Journal of Chemical Physics最新文献_第4页

Series expansion of a scalable Hermitian excitonic renormalization method. 可伸缩厄密激子重整化方法的级数展开。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0238707

Marco Bauer, Andreas Dreuw, Anthony D Dutoi

{"title":"Series expansion of a scalable Hermitian excitonic renormalization method.","authors":"Marco Bauer, Andreas Dreuw, Anthony D Dutoi","doi":"10.1063/5.0238707","DOIUrl":"https://doi.org/10.1063/5.0238707","url":null,"abstract":"Utilizing the sparsity of the electronic structure problem, fragmentation methods have been researched for decades with great success, pushing the limits of ab initio quantum chemistry ever further. Recently, this set of methods has been expanded to include a fundamentally different approach called excitonic renormalization, providing promising initial results. It builds a supersystem Hamiltonian in a second-quantized-like representation from transition-density tensors of isolated fragments, contracted with biorthogonalized molecular integrals. This makes the method fully modular in terms of the quantum chemical methods applied to each fragment and enables massive truncation of the state-space required. Proof-of-principle tests have previously shown that an excitonically renormalized Hamiltonian can efficiently scale to hundreds of fragments, but the ad hoc approach to building the Hamiltonian was not scalable to larger fragments. On the other hand, initial tests of the originally proposed modular Hamiltonian build, presented here, show the accuracy to be poor on account of its non-Hermitian character. In this study, we bridge the gap between these with an operator expansion that is shown to converge rapidly, tending toward a Hermitian Hamiltonian while retaining the modularity, yielding an accurate, scalable method. The accuracy is tested here for a beryllium dimer. At distances near equilibrium and longer, the zeroth-order method is comparable to coupled-cluster singles, doubles, and perturbative triples and the first-order method is comparable to full configuration interaction (FCI). The second-order method agrees with FCI for distances well up the inner repulsive wall of the potential. Deviations occurring at shorter bond distances are discussed along with approaches to scaling to larger fragments.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Spectroscopic study of energy transfer in collisions between vibrational excited H2 and CO2. 振动激发H2与CO2碰撞中能量传递的光谱研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0239602

Chu Qin, Xiaofang Zhao, Shuying Wang, Yifan Shen

{"title":"Spectroscopic study of energy transfer in collisions between vibrational excited H2 and CO2.","authors":"Chu Qin, Xiaofang Zhao, Shuying Wang, Yifan Shen","doi":"10.1063/5.0239602","DOIUrl":"https://doi.org/10.1063/5.0239602","url":null,"abstract":"The collisional energy transfer between vibrational excited H2(1, 7) and CO2 was investigated by exciting H2 to a vibrational excited state of v = 1, J = 7 by the stimulated Raman scattering technique. The coherent anti-Stokes Raman spectroscopy (CARS) technique determined that H2 was excited to the H2(1, 7) state. Varying the cuvette temperature, the number of H2(1, 7) particles was found to increase with the increase in H2 molar ratio α by scanning the intensity of the CARS spectrum, with peaks at different α at a temperature of 363 ± 15 K, but the peak temperature was not sensitive to α. Scanning CARS spectra after H2 collisions yielded that the energies of the excited states of H2 were mainly distributed in the vibrational and translational states, proving that the collisions between the excited states of H2 were linear collisions. The collisional transfer rate coefficients of H2(1, 7) and CO2 were obtained by fitting the Stern-Volmer equation as kv(H2) = (2.89 ± 0.30) × 10-13 cm3 s-1 and kv(CO2) = (8.23 ± 0.42) × 10-13 cm3 s-1. Exciting H2 to different states, it was found that the collisional transfer rate coefficient of CO2 was less affected by the energy of the vibrational excited H2. The rotational temperature was obtained from the Boltzmann distribution of the rotational dynamics, and it was found that the rotational temperature of CO2(0000, J) was about 3.4 times higher than that of CO2(0001, J), which proved that the energy of the vibrational excited H2 was mainly allocated to the higher rotational state of CO2(0000).","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Photon-mediated energy transfer between molecules and atoms in a cavity: A numerical study. 腔中分子与原子间光子介导的能量传递：数值研究。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0242420

Jun Zhang, Shaohong Wang, Mengdi Guo, Xin-Ke Li, Yong-Chen Xiong, Wanghuai Zhou

{"title":"Photon-mediated energy transfer between molecules and atoms in a cavity: A numerical study.","authors":"Jun Zhang, Shaohong Wang, Mengdi Guo, Xin-Ke Li, Yong-Chen Xiong, Wanghuai Zhou","doi":"10.1063/5.0242420","DOIUrl":"https://doi.org/10.1063/5.0242420","url":null,"abstract":"The molecular energy transfer is crucial for many different physicochemical processes. The efficiency of traditional resonance energy transfer relies on dipole-dipole distance between molecules and becomes negligible when the distance is larger than ∼10 nm, which is difficult to overcome. Cavity polariton, formed when placing molecules inside the cavity, is a promising way to surmount the distance limit. By hybridizing a two-level atom (TLA) and a lithium fluoride (LiF) molecule with a cavity, we numerically simulate the reaction process and the energy transfer between them. Our results show that the TLA can induce a deep potential well, which can be seen as a replica of the potential energy surface of bare LiF, acting as a reservoir to absorb/release the molecular kinetic energy. In addition, the energy transfer shows a molecular nuclear kinetic energy dependent behavior, namely, more nuclear kinetic energy igniting more energy transfer. These findings show us a promising way to manipulate the energy transfer process within the cavity using an intentional TLA, which can also serve as a knob to control the reaction process.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142949429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Disentangling collective coupling in vibrational polaritons with double quantum coherence spectroscopy. 用双量子相干光谱解纠缠振动极化子中的集体耦合。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0239877

Thomas Schnappinger, Cyril Falvo, Markus Kowalewski

{"title":"Disentangling collective coupling in vibrational polaritons with double quantum coherence spectroscopy.","authors":"Thomas Schnappinger, Cyril Falvo, Markus Kowalewski","doi":"10.1063/5.0239877","DOIUrl":"10.1063/5.0239877","url":null,"abstract":"Vibrational polaritons are formed by strong coupling of molecular vibrations and photon modes in an optical cavity. Experiments have demonstrated that vibrational strong coupling can change molecular properties and even affect chemical reactivity. However, the interactions in a molecular ensemble are complex, and the exact mechanisms that lead to modifications are not fully understood yet. We simulate two-dimensional infrared spectra of molecular vibrational polaritons based on the double quantum coherence technique to gain further insight into the complex many-body structure of these hybrid light-matter states. Double quantum coherence uniquely resolves the excitation of hybrid light-matter polaritons and allows one to directly probe the anharmonicities of the resulting states. By combining the cavity Born-Oppenheimer Hartree-Fock ansatz with a full quantum dynamics simulation of the corresponding eigenstates, we go beyond simplified model systems. This allows us to study the influence of self-polarization and the response of the electronic structure to the cavity interaction on the spectral features even beyond the single-molecule case.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Anisotropic interactions for continuum modeling of protein-membrane systems. 蛋白质-膜系统连续模型的各向异性相互作用。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0237408

T Oppelstrup, L G Stanton, J O B Tempkin, T N Ozturk, H I Ingólfsson, T S Carpenter

引用次数: 0

Electronic states of the N2+ ion dissociating to the four lowest dissociation limits: Energies, transition dipole moments, and Einstein coefficients. 解离到四个最低解离极限的N2+离子的电子态：能量、跃迁偶极矩和爱因斯坦系数。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0245622

Chaima Hammami, Conner Penson, Mehdi Adrien Ayouz, Viatcheslav Kokoouline

引用次数: 0

Generalized Langevin equation for a tagged monomer in a Gaussian semiflexible polymer. 高斯半柔性聚合物中标记单体的广义朗之万方程。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0229919

Xavier Durang, Chan Lim, Jae-Hyung Jeon

引用次数: 0

Variance-reduced random batch Langevin dynamics. 方差减少随机批朗之万动力学。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0246661

Zhenli Xu, Yue Zhao, Qi Zhou

引用次数: 0

A brief introduction to the diffusion Monte Carlo method and the fixed-node approximation. 简单介绍扩散蒙特卡罗方法和固定节点近似。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-28 DOI: 10.1063/5.0232424

Alfonso Annarelli, Dario Alfè, Andrea Zen

{"title":"A brief introduction to the diffusion Monte Carlo method and the fixed-node approximation.","authors":"Alfonso Annarelli, Dario Alfè, Andrea Zen","doi":"10.1063/5.0232424","DOIUrl":"https://doi.org/10.1063/5.0232424","url":null,"abstract":"Quantum Monte Carlo (QMC) methods represent a powerful family of computational techniques for tackling complex quantum many-body problems and performing calculations of stationary state properties. QMC is among the most accurate and powerful approaches to the study of electronic structure, but its application is often hindered by a steep learning curve; hence it is rarely addressed in undergraduate and postgraduate classes. This tutorial is a step toward filling this gap. We offer an introduction to the diffusion Monte Carlo (DMC) method, which aims to solve the imaginary time Schrödinger equation through stochastic sampling of the configuration space. Starting from the theoretical foundations, the discussion leads naturally to the formulation of a step-by-step algorithm. To illustrate how the method works in simplified scenarios, examples such as the harmonic oscillator and the hydrogen atom are provided. The discussion extends to the fixed-node approximation, a crucial approach for addressing the fermionic sign problem in multi-electron systems. In particular, we examine the influence of trial wave function nodal surfaces on the accuracy of DMC energy by evaluating results from a non-interacting two-fermion system. Extending the method to excited states is feasible in principle, but some additional considerations are needed, supported by practical insights. By addressing the fundamental concepts from a hands-on perspective, we hope this tutorial will serve as a valuable guide for researchers and students approaching DMC for the first time.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 24","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 impact of charge regulation and ionic intranuclear environment on the nucleosome core particle. 电荷调节和离子核内环境对核小体核心粒子的影响。

IF 3.1 2区化学

Journal of Chemical Physics Pub Date : 2024-12-21 DOI: 10.1063/5.0241529

Rikkert J Nap, Paola Carillo Gonzalez, Aria E Coraor, Ranya K A Virk, Juan J de Pablo, Vadim Backman, Igal Szleifer

{"title":"The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.","authors":"Rikkert J Nap, Paola Carillo Gonzalez, Aria E Coraor, Ranya K A Virk, Juan J de Pablo, Vadim Backman, Igal Szleifer","doi":"10.1063/5.0241529","DOIUrl":"10.1063/5.0241529","url":null,"abstract":"We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)-the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformation, charge, and chemical state of all molecular species-thereby linking the structural state with the chemical/charged state of the system. We investigate how variations in monovalent and divalent salt concentrations, as well as pH, affect the charge distribution across different regions of an NCP and quantify the impact of charge regulation. The effective charge of an NCP emerges from a delicate and complex balance involving the chemical dissociation equilibrium of the amino acids and the DNA-phosphates, the electrostatic interaction between them, and the translational entropy of the mobile solution ions, i.e., counter ion release and ion condensation. From our results, we note the significant effect of divalent magnesium ions on the charge and electrostatic energy as well as the counterion cloud that surrounds an NCP. As a function of magnesium concentration, charge neutralization, and even charge inversion is predicted-in line with experimental observation of NCPs. The strong Mg-dependence of the nucleosome charge state arises from ion bridges between two DNA-phosphates and one Mg2+ ion. We demonstrate that to describe and predict the charged state of an NCP properly, it is essential to consider molecular details, such as DNA-phosphate ion condensation and the acid-base equilibrium of the amino acids that comprise the core histone proteins.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 23","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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