Journal of Chemical Theory and Computation最新文献_第3页

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.5c0002210.1021/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 and 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 and Nikolaj Thomas Zinner, ","doi":"10.1021/acs.jctc.5c0002210.1021/acs.jctc.5c00022","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00022https://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":"21 7","pages":"3493–3503 3493–3503"},"PeriodicalIF":5.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790672","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

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

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.5c0010310.1021/acs.jctc.5c00103

Daeseong Yong*, and , Jaeup U. Kim,

{"title":"Dynamic Programming for Chain Propagator Computation of Branched Block Copolymers in Polymer Field Theory Simulations","authors":"Daeseong Yong*,  and , Jaeup U. Kim, ","doi":"10.1021/acs.jctc.5c0010310.1021/acs.jctc.5c00103","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00103https://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":"21 7","pages":"3676–3690 3676–3690"},"PeriodicalIF":5.7,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790459","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.4c0144810.1021/acs.jctc.4c01448

Qiujiang Liang*, and , Jun Yang*,

{"title":"Polarizable Water Model with Ab Initio Neural Network Dynamic Charges and Spontaneous Charge Transfer","authors":"Qiujiang Liang*,  and , Jun Yang*, ","doi":"10.1021/acs.jctc.4c0144810.1021/acs.jctc.4c01448","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01448https://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":"21 7","pages":"3360–3373 3360–3373"},"PeriodicalIF":5.7,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c01448","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790310","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

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

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.4c0165910.1021/acs.jctc.4c01659

Siu Ting Tai, Chen Wang, Ruihuan Cheng and 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 and Yue Chen*, ","doi":"10.1021/acs.jctc.4c0165910.1021/acs.jctc.4c01659","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01659https://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":"21 7","pages":"3649–3657 3649–3657"},"PeriodicalIF":5.7,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c01659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790455","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

The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H-Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States.

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-28 DOI: 10.1021/acs.jctc.4c01694

Yingfeng Zhang, Jin Xiao, Shunyu Wang, Tong Zhu, John Z H Zhang

引用次数: 0

The Atomic Density-Based Tight-Binding (aTB) Model: A Robust and Accurate Semiempirical Method Parametrized for H–Ra; Applied to Structures, Vibrational Frequencies, Noncovalent Interactions, and Excited States

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-03-28 DOI: 10.1021/acs.jctc.4c0169410.1021/acs.jctc.4c01694

Yingfeng Zhang*, Jin Xiao, Shunyu Wang, Tong Zhu* and John Z. H. Zhang*,

引用次数: 0