Journal of Chemical Theory and Computation最新文献

{"title":"Ground-State Energy Estimation on Current Quantum Hardware through the Variational Quantum Eigensolver: A Practical Study.","authors":"Nacer Eddine Belaloui, Abdellah Tounsi, Abdelmouheymen Rabah Khamadja, Mohamed Messaoud Louamri, Achour Benslama, David E Bernal Neira, Mohamed Taha Rouabah","doi":"10.1021/acs.jctc.4c01657","DOIUrl":"10.1021/acs.jctc.4c01657","url":null,"abstract":"<p><p>We investigate the variational quantum eigensolver (VQE) for estimating the ground-state energy of the BeH₂ molecule, emphasizing practical implementation and performance on current quantum hardware. Our research presents a comparative study of HEA and UCCSD ansätze on noiseless and noisy simulations and implements VQE on recent IBM quantum computer noise models and a real quantum computer, IBM Fez, providing a fully functional code employing Qiskit 1.2. Our experiments confirm UCCSD's reliability in ideal conditions, while the HEA demonstrates greater robustness to hardware noise, achieving chemical accuracy on state-vector simulation (SVS). The results reveal that achieving ground-state energy within chemical accuracy is feasible without error mitigation during VQE convergence. We demonstrate that current quantum devices effectively optimize circuit parameters despite misestimating simulated energies. The SVS-evaluated energies provide a more accurate representation of the solution quality compared to QPU-estimated energy values, indicating that VQE converges to the correct ground state despite quantum noise. Our study also applies noise mitigation as a postprocessing technique, using zero-noise extrapolation (ZNE) on a real quantum computer. The detailed methodologies presented in this study, including Hamiltonian construction and Fermionic-to-qubit transformations, facilitate flexible adaptation of the VQE approach for various algorithm variants and across different levels of algorithmic implementation.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6777-6792"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12288014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525461","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":"Atomistic Approach for Modeling of Polarizability and Raman Scattering of Water Clusters and Liquid Water.","authors":"Atanu Paul, Ilya Grinberg","doi":"10.1021/acs.jctc.5c00452","DOIUrl":"10.1021/acs.jctc.5c00452","url":null,"abstract":"<p><p>In this work, we develop a framework for atomistic modeling of the electronic polarizability to predict the Raman spectra of hydrogen-bonded clusters and liquids from molecular dynamics (MD) simulations. The total polarizability of the system is assumed to arise from the contributions of both the monomer unit and intermolecular interactions. The generalized bond-polarizability model (GBPM), inspired by the classic bond-polarizability model, effectively describes the electronic polarizability of a monomer. To account for the electronic polarizability arising from intermolecular interactions, we use a basis set of rapidly decaying functions of interatomic distances. We apply this model to calculate the electronic polarizability and Raman spectra of water clusters ((H₂O)_<i>r</i>, <i>r</i> = 2, 3, 4, 5, 6) and liquid water. The computational results are compared with the results of quantum mechanical calculations for clusters and experimental data for the liquid. It is demonstrated that this simple and physically motivated model, which relies on a small number of parameters, performs well for clusters at both low and high temperatures, capturing strong anharmonic effects. Moreover, its high transferability suggests its applicability to other water clusters. These results suggest that a hierarchical approach based on Jacob's ladder of increasingly sophisticated and accurate atomistic polarizability models incorporating additional effects can be used for efficient modeling of Raman spectra from MD simulations of clusters, liquids, and solids.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"7017-7026"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537406","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":"Permutationally Invariant Fourier Series for Accurate and Robust Data-Driven Many-Body Potentials.","authors":"Xuanyu Zhu, Francesco Paesani","doi":"10.1021/acs.jctc.5c00407","DOIUrl":"10.1021/acs.jctc.5c00407","url":null,"abstract":"<p><p>We present a robust solution to the long-standing challenge of eliminating unphysical energy predictions, or \"holes,\" in machine-learned many-body potentials, which can destabilize simulations when encountering configurations beyond the training set. By leveraging permutationally invariant Fourier series (PIFSs) within the MB-nrg data-driven many-body formalism, we introduce a new approach that significantly enhances the numerical stability of MB-nrg potential energy functions (PEFs) while preserving accuracy and transferability. Unlike conventional strategies that attempt to \"plug holes\" by expanding training data sets, PIFSs provide a more fundamental and efficient means of ensuring physically meaningful extrapolation across diverse molecular configurations. Using water as a benchmark system, we demonstrate that the MB-pol(PIFS) PEF retains the high accuracy of MB-pol across gas and condensed phases while extending the PEF's stability to a much broader range of thermodynamic conditions. Our results suggest that the PIFS-based MB-nrg many-body formalism provides a general framework for constructing accurate and robust physics-based/machine-learned potentials applicable to a broad range of molecular systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6950-6963"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566848","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":"","authors":"Liangxu Xie*,&nbsp;Yingdi Jin,&nbsp;Lei Xu,&nbsp;Shan Chang and Xiaojun Xu*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00605","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671704","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":"","authors":"Kartick Ramakrishnan,&nbsp;Gopalakrishnan Sai Gautam* and Phani Motamarri*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00513","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671743","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":"","authors":"Riccardo Alessandro,&nbsp;Matteo Castagnola,&nbsp;Henrik Koch and Enrico Ronca*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00519","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671744","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":"Identifying Band Inversions in Topological Materials Using Diffusion Monte Carlo.","authors":"Annette Lopez, Cody A Melton, Jeonghwan Ahn, Brenda M Rubenstein, Jaron T Krogel","doi":"10.1021/acs.jctc.5c00838","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00838","url":null,"abstract":"<p><p>Topological insulators are characterized by insulating bulk states and robust metallic surface states. Band inversion is a hallmark of topological insulators. At time-reversal invariant points in the Brillouin zone, spin-orbit coupling (SOC) induces a swapping of orbital character at the bulk band edges. Reliably detecting band inversion in solid-state systems with many-body methods would aid in identifying possible candidates for spintronics and quantum computing applications and improve our understanding of the physics behind topologically nontrivial systems. Density functional theory (DFT) methods are a well-established means of investigating these interesting materials due to their favorable balance of computational cost and accuracy but often struggle to accurately model the electron-electron correlations present in the many materials containing heavier elements. In this work, we develop a novel method to detect band inversion within continuum quantum Monte Carlo (QMC) methods that can accurately treat the electron correlation and spin-orbit coupling that are crucial to the physics of topological insulators. Our approach applies a momentum-space-resolved atomic population analysis throughout the first Brillouin zone utilizing the Löwdin method and the one-body reduced density matrix produced with diffusion Monte Carlo (DMC). We integrate this method into QMCPACK, an open source <i>ab initio</i> QMC package, so that these ground-state methods can be used to complement experimental studies and validate prior DFT work on predicting the band structures of correlated topological insulators. We demonstrate this new technique on the topological insulator bismuth telluride, which displays band inversion between its Bi-p and Te-p states at the Γ-point. We show an increase in charge on the bismuth-p orbital and a decrease in charge on the tellurium-p orbital when comparing band structures with and without SOC. Additionally, we use our method to compare the degree of band inversion present in monolayer Bi₂Te₃, which has no interlayer van der Waals interactions, to that seen in the bilayer and bulk. The method presented here will enable future many-body studies of band inversion that can shed light on the delicate interplay between correlation and topology in correlated topological materials.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673321","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":"Reducing the Sampling Complexity of Energy Estimation in Quantum Many-Body Systems Using Empirical Variance Information.","authors":"Alexander Gresch, Uğur Tepe, Martin Kliesch","doi":"10.1021/acs.jctc.5c00370","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00370","url":null,"abstract":"<p><p>We consider the problem of estimating the energy of a quantum state preparation for a given Hamiltonian in Pauli decomposition. For various quantum algorithms, in particular, in the context of quantum chemistry, it is crucial to have energy estimates with error bounds, as captured by guarantees on the problem's sampling complexity. In particular, when limited to Pauli basis measurements, the smallest sampling complexity guarantee comes from a simple single-shot estimator via a straightforward argument based on Hoeffding's inequality. In this work, we construct an adaptive estimator using the state's actual variance. Technically, our estimation method is based on the empirical Bernstein stopping (EBS) algorithm and grouping schemes, and we provide a rigorous tail bound, which leverages the state's empirical variance. In a numerical benchmark of estimating ground-state energies of several Hamiltonians, we demonstrate that EBS consistently improves upon elementary readout guarantees up to 1 order of magnitude.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673322","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":"\"Beyond-Zero-Sum\" Range-Separated Local Hybrid Functional with Improved Dynamical Correlation.","authors":"Artur Wodyński, Martin Kaupp","doi":"10.1021/acs.jctc.5c00699","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00699","url":null,"abstract":"<p><p>Recent work has shown that range-separated local hybrid (RSLH) functionals containing correction terms for strong correlation and delocalization errors, such as ωLH23tdE, allow a remarkable paradigm change in the context of the usual zero-sum game between delocalization and static correlation errors in the development of density functional approximations. In this work, we evaluate the modification of the dynamical correlation contribution for such strong correlation-corrected RSLHs (scRSLHs) and how it affects the performance of the large GMTKN55 database of main-group thermochemistry, kinetics, and noncovalent interactions. Replacing the B95c correlation in the previous functionals by a more flexible reoptimized B97c power-series expansion leads to substantial improvements. The ωLH25tdE scRSLH provides a GMTKN55 WTMAD-2 value of 2.64 kcal/mol in self-consistent calculations, when augmented by DFT-D4 corrections. This is the lowest for any rung 4 functional today. At the same time, ωLH25tdE retains the favorable performance for spin-restricted bond dissociation, the removal of unphysical spin contamination in certain open-shell transition-metal complexes, and the correct long-range asymptotic potential, resulting in excellent results for quasiparticle computations of ionization potentials, electron affinities, and band gaps.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657869","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":"Cytochrome c Facilitates Binding between Lipid Bilayers and Citrate-Coated Gold Nanoparticles in Coarse-Grained Simulations.","authors":"Yinhan Wang, Rigoberto Hernandez","doi":"10.1021/acs.jctc.5c00454","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00454","url":null,"abstract":"<p><p>Characterization and prediction of the interactions between engineered nanoparticles (ENPs), proteins, and biological membranes is critical for advancing applications to nanomedicine and nanomanufacturing while mitigating nanotoxicological risks. In this work, we employ a coarse-grained dissipative particle dynamics (DPD) simulation to investigate the interactions among cytochrome c (CytC), lipid bilayers, and citrate-coated gold nanoparticles (AuNPs). We updated the DPD potential to accurately represent binding potentials between molecules, and validated the model relative to an all-atom representation. The DPD simulations successfully replicate experimental observations: CytC facilitates the binding of citrate-coated AuNPs to lipid bilayers composed of 90% dioleoylphosphatidylcholine (DOPC) mixed with 10% stearoylphosphatidylinositol (SAPI) or 10% tetraoleoyl cardiolipin (TOCL) but not to pure 100% DOPC bilayers. In addition, the simulations reveal nuanced differences in binding preferences between CytC, the lipid bilayers, and the ENP, at a scale that is not presently directly observable in experiments. Specifically, we found that the surface coating of the nanoparticles─viz variations in the CytC surface density─affects the protein-mediated binding with the bilayers. Such a molecular-sensitive result underscores the utility of DPD simulations in simulating complex biological systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144657871","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}