoms) in Zinc-embedded Lantern Organic Frameworks (Zn@LOFs) to resolve this design. By systematically comparing sp- and sp³-bridging motifs, we reveal a critical structural dichotomy: while flexible sp³-frameworks favor endo-configuration, rigid sp-bridging systems introduce a unique kinetic trap that stabilizes accessible exo-configuration. Crucially, agglomeration analysis confirms that the sp-LOF architecture could suppress ZnZn clustering. Beyond stability, we demonstrate precise electronic tunability; endo-Zn_n@sp-LOFs leverage metal-ligand π-conjugation to significantly narrow the HOMO-LUMO gap, whereas endo-Zn_n@sp³-LOF affects the gap slightly. Furthermore, electron transport analysis based on Yoshizawa's orbital rules confirms that these constructs maintain good molecular conductance between two ends of the framework-protected Zn-Zn metal chains (10^-2 to 10^-3 G₀; Log[G₀] from -2 to -3), despite smaller values in comparison to the free-standing zinc metal chains. Moreover, the predicted gas adsorption behavior indicates that CO₂ is predicted to interact more strongly than CO, with adsorption strength modulated by the LOF motifs and the presence and position of Zn centers. These findings establish Zn@LOFs not merely as passive supports, but as tunable, dual-function platforms capable of integrating potential single-atom catalysis with efficient charge transport.</p>","PeriodicalId":188,"journal":{"name":"Journal of Computational Chemistry","volume":"47 14","pages":"e70404"},"PeriodicalIF":4.8,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012816","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}