Journal of Chemical Theory and Computation最新文献_第2页

Bayesian Nonparametric Analysis of Residence Times for Protein-Lipid Interactions in Molecular Dynamics Simulations.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-02 DOI: 10.1021/acs.jctc.4c01522

Ricky Sexton, Mohamadreza Fazel, Maxwell Schweiger, Steve Pressé, Oliver Beckstein

{"title":"Bayesian Nonparametric Analysis of Residence Times for Protein-Lipid Interactions in Molecular Dynamics Simulations.","authors":"Ricky Sexton, Mohamadreza Fazel, Maxwell Schweiger, Steve Pressé, Oliver Beckstein","doi":"10.1021/acs.jctc.4c01522","DOIUrl":"10.1021/acs.jctc.4c01522","url":null,"abstract":"Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular, of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid-protein binding kinetics has remained challenging due to considerable noise and low frequency of long binding events, even in hundreds of microseconds of simulation data. Here, we apply Bayesian nonparametrics to compute residue-resolved residence time distributions from MD trajectories. Such an analysis characterizes binding processes at different time scales (quantified by their kinetic off-rate) and assigns to each trajectory frame a probability of belonging to a specific process. In this way, we classify trajectory frames in an unsupervised manner and obtain, for example, different binding poses or molecular densities based on the time scale of the process. We demonstrate our approach by characterizing interactions of cholesterol with six different G-protein-coupled receptors (A2AAR, β2AR, CB1R, CB2R, CCK1R, and CCK2R) simulated with coarse-grained MD simulations with the MARTINI model. The nonparametric Bayesian analysis allows us to connect the coarse binding time series data to the underlying molecular picture and thus not only infers accurate binding kinetics with error distributions from MD simulations but also describes molecular events responsible for the broad range of kinetic rates.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762540","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

Quantum Circuit and Mapping Algorithms for Wavepacket Dynamics: Case Study of Anharmonic Hydrogen Bonds in Protonated and Hydroxide Water Clusters.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-02 DOI: 10.1021/acs.jctc.4c01343

Debadrita Saha, Philip Richerme, Srinivasan S Iyengar

{"title":"Quantum Circuit and Mapping Algorithms for Wavepacket Dynamics: Case Study of Anharmonic Hydrogen Bonds in Protonated and Hydroxide Water Clusters.","authors":"Debadrita Saha, Philip Richerme, Srinivasan S Iyengar","doi":"10.1021/acs.jctc.4c01343","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01343","url":null,"abstract":"The accurate computational study of wavepacket nuclear dynamics is considered to be a classically intractable problem, particularly with increasing dimensions. Here, we present two algorithms that, in conjunction with other methods developed by us, may result in one set of contributions for performing quantum nuclear dynamics in arbitrary dimensions. For one of the two algorithms discussed here, we present a direct map between the Born-Oppenheimer Hamiltonian describing the nuclear wavepacket time evolution and the control parameters of a spin-lattice Hamiltonian that describes the dynamics of qubit states in an ion-trap quantum computer. This map is exact for three qubits, and when implemented, the dynamics of the spin states emulates those of the nuclear wavepacket in a continuous representation. However, this map becomes approximate as the number of qubits grows. In a second algorithm, we present a general quantum circuit decomposition formalism for such problems using a method called the Quantum Shannon Decomposition. This algorithm is more robust and is exact for any number of qubits at the cost of increased circuit complexity. The resultant circuit is implemented on IBM's quantum simulator (QASM) for 3-7 qubits, without using a noise model so as to test the intrinsic accuracy of the method. In both cases, the wavepacket dynamics is found to be in good agreement with the classical propagation result and the corresponding vibrational frequencies obtained from the wavepacket density time evolution are in agreement to within a few tenths of a wavenumber.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762526","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

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-01 DOI: 10.1021/acs.jctc.5c00102

Emmit K Pert, Clay H Batton, Xiang Li, Steven Dunne, Grant M Rotskoff

{"title":"Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators.","authors":"Emmit K Pert, Clay H Batton, Xiang Li, Steven Dunne, Grant M Rotskoff","doi":"10.1021/acs.jctc.5c00102","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00102","url":null,"abstract":"Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762453","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

Optimal-Reference Excited State Methods: Static Correlation at Polynomial Cost with Single-Reference Coupled-Cluster Approaches.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-01 DOI: 10.1021/acs.jctc.5c00172

Sylvia J Bintrim, Kevin Carter-Fenk

{"title":"Optimal-Reference Excited State Methods: Static Correlation at Polynomial Cost with Single-Reference Coupled-Cluster Approaches.","authors":"Sylvia J Bintrim, Kevin Carter-Fenk","doi":"10.1021/acs.jctc.5c00172","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00172","url":null,"abstract":"Accurate yet efficient modeling of chemical systems with pronounced static correlation in their excited states remains a significant challenge in quantum chemistry, as most electronic structure methods that can adequately capture static correlation scale factorially with system size. Researchers are often left with no option but to use more affordable methods that may lack the accuracy required to model critical processes in photochemistry such as photolysis, photocatalysis, and nonadiabatic relaxation. A great deal of work has been dedicated to refining single-reference descriptions of static correlation in the ground state via \"addition-by-subtraction\" coupled cluster methods such as pair coupled cluster with double substitutions (pCCD), singlet-paired CCD (CCD0), triplet-paired CCD (CCD1), and CCD with frozen singlet- or triplet-paired amplitudes (CCDf0/CCDf1). By combining wave functions derived from these methods with the intermediate state representation (ISR), we gain insights into the extensibility of single-reference coupled cluster theory's coverage of static correlation to the excited state problem. Our CCDf1-ISR(2) approach is robust in the face of static correlation and provides enough dynamical correlation to accurately predict excitation energies to within about 0.2 eV in small organic molecules. We also highlight distinct advantages of the Hermitian ISR construction, such as the avoidance of pathological failures of equation-of-motion methods for excited state potential energy surface topology. Our results prompt us to continue exploring optimal single-reference theories (excited state approaches that leverage dependence on the initial reference wave function) as a potentially economical approach to the excited state static correlation problem.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750261","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

Discovery of Spin-Crossover Materials with Equivariant Graph Neural Networks and Relevance-Based Classification.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-04-01 DOI: 10.1021/acs.jctc.4c01690

Angel Albavera-Mata, Pawan Prakash, Jason B Gibson, Eric Fonseca, Sijin Ren, Xiao-Guang Zhang, Hai-Ping Cheng, Michael Shatruk, S B Trickey, Richard G Hennig

引用次数: 0

Strong Coupling Møller-Plesset Perturbation Theory.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-31 DOI: 10.1021/acs.jctc.5c00055

Yassir El Moutaoukal, Rosario R Riso, Matteo Castagnola, Enrico Ronca, Henrik Koch

引用次数: 0

Calculating the Energy Profile of an Enzymatic Reaction on a Quantum Computer.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-31 DOI: 10.1021/acs.jctc.5c00022

Patrick Ettenhuber, Mads Bøttger Hansen, Pier Paolo Poier, Irfansha Shaik, Stig Elkjaer Rasmussen, Niels Kristian Madsen, Marco Majland, Frank Jensen, Lars Olsen, Nikolaj Thomas Zinner

{"title":"Calculating the Energy Profile of an Enzymatic Reaction on a Quantum Computer.","authors":"Patrick Ettenhuber, Mads Bøttger Hansen, Pier Paolo Poier, Irfansha Shaik, Stig Elkjaer Rasmussen, Niels Kristian Madsen, Marco Majland, Frank Jensen, Lars Olsen, Nikolaj Thomas Zinner","doi":"10.1021/acs.jctc.5c00022","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00022","url":null,"abstract":"Quantum computing (QC) provides a promising avenue for enabling quantum chemistry calculations, which are classically impossible due to computational complexity that increases exponentially with system size. As fully fault-tolerant algorithms and hardware, for which an exponential speedup is predicted, are currently out of reach, recent research efforts have been dedicated to developing and scaling algorithms for Noisy Intermediate-Scale Quantum (NISQ) devices to showcase the practical usefulness of such machines. To demonstrate the usefulness of NISQ devices in the field of chemistry, we apply our recently developed FAST-VQE algorithm and a state-of-the-art quantum gate reduction strategy based on propositional satisfiability together with standard optimization tools for the simulation of the rate-determining proton transfer step for CO2 hydration catalyzed by carbonic anhydrase resulting in the first application of a quantum computing device for the simulation of an enzymatic reaction. To this end, we have combined classical force field simulations with quantum mechanical methods on classical and quantum computers in a hybrid calculation approach. The presented technique significantly enhances the accuracy and capabilities of QC-based molecular modeling and finally pushes it into compelling and realistic applications. The framework is general and can be applied beyond the case of computational enzymology.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750259","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

Dynamic Programming for Chain Propagator Computation of Branched Block Copolymers in Polymer Field Theory Simulations.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-30 DOI: 10.1021/acs.jctc.5c00103

Daeseong Yong, Jaeup U Kim

{"title":"Dynamic Programming for Chain Propagator Computation of Branched Block Copolymers in Polymer Field Theory Simulations.","authors":"Daeseong Yong, Jaeup U Kim","doi":"10.1021/acs.jctc.5c00103","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00103","url":null,"abstract":"We present an algorithmic approach to optimize chain propagator computations in polymer field theory simulations, including self-consistent field theory (SCFT) calculations and field-theoretic simulations (FTSs). Propagator calculations for branched block copolymers often involve recursive structures and overlapping subproblems, resulting in redundant computations. By employing dynamic programming (DP) and encoding computational dependencies as strings, our method systematically eliminates these redundancies in mixtures of branched polymers. The algorithm achieves optimal time complexity for various polymeric systems, including star-shaped, comb, dendrimer polymers, and homopolymer mixtures, by reusing and aggregating propagators for symmetric and repetitive structures. This enhances computational efficiency and reduces memory usage, addressing a key limitation in developing versatile polymer field theory simulation software. Our approach streamlines the simulation of complex branched polymers without requiring manual software adjustments, facilitating more efficient workflows for polymer researchers. Furthermore, the method enables automated searches for inverse design by optimizing computations across diverse branched polymer architectures, contributing to the discovery and design of novel polymeric materials. The algorithm is implemented in open-source software, ensuring accessibility for further development and broader application in computational polymer science.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750260","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

Revisiting Many-Body Interaction Heat Current and Thermal Conductivity Calculations Using the Moment Tensor Potential/LAMMPS Interface.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-29 DOI: 10.1021/acs.jctc.4c01659

Siu Ting Tai, Chen Wang, Ruihuan Cheng, Yue Chen

{"title":"Revisiting Many-Body Interaction Heat Current and Thermal Conductivity Calculations Using the Moment Tensor Potential/LAMMPS Interface.","authors":"Siu Ting Tai, Chen Wang, Ruihuan Cheng, Yue Chen","doi":"10.1021/acs.jctc.4c01659","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01659","url":null,"abstract":"The definition of heat current operator for systems for nonpairwise additive interactions and its impact on related lattice thermal conductivity (κL) via molecular dynamics (MD) simulation are ambiguous and controversial when migrating from empirical potential models to machine learning potential (MLP) models. Herein, we study and compare the significance of many-body interaction with heat current computation in one of the most popular MLP models, the moment tensor potential (MTP). Nonequilibrium MD simulations and equilibrium MD simulations among four different materials were performed, and inconsistencies in energy conservation between the simulation thermostat and the pairwise calculator were found. A new virial stress tensor expression with a many-body heat current description was integrated inside the MTP, and we uncovered the influence of the modification that could alter the κL results by 29-64% using the equilibrium MD computational approach. Our work demonstrates the importance of a many-body description during thermal analysis in MD simulations when MLPs are of concern.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741743","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

Polarizable Water Model with Ab Initio Neural Network Dynamic Charges and Spontaneous Charge Transfer.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-29 DOI: 10.1021/acs.jctc.4c01448

Qiujiang Liang, Jun Yang

{"title":"Polarizable Water Model with Ab Initio Neural Network Dynamic Charges and Spontaneous Charge Transfer.","authors":"Qiujiang Liang, Jun Yang","doi":"10.1021/acs.jctc.4c01448","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01448","url":null,"abstract":"Simulating water accurately has been a challenge due to the complexity of describing polarization and intermolecular charge transfer. Quantum mechanical (QM) electronic structures provide an accurate description of polarization in response to local environments, which is nevertheless too expensive for large water systems. In this study, we have developed a polarizable water model integrating Charge Model 5 atomic charges at the level of the second-order Mo̷ller-Plesset perturbation theory, predicted by an accurate and transferable charge neural network (ChargeNN) model. The spontaneous intermolecular charge transfer has been explicitly accounted for, enabling a precise treatment of hydrogen bonds and out-of-plane polarization. Our ChargeNN water model successfully reproduces various properties of water in gas, liquid, and solid phases. For example, ChargeNN correctly captures the hydrogen-bond stretching peak and bending-libration combination band, which are absent in the spectra using fixed charges, highlighting the significance of accurate polarization and charge transfer. Finally, the molecular dynamical simulations using ChargeNN for liquid water and a large water droplet with a ∼4.5 nm radius reveal that the strong interfacial electric fields are concurrently induced by the partial collapse of the hydrogen-bond network and surface-to-interior charge transfer. Our study paves the way for QM-polarizable force fields, aiming for large-scale molecular simulations with high accuracy.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741740","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