Journal of Chemical Theory and Computation最新文献_第9页

Conical Intersections Studied by the Configuration-Interaction-Corrected Tamm-Dancoff Method.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-18 DOI: 10.1021/acs.jctc.4c01768

Lei Xu, Victor M Freixas, Flavia Aleotti, Donald G Truhlar, Sergei Tretiak, Marco Garavelli, Shaul Mukamel, Niranjan Govind

{"title":"Conical Intersections Studied by the Configuration-Interaction-Corrected Tamm-Dancoff Method.","authors":"Lei Xu, Victor M Freixas, Flavia Aleotti, Donald G Truhlar, Sergei Tretiak, Marco Garavelli, Shaul Mukamel, Niranjan Govind","doi":"10.1021/acs.jctc.4c01768","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01768","url":null,"abstract":"Conical intersections directly mediate the internal energy conversion in photoinduced processes in a wide range of chemical and biological systems. Because of the Brillouin theorem, many conventional electronic structure methods, including configuration interaction with single excitations from a Hartree-Fock reference and time-dependent density functional theory in either the linear response approximation (TDDFT) or Tamm-Dancoff approximation (DFT-TDA), have the wrong dimensionality for conical intersections between the ground state (S0) and the first excited state (S1) of the same multiplicity. This leads to unphysical state crossings. Here, we implement and assess the configuration-interaction-corrected Tamm-Dancoff approximation (CIC-TDA) that restores the correct dimensionality of conical intersections by including the coupling between the reference state and the intersecting excited state. We apply the CIC-TDA method to the S1/S0 conical intersections in ammonia (NH3), ethylene (C2H4), bithiophene (C8H6S2), azobenzene (C12H10N2), and 11-cis retinal protonated Schiff base (PSB11) in vacuo. We show that this black-box approach can produce potential energy surfaces (PESs) of comparable accuracy to multireference wave function methods. The method validated here can allow cost-efficient explorations of photoinduced electronically nonadiabatic dynamics, especially for large molecules and complex systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ion Channel Reaction Networks: Dielectric Screening and the Importance of Off-Pathway Flux.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-18 DOI: 10.1021/acs.jctc.4c01569

Hannah Weckel-Dahman, Ryan Carlsen, Alexander Daum, Maxwell He, Tyler G Southam, Jessica M J Swanson

{"title":"Ion Channel Reaction Networks: Dielectric Screening and the Importance of Off-Pathway Flux.","authors":"Hannah Weckel-Dahman, Ryan Carlsen, Alexander Daum, Maxwell He, Tyler G Southam, Jessica M J Swanson","doi":"10.1021/acs.jctc.4c01569","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01569","url":null,"abstract":"The transport of ions through channels involves multiple rare-event transitions through a web of interconnected intermediates. Extracting open channel mechanisms generally requires quantifying the relative flux through these intermediates in response to a range of electrochemical gradients. Although this is ideally suited to network-based representations like Markov state models (MSMs), the relative contributions from different pathways and the importance of network resolution remain open areas of research. Herein, we use a complementary approach called multiscale responsive kinetic modeling (MsRKM) to explore how the screening of ionic interactions and the competition between multiple mechanistic pathways contribute to channel mechanisms and current profiles of ion channels. We find that explicitly optimizing screened ionic interactions in the MsRKM framework vastly reduces the solution search space, enabling more efficient identification of physically robust solutions. Using a model of the Shaker Kv channel, we demonstrate that even when systems are well described by a single dominant flux pathway, the remaining contributing pathways and off-pathway flux play multiple essential roles, including shifting current profiles and mechanisms in response to different electrochemical gradients. We additionally discover that the current continues to change above the experimentally predicted saturation point. Model systems explain how the degree of dielectric screening influences channel occupancy, the number of contributing pathways, and why current increases or decreases above its experimental saturation point. Our findings emphasize the importance of retaining a full network description to identify and understand ion channel mechanisms.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Can Coarse-Grained Molecular Dynamics Simulations Predict Pharmaceutical Crystal Growth?

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.5c00040

Linghao Shi, Futianyi Wang, Taraknath Mandal, Ronald G Larson

{"title":"Can Coarse-Grained Molecular Dynamics Simulations Predict Pharmaceutical Crystal Growth?","authors":"Linghao Shi, Futianyi Wang, Taraknath Mandal, Ronald G Larson","doi":"10.1021/acs.jctc.5c00040","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00040","url":null,"abstract":"To investigate the ability of coarse-grained molecular dynamics simulations to predict the relative growth rates of crystal facets of pharmaceutical molecules, we apply two coarse-graining strategies to two drug molecules, phenytoin and carbamazepine. In the first method, we map an atomistic model to a MARTINI-level coarse-grained (CG) force field that uses 2 or 3 heavy atoms per bead. This is followed by applying Particle Swarm Optimization (PSO), a global optimum searching algorithm, to the CG Lennard-Jones intermolecular potentials to fit the radial distribution functions of both the crystalline and melt structures. In the second, a coarser-grained method, we map 5 or more heavy atoms into one bead with the help of the Iterative Boltzmann Inversion (IBI) method to derive a tabulated longer-range force field (FF). Simulations using the FF's derived from both strategies were able to stabilize the crystal in the correct structure and to predict crystal growth from the melt with modest computational resources. We evaluate the advantages and limitations of both methods and compare the relative growth rates of various facets of both drug crystals with those predicted by the Bravais-Friedel-Donnay-Harker (BFDH) and attachment energy (AE) theories. While all methods, except for the simulations conducted with the coarser-grained IBI-generated model, produced similarly good results for phenytoin, the finer-grained PSO-generated FF using MARTINI mapping rules outperformed the other methods in its prediction of the facet growth rates and resulting crystalline morphology for carbamazepine.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coarse-Grained Modeling of a Metal–Organic Framework/Polymer Composite and Its Gas Adsorption at the Nanoparticle Level

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.4c0134110.1021/acs.jctc.4c01341

Cecilia M. S. Alvares, and , Rocio Semino*,

{"title":"Coarse-Grained Modeling of a Metal–Organic Framework/Polymer Composite and Its Gas Adsorption at the Nanoparticle Level","authors":"Cecilia M. S. Alvares,  and , Rocio Semino*, ","doi":"10.1021/acs.jctc.4c0134110.1021/acs.jctc.4c01341","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01341https://doi.org/10.1021/acs.jctc.4c01341","url":null,"abstract":"Simulations have acted as a cornerstone to understand the MOF/polymer interface structure; however, no molecular-level simulation has yet been performed at the nanoparticle scale. In this work, a hybrid MARTINI/force matching (FM) force field was developed and successfully implemented to model the ZIF-8/PVDF composite at a coarse-grained resolution. Interphase interactions were modeled using FM potentials, which strive to reasonably reproduce the forces from an atomistic benchmark model, while intraphase interactions were modeled using the general-purpose MARTINI potentials. Systems made of a ZIF-8 nanoparticle embedded into a PVDF matrix were considered to evaluate the effect of nanoparticle size and morphology in the polymer structuration and in the CO2 adsorption. Results show that simulations at the nanoparticle level are crucial for depicting polymer penetration. Notably, the smallest nanoparticle exhibited the least extent of polymer penetration, while the cubic nanoparticle exhibited the highest amount. Polymer conformation and local density values change following the same trend in all ZIF-8/PVDF systems depending on whether the polymer lies inside or outside the nanoparticle domain. All composite models present more significant CO2 adsorption in the nanoparticle domain than in the PVDF phase, in agreement with experiments. More remarkably, the small rhombic dodecahedron ZIF-8/PVDF system presents a larger equilibrium amount of gas adsorbed at ambient conditions compared to the other two systems, in alignment with the observed polymer penetration trend. On the other hand, comparison of CO2 adsorption capacities in cubic and rhombic dodecahedron ZIF-8 nanoparticles of similar sizes reveals that the former is more advantageous for CO2 adsorption.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3142–3155 3142–3155"},"PeriodicalIF":5.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Theoretical Model for Linear and Nonlinear Spectroscopy of Plexcitons.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.5c00048

Chenghong Huang, Shuming Bai, Qiang Shi

{"title":"A Theoretical Model for Linear and Nonlinear Spectroscopy of Plexcitons.","authors":"Chenghong Huang, Shuming Bai, Qiang Shi","doi":"10.1021/acs.jctc.5c00048","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00048","url":null,"abstract":"We present a theoretical model to investigate the dynamics and spectroscopic properties of a plexciton system consisting of a molecular exciton coupled to a single short-lived plasmonic mode. The exciton is described as a two-level system (TLS), while the plasmonic mode is treated as a dissipative harmonic oscillator. The hierarchical equations of motion method is employed to simulate energy transfer dynamics, absorption spectra, and two-dimensional electronic spectra (2DES) of the system across a range of coupling strengths. It is shown that increasing the exciton-plasmon coupling strength drives a transition in the absorption spectra from an asymmetric Fano line shape to a Rabi splitting pattern, while coupling the TLS to intramolecular vibrational modes reduces the central dip of the absorption spectra and makes the line shape more symmetric. The simulated 2DES exhibit distinct features compared to those of a coupled molecular dimer, highlighting the unique nonlinear response of plexciton systems. In addition, a \"breathing mode\" pattern observed in the strong coupling regime can serve as a direct evidence of Rabi oscillation.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeted TPS Shooting Using Computer Vision to Generate Ensemble of Trajectories.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.4c01725

Kseniia Korchagina, Steven D Schwartz

引用次数: 0

Implementation of an Ellipsoidal-Cavity Field Correction for Computed Molecular Oscillator Strengths in Solution: A(nother) Benchmark Study

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.5c0007010.1021/acs.jctc.5c00070

Jorge C. Garcia-Alvarez*, and , Samer Gozem*,

{"title":"Implementation of an Ellipsoidal-Cavity Field Correction for Computed Molecular Oscillator Strengths in Solution: A(nother) Benchmark Study","authors":"Jorge C. Garcia-Alvarez*,  and , Samer Gozem*, ","doi":"10.1021/acs.jctc.5c0007010.1021/acs.jctc.5c00070","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00070https://doi.org/10.1021/acs.jctc.5c00070","url":null,"abstract":"We recently compared oscillator strengths (OS) obtained from electronic structure calculations (fcomp) to OSs derived from experimental spectra (fexp) multiplied by the refractive index (n) of the solution in which the spectra were measured. The choice of nfexp instead of fexp as a reference accounts for the macroscopic flux of energy in a dielectric (the experimental solvent). Here, we apply an approximate correction to fcomp values that accounts for the local electromagnetic field driving the absorption transition (which is generally different from the macroscopic field). We refer to these modified OSs as fcompS. The correction is obtained by assuming that each molecule occupies an ellipsoidal cavity, fitted to its van der Waals surface, surrounded by a continuum dielectric model representing the solvent. Sets ranging from 33 to 85 experimental transitions are used for the benchmark. For LR-CCSD and EOM-CCSD, we find that fcompS generally gives a better agreement with experimental strengths than fcomp. For LR-CCSD in the length gauge, for instance, there is a 1 to 1 scaling of the (nfexp, fcompS) pairs. Instead, the results for TD-DFT depend on the amount of HF exchange used in the functional: pure functionals typically also have a 1 to 1 scaling of the (nfexp, fcompS) pairs, while for hybrid functionals fcompS overestimates nfexp to a degree that appears proportional to the amount of HF exchange present in the functional.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3120–3131 3120–3131"},"PeriodicalIF":5.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.5c00070","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitative Theory for Critical Conditions of Like-Charge Attraction between Polarizable Spheres

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-17 DOI: 10.1021/acs.jctc.5c0014410.1021/acs.jctc.5c00144

Yanyu Duan, and , Zecheng Gan*,

引用次数: 0

Fast and Accurate Prediction of Tautomer Ratios in Aqueous Solution via a Siamese Neural Network

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-16 DOI: 10.1021/acs.jctc.5c0004110.1021/acs.jctc.5c00041

Xiaolin Pan, Xudong Zhang, Song Xia and Yingkai Zhang*,

{"title":"Fast and Accurate Prediction of Tautomer Ratios in Aqueous Solution via a Siamese Neural Network","authors":"Xiaolin Pan, Xudong Zhang, Song Xia and Yingkai Zhang*, ","doi":"10.1021/acs.jctc.5c0004110.1021/acs.jctc.5c00041","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00041https://doi.org/10.1021/acs.jctc.5c00041","url":null,"abstract":"Tautomerization plays a critical role in chemical and biological processes, influencing molecular stability, reactivity, biological activity, and ADME-Tox properties. Many drug-like molecules exist in multiple tautomeric states in aqueous solution, complicating the study of protein–ligand interactions. Rapid and accurate prediction of tautomer ratios and identification of predominant species are therefore crucial in computational drug discovery. In this study, we introduce sPhysNet-Taut, a deep learning model fine-tuned on experimental data using a Siamese neural network architecture. This model directly predicts tautomer ratios in aqueous solution based on MMFF94-optimized molecular geometries. On experimental test sets, sPhysNet-Taut achieves state-of-the-art performance with root-mean-square error (RMSE) of 1.9 kcal/mol on the 100-tautomers set and 1.0 kcal/mol on the SAMPL2 challenge, outperforming all other methods. It also provides superior ranking power for tautomer pairs on multiple test sets. Our results demonstrate that fine-tuning on experimental data significantly enhances model performance compared to training from scratch. This work not only offers a valuable deep learning model for predicting tautomer ratios but also presents a protocol for modeling pairwise data. To promote usability, we have developed an accessible tool that predicts stable tautomeric states in aqueous solution by enumerating all possible tautomeric states and ranking them using our model. The source code and web server are freely accessible at https://github.com/xiaolinpan/sPhysNet-Taut and https://yzhang.hpc.nyu.edu/tautomer.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3132–3141 3132–3141"},"PeriodicalIF":5.7,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.5c00041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A General Formalism of Excitation-Dependent Luminescence Properties in Triplet–Triplet Annihilation Systems

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-14 DOI: 10.1021/acs.jctc.4c0171210.1021/acs.jctc.4c01712

Wenwan Zeng, Yincheng Zhang, Hao Chen, Hui Huang and Qian Peng*,

{"title":"A General Formalism of Excitation-Dependent Luminescence Properties in Triplet–Triplet Annihilation Systems","authors":"Wenwan Zeng, Yincheng Zhang, Hao Chen, Hui Huang and Qian Peng*, ","doi":"10.1021/acs.jctc.4c0171210.1021/acs.jctc.4c01712","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01712https://doi.org/10.1021/acs.jctc.4c01712","url":null,"abstract":"Triplet–triplet annihilation (TTA) has promising applications in optical functional devices and technologies due to its efficient exciton utilization and up-conversion. Traditionally, the change in the slope of the dual logarithmic relationship curve between emission and excitation light intensity from 2 to 1 has been regarded as evidence of the occurrence of TTA. However, this characteristic change was not observed in many single-component organic TTA systems in recent experiments. In this work, we develop new models for TTA processes by introducing more electronic states and transitions than those considered in the traditional model and derive a general formalism of excitation-dependent luminescence intensity, Iem = N(Ckex + Akex + B – <math><mrow><msqrt><mrow><msup><mrow><mi>B</mi></mrow><mrow><mn>2</mn></mrow></msup><mo>+</mo><mn>2</mn><mi>AB</mi><msub><mrow><mi>k</mi></mrow><mrow><mrow><mi>e</mi></mrow><mrow><mi>x</mi></mrow></mrow></msub></mrow></msqrt></mrow></math>). This formalism can be applied not only to typical TTA systems but also to systems whose dynamics cannot be accurately described using traditional models. As kex increases, the slope of log Iem ∼ log kex changes from 1 to n and then back to 1 (where 1 < n ≤ 2) with two distinct turning points, and the corresponding luminescence quantum yield (Φem) increases monotonically until it reaches saturation, which are fully confirmed by the steady-state spectrum experiments. The characteristic change in Φem is a more suitable universal criterion for judging the occurrence of TTA. These findings provide a valuable novel tool for probing the kinetic processes in TTA systems that are challenging to model.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3092–3100 3092–3100"},"PeriodicalIF":5.7,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0