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

Automatic Differentiation for Explicitly Correlated MP2. 显式相关 MP2 的自动微分。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-23 DOI: 10.1021/acs.jctc.4c00818

Erica C Mitchell, Justin M Turney, Henry F Schaefer

引用次数: 0

Two-Tier Modular Anharmonic Small Matrix Path Integral with Composite Spin-Boson Baths 带复合自旋玻色子浴的两层模块化非谐波小矩阵路径积分

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-20 DOI: 10.1021/acs.jctc.4c00980

Nancy Makri

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Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning. 利用自适应采样和机器学习增强对生物分子慢构象转变的采样。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-20 DOI: 10.1021/acs.jctc.4c00764

Mingyuan Zhang,Hao Wu,Yong Wang

{"title":"Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning.","authors":"Mingyuan Zhang,Hao Wu,Yong Wang","doi":"10.1021/acs.jctc.4c00764","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00764","url":null,"abstract":"Biomolecular simulations often suffer from the \"time scale problem\", hindering the study of rare events occurring over extended time scales. Enhanced sampling techniques aim to alleviate this issue by accelerating conformational transitions, yet they typically necessitate well-defined collective variables (CVs), posing a significant challenge. Machine learning offers promising solutions but typically requires rich training data encompassing the entire free energy surface (FES). In this work, we introduce an automated iterative pipeline designed to mitigate these limitations. Our protocol first utilizes a CV-free count-based adaptive sampling method to generate a data set rich in rare events. From this data set, slow modes are identified using Koopman-reweighted time-lagged independent component analysis (KTICA), which are subsequently leveraged by on-the-fly probability enhanced sampling (OPES) to efficiently explore the FES. The effectiveness of our pipeline is demonstrated and further compared with the common Markov State Model (MSM) approach on two model systems with increasing complexity: alanine dipeptide (Ala2) and deca-alanine (Ala10), underscoring its applicability across diverse biomolecular simulations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142273452","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

Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase 荧光光谱调谐机制的理论洞察：依赖黄素的细菌荧光素酶案例研究

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-19 DOI: 10.1021/acs.jctc.4c00950

Xiaodi Fu, Wenwen Diao, Yanling Luo, Yajun Liu, Zhanfeng Wang

{"title":"Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase","authors":"Xiaodi Fu, Wenwen Diao, Yanling Luo, Yajun Liu, Zhanfeng Wang","doi":"10.1021/acs.jctc.4c00950","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00950","url":null,"abstract":"Bioluminescence of bacteria is widely applied in biological imaging, environmental toxicant detection, and many other situations. Understanding the spectral tuning mechanism not only helps explain the diversity of colors observed in nature but also provides principles for bioengineering new color variants for practical applications. In this study, time-dependent density functional theory (TD-DFT) and quantum mechanics and molecular mechanics (QM/MM) calculations have been employed to understand the fluorescence spectral tuning mechanism of bacterial luciferase with a focus on the electrostatic effect. The spectrum can be tuned by both a homogeneous dielectric environment and oriented external electric fields (OEEFs). Increasing the solvent polarity leads to a redshift of the fluorescence emission maximum, λF, accompanied by a substantial increase in density. In contrast, applying an OEEF along the long axis of the isoalloxazine ring (X-axis) leads to a significant red- or blue-shift in λF, depending on the direction of the OEEF, yet with much smaller changes in intensity. The effect of polar solvents is directionless, and the red-shifts can be attributed to the larger dipole moment of the S1 state compared with that of the S0 state. However, the effect of OEEFs directly correlates with the difference dipole moment between the S1 and S0 states, which is directional and is determined by the charge redistribution upon deexcitation. Moreover, the electrostatic effect of bacterial luciferase is in line with the presence of an internal electric field (IEF) pointing in the negative X direction. Finally, the key residues that contribute to this IEF and strategies for modulating the spectrum through site-directed point mutations are discussed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246154","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

Parallel Implementation of the Density Matrix Renormalization Group Method Achieving a Quarter petaFLOPS Performance on a Single DGX-H100 GPU Node 在单个 DGX-H100 GPU 节点上实现四分之一 petaFLOPS 性能的密度矩阵重正化群方法并行实施

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-19 DOI: 10.1021/acs.jctc.4c00903

Andor Menczer, Maarten van Damme, Alan Rask, Lee Huntington, Jeff Hammond, Sotiris S. Xantheas, Martin Ganahl, Örs Legeza

{"title":"Parallel Implementation of the Density Matrix Renormalization Group Method Achieving a Quarter petaFLOPS Performance on a Single DGX-H100 GPU Node","authors":"Andor Menczer, Maarten van Damme, Alan Rask, Lee Huntington, Jeff Hammond, Sotiris S. Xantheas, Martin Ganahl, Örs Legeza","doi":"10.1021/acs.jctc.4c00903","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00903","url":null,"abstract":"We report cutting edge performance results on a single node hybrid CPU-multi-GPU implementation of the spin adapted ab initio Density Matrix Renormalization Group (DMRG) method on current state-of-the-art NVIDIA DGX-H100 architectures. We evaluate the performance of the DMRG electronic structure calculations for the active compounds of the FeMoco, the primary cofactor of nitrogenase, and cytochrome P450 (CYP) enzymes with complete active space (CAS) sizes of up to 113 electrons in 76 orbitals [CAS(113, 76)] and 63 electrons in 58 orbitals [CAS(63, 58)], respectively. We achieve 246 teraFLOPS of sustained performance, an improvement of more than 2.5× compared to the performance achieved on the DGX-A100 architectures and an 80× acceleration compared to an OpenMP parallelized implementation on a 128-core CPU architecture. Our work highlights the ability of tensor network algorithms to efficiently utilize high-performance multi-GPU hardware and shows that the combination of tensor networks with modern large-scale GPU accelerators can pave the way toward solving some of the most challenging problems in quantum chemistry and beyond.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246153","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

Excited-State Forces with the Gaussian and Augmented Plane Wave Method for the Tamm–Dancoff Approximation of Time-Dependent Density Functional Theory 用高斯和增强平面波方法计算时变密度泛函理论的激发态作用力

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-18 DOI: 10.1021/acs.jctc.4c00614

Beliz Sertcan Gökmen, Jürg Hutter, Anna-Sophia Hehn

{"title":"Excited-State Forces with the Gaussian and Augmented Plane Wave Method for the Tamm–Dancoff Approximation of Time-Dependent Density Functional Theory","authors":"Beliz Sertcan Gökmen, Jürg Hutter, Anna-Sophia Hehn","doi":"10.1021/acs.jctc.4c00614","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00614","url":null,"abstract":"Augmented plane wave methods enable an efficient description of atom-centered or localized features of the electronic density, circumventing high energy cutoffs and thus prohibitive computational costs of pure plane wave formulations. To complement existing implementations for ground-state properties and excitation energies, we present the extension of the Gaussian and augmented plane wave method to excited-state nuclear gradients within the Tamm–Dancoff approximation of time-dependent density functional theory and its implementation in the CP2K program package. Benchmarks for a test set of 35 small molecules demonstrate that maximum errors in the nuclear forces for excited states of singlet and triplet spin multiplicity are smaller than 0.1 eV/Å. The method is furthermore applied to the calculation of the zero-phonon line of defective hexagonal boron nitride. This spectral feature is reproduced with an error of 0.6 eV in comparison to GW–Bethe–Salpeter reference computations and 0.4 eV in comparison to experimental measurements. Accuracy assessments and applications thus demonstrate the potential use of the outlined developments for large-scale applications on excited-state properties of extended systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237185","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

Configuration Interaction in Frontier Molecular Orbital Basis for Screening the Spin-Correlated, Spatially Separated Triplet Pair State 1(T···T) Formation 用于筛选自旋相关、空间分离的三重对态 1(T---T) 形成的前沿分子轨道基础中的构型相互作用

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-18 DOI: 10.1021/acs.jctc.4c00473

Anurag Singh, Merle I. S. Röhr

引用次数: 0

From Many-Body Ab Initio to Effective Excitonic Models: A Versatile Mapping Approach Including Environmental Embedding Effects 从多体 Ab Initio 到有效激子模型：包括环境嵌入效应的多功能映射方法

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-18 DOI: 10.1021/acs.jctc.4c00756

Mauricio Rodriguez-Mayorga, Xavier Blase, Ivan Duchemin, Gabriele D’Avino

引用次数: 0

Halogen Bonding on Water─A Drop in the Ocean? 水的卤素键合--沧海一粟？

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-18 DOI: 10.1021/acs.jctc.4c00834

Marc U Engelhardt,Markus O Zimmermann,Marcel Dammann,Jason Stahlecker,Antti Poso,Thales Kronenberger,Conrad Kunick,Thilo Stehle,Frank M Boeckler

{"title":"Halogen Bonding on Water─A Drop in the Ocean?","authors":"Marc U Engelhardt,Markus O Zimmermann,Marcel Dammann,Jason Stahlecker,Antti Poso,Thales Kronenberger,Conrad Kunick,Thilo Stehle,Frank M Boeckler","doi":"10.1021/acs.jctc.4c00834","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00834","url":null,"abstract":"Halogen bonding is a valuable interaction in drug design, offering an unconventional way to influence affinity and selectivity by leveraging the halogen atoms' ability to form directional bonds. The present study evaluates halogen-water interactions within protein binding sites, demonstrating that targeting a water molecule via halogen bonding can in specific cases contribute beneficially to ligand binding. In solving and examining the crystal structure of 2-cyclopentyl-7-iodo-1H-indole-3-carbonitrile bound to DYRK1a kinase, we identified a notable iodine-water interaction, where water accepts a halogen bond with good geometric and energetic features. This starting point triggered further investigations into the prevalence of such interactions across various halogen-bearing ligands (chlorine, bromine, iodine) in the PDB. Using QM calculations (MP2/TZVPP), we highlight the versatility and potential benefits of such halogen-water interactions, particularly when the water molecule is a stable part of the binding site's structured environment. While the interaction energies with water are lower compared to other typical halogen bond acceptors, we deem this different binding strength essential for reducing desolvation costs. We suggest that \"interstitial\" water molecules, as stable parts of the binding site engaging in multiple strong interactions, could be prime targets for halogen bonding. Further systematic studies, combining high-resolution crystal structures and quantum chemistry, are required to scrutinize whether halogen bonding on water is more than a \"drop in the ocean\".","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245358","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

pyMSER─An Open-Source Library for Automatic Equilibration Detection in Molecular Simulations pyMSER--分子模拟中自动平衡检测的开源库

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-18 DOI: 10.1021/acs.jctc.4c00417

Felipe L. Oliveira, Binquan Luan, Pierre M. Esteves, Mathias Steiner, Rodrigo Neumann Barros Ferreira

{"title":"pyMSER─An Open-Source Library for Automatic Equilibration Detection in Molecular Simulations","authors":"Felipe L. Oliveira, Binquan Luan, Pierre M. Esteves, Mathias Steiner, Rodrigo Neumann Barros Ferreira","doi":"10.1021/acs.jctc.4c00417","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00417","url":null,"abstract":"Automated molecular simulations are used extensively for predicting material properties. Typically, these simulations exhibit two regimes: a dynamic equilibration part, followed by a steady state. For extracting observable properties, the simulations must first reach a steady state so that thermodynamic averages can be taken. However, as equilibration depends on simulation conditions, predicting the optimal number of simulation steps a priori is impossible. Here, we demonstrate the application of the Marginal Standard Error Rule (MSER) for automatically identifying the optimal truncation point in Grand Canonical Monte Carlo (GCMC) simulations. This novel automatic procedure determines the point at which a steady state is reached, ensuring that figures of merit are extracted in an objective, accurate, and reproducible fashion. In the case of GCMC simulations of gas adsorption in metal–organic frameworks, we find that this methodology reduces the computational cost by up to 90%. As MSER statistics are independent of the simulation method that creates the data, this library is, in principle, applicable to any time series analysis in which equilibration truncation is required. The open-source Python implementation of our method, pyMSER, is publicly available for reuse and validation at https://github.com/IBM/pymser.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247051","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