Journal of Chemical Physics最新文献

Elucidating the relationship between protein amide I, II, and III bands and secondary structures by localized anharmonic vibrational calculations. 用局域非谐振动计算阐明蛋白酰胺I、II和III波段与二级结构的关系。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0355079

Nao Matsuyama, Kiyoshi Yagi

{"title":"Elucidating the relationship between protein amide I, II, and III bands and secondary structures by localized anharmonic vibrational calculations.","authors":"Nao Matsuyama, Kiyoshi Yagi","doi":"10.1063/5.0355079","DOIUrl":"https://doi.org/10.1063/5.0355079","url":null,"abstract":"The amide I, II, and III spectra of the insulin dimer and ubiquitin were investigated using our recently developed localized, second-order vibrational quasi-degenerate perturbation theory (VQDPT2) combined with quantum mechanics/molecular mechanics calculations. By averaging over ten snapshots from molecular dynamics trajectories, we confirmed that the computed spectra converged to a sufficient degree. Although the method has intrinsic limitations due to the neglect of vibrational coupling between neighboring amide groups, we found that the method provides a useful basis for spectral analysis of these proteins. The analysis of the averaged amide I, II, and III bands revealed that, for both proteins, the amide II and III peak positions tend to be closely associated with the coil contribution, whereas the origin of the amide I maximum is more protein dependent. The calculated amide I and III frequencies of the coil structures showed good agreement with experimental values. The spectra of each secondary structure were further subdivided according to the type of hydrogen bonding within the secondary structure. For structurally constrained α-helix and β-sheet structures, hydrogen-bond-dependent amide I frequency shifts were found to correlate with changes in the amide dihedral angles (O=C-N-H). Localized VQDPT2 enables direct interpretation of amide band shifts associated with conformational changes and provides a deeper understanding of the structural origin responsible for these band shifts.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220263","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

Sum-frequency order parameter ratio determination for molecules with high-symmetry vibrational modes. 高对称振动模式分子的和频阶参数比测定。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0350318

Aruna Kumarasiri, Amin Yousefi, Dennis Hore

{"title":"Sum-frequency order parameter ratio determination for molecules with high-symmetry vibrational modes.","authors":"Aruna Kumarasiri, Amin Yousefi, Dennis Hore","doi":"10.1063/5.0350318","DOIUrl":"https://doi.org/10.1063/5.0350318","url":null,"abstract":"The structure of molecules at surfaces and buried interfaces can be probed by second-order nonlinear optical techniques that derive their response from environments with broken centrosymmetry, thereby simultaneously enhancing the signal from the molecules of interest and suppressing the responses of the adjacent bulk phases. However, even though these methods are surface-sensitive, extracting orientation information has often relied on significant assumptions about the shape of the orientation distribution and the underlying molecular electronic structure. Here, we illustrate that the measurement of the relative magnitude and the phase of tensor elements that govern the vibrational sum frequency response can be used to construct a ratio of order parameters ⟨P3⟩/⟨P1⟩. This structural parameter does not require knowledge of the hyperpolarizability or even the hyperpolarizability ratio, thereby dramatically increasing the accuracy of its determination. We then show how this parameter can be used to comment on the most probable distribution of tilt angles. This is demonstrated for para-cyanophenol at three different interfaces.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220244","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 development of a high-accuracy, low-cost, numerical tensor method for the P states of three-particle systems. 一种高精度、低成本的三粒子系统P态数值张量方法的发展。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0356420

Brice Kammegne Tcheugam, Henryk A Witek, Hazel Cox

{"title":"The development of a high-accuracy, low-cost, numerical tensor method for the P states of three-particle systems.","authors":"Brice Kammegne Tcheugam, Henryk A Witek, Hazel Cox","doi":"10.1063/5.0356420","DOIUrl":"https://doi.org/10.1063/5.0356420","url":null,"abstract":"In this paper, we solve the non-relativistic many-body Schrödinger equation (SE) for the excited P states (L = 1) of three-particle systems with natural and unnatural parity. The exact separation of the rotational degrees of freedom from the internal degrees of freedom presented by Sadhukhan et al. [arXiv:2506.23962 (2025)] is exploited. The angular matrix elements involve the product of two bipolar harmonics and are calculated using an explicit analytical expression containing the Wigner 3j- and 6j-symbols. Using a symmetry and parity adapted wavefunction for P states in perimetric coordinates, the variational form of the SE in canonical tensor format is derived. This consists of a sum of triple tensor products of factor matrices and is an exact representation. From this canonical format, the SE can be solved in full tensor format or used to derive an exact representation as a second-order tensor train. Two formulations are presented. In the first, scaled perimetric coordinates are used; it is assumed that the like-charged particles have the same asymptotic behavior so that the orthonormality of the Laguerre functions can be exploited and the matrices are sparse. In the second, the like-charged particles are not constrained to have the same asymptotic behavior and an analytical integral is used which results in dense matrices. It is shown that by optimizing either one or two non-linear variational parameters, it is possible to obtain excited P state energies that are accurate to the picohartree, for atomic and molecular systems in less than 25 min on a standard desktop computer.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220281","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

Quantum simulation of ligand-like molecules through sample-based quantum diagonalization in density matrix embedding framework. 密度矩阵嵌入框架中基于样品的量子对角化配体类分子的量子模拟。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0338676

Ashish Kumar Patra, Anurag K S V, Sai Shankar P, Ruchika Bhat, Raghavendra V, Rahul Maitra, Jaiganesh G

{"title":"Quantum simulation of ligand-like molecules through sample-based quantum diagonalization in density matrix embedding framework.","authors":"Ashish Kumar Patra, Anurag K S V, Sai Shankar P, Ruchika Bhat, Raghavendra V, Rahul Maitra, Jaiganesh G","doi":"10.1063/5.0338676","DOIUrl":"https://doi.org/10.1063/5.0338676","url":null,"abstract":"The accurate treatment of electron correlation in extended molecular systems remains computationally challenging using classical electronic structure methods. Hybrid quantum-classical algorithms offer a potential route to overcome these limitations; however, their practical deployment on existing quantum computers requires strategies that both reduce problem size and mitigate hardware noise. In this work, we investigate ground-state energy calculations of ligand-like molecules using Sample-based Quantum Diagonalization (SQD) within the Density Matrix Embedding Theory (DMET) framework, focusing on low-symmetry systems with diverse bonding motifs that exhibit subsystem-dependent variations in fragment-environment entanglement. These entanglement-based variations directly influence bath orbital construction, impurity sizes, and the structure of the embedded Hamiltonians, posing nontrivial challenges for both embedding and quantum sampling. By combining DMET fragmentation with SQD-based construction of reduced configuration spaces through quantum sampling and iterative configuration recovery, we perform quantum simulations on IBM's Eagle R3 (ibm_sherbrooke) and IBM's Heron R3 (ibm_boston) superconducting quantum hardware, thereby showing that the entanglement structure across embedding subsystems plays a central role in determining the efficiency and accuracy of the simulations. Despite these complexities, we show that the DMET-SQD framework yields ground-state energies in strong agreement with DMET-full configuration interaction benchmarks, achieving chemical accuracy (1 kcal/mol) across all systems studied. These results demonstrate that SQD-based quantum simulations can be robustly extended to low-symmetry, chemically realistic, industry relevant molecules and highlight the importance of entanglement-aware embedding strategies for scalable quantum electronic structure calculations.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220269","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

Microscopic origin of polytype-dependent melting in SiC revealed by machine-learning molecular dynamics. 机器学习分子动力学揭示了SiC中多型依赖熔化的微观起源。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0350682

Ljiljana Stojanović, Samuel J Magorrian, Lara Kabalan, Richard N White, Fabian L Thiemann, Viktor Zólyomi

{"title":"Microscopic origin of polytype-dependent melting in SiC revealed by machine-learning molecular dynamics.","authors":"Ljiljana Stojanović, Samuel J Magorrian, Lara Kabalan, Richard N White, Fabian L Thiemann, Viktor Zólyomi","doi":"10.1063/5.0350682","DOIUrl":"https://doi.org/10.1063/5.0350682","url":null,"abstract":"Predicting how crystal structure influences high-temperature stability remains a key challenge in materials modeling and design. Silicon carbide (SiC), one of the most thermally and chemically stable materials known, provides an ideal system for studying this problem because its many polytypes preserve similar local tetrahedral bonding while differing in long-range stacking geometry. To determine the impact of polytype structure on the high-temperature stability of SiC, we combine phase-coexistence machine-learning molecular dynamics with finite-temperature phonon analysis, enabled by a fine-tuned MACE interatomic potential that accurately describes crystalline, high-temperature, and disordered configurations across multiple SiC polytypes. We identify a clear stability ordering, 3C > 2H > 9R, reflected consistently in structural disordering, interlayer sliding, and finite-temperature phonon spectra. Across all polytypes, melting initiates through the formation of short C-C contacts and carbon-rich local regions, followed by a progressive loss of tetrahedral Si-C connectivity. The reduced stability of the long-period 9R polytype is associated with a denser manifold of low-frequency transverse-acoustic modes arising from its stacking periodicity and associated zone folding, which broaden and soften further at high temperature. These modes can provide additional low-energy channels for thermally activated lateral bilayer motion, consistent with the larger sliding amplitudes observed in 9R and their positive correlation with local structural disorder.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220298","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

Variational block-correlated coupled-cluster Monte Carlo. 变分块相关耦合簇蒙特卡罗。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0351856

Hunter Brodie, Alexander Shilcusky, Adrian Feiguin

引用次数: 0

Revisiting the visible B̃2A2 ← X̃2B1 spectrum of the phenoxy radical: Multireference energetics and finite-temperature Franck-Condon simulations. 苯氧自由基的可见B ^ 2A2←X ^ 2B1光谱：多参考能量学和有限温度frank - condon模拟。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0351073

Kohsuke Suma

{"title":"Revisiting the visible B̃2A2 ← X̃2B1 spectrum of the phenoxy radical: Multireference energetics and finite-temperature Franck-Condon simulations.","authors":"Kohsuke Suma","doi":"10.1063/5.0351073","DOIUrl":"https://doi.org/10.1063/5.0351073","url":null,"abstract":"The visible B̃2A2 ← X̃2B1 absorption system of the phenoxy radical is characterized by a pronounced ∼500 cm-1 vibronic progression and broad, asymmetric band profiles. The assignment of the lowest-wavenumber component to the 0-0 band is supported by the 7 K Ar-matrix spectra, whereas the progression and room-temperature asymmetry have been assigned to the Wilson 6a vibration and sequence structure involving the low-frequency 10b vibration, respectively. Reference SA-CASSCF and TD-B3LYP Franck-Condon simulations show complementary limitations: CASSCF gives an overly compact 6a progression, whereas TD-B3LYP gives an overly extended cold-band envelope. The X̃2B1 and B̃2A2 states are therefore treated by second-order multireference Rayleigh-Schrödinger perturbation theory using a common state-averaged CASSCF reference. The resulting structures and harmonic force fields define a Duschinsky transformation involving all 30 normal coordinates. The finite-temperature vibrational basis was then expanded across all four C2v symmetry species and converged using mode-specific vibrational limits and state-energy cutoffs. The converged 30-mode model is compared directly with the room-temperature cavity-ringdown spectra of Araki et al. after one common wavenumber shift and an explicitly defined local normalization. It reproduces the principal 6a progression and parts of the asymmetric local envelopes qualitatively, but overestimates several wings and the high-wavenumber congestion. A calculation differing only in population temperature shows that this global high-wavenumber rise disappears at 7 K, identifying it as an accumulation of transitions from thermally populated lower states. The room-temperature spectrum is better described as a congested 6a progression with contributions from 10b and other modes than as a single 10b sequence.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 15","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220289","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

Collective intermolecular Coulombic decay beyond Coulomb. 集体分子间库仑衰变超越库仑。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-21 DOI: 10.1063/5.0356165

Alan G Falkowski, Lorenz S Cederbaum

引用次数: 0

Using large language models to probe the limits of atom-centered structural descriptors. 使用大型语言模型探索以原子为中心的结构描述符的局限性。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-14 DOI: 10.1063/5.0354408

Michelangelo Domina, Michele Ceriotti

{"title":"Using large language models to probe the limits of atom-centered structural descriptors.","authors":"Michelangelo Domina, Michele Ceriotti","doi":"10.1063/5.0354408","DOIUrl":"https://doi.org/10.1063/5.0354408","url":null,"abstract":"Mapping an atomic structure to a compact set of geometric descriptors is an essential step in any machine-learning application to atomic-scale modeling. A powerful and widely used approach can be understood as a discretization of the histogram of pair distances, triangles, etc., which results in a hierarchy of symmetry-invariant atom-centered descriptors. Unfortunately, the lower rungs on this hierarchy (two, three, four-body clusters) were found to be incomplete, with symmetry-unrelated pairs of structures having exactly the same descriptors. However, all the \"degeneracies\" reported so far are resolved by considering larger clusters of neighbors to build the descriptors. We report examples of 3D structures that are indistinguishable even if one considers clusters of up to seven neighbors, and to arbitrary order when considering a practical level of discretization of the descriptors, discovered with the assistance of large language models. The key ingredients in their construction can be traced to results that have been known for decades in different communities: the model was able to find the references and recognize their significance for the problem at hand. We believe that this experiment exposes an extremely fruitful usage pattern for Artificial Intelligence in science: translating results between different communities and application domains, accelerating the process by which serendipitous discoveries in a field become breakthroughs in another.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 14","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164484","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

Symmetry-driven correlation patterns in one-dimensional periodic fermionic systems: Closed-form expressions and exact selection rules for correlation functions, entanglement entropies, and mutual information. 一维周期费米子系统中对称驱动的相关模式：相关函数、纠缠熵和互信息的封闭形式表达式和精确选择规则。

IF 3.7 2区化学

Journal of Chemical Physics Pub Date : 2026-10-14 DOI: 10.1063/5.0350248

Celestino Angeli

{"title":"Symmetry-driven correlation patterns in one-dimensional periodic fermionic systems: Closed-form expressions and exact selection rules for correlation functions, entanglement entropies, and mutual information.","authors":"Celestino Angeli","doi":"10.1063/5.0350248","DOIUrl":"https://doi.org/10.1063/5.0350248","url":null,"abstract":"We present an analytical study of the spatial structure of correlations in periodic fermionic systems at the single Slater determinant level, focusing on the cyclic case. Exploiting cyclic symmetry, the transformation from localized orbitals to molecular orbitals is simultaneously a discrete Fourier transform, a Vandermonde matrix on the roots of unity, a complex Hadamard matrix, and the character table of the cyclic group Cm. Within this framework, the spatial structure of correlations is fully determined by the occupied irreducible representations (Fourier modes), independently of the specific Hamiltonian generating them. In particular, the fermionic two-point correlator is expressed as a truncated Fourier sum over the occupied orbitals, leading to exact analytical expressions for symmetric occupation patterns of Fourier modes (ℓ and -ℓ pairs), corresponding in quantum chemistry to aromatic fillings, i.e., fillings satisfying Hückel's 4n + 2 rule. For the half filling case, we derive exact spatial selection rules. In particular, the two-point correlator vanishes identically for all even distances along the ring. This property propagates to reduced density matrices and implies a complete absence of mutual information between the corresponding orbitals. These results reveal that, despite the global delocalization of molecular orbitals, the correlation structure in cyclic systems is highly non-uniform and governed by symmetry-induced interference. Although formulated in terms of cyclic lattice systems, the present results extend straightforwardly to one-dimensional fermionic chains with periodic conditions, reflecting the underlying translational symmetry of the problem. The framework, therefore, provides a Hamiltonian-independent and universal reference for understanding correlation patterns in one-dimensional periodic fermionic systems.","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"165 14","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167090","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