Journal of Chemical Theory and Computation最新文献_第4页

FC2DES: Modeling 2D Electronic Spectroscopy for Harmonic Hamiltonians. 谐波哈密顿量的二维电子能谱建模。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-29 DOI: 10.1021/acs.jctc.5c00349

Lucas Allan, Tim J Zuehlsdorff

{"title":"FC2DES: Modeling 2D Electronic Spectroscopy for Harmonic Hamiltonians.","authors":"Lucas Allan, Tim J Zuehlsdorff","doi":"10.1021/acs.jctc.5c00349","DOIUrl":"10.1021/acs.jctc.5c00349","url":null,"abstract":"Two-dimensional electronic spectroscopy (2DES) can provide detailed insight into the energy transfer and relaxation dynamics of chromophores by directly measuring the nonlinear response function of the system. However, experiments are often difficult to interpret, and the development of computationally affordable approaches to simulate experimental signals is desirable. For linear spectroscopy, optical spectra of small to medium-sized molecules can be efficiently calculated in the Franck-Condon approach. Approximating the nuclear degrees of freedom as harmonic around the ground- and excited-state minima, closed-form expressions for the exact finite-temperature linear response function can be derived using known solutions for the propagation operator between normal mode coordinate sets, fully accounting for Duschinsky mode-mixing effects. In the present work, we demonstrate that a similar approach can be utilized to yield analogous closed-form expression for the finite-temperature nonlinear (third-order) response function of harmonic nuclear Hamiltonians. The resulting approach, named FC2DES, is implemented on graphics processing units, allowing efficient computations of 2DES signals for medium-sized molecules containing hundreds of normal modes. Benchmark comparisons against the widely used cumulant method for computing 2DES signals are performed on small model systems, as well as the nile red molecule. We highlight the advantages of the FC2DES approach, especially in systems with moderate Duschinsky mode mixing and for long delay times in the nonlinear response function, where low-order cumulant approximations are shown to fail.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5625-5641"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180458","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

Anharmonic Vibrational States of Double-Well Potentials in the Solid State from DFT Calculations. 用DFT计算固态中双阱势的非调和振动态。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-03-10 DOI: 10.1021/acs.jctc.4c01394

Davide Mitoli, Maria Petrov, Jefferson Maul, William B Stoll, Michael T Ruggiero, Alessandro Erba

{"title":"Anharmonic Vibrational States of Double-Well Potentials in the Solid State from DFT Calculations.","authors":"Davide Mitoli, Maria Petrov, Jefferson Maul, William B Stoll, Michael T Ruggiero, Alessandro Erba","doi":"10.1021/acs.jctc.4c01394","DOIUrl":"10.1021/acs.jctc.4c01394","url":null,"abstract":"We introduce a general approach for the simulation of quantum vibrational states of (symmetric and asymmetric) double-well potentials in molecules and materials for thermodynamic and spectroscopic applications. The method involves solving the nuclear Schrödinger equation associated with a one-mode potential of the type V(Q) = aQ2 + bQ3 + cQ4 (with a < 0 and c > 0) and thus explicitly includes nuclear quantum effects. The potential, V(Q), is obtained from density functional theory (DFT) calculations performed at displaced nuclear configurations along the selected normal mode, Q. The strategy has been implemented into the Crystal electronic structure package and allows for (i) the use of many density functional approximations, including hybrid ones, and (ii) integration with a quasi-harmonic module. The method is applied to the spectroscopic characterization of soft lattice modes in two phases of the molecular crystal of thiourea: a low-temperature ferroelectric phase and a high-temperature paraelectric phase. Signature peaks associated with structural changes between the two phases are found in the terahertz region of the electromagnetic spectrum, which exhibit strong anharmonic character in their thermal evolution, as measured by temperature-dependent terahertz time-domain spectroscopy.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5365-5371"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595808","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

A Quantum Computational Method for Corrosion Inhibition. 一种缓蚀的量子计算方法。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-28 DOI: 10.1021/acs.jctc.5c00469

Naman Jain, Rosa Di Felice

引用次数: 0

Multi-Level Coupled-Cluster Description of Crystal Lattice Energies. 晶体点阵能量的多级耦合簇描述。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-29 DOI: 10.1021/acs.jctc.5c00428

Krystyna Syty, Grzegorz Czekało, Khanh Ngoc Pham, Marcin Modrzejewski

{"title":"Multi-Level Coupled-Cluster Description of Crystal Lattice Energies.","authors":"Krystyna Syty, Grzegorz Czekało, Khanh Ngoc Pham, Marcin Modrzejewski","doi":"10.1021/acs.jctc.5c00428","DOIUrl":"10.1021/acs.jctc.5c00428","url":null,"abstract":"The many-body expansion (MBE) of the lattice energy enables an ab initio description of molecular solids using correlated wave function approximations. However, the practical application of MBE requires computing the large number of n-body contributions efficiently. To this end, we employ a multi-level coupled-cluster approach which adapts the approximation level based on interaction type and intermolecular distance. The high-level method, including connected triple excitations, is applied only to monomer relaxation and dimer interactions roughly within the first and second coordination shells. Long-range dimers and trimers are treated using a simplified coupled-cluster description based on the random-phase approximation (RPA). A key feature is an energy correction which mitigates the underbinding error of the base RPA. Convergence to the bulk limit is accelerated by the addition of the periodic Hartree-Fock correction. The proposed approach is validated against recent diffusion Monte Carlo reference data for the X23 data set, achieving a mean absolute error of 3.1 kJ/mol, i.e., chemical accuracy for absolute lattice energies.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5533-5544"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172215","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

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-23 DOI: 10.1021/acs.jctc.5c00322

Chenyang Li, Xiaoxue Wang, Huanchen Zhai, Wei-Hai Fang

{"title":"Driven Similarity Renormalization Group with a Large Active Space: Applications to Oligoacenes, Zeaxanthin, and Chromium Dimer.","authors":"Chenyang Li, Xiaoxue Wang, Huanchen Zhai, Wei-Hai Fang","doi":"10.1021/acs.jctc.5c00322","DOIUrl":"10.1021/acs.jctc.5c00322","url":null,"abstract":"We present a new implementation of the driven similarity renormalization group (DSRG) based on a density matrix renormalization group (DMRG) reference. The explicit build of high-order reduced density matrices is avoided by forming matrix-product-state compressed intermediates. This algorithm facilitates the application of DSRG second- and third-order perturbation theories to dodecacene with an active space of 50 electrons in 50 orbitals. This active space appears the largest employed to date within the framework of internally contracted multireference formalism. The DMRG-DSRG approach is applied to several challenging systems, including the singlet-triplet gaps (ΔST) of oligoacenes ranging from naphthalene to dodecacene, the vertical excitation energies of zeaxanthin, and the ground-state potential energy curve (PEC) of Cr2 molecule. Our best estimate for the vertical ΔST of dodecacene is 0.22 eV, showing an excellent agreement with that of the linearized adiabatic connection method (0.24 eV). For zeaxanthin, all DSRG schemes suggest the order of <math><mn>2</mn><mspace></mspace><mmultiscripts><msubsup><mi>A</mi><mi>g</mi><mo>-</mo></msubsup><mprescripts></mprescripts><none></none><mn>1</mn></mmultiscripts><mo><</mo><mn>1</mn><mspace></mspace><mmultiscripts><msubsup><mi>B</mi><mi>u</mi><mo>+</mo></msubsup><mprescripts></mprescripts><none></none><mn>1</mn></mmultiscripts><mo><</mo><mn>1</mn><mspace></mspace><mmultiscripts><msubsup><mi>B</mi><mi>u</mi><mo>-</mo></msubsup><mprescripts></mprescripts><none></none><mn>1</mn></mmultiscripts></math> for excited states. Both the equilibrium and the shoulder regions of the Cr2 PEC are reasonably reproduced by the linearized DSRG with one- and two-body operators.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5445-5456"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126131","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

Analytical Gradient Theory for Density-Fitted Exact Two-Component Hartree-Fock, State-Specific Complete Active Space Self-Consistent Field, and Second-Order Møller-Plesset Perturbation Theories. 密度拟合精确双分量Hartree-Fock的解析梯度理论，状态特定完全活动空间自洽场，二阶Møller-Plesset微扰理论。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-29 DOI: 10.1021/acs.jctc.5c00405

Jae Woo Park

{"title":"Analytical Gradient Theory for Density-Fitted Exact Two-Component Hartree-Fock, State-Specific Complete Active Space Self-Consistent Field, and Second-Order Møller-Plesset Perturbation Theories.","authors":"Jae Woo Park","doi":"10.1021/acs.jctc.5c00405","DOIUrl":"10.1021/acs.jctc.5c00405","url":null,"abstract":"The exact two-component (X2C) relativistic quantum chemistry calculations can be used to describe scalar relativistic effects and spin-orbit couplings at reasonable computational cost. However, they have limited applicability to wave function-based quantum chemistry methods, particularly geometric optimizations and dynamics simulations, owing to the high computational demands of these methods in sizable molecular systems. In this work, we report our implementation of an analytical gradient algorithm with a density-fitting approximation for Hartree-Fock, state-specific complete active space self-consistent field (CASSCF), and second-order Møller-Plesset perturbation theory (MP2) calculations with the X2C one-electron Hamiltonian. This implementation uses a second-order orbital optimization scheme to facilitate convergence in X2C-CASSCF calculations, as well as a response (Z-vector) equation for evaluation of the X2C-MP2 nuclear gradient. We demonstrate the applicability of the algorithm for optimization of the geometry of Ir(ppy)2(bpy)+ and evaluate its computational cost and parallelization (multithreading) efficiency.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5523-5532"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179690","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

PHAST-MBD: Implementing Many-Body Dispersion in the PHAST 2.0 Potential, Results for Noble Gases. PHAST- mbd：在PHAST 2.0电位中实现多体色散，惰性气体的结果。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 DOI: 10.1021/acs.jctc.5c00448

Matthew Mostrom, Adam Hogan, Logan Ritter, William Morris, Brian Space

{"title":"PHAST-MBD: Implementing Many-Body Dispersion in the PHAST 2.0 Potential, Results for Noble Gases.","authors":"Matthew Mostrom, Adam Hogan, Logan Ritter, William Morris, Brian Space","doi":"10.1021/acs.jctc.5c00448","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00448","url":null,"abstract":"A recently published empirical force field (herein PHAST or PHAST 2.0) is employed in its many-body dispersion-corrected form (PHAST-MBD) to examine the effects of collective dispersion interactions. Rare gases are used as a systematic way to test increasing importance of van der Waals attractions in systems dominated by repulsion-dispersion that are a challenge to extant force fields. The effects of many-body dispersion were studied for liquid and supercritical fluid regime for the series Neon, Argon, Krypton and Xenon. The PHAST force field is a condensed phase atomistic molecular modeling potential that includes contributions from repulsion-dispersion, permanent electrostatics, and many-body polarization. Each of these pieces is physics based and seeks to mimic their constituent first-principles counterparts with as few fitting parameters as possible. Critically, it is built to reproduce accurate gas phase pair interactions. This facilitates the efficacy of mixing rules for unlike interactions while many-body effects are added via explicit polarization and dispersion models. The effectiveness of PHAST-MBD is demonstrated calculating rare gas densities as compared to experiment over a wide pressure range. Pair potentials fail systematically at high pressure and density as dispersion grows while PHAST-MBD reproduces experiment in all regimes. This is strong evidence in favor of the PHAST 2.0 paradigm of physically motivated empirical potentials that reproduce gas phase interactions and facilitate accurate mixing rules with many-body effects included explicitly. This work suggests a hybrid future approach that will be adopted in PHAST-MBD that keeps the accurate PHAST pair interactions and only includes many-body terms via the coupled dipole method (CDM); such an approach avoids the issues identified here that the CDM many body van der Waals (MBVDWs) formalism has reasonable but nonoptimal implicit mixing rules and can alter pair potentials.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256714","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

Approximation to Second Order N-Electron Valence State Perturbation Theory: Limiting the Wave Function within Singles. 二阶n电子价态摄动理论的近似：限制波函数在单波内。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-28 DOI: 10.1021/acs.jctc.5c00582

Yang Guo, Katarzyna Pernal

引用次数: 0

Quantifying Cooperativity through Binding Free Energies in Molecular Glue Degraders. 用结合自由能量化分子胶水降解剂的协同性。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-06 DOI: 10.1021/acs.jctc.5c00064

Balint Dudas, Christina Athanasiou, Juan Carlos Mobarec, Edina Rosta

{"title":"Quantifying Cooperativity through Binding Free Energies in Molecular Glue Degraders.","authors":"Balint Dudas, Christina Athanasiou, Juan Carlos Mobarec, Edina Rosta","doi":"10.1021/acs.jctc.5c00064","DOIUrl":"10.1021/acs.jctc.5c00064","url":null,"abstract":"Molecular glues represent a novel therapeutic modality facilitating the stabilization of protein-protein interactions (PPIs), thus enabling the targeting of previously \"undruggable\" proteins. We develop a computational procedure to screen for molecular glues using a pathway-independent free energy calculation method for accurately assessing the cooperativity. We employ a combined ligand and protein free energy perturbation (FEP) method to calculate the cooperative effect of a ligand for ternary binding. We study the cooperative binding mechanisms of molecular glue degraders, specifically cereblon (CRBN) modulators targeting Ikaros family zinc finger 2 (IKZF2), a transcription factor implicated in cancer immunotherapy. We present a comprehensive computational protocol for screening large molecular libraries to identify potent molecular glues. By leveraging cooperative binding principles in ternary complex formation, our approach effectively predicts ligand-induced PPIs and their degradation potential. Benchmarking against experimental data for CRBN-Ikaros complexes, our protocol demonstrates high accuracy in identifying superior molecular glues, highlighting L4 and L5 as top performers. Furthermore, our high-throughput screening identified novel candidates from extensive chemical libraries, validated through advanced FEP+ simulations. This study not only underscores the transformative potential of molecular glues in targeted protein degradation but also sets the stage for their broader application across diverse protein targets, paving the way for innovative therapeutic strategies in drug discovery.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5712-5723"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143952402","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

Spin-Symmetry Projected Constrained Unrestricted Hartree-Fock. 自旋对称投影约束不受限制Hartree-Fock。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-21 DOI: 10.1021/acs.jctc.5c00068

Amir Ayati, Hugh G A Burton, Stijn De Baerdemacker

引用次数: 0