Journal of Chemical Theory and Computation最新文献

{"title":"Rigid Molecule Packing Similarity Index Based on Dual Quaternions","authors":"Hazel Vázquez-Hernández,Joel Ireta","doi":"10.1021/acs.jctc.6c01293","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01293","url":null,"abstract":"Mapping comparisons between periodic 3D rigid-molecule (or fixed molecular conformer) arrangements to a scalar value, typically referred to as a similarity index, is essential in fields such as crystal structure prediction (CSP) and molecular engineering. Evaluating crystal lattice similarity is crucial for filtering random structure pools and differentiating polymorphs. Here, we introduce a configurational similarity index based on dual quaternions to simultaneously capture relative rigid-molecule (fixed molecular-conformer) positions and orientations in crystal lattices. Within this framework, pairs of molecular configurations with known atomic correspondence are compared using a metric derived from the product of their dual quaternions. After validating the metric on water dimer configurations, we employ it to contrast clusters of molecules representing different molecular packing motifs. This pairwise comparison is condensed into a single index, Drt, which measures total crystal packing similarity. Using Drt to screen pools of randomly generated structures for oxalic acid, maleic hydrazide, and formamide, we successfully retrieve packing motifs similar to the experimental references. Upon geometry optimization, these identified structures converge to the corresponding optimized experimental configurations, highlighting the reliability of this metric for integration into CSP methodologies.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"16 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360521","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}

{"title":"Real-Time Multidimensional Spectroscopy for Organic Molecules in Cavities: Dark-State Dynamics and Optical Signatures","authors":"Yihe Xu,Zhedong Zhang","doi":"10.1021/acs.jctc.6c01245","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01245","url":null,"abstract":"Ultrafast multidimensional spectroscopy has emerged as a powerful tool for probing organic exciton–polaritons in optical microcavities, revealing rich dynamical properties at the femtosecond timescale. However, the dark states and their crosstalk with polaritons still remain challenging, due to the ultrafast dynamics and optical responses that lead to large ambiguities in the interpretation of time-domain spectroscopic experiments, which signify the properties of highly excited states. Here, we develop a fully quantum-mechanical approach to simulate ultrafast two-dimensional polaritonic spectroscopy (2DPS) of organic systems with strong vibronic coupling. By incorporating the time-dependent density matrix renormalization group (TD-DMRG) method into spectroscopic simulations, our approach enables direct visualization of dark-state dynamics and their excited-state absorption (ESA) signals in organic molecules confined in Fabry–Pérot cavities with realistic vibrational environments. Our results reveal two distinct classes of dark states, namely, lower-polariton (LP) polarons and dark polaritons, which are clearly distinguishable from bright polaritons in 2DPS signals. Time-resolved spectra further exhibit their relaxation dynamics, showing by separated timescales and pathways for energy migration, e.g., ∼200 fs for polaron decoupling. Furthermore, these findings provide new theoretical insights into light-induced phases in organic materials and offer guidance for the design of polaritonic devices.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"14 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149360585","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}

{"title":"Systematic Improvement of Trial States in Phaseless Auxiliary-Field Quantum Monte Carlo","authors":"Eirik F. Kjønstad,Yann Damour,Sandeep Sharma,Garnet Kin-Lic Chan","doi":"10.1021/acs.jctc.6c01750","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01750","url":null,"abstract":"We extend the use of coupled cluster (CC) trial states in the phaseless auxiliary-field quantum Monte Carlo (AFQMC) method beyond single and double excitations to include both triple and quadruple excitations. With this AFQMC/CC hierarchy, we are able to systematically benchmark the method’s performance on molecular systems as the quality of the trial is improved. Our results show that the phaseless AFQMC energy improves systematically and is typically significantly more accurate than the energy of the underlying trial state. However, the relative improvement compared to the trial CC energy decreases as we ascend the CC hierarchy. As the CC wave function is usually further approximated when used as an AFQMC trial, we also explore the relationship between the components of the CC wave function and the resulting AFQMC/CC error. Our results suggest that improving the representation of the CC wave function in the AFQMC trial does not always lower the bias even when it increases the fidelity of the trial with the exact ground state.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"262 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359389","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}

{"title":"Free Energy Landscape Perturbation for Estimating Mutation-Induced Population Shifts from Reference Molecular Dynamics Ensembles","authors":"Tatum E. Murdock,Benjamin P. Brown","doi":"10.1021/acs.jctc.6c01098","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01098","url":null,"abstract":"Mutations can alter protein function by redistributing probability among conformational states, even when structural changes are modest. Directly estimating a perturbed conformational free energy landscape with molecular dynamics is expensive because each mutation requires a new converged simulation. Here, we introduce Free Energy Landscape Perturbation (FELP), a state-local reweighting framework that estimates mutation-induced population shifts from a reference ensemble. FELP partitions a reference trajectory into discrete microstates, evaluates restrained reference-to-perturbed energy differences for configurations sampled within each state, and combines spatially regularized state-local Zwanzig factors with the reference state probabilities to estimate the perturbed state distribution. FELP estimates how a perturbation changes the relative probabilities of conformational basins and reports effective-sample and overlap diagnostics that identify when the predicted shift lacks support in the sampled reference ensemble. We describe the FELP estimator, its implementation, and its performance on capped dipeptides, chignolin, T4 lysozyme, and the EGFR kinase domain. FELP is intended for perturbations that reshape populations within a sufficiently sampled reference landscape, providing a practical bridge between local alchemical energy evaluation and ensemble-level mechanistic interpretation.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"5 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359426","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}

{"title":"DEGAUSS-3p: A Three-Site Water Model from Soft Gaussian-Charge Electrostatics and a Rare-Gas-Informed Double-Exponential Potential","authors":"Zhen Huang,Yong Duan,Xiongwu Wu,Ray Luo","doi":"10.1021/acs.jctc.6c01678","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01678","url":null,"abstract":"Classical fixed-charge water models combine point-charge Coulomb interactions, which diverge at short distances and neglect charge penetration, with a Lennard–Jones 12–6 repulsion whose r–12 dependence does not reflect the near-exponential decay of quantum-mechanical exchange repulsion. The DEGAUSS force field replaces both with finite, Gaussian-smeared charge densities and a double-exponential van der Waals potential, with adjustable short-range softness and rare-gas-informed starting values for the double-exponential exponents. DEGAUSS-3p is parametrized directly for liquid water using these interaction forms. The resulting rigid three-site model captures the density anomaly and tetrahedral organization of liquid water, with a balanced description of structural, thermodynamic, and dynamic properties. Gaussian electrostatics and double-exponential repulsion thus provide an effective basis for modeling liquid water with finite interactions at short distances.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"18 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149359390","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}

{"title":"Capturing Transient Polaron Formation Dynamics: A Time-Dependent Polaron Transformation Approach","authors":"Zeyu Dong,Wenxiang Ying,Feng-Feng Song,Peng Zhang,Hanggai Nuomin","doi":"10.1021/acs.jctc.6c01636","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01636","url":null,"abstract":"Static polaron transformations impose an equilibrium environmental displacement at the initial time and can therefore misrepresent transient polaron formation. We introduce a time-dependent (TD) polaron transformation that describes the dynamical formation of polarons. We first present the TD polaron transformation for the spin–boson model via an infinite sequence of interaction-picture transformations. Each transformation in the sequence cancels the residual term generated by its predecessor; the ordered transformation sequence combines exactly into a displacement operator whose amplitude is zero at the initial time. We then generalize this recursive elimination to any suitably partitioned Hamiltonian. When the generated operator algebra closes, the ordered sequence of transformations reduces to an exact closed form; otherwise, a truncated sequence provides a systematic short-time approximation. For the transformed spin–boson Hamiltonian, we derive a second-order Nakajima–Zwanzig quantum master equation with two-time bath correlation functions. We benchmark this quantum master equation against numerically exact matrix-product-state dynamics and hierarchical equations of motion using Landau–Zener sweeps coupled to a thermal bath, whose tunable crossing time acts as a clock for polaron formation. We find that the TD-polaron quantum master equation outperforms the static formulation in regimes where transient polaron formation competes with the system evolution. The TD-polaron transformation is therefore applicable to nonequilibrium processes such as sudden charge injection, while the underlying sequential elimination scheme extends to other suitably partitioned Hamiltonians.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"379 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305311","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}

{"title":"Smoothed Truncated Coulomb Potential for Periodic Gaussian-Basis Hartree–Fock Exchange","authors":"Gengzhi Yang,Aamy Bakry,Hong-Zhou Ye","doi":"10.1021/acs.jctc.6c01829","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01829","url":null,"abstract":"Truncated Coulomb (TC) potentials reduce finite-size errors and accelerate thermodynamic-limit convergence in periodic Hartree–Fock (HF) calculations, but their use with Gaussian basis sets is complicated by the evaluation of electron repulsion integrals (ERIs), particularly for nonspherical truncation domains and all-electron calculations. We introduce the smoothed truncated Coulomb (sTC) potential as a systematically improvable approximation to a parent TC potential. A real-space Gaussian convolution smooths the sharp truncation boundary, and a single dimensionless parameter, η, controls the width of the smoothing window, which can be tightened to systematically approach the TC reference. The smoothing by sTC enables a dual-space algorithm for evaluating periodic Gaussian-basis ERIs that requires neither a large plane-wave basis nor new molecular integral kernels and is applicable to both pseudopotential and all-electron calculations, including the important Wigner–Seitz-cell truncation boundaries. Benchmarks spanning insulating, semiconducting, layered, metallic, and molecular-crystal systems show that sTC-based HF closely reproduces TC results in pseudopotential calculations and extends TC-quality calculations to all-electron settings. Across these systems, sTC substantially improves thermodynamic-limit convergence relative to the probe-charge Ewald method while remaining practical for all-electron calculations in which direct TC-based calculations are computationally challenging.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"14 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305310","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}

{"title":"Adaptive Substructure Sampling for Molecules with Flexible Alkyl Substituents","authors":"Lukas S. Rindt,Philipp Pracht","doi":"10.1021/acs.jctc.6c01611","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01611","url":null,"abstract":"The exponential growth of conformational space in molecules with flexible side chains presents a fundamental bottleneck for atomistic sampling methods. A large fraction of this complexity arises from weakly coupled, quasi-degenerate torsional degrees of freedom that contribute little to chemically meaningful structural diversity while dramatically increasing computational cost. We present a substructure-based conformational sampling framework that separates flexible side chains from the molecular core at the graph level. Detached substituents are replaced by capped surrogate groups, enabling independent sampling of subsystems and systematic reconstruction of approximate full-molecule ensembles. A limiting variant neglects explicit sampling of the side chains and assumes extended reference conformations. This approximation is rationalized using high-level electronic-structure data for linear alkyl chains, which show that folded conformations become thermodynamically competitive only beyond well-defined lengths, particularly in solution. The approach is implemented within CREST and reduces the effective dimensionality of conformational sampling for molecules with extended flexible substituents.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"2 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149304895","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}

{"title":"A Two-Bead-Per-Amino Acid Coarse-Grained MD Model with Hydrogen Bonding (2BPA-HB) to Probe DNAJB6b-Mediated Suppression of Polyglutamine Aggregation in Huntington’s Disease","authors":"Vasista Adupa,Johan D. Polet,Maurice Dekker,Patrick R. Onck","doi":"10.1021/acs.jctc.6c01461","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01461","url":null,"abstract":"Polyglutamine (polyQ) aggregation plays a central role in several neurodegenerative diseases, including Huntington’s disease. DNAJB6b, a molecular chaperone involved in protein quality control, is known to efficiently suppress polyQ aggregation, but its antiaggregation mechanism remains unclear. In this work, we investigate the interaction between DNAJB6b and the polyQ region (Q48) of mutant Huntingtin Exon 1 (mHttEx1) using a custom-built coarse-grained molecular dynamics model. The model incorporates a two-bead-per-amino-acid representation with hydrogen bonding (termed 2BPA-HB) and is calibrated against all-atom molecular dynamics data in terms of geometry, hydrophobicity, and hydrogen bonding. The model reproduces the tertiary structure of DNAJB6b and its interactions with Q48 and reveals an inverse correlation between DNAJB6b concentration and Q48 aggregation propensity. Our simulations show that DNAJB6b undergoes cocondensation with polyQ molecules, thereby shielding the polyQ from forming the intermolecular hydrogen bonds necessary for amyloid formation. The 2BPA-HB CGMD model enables efficient exploration of DNAJB6b conformations, supporting future studies of chaperone-mediated aggregation suppression and therapeutic development.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"12 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305312","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}

{"title":"Systematic Correction of Kohn–Sham-Derived Excitation Energies via a Quantum Monte Carlo Approach","authors":"Kayahan Saritas,Jaron T. Krogel,Fernando A. Reboredo","doi":"10.1021/acs.jctc.6c01490","DOIUrl":"https://doi.org/10.1021/acs.jctc.6c01490","url":null,"abstract":"Developing and applying accurate methods for the calculation of excitation spectra remains an outstanding problem in electronic structure. Here, we present the first application of auxiliary boson-corrected diffusion Monte Carlo (ABCDMC) to ab initio systems of atoms and ions in the second row of the periodic table and molecules. In ABCDMC, the many-body electron–electron correction to the density functional theory (DFT) exchange-correlation energy is captured statistically via an auxiliary boson ground state obtained with diffusion Monte Carlo. Moreover, the kinetic-energy contribution to correlation is included up to the limit of a finite active-space expansion. The excitations are described as a product of a linear combination of Fermionic functions derived from DFT and the auxiliary boson state. The corrections to the DFT-derived excitation spectra are obtained by statistically sampling an observable on the auxiliary boson state. We benchmark ABCDMC on the experimental excitation spectra of second-row neutral atoms (Li–F), cations (Be+–Ne+), dications (B2+–Na2+), and the carbon dimer against full configuration interaction (FCI). For the atomic set (96 excitations), ABCDMC improves local density approximation excitation energies for low-lying single excitations up to the n = 3 shell, reducing the mean signed error from −0.059 to less than 0.001 Ha and the root-mean-square deviation (RMSD) from 0.102 to 0.037 Ha using at most 25 determinants per species. An O+ convergence study shows systematic improvement as the determinant space is enlarged and double excitations are included. For the carbon dimer, ABCDMC matches FCI within 9 mHa RMSD for 11 low-lying excitations using 16 determinants. Overall, these results indicate that ABCDMC is particularly promising for the calculation of low-energy excitations with very small active spaces. However, the method is not designed to correct basis-set errors associated with diffuse wave functions and the cusp condition errors at the core in atomic systems using Gaussian bases which are also present in the underlying DFT. The compact determinant expansions used here suggest that ABCDMC may be useful for larger systems and, in future work, for correcting DFT band structures of solids, provided a sparse multireference basis can be constructed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"12 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2026-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149305314","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}