Journal of Chemical Theory and Computation最新文献_第7页

Polaritonic Chemistry Using the Density Matrix Renormalization Group Method 使用密度矩阵重正化群法的极性化学

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-23 DOI: 10.1021/acs.jctc.4c00986

Mikuláš Matoušek, Nam Vu, Niranjan Govind, Jonathan J. Foley, IV, Libor Veis

{"title":"Polaritonic Chemistry Using the Density Matrix Renormalization Group Method","authors":"Mikuláš Matoušek, Nam Vu, Niranjan Govind, Jonathan J. Foley, IV, Libor Veis","doi":"10.1021/acs.jctc.4c00986","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00986","url":null,"abstract":"The emerging field of polaritonic chemistry explores the behavior of molecules under strong coupling with cavity modes. Despite recent developments in ab initio polaritonic methods for simulating polaritonic chemistry under electronic strong coupling, their capabilities are limited, especially in cases where the molecule also features strong electronic correlation. To bridge this gap, we have developed a novel method for cavity QED calculations utilizing the Density Matrix Renormalization Group (DMRG) algorithm in conjunction with the Pauli–Fierz Hamiltonian. Our approach is applied to investigate the effect of the cavity on the S0–S1 transition of n-oligoacenes, with n ranging from 2 to 5, encompassing 22 fully correlated π orbitals in the largest pentacene molecule. Our findings indicate that the influence of the cavity intensifies with larger acenes. Additionally, we demonstrate that, unlike the full determinantal representation, DMRG efficiently optimizes and eliminates excess photonic degrees of freedom, resulting in an asymptotically constant computational cost as the photonic basis increases.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488005","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

Acceleration of Diffusion in Ab Initio Nanoreactor Molecular Dynamics and Application to Hydrogen Sulfide Oxidation 加速扩散的 Ab Initio 纳米反应器分子动力学及硫化氢氧化应用

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-23 DOI: 10.1021/acs.jctc.4c00826

Jan A. Meissner, Jan Meisner

{"title":"Acceleration of Diffusion in Ab Initio Nanoreactor Molecular Dynamics and Application to Hydrogen Sulfide Oxidation","authors":"Jan A. Meissner, Jan Meisner","doi":"10.1021/acs.jctc.4c00826","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00826","url":null,"abstract":"The computational description of chemical reactivity can become extremely complex when multiple different reaction products and intermediates come into play, forming a chemical reaction network. Therefore, computational methods for the automated construction of chemical reaction networks have been developed in the last decades. One of these methods, ab initio nanoreactor molecular dynamics (NMD), is based on external forces enhancing reactivity by e.g., periodically compressing the system and allowing it to relax. However, during the relaxation process, a significant simulation time is required to allow energy to dissipate and molecules to diffuse, making this part of the NMD simulation computationally intensive. This work aims to improve NMD by accelerating the diffusion process in the relaxation phase. We systematically investigate the speedup of reaction discovery gained by diffusion acceleration, leading to a factor of up to 28 in discovery frequency. Diffusion-accelerated nanoreactor molecular dynamics (DA-NMD) is then used to construct a reaction network of hydrogen sulfide oxidation under atmospheric conditions, where reactions are automatically detected by a change in the bond order and bond distance. A reaction network of 108 molecular species and 399 elementary reactions was constructed starting from hydrogen sulfide, hydroxy radicals, and molecular oxygen covering a broad variety of sulfur–oxygen chemistry and oxidation states of the sulfur atom ranging from −II to +VI.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142487983","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

Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals. 使用 Tamm-Dancoff 近似和范围分离混合函数的超大规模 GPU 加速时变密度泛函理论的核梯度。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI: 10.1021/acs.jctc.4c01003

Inkoo Kim, Daun Jeong, Leah P Weisburn, Alexandra Alexiu, Troy Van Voorhis, Young Min Rhee, Won-Joon Son, Hyung-Jin Kim, Jinkyu Yim, Sungmin Kim, Yeonchoo Cho, Inkook Jang, Seungmin Lee, Dae Sin Kim

{"title":"Very-Large-Scale GPU-Accelerated Nuclear Gradient of Time-Dependent Density Functional Theory with Tamm-Dancoff Approximation and Range-Separated Hybrid Functionals.","authors":"Inkoo Kim, Daun Jeong, Leah P Weisburn, Alexandra Alexiu, Troy Van Voorhis, Young Min Rhee, Won-Joon Son, Hyung-Jin Kim, Jinkyu Yim, Sungmin Kim, Yeonchoo Cho, Inkook Jang, Seungmin Lee, Dae Sin Kim","doi":"10.1021/acs.jctc.4c01003","DOIUrl":"10.1021/acs.jctc.4c01003","url":null,"abstract":"Modern graphics processing units (GPUs) provide an unprecedented level of computing power. In this study, we present a high-performance, multi-GPU implementation of the analytical nuclear gradient for Kohn-Sham time-dependent density functional theory (TDDFT), employing the Tamm-Dancoff approximation (TDA) and Gaussian-type atomic orbitals as basis functions. We discuss GPU-efficient algorithms for the derivatives of electron repulsion integrals and exchange-correlation functionals within the range-separated scheme. As an illustrative example, we calculate the TDA-TDDFT gradient of the S1 state of a full-scale green fluorescent protein with explicit water solvent molecules, totaling 4353 atoms, at the ωB97X/def2-SVP level of theory. Our algorithm demonstrates favorable parallel efficiencies on a high-speed distributed system equipped with 256 Nvidia A100 GPUs, achieving >70% with up to 64 GPUs and 31% with 256 GPUs, effectively leveraging the capabilities of modern high-performance computing systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379412","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

Changing Your Martini Can Still Give You a Hangover. 换一杯马提尼还是会让你宿醉。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-03 DOI: 10.1021/acs.jctc.4c00868

Timothy D Loose, Patrick G Sahrmann, Thomas S Qu, Gregory A Voth

{"title":"Changing Your Martini Can Still Give You a Hangover.","authors":"Timothy D Loose, Patrick G Sahrmann, Thomas S Qu, Gregory A Voth","doi":"10.1021/acs.jctc.4c00868","DOIUrl":"10.1021/acs.jctc.4c00868","url":null,"abstract":"The Martini 3.0 coarse-grained force field, which was parametrized to better capture transferability in top-down coarse-grained models, is analyzed to assess its accuracy in representing thermodynamic and structural properties with respect to the underlying atomistic representation of the system. These results are compared to those obtained following the principles of statistical mechanics that start from the same underlying atomistic system. To this end, the potentials of mean force for lateral association in Martini 3.0 binary lipid bilayers are decomposed into their entropic and enthalpic components and compared to those of corresponding atomistic bilayers that have been projected onto equivalent coarse-grained mappings but evolved under the fully atomistic forces. This is accomplished by applying the reversible work theorem to lateral pair correlation functions between coarse-grained lipid beads taken at a range of different temperatures. The entropy-enthalpy decompositions provide a metric by which the underlying statistical mechanical properties of Martini can be investigated. Overall, Martini 3.0 is found to fail to properly partition entropy and enthalpy for the PMFs compared to the mapped all-atom results, despite changes made to the force field from the Martini 2.0 version. This outcome points to the fact that the development of more accurate top-down coarse-grained models such as Martini will likely necessitate temperature-dependent terms in the corresponding CG force-field; although necessary, this may not be sufficient to improve Martini. In addition to the entropy-enthalpy decompositions, Martini 3.0 produces an incorrect undulation spectrum, in particular at intermediate length scales of biophysical pertinence.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363441","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

Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods 阐明气相中的蛋白质结构：用偏置方法穿越构型空间

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 DOI: 10.1021/acs.jctc.4c0028810.1021/acs.jctc.4c00288

Viraj D. Gandhi, Leyan Hua, Morgan Lawrenz, Mohsen Latif, Amber D. Rolland, Iain D. G. Campuzano and Carlos Larriba-Andaluz*,

{"title":"Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods","authors":"Viraj D. Gandhi, Leyan Hua, Morgan Lawrenz, Mohsen Latif, Amber D. Rolland, Iain D. G. Campuzano and Carlos Larriba-Andaluz*, ","doi":"10.1021/acs.jctc.4c0028810.1021/acs.jctc.4c00288","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00288https://doi.org/10.1021/acs.jctc.4c00288","url":null,"abstract":"Achieving accurate characterization of protein structures in the gas phase continues to be a formidable challenge. To tackle this issue, the present study employs Molecular Dynamics (MD) simulations in tandem with enhanced sampling techniques (methods designed to efficiently explore protein conformations). The objective is to identify suitable structures of proteins by contrasting their calculated Collision Cross-Section (CCS) with those observed experimentally. Significant discrepancies were observed between the initial MD-simulated and experimentally measured CCS values through Ion Mobility–Mass Spectrometry (IMS-MS). To bridge this gap, we employed two distinct enhanced sampling methods, Harmonic Biasing Potential and Adaptive Biasing Force, which help the proteins overcome energy barriers to adopt more compact configurations. These techniques leverage the radius of gyration as a reaction coordinate (guiding parameter), guiding the system toward compressed states that potentially match experimental configurations more closely. The guiding forces are only employed to overcome existing barriers and are removed to allow the protein to naturally arrive at a potential gas phase configuration. The results demonstrated close alignment (within ∼4%) between simulated and experimental CCS values despite using different strengths and/or methods, validating their efficacy. This work lays the groundwork for future studies aimed at optimizing biasing methods and expanding the collective variables used for more accurate gas-phase structural predictions.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142608059","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

Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments. 通过半实验和耦合簇模板片段，以 DFT 成本获得大分子的精确几何图形。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI: 10.1021/acs.jctc.4c00900

Silvia Di Grande, Federico Lazzari, Vincenzo Barone

{"title":"Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments.","authors":"Silvia Di Grande, Federico Lazzari, Vincenzo Barone","doi":"10.1021/acs.jctc.4c00900","DOIUrl":"10.1021/acs.jctc.4c00900","url":null,"abstract":"Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379408","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

Chemically Transferable Electronic Coarse Graining for Polythiophenes. 聚噻吩的化学可转移电子粗粒化。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-07 DOI: 10.1021/acs.jctc.4c00804

Zheng Yu, Nicholas E Jackson

{"title":"Chemically Transferable Electronic Coarse Graining for Polythiophenes.","authors":"Zheng Yu, Nicholas E Jackson","doi":"10.1021/acs.jctc.4c00804","DOIUrl":"10.1021/acs.jctc.4c00804","url":null,"abstract":"Recent advances in machine-learning-based electronic coarse graining (ECG) methods have demonstrated the potential to enable electronic predictions in soft materials at mesoscopic length scales. However, previous ECG models have yet to confront the issue of chemical transferability. In this study, we develop chemically transferable ECG models for polythiophenes using graph neural networks. Our models are trained on a data set that samples over the conformational space of random polythiophene sequences generated with 15 different monomer chemistries and three different degrees of polymerization. We systematically explore the impact of coarse-grained representation on ECG accuracy, highlighting the significance of preserving the C-β coordinates in thiophene. We also find that integrating unique polymer sequences into training enhances the model performance more efficiently than augmenting conformational sampling for sequences already in the training data set. Moreover, our ECG models, developed initially for one property and one level of quantum chemical theory, can be efficiently transferred to related properties and higher levels of theory with minimal additional data. The chemically transferable ECG model introduced in this work will serve as a foundation model for new classes of chemically transferable ECG predictions across chemical space.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379410","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

Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods 阐明气相中的蛋白质结构：用偏置方法穿越构型空间

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 DOI: 10.1021/acs.jctc.4c00288

Viraj D. Gandhi, Leyan Hua, Morgan Lawrenz, Mohsen Latif, Amber D. Rolland, Iain D. G. Campuzano, Carlos Larriba-Andaluz

{"title":"Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods","authors":"Viraj D. Gandhi, Leyan Hua, Morgan Lawrenz, Mohsen Latif, Amber D. Rolland, Iain D. G. Campuzano, Carlos Larriba-Andaluz","doi":"10.1021/acs.jctc.4c00288","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00288","url":null,"abstract":"Achieving accurate characterization of protein structures in the gas phase continues to be a formidable challenge. To tackle this issue, the present study employs Molecular Dynamics (MD) simulations in tandem with enhanced sampling techniques (methods designed to efficiently explore protein conformations). The objective is to identify suitable structures of proteins by contrasting their calculated Collision Cross-Section (CCS) with those observed experimentally. Significant discrepancies were observed between the initial MD-simulated and experimentally measured CCS values through Ion Mobility–Mass Spectrometry (IMS-MS). To bridge this gap, we employed two distinct enhanced sampling methods, Harmonic Biasing Potential and Adaptive Biasing Force, which help the proteins overcome energy barriers to adopt more compact configurations. These techniques leverage the radius of gyration as a reaction coordinate (guiding parameter), guiding the system toward compressed states that potentially match experimental configurations more closely. The guiding forces are only employed to overcome existing barriers and are removed to allow the protein to naturally arrive at a potential gas phase configuration. The results demonstrated close alignment (within ∼4%) between simulated and experimental CCS values despite using different strengths and/or methods, validating their efficacy. This work lays the groundwork for future studies aimed at optimizing biasing methods and expanding the collective variables used for more accurate gas-phase structural predictions.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142487985","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

Comparison of Matrix Product State and Multiconfiguration Time-Dependent Hartree Methods for Nonadiabatic Dynamics of Exciton Dissociation. 基质积态与多配置时变哈特里方法在激子解离非绝热动力学方面的比较。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-04 DOI: 10.1021/acs.jctc.4c00751

Maximilian F X Dorfner, Dominik Brey, Irene Burghardt, Frank Ortmann

{"title":"Comparison of Matrix Product State and Multiconfiguration Time-Dependent Hartree Methods for Nonadiabatic Dynamics of Exciton Dissociation.","authors":"Maximilian F X Dorfner, Dominik Brey, Irene Burghardt, Frank Ortmann","doi":"10.1021/acs.jctc.4c00751","DOIUrl":"10.1021/acs.jctc.4c00751","url":null,"abstract":"The excited-state dynamics of organic molecules, molecular aggregates, and donor-acceptor clusters is typically governed by the interplay of electronic excitations and, due to their flexibility and soft bonding, by the interaction with their vibrations. This interaction in these systems can be characterized by a few relevant electronic states that are coupled to numerous vibrational normal modes, encompassing a vast configurational space of the molecules. The full quantum simulation of these type of systems has been long dominated by the multiconfiguration time-dependent Hartree (MCTDH) approach and its multilayer variants, which are considered the gold standard in the presence of electron-vibration coupling with a large number of modes. Recently, also the matrix product state ansatz (MPS) with appropriate time-evolution schemes has been applied to these types of Hamiltonians. In this article, we provide a numerical comparison of excited-state dynamics between the MCTDH and MPS approaches for two electron-vibration coupled systems. Notably, we consider two models for exciton dissociation at a P3HT:PCBM heterojunction, comprising two electronic states and 100 vibrational modes, and 26 electronic states and 113 vibrational modes, respectively. While both methods agree very well for the first model, more pronounced deviations are found for the second model. We trace back the divergence between the methods to the different way entanglement is treated.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142370217","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

Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy. 改进六糖单糖的 Drude 可极化力场：更精确地捕捉环状构象动力学

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-10-22 Epub Date: 2024-10-09 DOI: 10.1021/acs.jctc.4c00656

Chythra J N, Olgun Guvench, Alexander D MacKerell, Takumi Yamaguchi, Sairam S Mallajosyula

{"title":"Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.","authors":"Chythra J N, Olgun Guvench, Alexander D MacKerell, Takumi Yamaguchi, Sairam S Mallajosyula","doi":"10.1021/acs.jctc.4c00656","DOIUrl":"10.1021/acs.jctc.4c00656","url":null,"abstract":"We present a revised version of the Drude polarizable carbohydrate force field (FF), focusing on refining the ring and exocyclic torsional parameters for hexopyranose monosaccharides. This refinement addresses the previously observed discrepancies between calculated and experimental NMR 3J coupling values, particularly in describing ring dynamics and exocyclic rotamer populations within major hexose monosaccharides and their anomers. Specifically, α-MAN, β-MAN, α-GLC, β-GLC, α-GAL, β-GAL, α-ALT, β-ALT, α-IDO, and β-IDO were targeted for optimization. The optimization process involved potential energy scans (PES) of the ring and exocyclic dihedral angles computed using quantum mechanical (QM) methods. The target data for the reoptimization included PES of the inner ring dihedrals (C1-C2-C3-C4, C2-C3-C4-C5, C5-O5-C1-C2, C4-C5-O5-C1, O5-C1-C2-C3, C3-C4-C5-O5) and the exocyclic torsions, other than the pseudo ring dihedrals (O1-C1-O5-C5, O2-C2-C1-O5, and O4-C4-C5-O5) and hydroxyl torsions used in the previous parametrization efforts. These parameters, in conjunction with previously developed Drude parameters for hexopyranose monosaccharides, were validated against experimental observations, including NMR data and conformational energetics, in aqueous environments. The resulting polarizable model is shown to be in good agreement with a range of QM data, experimental NMR data, and conformational energetics of monosaccharides in aqueous solutions. This offers a significant improvement of the Drude carbohydrate force field, wherein the refinement enhances the accuracy of accessing the conformational dynamics of carbohydrates in biomolecular simulations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11495998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386399","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