Journal of Chemical Physics最新文献

{"title":"Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.","authors":"Prabin Baral, Mert Y Sengul, Alexander D MacKerell","doi":"10.1063/5.0241246","DOIUrl":"10.1063/5.0241246","url":null,"abstract":"<p><p>Molecular dynamics simulations are crucial for understanding the structural and dynamical behavior of biomolecular systems, including the impact of their environment. However, there is a gap between the time scale of these simulations and that of real-world experiments. To address this problem, various enhanced simulation methods have been developed. In addition, there has been a significant advancement of the force fields used for simulations associated with the explicit treatment of electronic polarizability. In this study, we apply oscillating chemical potential grand canonical Monte Carlo and machine learning methods to determine reaction coordinates combined with metadynamics simulations to explore the role of Mg2+ distribution and electronic polarizability in the context of the classical Drude oscillator polarizable force field on the stability of the twister ribozyme. The introduction of electronic polarizability along with the details of the distribution of Mg2+ significantly stabilizes the simulations with respect to sampling the crystallographic conformation. The introduction of electronic polarizability leads to increased stability over that obtained with the additive CHARMM36 FF reported in a previous study, allowing for a distribution of a wider range of ions to stabilize twister. Specific interactions contributing to stabilization are identified, including both those observed in the crystal structures and additional experimentally unobserved interactions. Interactions of Mg2+ with the bases are indicated to make important contributions to stabilization. Notably, the presence of specific interactions between the Mg2+ ions and bases or the non-bridging phosphate oxygens (NBPOs) leads to enhanced dipole moments of all three moieties. Mg2+-NBPO interactions led to enhanced dipoles of the phosphates but, interestingly, not in all the participating ions. The present results further indicate the importance of electronic polarizability in stabilizing RNA in molecular simulations and the complicated nature of the relationship of Mg2+-RNA interactions with the polarization response of the bases and phosphates.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813289","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}

{"title":"Variance-based wave function optimization within the unrestricted doubly occupied configuration interaction framework: A half-projection treatment.","authors":"Javier Garcia, Diego R Alcoba, Alicia Torre, Luis Lain, Ofelia B Oña, Gustavo E Massaccesi","doi":"10.1063/5.0242174","DOIUrl":"https://doi.org/10.1063/5.0242174","url":null,"abstract":"<p><p>The energy-variance-based optimization procedures have proven to be useful tools to describe N-electron spectra. However, the resulting wave functions usually present spin-contaminant contributions. The goal of this work is to reduce the spin contamination of the results arising from the unrestricted doubly occupied configuration interaction method in its energy variance minimization version [Alcoba et al., J. Chem. Phys. 160, 164107 (2024)]. We propose to incorporate the half-projection technique, which allows removing the spin components with even or odd spin quantum number of an approximate N-electron wave function, into the framework of the unrestricted doubly occupied configuration interaction treatment. This implementation can be carried out following several possible ways, whose results are analyzed in detail, in order to show the behavior of each procedure. Numerical determinations performed on selected strongly correlated N-electron systems, in ground and excited states, allow us to assess the most suitable procedure.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818220","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}

{"title":"Calculation of thermodynamic properties of helium using path integral Monte Carlo simulations in the NpT ensemble and ab initio potentials.","authors":"Philipp Marienhagen, Karsten Meier","doi":"10.1063/5.0243210","DOIUrl":"https://doi.org/10.1063/5.0243210","url":null,"abstract":"<p><p>We apply the methodology of Lustig, with which rigorous expressions for all thermodynamic properties can be derived in any statistical ensemble, to derive expressions for the calculation of thermodynamic properties in the path integral formulation of the quantum-mechanical isobaric-isothermal (NpT) ensemble. With the derived expressions, thermodynamic properties such as the density, speed of sound, or Joule-Thomson coefficient can be calculated in path integral Monte Carlo simulations, fully incorporating quantum effects without uncontrolled approximations within the well-known isomorphism between the quantum-mechanical partition function and a classical system of ring polymers. The derived expressions are verified by simulations of supercritical helium above the vapor-liquid critical point at selected state points using recent highly accurate ab initio potentials for pairwise and nonadditive three-body interactions. We observe excellent agreement of our results with the most accurate experimental data for the density and speed of sound and a reference virial equation of state for helium in the region where the virial equation of state is converged. Moreover, our results agree closer with the experimental data and virial equation of state than the results of semiclassical simulations using the Feynman-Hibbs correction for quantum effects, which demonstrates the necessity to fully include quantum effects by path integral simulations. Our results also show that nonadditive three-body interactions must be accounted for when accurately predicting thermodynamic properties of helium by solely theoretical means.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828273","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}

{"title":"Density functional theory for fractional charge: Locality, size consistency, and exchange-correlation.","authors":"Jing Kong","doi":"10.1063/5.0234907","DOIUrl":"https://doi.org/10.1063/5.0234907","url":null,"abstract":"<p><p>We show that the exact universal density functional of integer electronic charge leads to an extension to fractional charge in an asymptotic sense when it is applied to a system made of asymptotically separated densities. The extended functional is asymptotically local and is said to be i-local. The concept of i-locality is also applicable to nuclear external potentials, and a natural association exists between the localities of a density and a set of nuclei. Applying the functional to a system with nuclei distributed in two asymptotically separated locales requires an explicit search of the electronic charge at each locale with the constraint of the global charge. The determined number of electrons at each locale can be fractional. The molecular size consistency principle is realized as the result of the search. It is physically sensible to extend the molecule concept to include a fractional number of electrons (called fractional molecule henceforth) as a localized observable. The physical validity of fractional molecules is equivalent to the asymptotic separability of molecules, a basic assumption in molecular research. A one-to-one mapping between a fractional molecule's density and external potential is shown to exist with a nondegenerate condition. The global one-to-one mapping required by the Hohenberg-Kohn first theorem is realized through the aforementioned global search for molecular charges. Furthermore, the well-known piecewise linearity of the universal functional with respect to the number of electrons is necessary for an approximate i-local universal functional to be broadly accurate for any integer number of electrons. The Kohn-Sham (KS) noninteracting kinetic energy functional for a fractional molecule is well-defined and has the same form as that for a system of an integer number of electrons. It is shown to be i-local. A nondegenerate, noninteracting ensemble v-representable fractional density is simultaneously noninteracting wavefunction representable. A constrained search over those representing wavefunctions yields the definition of an exchange-correlation functional pertaining to fractional occupancies of KS orbitals. The functional is shown to be an upper bound to the formal KS exchange-correlation energy of a fractional molecule and includes a strong correlation. It yields the correct result for a well-designed example of effective fractional occupancies in the literature.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813156","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}

{"title":"First-principles study of electron dynamics of MoS2 under femtosecond laser irradiation from deep ultraviolet to near-infrared wavelengths.","authors":"Huimin Qi, Jinshi Wang, Zongwei Xu, Fengzhou Fang","doi":"10.1063/5.0232520","DOIUrl":"https://doi.org/10.1063/5.0232520","url":null,"abstract":"<p><p>Time-dependent density functional theory was employed to investigate the electron dynamics of MoS2 following femtosecond pulse irradiation. The study concerned the effects of laser wavelength, intensities, and polarization and elucidated the ionization mechanisms across the intensity range of 1010-1014 W/cm2. As laser intensity increases, MoS2 irradiated with an infrared (IR) laser (800 nm) deviates from single-photon absorption at lower intensities compared to that subjected to an ultraviolet (UV) laser (266 nm), and nonlinear effects in the current arise at lower intensities for the 800 nm laser. At a wavelength of 266 nm, MoS2 irradiated with an a-axis polarized laser deposited more energy and generated more electron-hole pairs compared to c-axis polarization. Rate equations were used to estimate the total number of excited electrons in MoS2 and the corresponding plasma frequency. Simulation results indicate that the damage threshold of the UV laser is higher than that of the IR laser, which contradicts the experimental results. This outcome suggests that the mechanism of material damage induced by the UV femtosecond laser near the damage threshold is independent of optical breakdown. The findings of this research are significant for enhancing the performance of MoS2-based photodetectors and optimizing their stability and reliability in high-power, short-wavelength laser applications.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 22","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142818218","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}

{"title":"Recasting the wobbling-in-a-cone model for the rotational anisotropy of phenylselenocyanate in poly(methyl methacrylate): Effect of internal bond rotation and polymer segmental motion.","authors":"Sourav Palchowdhury, Saptarsi Mondal, Kyungwon Kwak, Minhaeng Cho","doi":"10.1063/5.0239896","DOIUrl":"https://doi.org/10.1063/5.0239896","url":null,"abstract":"<p><p>The rotational anisotropy of a molecule in a constrained environment is modeled by wobbling-in-a-cone (WIAC) motion, which describes the angular space sampled by the molecule. Recent polarization-selective IR pump-probe measurements have applied this model to phenylselenocyanate in amorphous polymers, aiming to probe the surrounding free volume. A faster rotational timescale was hypothesized to reflect the angular space within the static voids of the polymer matrix, while a slower timescale relates to constraint release by the polymer backbones. To better quantify the contributions of internal bond rotation and polymer segmental motion, we conduct molecular dynamics simulations on two phenylselenocyanate variants with different internal rotational barriers, as well as on p-chlorobenzonitrile, which lacks such internal rotational freedom, within a polymer matrix. Our analyses reveal that the faster (∼10 ps) component of the cyano group's anisotropy decay arises from concurrent angular sampling due to internal bond rotation and WIAC motion. Conversely, polymer segmental motion was found to have a minimal influence on the slow (∼200 ps) anisotropy component. Based on these findings, we refine the WIAC model to better link rotational diffusion with the distinct free volume elements accessed by the probe molecule. This revised model allows the quantification of free volume elements associated with both internal bond rotation and wobbling motion within the polymer cage.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785888","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}

{"title":"Data-assimilated crystal growth simulation for multiple crystalline phases.","authors":"Yuuki Kubo, Ryuhei Sato, Yuansheng Zhao, Takahiro Ishikawa, Shinji Tsuneyuki","doi":"10.1063/5.0223390","DOIUrl":"https://doi.org/10.1063/5.0223390","url":null,"abstract":"<p><p>To determine crystal structures from a powder x-ray diffraction (PXRD) pattern containing multiple unknown phases, a data-assimilated crystal growth (DACG) simulation method has been developed. The PXRD penalty function selectively stabilizes the structures in the experimental data, promoting their grain growth during simulated annealing. Since the PXRD pattern is calculated as the Fourier transform of the pair distribution function, the DACG simulation can be performed without prior determination of the lattice parameters. We applied it to carbon (graphite and diamond) and SiO2 (low-quartz, low-cristobalite, and coesite) systems, demonstrating that the DACG simulation successfully reproduced multiple crystal structures.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785886","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}

{"title":"Response to \"Comment on 'On the intensity of light scattered by molecular liquids-Comparison of experiment and quantum chemical calculations'\" [J. Chem. Phys. 161, 217101 (2024)].","authors":"Florian Pabst, Pierre-Michel Déjardin, Thomas Blochowicz","doi":"10.1063/5.0233386","DOIUrl":"https://doi.org/10.1063/5.0233386","url":null,"abstract":"","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785892","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}

{"title":"The bonded interfacial layer structure of α-Al2O3 (0001)/water at different pH values studied by sum frequency vibrational spectroscopy.","authors":"Shumei Sun, Huanzhen Yao, Jiabao Pan, Zhenzhe Xian","doi":"10.1063/5.0235695","DOIUrl":"https://doi.org/10.1063/5.0235695","url":null,"abstract":"<p><p>Oxide/water interfaces are ubiquitous, with alumina/water drawing particular interest due to its environmental and industrial applications. Understanding the interfacial structure at the molecular level is crucial for many physical and chemical processes occurring there. However, the exact structure of interfacial H-bonded network at different pH values remains unclear. Here, sum-frequency vibrational spectroscopy in the OH stretch region was employed to study α-Al2O3 (0001)/water interface at different pH values, while suppressing the contribution of the diffusion layer by adding salts. The experimental results revealed although the variation of pH can charge the surface, it has little impact on the structure of the bonded interfacial layer (BIL). The interaction between alumina and water is mainly governed by weak hydrogen bonds. Furthermore, the templating effect of α-Al2O3 (0001) on the interfacial H-bonded network was observed, with the O-H stretch mode of ∼3430 cm-1 exhibiting anisotropy consistent with the (0001) surface symmetry. These findings indicate that the BIL structure on Al2O3 (0001) is predominantly influenced by the surface atom configuration, and the effect of charge changes induced by pH on the BIL structure is negligible.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785821","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}

{"title":"Comment on \"On the intensity of light scattered by molecular liquids-Comparison of experiment and quantum chemical calculations\" [J. Chem. Phys. 157, 244501 (2022)].","authors":"Tom Keyes","doi":"10.1063/5.0220390","DOIUrl":"https://doi.org/10.1063/5.0220390","url":null,"abstract":"","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"161 21","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785879","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}