Journal of Chemical Theory and Computation最新文献

{"title":"Structural and Energetic Analysis of the CmABCB1 Substrate Transport","authors":"Kei Moritsugu*,&nbsp;, ,&nbsp;Ryuji Ishida,&nbsp;, ,&nbsp;Takumi Someya,&nbsp;, ,&nbsp;Akinori Kidera,&nbsp;, ,&nbsp;Hiroaki Kato,&nbsp;, and ,&nbsp;Hiroshi Fujisaki,&nbsp;","doi":"10.1021/acs.jctc.5c00852","DOIUrl":"10.1021/acs.jctc.5c00852","url":null,"abstract":"<p >P-Glycoprotein, a member of the ATP-binding cassette (ABC) transporter family (ABCB1), actively exports various hydrophobic compounds from the cell. Crystal structures of the eukaryotic <i>Cyanidioschyzon merolae</i> homologue (CmABCB1) in both inward-facing (IF) and outward-facing (OF) conformations have suggested a transport mechanism involving conformational changes in the transmembrane helices (TMHs) and nucleotide-binding domain (NBD) dimerization. In this study, we employed the string method to compute the minimum free energy path (MFEP) of the conformational transition from IF to OF crystal structure, with a focus on elucidating the structural and energetic basis of a model substrate (rhodamine 6G (R6G)) transport as a most probable path derived from the crystallographic data. ATP binding and subsequent NBD dimerization act as driving forces to overcome the energy barrier associated with frustration occurring in TMH. This process disrupts the aromatic hydrophobic network (AHN), facilitates nonspecific R6G binding, and leads to an intermediate substrate-occluded (Occ) state. R6G interactions weaken the dimer interface and destabilize the Occ state, promoting transition to the stable OF conformation through TMH twisting and squeezing motions. These results highlight the power of MFEP-based free energy landscapes in uncovering the molecular mechanisms of membrane transporters.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9935–9942"},"PeriodicalIF":5.5,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215851","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":"Cavity Field-Driven Symmetry Breaking and Modulation of Vibrational Properties: Insights from the Analytical QED-HF Hessian","authors":"Alberto Barlini,&nbsp;, ,&nbsp;Andrea Bianchi,&nbsp;, ,&nbsp;Jan Haakon M. Trabski,&nbsp;, ,&nbsp;Julien Bloino,&nbsp;, and ,&nbsp;Henrik Koch*,&nbsp;","doi":"10.1021/acs.jctc.5c00680","DOIUrl":"10.1021/acs.jctc.5c00680","url":null,"abstract":"<p >In this work, we present the analytical derivation and implementation of the quantum electrodynamics Hartree–Fock Hessian. We investigate how electronic strong coupling influences molecular vibrational properties, applying this framework to formaldehyde, <i>p</i>-nitroaniline, and adamantane. Our analysis reveals cavity-induced changes in vibrational frequencies and intensities. Additionally, we show how the quantum electromagnetic field breaks molecular symmetry, activating previously forbidden infrared transitions. Our findings highlight the potential of coupling photonic and electronic degrees of freedom to control and modulate molecular vibrational properties in the ground state.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9323–9334"},"PeriodicalIF":5.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00680","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211161","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}

{"title":"Molecular Polariton Dynamics in Realistic Cavities","authors":"Carlos M. Bustamante*,&nbsp;, ,&nbsp;Franco P. Bonafé,&nbsp;, ,&nbsp;Maxim Sukharev,&nbsp;, ,&nbsp;Michael Ruggenthaler,&nbsp;, ,&nbsp;Abraham Nitzan,&nbsp;, and ,&nbsp;Angel Rubio,&nbsp;","doi":"10.1021/acs.jctc.5c01318","DOIUrl":"10.1021/acs.jctc.5c01318","url":null,"abstract":"<p >The large number of degrees of freedom involved in polaritonic chemistry processes considerably restricts the systems that can be described by any ab initio approach, due to the resulting high computational cost. Semiclassical methods that treat light classically offer a promising route for overcoming these limitations. In this work, we present a new implementation that combines the numerical propagation of Maxwell’s equations to simulate realistic cavities with quantum electron dynamics at the density functional tight-binding (DFTB) theory level. This implementation allows for the simulation of a large number of molecules described at the atomistic level, interacting with cavity modes obtained by numerically solving Maxwell’s equations. By mimicking experimental setups, our approach enables the calculation of transmission spectra, in which we observe the corresponding polaritonic signals. In addition, we have access to local information, revealing complex responses of individual molecules that depend on the number, geometry, position, and orientation of the molecules inside the cavity.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9823–9831"},"PeriodicalIF":5.5,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01318","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211109","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}

{"title":"Semiclassical Multistate Quantum Dynamics Using Thermalized Gaussian Wavepacket","authors":"Yoosang Son,&nbsp;, ,&nbsp;Yeseong Choi,&nbsp;, ,&nbsp;Oleg V. Prezhdo*,&nbsp;, and ,&nbsp;Hyungjun Kim*,&nbsp;","doi":"10.1021/acs.jctc.5c01001","DOIUrl":"10.1021/acs.jctc.5c01001","url":null,"abstract":"<p >Electronic dynamics in condensed-phase systems are predominantly influenced by thermal effects and decoherence arising from the quantum bath coupled to the system. A system–bath Hamiltonian, where the ″system″ interacts with a ″bath″ of many harmonic oscillators, provides a foundational framework for investigating quantum dynamics with environmental effects. Here, we introduce a novel wave function-based method that enables real-time propagation of a finite-temperature harmonic bath wave function using classical equations of motion. We begin by purifying the thermal density matrix of a harmonic oscillator through the introduction of an auxiliary function, which corrects the decoherence behavior of standard Gaussian wavepackets. Using the path-integral formalism, we show that the resulting wavepacket evolves along classical trajectories under a sequence of shifted harmonic potentials. We then derive an explicit analytical form of this state, termed the thermalized Gaussian wavepacket (TGW). To propagate the TGW, we develop two numerical schemes; a stochastic hopping method for the finite coupling regime and a perturbative method tailored for the weak-coupling limit. Our simulations demonstrate that the TGW not only recovers Marcus theory rates in the weak-coupling limit for two-state systems, but also accurately reproduces numerically exact time-dependent Schrödinger equation (TDSE) or multiconfiguration time-dependent Hartree (MCTDH) results for two- and three-state models. These findings demonstrate that the density matrix evolution can be accurately simulated only by forward-propagating the TGW based on the classical trajectories. We envision that the TGW framework offers an efficient and accurate route to simulate electronic transition dynamics in real time, while rigorously incorporating both decoherence and thermal effects, making it a promising tool for investigating quantum dynamics in more complex and realistic systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9772–9783"},"PeriodicalIF":5.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209111","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":"Operator Formalism for Noncollinear Functionals in the Multicollinear Approach","authors":"Xiaoyu Zhang*,&nbsp; and ,&nbsp;Taoni Bao,&nbsp;","doi":"10.1021/acs.jctc.5c01305","DOIUrl":"10.1021/acs.jctc.5c01305","url":null,"abstract":"<p >Accurate modeling of spin–orbit coupling and noncollinear magnetism requires noncollinear density functionals within the two-component generalized Kohn–Sham framework, yet constructing and implementing noncollinear functionals remains challenging. Recently, a well-defined methodology called the multicollinear approach was proposed to extend collinear functionals into noncollinear ones. While previous research focuses on its matrix representation, the present work derives its operator formalism. We implement these new equations in our noncollinear functional ensemble named NCXC, which is expected to facilitate compatibility with most DFT software packages. Since the multicollinear approach was proposed for solving nonphysical properties and mathematical singularities in noncollinear functionals, we validate its accuracy in practical periodic systems, including noncollinear magnetism in spin spirals, band structures in topological insulators, and band gaps in semiconducting inorganic materials.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9620–9630"},"PeriodicalIF":5.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209183","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":"The Grand Canonical General-Purpose Reactivity Indicator: A Conceptual DFT Approach to Predict Molecular Reactivity and Experimental Electrophilicity and Nucleophilicity Scales.","authors":"Yoshio Barrera,Tomás Rocha-Rinza,Florian F Mulks,Paul W Ayers,James S M Anderson","doi":"10.1021/acs.jctc.5c00849","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00849","url":null,"abstract":"The Grand Canonical General-Purpose Reactivity Indicator (GC-GPRI) is introduced as a tool for predicting reactivity and for discerning the relative electrophilicity and nucleophilicity of electrophiles and nucleophiles, respectively. The GC-GPRI is derived within the zero-temperature grand canonical ensemble conceptual density-functional theory (CDFT) framework using a perturbative approach. In this model, the electrophile-nucleophile interaction energy is modeled by perturbations in the chemical and external potentials of the isolated species. The GC-GPRI accurately identifies the most reactive hard and soft atoms in complex molecules with multiple reactive sites. This model also reproduces experimental electrophilicity and nucleophilicity scales for 21 electrophiles and 20 nucleophiles, with R2 correlations of 0.98 and 0.94, respectively.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"114 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145209277","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":"Computational Characterization of DNA Catenanes","authors":"Yeonho Song,&nbsp;, ,&nbsp;Minjung Kim,&nbsp;, ,&nbsp;Bong June Sung,&nbsp;, and ,&nbsp;Jun Soo Kim*,&nbsp;","doi":"10.1021/acs.jctc.5c01224","DOIUrl":"10.1021/acs.jctc.5c01224","url":null,"abstract":"<p >DNA catenanes are molecular structures composed of two interlocked circular DNA molecules, held together by a mechanical bond─a topological constraint arising from their mutual interlocking. Using all-atom molecular dynamics simulations, we investigated the structural and dynamical properties of DNA catenanes formed by small double-stranded DNA minicircles. In homocatenanes with mild torsional stress (82 bp–82 bp and 92 bp–92 bp), the minicircles largely retain circular conformations, and the mechanical bond exhibits constrained fluctuations in both bond length and twist angle. Rotational diffusion occurs on the microsecond time scale. In the heterocatenane (76 bp–82 bp), elevated torsional stress promotes kink formation in the 76-bp minicircle, leading to a distorted elliptical shape, enhanced DNA–DNA contacts, and anisotropic relaxation characterized by double-exponential decay in both relative translation and twist. Ion distribution analysis shows Na⁺ enrichment in the interstitial region between the two DNA minicircles, indicating that counterion condensation also occurs within the interlocked structures. Taken together, these results provide quantitative characterization of relative translation, twisting, and rotation in homocatenanes, while for the heterocatenane the emphasis is placed on qualitative interpretation of anisotropic relaxation. This study highlights how DNA conformation and topological constraints shape the structural and dynamic behavior of DNA catenanes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9967–9981"},"PeriodicalIF":5.5,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145205005","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":"NNQS-AFQMC: Neural Network Quantum States Enhanced Fermionic Quantum Monte Carlo","authors":"Zhi-Yu Xiao*,&nbsp;, ,&nbsp;Bowen Kan,&nbsp;, ,&nbsp;Huan Ma,&nbsp;, ,&nbsp;Bowen Zhao,&nbsp;, and ,&nbsp;Honghui Shang*,&nbsp;","doi":"10.1021/acs.jctc.5c01138","DOIUrl":"10.1021/acs.jctc.5c01138","url":null,"abstract":"<p >We introduce an efficient approach to implement neural network quantum states (NNQS) as trial wave functions in auxiliary-field quantum Monte Carlo (AFQMC). NNQS are a recently developed class of variational ansätze capable of flexibly representing many-body wave functions, though they often incur a high computational cost during optimization. AFQMC, on the other hand, is a powerful stochastic projector approach for ground-state calculations, but it normally requires an approximate constraint via a trial wave function or trial density matrix, whose quality affects the accuracy. Recently, it has been shown (Xiao et al., arXiv2505.18519) that a broad class of highly correlated wave functions can be integrated into AFQMC through stochastic sampling techniques. In this work, we apply this approach and present a direct integration of NNQS with AFQMC, allowing NNQS to serve as high-quality trial wave functions for AFQMC with manageable computational cost. We test the NNQS-AFQMC method on the challenging nitrogen molecule (N₂) at stretched geometries. Our results demonstrate that AFQMC with an NNQS trial wave function can attain near-exact total energies, highlighting the potential of AFQMC with NNQS to overcome longstanding challenges in strongly correlated electronic structure calculations. We also outline future research directions for improving this promising methodology.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9587–9600"},"PeriodicalIF":5.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204965","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":"Quantum Statistical Mechanics of Electronically Open Molecules: Reduced Density Operators","authors":"Jacob Pedersen,&nbsp;, ,&nbsp;Bendik Støa Sannes,&nbsp;, and ,&nbsp;Ida-Marie Høyvik*,&nbsp;","doi":"10.1021/acs.jctc.5c00782","DOIUrl":"10.1021/acs.jctc.5c00782","url":null,"abstract":"<p >We present a reduced density operator for electronically open molecules by explicitly averaging over the environmental degrees of freedom of the composite Hamiltonian. Specifically, we include the particle-number nonconserving (particle-breaking) interactions responsible for the sharing of electrons between the molecule and the environment, which are neglected in standard formulations of quantum statistical mechanics. We propose an unambiguous definition of the partial trace operation in the composite fermionic Fock space based on composite states in a second quantization framework built from a common orthonormal set of orbitals. Thereby, we resolve the fermionic partial trace ambiguity. The common orbital basis is constructed by spatial localization of the full orbital space, in which the full composite Hamiltonian naturally partitions into a molecule Hamiltonian, an environment Hamiltonian, and an interaction Hamiltonian. The new reduced density operator is based on the approximation of commutativity between the subsystem Hamiltonians (i.e., molecule and environment Hamiltonians) and the interaction Hamiltonian, but our methodology provides a hierarchical approach for improving this approximation. The reduced density operator can be viewed as a generalization of the grand canonical density operator. We are prompted to define the generalized chemical potential, which aligns with the standard interpretation of the chemical potential, apart from the possibility of fractional rather than strictly integer electron transfer in our framework. In contrast to standard approaches, our framework enables an explicit consideration of the electron occupancy in the environment at any level of theory, irrespective of the model used to describe the molecule. Specifically, our reduced density operator is fully compatible with all possible level-of-theory treatments of the environment. The approximations that render our reduced density operator identical to the grand canonical density operator are (i) restriction of excitations to occur within the same orbitals and (ii) assumption of equal interaction with the environment for all molecule spin orbitals (i.e., the wide-band approximation).</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9415–9429"},"PeriodicalIF":5.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00782","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197500","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}

{"title":"Influences of Basis Set and Electronic Exchange-Correlation on Low-Frequency Vibrations and Stability of Paracetamol Polymorphs","authors":"Huanyu Zhou*,&nbsp;, ,&nbsp;Giuseppe Mallia,&nbsp;, and ,&nbsp;Nicholas M. Harrison,&nbsp;","doi":"10.1021/acs.jctc.5c00599","DOIUrl":"10.1021/acs.jctc.5c00599","url":null,"abstract":"<p >In molecular crystals, many solid state phase transitions can be attributed to the entropy of intermolecular vibrations at low frequencies, where the weak noncovalent interactions dominate, and simulations based on density functional theory (DFT) suffer from relatively large errors. In this work, the precision of two critical computational parameters are evaluated, namely the choice of local basis set and (DFT-based) Hamiltonian. Each is documented in detail for the vibrational properties and thermodynamic stability of two polymorphs of paracetamol, which are chosen due to the representative chemical interactions and the good availability of high-quality reference data. Comparisons are made with experimentally measured low-temperature geometries, Raman spectra, and temperature–pressure phase diagrams. These results highlight the substantial influences of basis set, revealing the importance of both the cardinality (i.e., ζ) and the diffuseness; the failure to account for either factor might lead to unexpected results. The features of low-frequency vibrations that most significantly affect the relative stability of molecular crystals are identified and shown to be captured when the triple-ζ def2-TZVP basis set is adopted; on the contrary, widely used double-ζ basis sets are shown to be inadequate. The improvement attributed to the inclusion of Fock exchange is revealed to be marginal, especially with triple-ζ basis sets. By systematically improving levels of precision, the current work disentangles competing sources of errors impeding accurate crystal structure predictions and polymorph energy rankings. This facilitates the predictability and reliability of DFT in thermodynamic modeling of molecular crystals.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9832–9843"},"PeriodicalIF":5.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00599","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195090","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}