Journal of Chemical Theory and Computation最新文献_第10页

Molecular Ionization Energies from GW and Hartree-Fock Theory: Polarizability, Screening, and Self-Energy Vertex Corrections. 来自 GW 和 Hartree-Fock 理论的分子电离能：极化性、筛选和自能顶点校正。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-27 DOI: 10.1021/acs.jctc.4c00795

Charles H Patterson

{"title":"Molecular Ionization Energies from GW and Hartree-Fock Theory: Polarizability, Screening, and Self-Energy Vertex Corrections.","authors":"Charles H Patterson","doi":"10.1021/acs.jctc.4c00795","DOIUrl":"10.1021/acs.jctc.4c00795","url":null,"abstract":"Accurate prediction of electron removal and addition energies is essential for reproducing neutral excitation spectra in molecules using Bethe-Salpeter equation methods. A Hartree-Fock starting point for GW/BSE calculations, combined with a random phase approximation (RPA) polarizability in the screened interaction, W, is well-known to overestimate neutral excitation energies. Using a Hartree-Fock starting point, we apply several different approximations for W to molecules in the Quest-3 database [Loos et al. J. Chem. Theory Comput. 2020, 16, 1711]. W is calculated using polarizabilities in RPA and time-dependent HF approximations. Inclusion of screened electron-hole attraction in the polarizability yields valence ionization energies in better agreement with experimental values and ADC(3) calculations than the more commonly applied RPA polarizability. Quasiparticle weights are also in better agreement with ADC(3) values when electron-hole attraction is included in W. Shake-up excitations for the 1π levels in benzene and azines are indicated only when electron-hole attraction is included. Ionization energies derived from HF eigenvalues via Koopmans theorem for molecules with nitrogen or oxygen lone pairs have the largest differences from experimental values in the molecules considered, leading to incorrect ordering of nonbonding and π bonding levels. Inclusion of electron-hole attraction in the polarizability results in correct ordering of ionization energies and marked improvement in agreement with experimental data. Vertex corrections to the self-energy further improve agreement with experimental ionization energies for these localized states.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071400","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

Cavity-Mediated Enhancement of the Energy Transfer in the Reduced Fenna-Matthews-Olson Complex. 空腔介导的还原 Fenna-Matthews-Olson 复合物能量转移的增强。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-27 DOI: 10.1021/acs.jctc.4c00626

Luis E Herrera Rodríguez, Aarti Sindhu, Kennet J Rueda Espinosa, Alexei A Kananenka

{"title":"Cavity-Mediated Enhancement of the Energy Transfer in the Reduced Fenna-Matthews-Olson Complex.","authors":"Luis E Herrera Rodríguez, Aarti Sindhu, Kennet J Rueda Espinosa, Alexei A Kananenka","doi":"10.1021/acs.jctc.4c00626","DOIUrl":"10.1021/acs.jctc.4c00626","url":null,"abstract":"Strong light-matter interaction leads to the formation of hybrid polariton states and can alter the light-harvesting properties of natural photosynthetic systems without modifying their chemical structure. In the present study, we computationally investigate the effect of the resonant cavity on the efficiency and the rate of the population transfer in a quantum system coupled to the cavity and the dissipative environment. The parameters of the model system were chosen to represent the Fenna-Matthews-Olson natural light-harvesting complex reduced to the three essential sites. The dynamics of the total system was propagated using the hierarchical equations of motion. Our results show that the strong light-matter interaction can accelerate the population transfer process compared to the cavity-free case but at the cost of lowering the transfer efficiency. The transition to the strong coupling regime was found to coincide with the degeneracy of polariton eigenvalues. Our findings indicate the potential and the limit of tuning the energy transfer in already efficient natural light-harvesting systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142078389","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

Multi-GPU RI-HF Energies and Analytic Gradients─Toward High-Throughput Ab Initio Molecular Dynamics. 多 GPU RI-HF 能量和分析梯度--面向高通量 Ab Initio 分子动力学。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-27 DOI: 10.1021/acs.jctc.4c00877

Ryan Stocks, Elise Palethorpe, Giuseppe M J Barca

引用次数: 0

Bond Lengths and Dipole Moments of Diatomic Molecules under Isotropic Pressure with the XP-PCM and GOSTSHYP Models. 用 XP-PCM 和 GOSTSHYP 模型计算各向同性压力下二价原子分子的键长和偶极矩。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-27 DOI: 10.1021/acs.jctc.4c00665

Jochen Eeckhoudt, Mercedes Alonso, Paul Geerlings, Frank De Proft

{"title":"Bond Lengths and Dipole Moments of Diatomic Molecules under Isotropic Pressure with the XP-PCM and GOSTSHYP Models.","authors":"Jochen Eeckhoudt, Mercedes Alonso, Paul Geerlings, Frank De Proft","doi":"10.1021/acs.jctc.4c00665","DOIUrl":"10.1021/acs.jctc.4c00665","url":null,"abstract":"While high-pressure chemistry has a well-established history, methods to simulate pressure at the single-molecule level have been somewhat lacking. The current work aims at comparing two static models (XP-PCM and GOSTSHYP) to apply isotropic pressure to single molecules, focusing on the equilibrium bond length and electric dipole moment of diatomic molecules. Numerical challenges arising in the potential energy surface using the XP-PCM method were examined, and a pragmatic approach was followed to mitigate these. The definition of the cavity was scrutinized, and two approaches to retrieve the isotropic character that could potentially be lost when using the standard methodology were suggested. Subsequently, equilibrium bond lengths under pressure were evaluated, showing reasonable agreement between GOSTSHYP and XP-PCM, but some discrepancies persist. A Taylor series analysis introduced elsewhere was then applied to rationalize the observed trends in terms of the bond surface. Finally, the dipole moment was shown to be highly sensitive to the cavity definition, and qualitative agreement necessitates the use of our adapted procedure.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071395","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

Convergence Analysis of the Stochastic Resolution of Identity: Comparing Hutchinson to Hutch++ for the Second-Order Green's Function. 同一性随机解析的收敛性分析：二阶格林函数的哈钦森与哈奇++比较

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-27 DOI: 10.1021/acs.jctc.4c00862

Leopoldo Mejía, Sandeep Sharma, Roi Baer, Garnet Kin-Lic Chan, Eran Rabani

{"title":"Convergence Analysis of the Stochastic Resolution of Identity: Comparing Hutchinson to Hutch++ for the Second-Order Green's Function.","authors":"Leopoldo Mejía, Sandeep Sharma, Roi Baer, Garnet Kin-Lic Chan, Eran Rabani","doi":"10.1021/acs.jctc.4c00862","DOIUrl":"10.1021/acs.jctc.4c00862","url":null,"abstract":"Stochastic orbital techniques offer reduced computational scaling and memory requirements to describe ground and excited states at the cost of introducing controlled statistical errors. Such techniques often rely on two basic operations, stochastic trace estimation and stochastic resolution of identity, both of which lead to statistical errors that scale with the number of stochastic realizations (Nξ) as <math><msqrt><mrow><msubsup><mi>N</mi><mi>ξ</mi><mrow><mo>-</mo><mn>1</mn></mrow></msubsup></mrow></msqrt></math>. Reducing the statistical errors without significantly increasing Nξ has been challenging and is central to the development of efficient and accurate stochastic algorithms. In this work, we build upon recent progress made to improve stochastic trace estimation based on the ubiquitous Hutchinson's algorithm and propose a two-step approach for the stochastic resolution of identity, in the spirit of the Hutch++ method. Our approach is based on employing a randomized low-rank approximation followed by a residual calculation, resulting in statistical errors that scale much better than <math><msqrt><mrow><msubsup><mi>N</mi><mi>ξ</mi><mrow><mo>-</mo><mn>1</mn></mrow></msubsup></mrow></msqrt></math>. We implement the approach within the second-order Born approximation for the self-energy in the computation of neutral excitations and discuss three different low-rank approximations for the two-body Coulomb integrals. Tests on a series of hydrogen dimer chains with varying lengths demonstrate that the Hutch++-like approximations are computationally more efficient than both deterministic and purely stochastic (Hutchinson) approaches for low error thresholds and intermediate system sizes. Notably, for arbitrarily large systems, the Hutchinson-like approximation outperforms both deterministic and Hutch++-like methods.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071396","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

Range Separation of the Interaction Potential in Intermolecular and Intramolecular Symmetry-Adapted Perturbation Theory 分子间和分子内对称相适应扰动理论中相互作用势的范围分离

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 DOI: 10.1021/acs.jctc.4c00608

Du Luu, Clemence Corminboeuf, Konrad Patkowski

{"title":"Range Separation of the Interaction Potential in Intermolecular and Intramolecular Symmetry-Adapted Perturbation Theory","authors":"Du Luu, Clemence Corminboeuf, Konrad Patkowski","doi":"10.1021/acs.jctc.4c00608","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00608","url":null,"abstract":"Symmetry-adapted perturbation theory (SAPT) is a popular and versatile tool to compute and decompose noncovalent interaction energies between molecules. The intramolecular SAPT (ISAPT) variant provides a similar energy decomposition between two nonbonded fragments of the same molecule, covalently connected by a third fragment. In this work, we explore an alternative approach where the noncovalent interaction is singled out by a range separation of the Coulomb potential. We investigate two common splittings of the 1/r potential into long-range and short-range parts based on the Gaussian and error functions, and approximate either the entire intermolecular/interfragment interaction or only its attractive terms by the long-range contribution. These range separation schemes are tested for a number of intermolecular and intramolecular complexes. We find that the energy corrections from range-separated SAPT or ISAPT are in reasonable agreement with complete SAPT/ISAPT data. This result should be contrasted with the inability of the long-range multipole expansion to describe crucial short-range charge penetration and exchange effects; it shows that the long-range interaction potential does not just recover the asymptotic interaction energy but also provides a useful account of short-range terms. The best consistency is attained for the error-function separation applied to all interaction terms, both attractive and repulsive. This study is the first step toward a fragmentation-free decomposition of intramolecular nonbonded energy.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161124","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 Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions. 针对溶解和裸露钠离子和氯离子的粗粒 SPICA 改造。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 Epub Date: 2024-08-19 DOI: 10.1021/acs.jctc.4c00529

Janak Prabhu, Matteo Frigerio, Emanuele Petretto, Pablo Campomanes, Stefan Salentinig, Stefano Vanni

{"title":"A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.","authors":"Janak Prabhu, Matteo Frigerio, Emanuele Petretto, Pablo Campomanes, Stefan Salentinig, Stefano Vanni","doi":"10.1021/acs.jctc.4c00529","DOIUrl":"10.1021/acs.jctc.4c00529","url":null,"abstract":"Aqueous ionic solutions are pivotal in various scientific domains due to their natural prevalence and vital roles in biological and chemical processes. Molecular dynamics has emerged as an effective methodology for studying the dynamic behavior of these systems. While all-atomistic models have made significant strides in accurately representing and simulating these ions, the challenge persists in achieving precise models for coarse-grained (CG) simulations. Our study introduces two optimized models for sodium and chloride ions within the nonpolarizable surface property fitting coarse-grained force field (SPICA-FF) framework. The two models represent solvated ions, such as the original FF model, and unsolvated or bare ions. The nonbonded Lennard-Jones interactions were reparameterized to faithfully reproduce bulk properties, including density and surface tension, in sodium chloride solutions at varying concentrations. Notably, these optimized models replicate experimental surface tensions at high ionic strengths, a property not well-captured by the ions of the original model in the SPICA-FF. The optimized unsolvated model also proved successful in reproducing experimental osmotic pressure. Additionally, the newly reparameterized ion models capture hydrophobic interactions within sodium chloride solutions and show qualitative agreement when modeling structural changes in phospholipid bilayers, aligning with experimental observations. For aqueous solutions, these optimized models promise a more precise representation of the ion behavior.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11391577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142002968","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

Driven Self-Assembly of Patchy Particles Overcoming Equilibrium Limitations 克服平衡限制的斑状颗粒驱动型自组装

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 DOI: 10.1021/acs.jctc.4c01118

Shubhadeep Nag, Gili Bisker

引用次数: 0

Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance 随机相位逼近相关能的静态子空间逼近：实现与性能

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 DOI: 10.1021/acs.jctc.4c00807

Daniel Weinberg, Olivia A. Hull, Jacob M. Clary, Ravishankar Sundararaman, Derek Vigil-Fowler, Mauro Del Ben

{"title":"Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance","authors":"Daniel Weinberg, Olivia A. Hull, Jacob M. Clary, Ravishankar Sundararaman, Derek Vigil-Fowler, Mauro Del Ben","doi":"10.1021/acs.jctc.4c00807","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00807","url":null,"abstract":"Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity. However, this is now a surmountable barrier due to the advances in computational power available, in particular through modern GPU-based supercomputers. In this work, we describe the implementation of RPA calculations within BerkeleyGW and show its favorable computational performance on large complex systems relevant for catalysis and electrochemistry applications. Our implementation builds off of the static subspace approximation which, by employing a compressed representation of the frequency dependent polarizability, enables the evaluation of the RPA correlation energy with significant acceleration and systematically controllable accuracy. We find that the computational cost of calculating the RPA correlation energy scales only linearly with system size for systems containing up to 50 thousand bands, and is expected to scale quadratically thereafter. We also show excellent strong scaling results across several supercomputers, demonstrating the performance and portability of this implementation.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142161126","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

The Localized Active Space Method with Unitary Selective Coupled Cluster 具有单元选择性耦合簇的局部主动空间法

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-10 DOI: 10.1021/acs.jctc.4c00528

Abhishek Mitra, Ruhee D’Cunha, Qiaohong Wang, Matthew R. Hermes, Yuri Alexeev, Stephen K. Gray, Matthew Otten, Laura Gagliardi

{"title":"The Localized Active Space Method with Unitary Selective Coupled Cluster","authors":"Abhishek Mitra, Ruhee D’Cunha, Qiaohong Wang, Matthew R. Hermes, Yuri Alexeev, Stephen K. Gray, Matthew Otten, Laura Gagliardi","doi":"10.1021/acs.jctc.4c00528","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00528","url":null,"abstract":"We introduce a hybrid quantum-classical algorithm, the localized active space unitary selective coupled cluster singles and doubles (LAS-USCCSD) method. Derived from the localized active space unitary coupled cluster (LAS-UCCSD) method, LAS-USCCSD first performs a classical LASSCF calculation, then selectively identifies the most important parameters (cluster amplitudes used to build the multireference UCC ansatz) for restoring interfragment interaction energy using this reduced set of parameters with the variational quantum eigensolver method. We benchmark LAS-USCCSD against LAS-UCCSD by calculating the total energies of (H2)2, (H2)4, and trans-butadiene, and the magnetic coupling constant for a bimetallic compound [Cr2(OH)3(NH3)6]3+. For these systems, we find that LAS-USCCSD reduces the number of required parameters and thus the circuit depth by at least 1 order of magnitude, an aspect which is important for the practical implementation of multireference hybrid quantum-classical algorithms like LAS-UCCSD on near-term quantum computers.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142171432","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