The Journal of chemical physics最新文献

{"title":"Sample size dependence of tagged molecule dynamics in steady-state networks with bimolecular reactions: Cycle times of a light-driven pump.","authors":"Daniele Asnicar, Emanuele Penocchio, D. Frezzato","doi":"10.1063/5.0089695","DOIUrl":"https://doi.org/10.1063/5.0089695","url":null,"abstract":"Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the small-volume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial \"compartmentalization\" may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic light-driven supramolecular pump composed of ring-like and axle-like molecules that dynamically assemble and disassemble, originating an average ring-through-axle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system's size. This is explained in the presence of rate-determining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"30-31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133476435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate description of the quantum dynamical surface temperature effects on the dissociative chemisorption of H2 from Cu(111).","authors":"B. Smits, L. Litjens, M. Somers","doi":"10.1063/5.0094985","DOIUrl":"https://doi.org/10.1063/5.0094985","url":null,"abstract":"Accurately describing surface temperature effects for the dissociative scattering of H2 on a metal surface on a quantum dynamical (QD) level is currently one of the open challenges for theoretical surface scientists. We present the first QD simulations of hydrogen dissociating on a Cu(111) surface, which accurately describe all relevant surface temperature effects, using the static corrugation model. The reaction probabilities we obtain show very good agreement with those found using quasi-classical dynamics (QCD), both for individual surface slabs and for an averaged, thus Monte Carlo sampled, set of thermally distorted surface configurations. Rovibrationally elastic scattering probabilities show a much clearer difference between the QCD and QD results, which appears to be traceable back toward thermally distorted surface configurations with very low dissociation probabilities and underlines the importance of investigating more observables than just dissociation. By reducing the number of distorted surface atoms included in the dynamical model, we also show that only including one surface atom, or even three surface atoms, is generally not enough to accurately describe the effects of the surface temperature on dissociation and elastic scattering. These results are a major step forward in accurately describing hydrogen scattering from a thermally excited Cu(111) surface and open up a pathway to better describe reaction and scattering from other relevant crystal facets, such as stepped surfaces, at moderately elevated surface temperatures where quantum effects are expected to play a more important role in the dissociation of H2 on Cu.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"185 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133607072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nuclear-electronic orbital approach to quantization of protons in periodic electronic structure calculations.","authors":"Jianhang Xu, Ruiyi Zhou, Z. Tao, Christopher L. Malbon, V. Blum, S. Hammes‐Schiffer, Y. Kanai","doi":"10.1063/5.0088427","DOIUrl":"https://doi.org/10.1063/5.0088427","url":null,"abstract":"The nuclear-electronic orbital (NEO) method is a well-established approach for treating nuclei quantum mechanically in molecular systems beyond the usual Born-Oppenheimer approximation. In this work, we present a strategy to implement the NEO method for periodic electronic structure calculations, particularly focused on multicomponent density functional theory (DFT). The NEO-DFT method is implemented in an all-electron electronic structure code, FHI-aims, using a combination of analytical and numerical integration techniques as well as a resolution of the identity scheme to enhance computational efficiency. After validating this implementation, proof-of-concept applications are presented to illustrate the effects of quantized protons on the physical properties of extended systems, such as two-dimensional materials and liquid-semiconductor interfaces. Specifically, periodic NEO-DFT calculations are performed for a trans-polyacetylene chain, a hydrogen boride sheet, and a titanium oxide-water interface. The zero-point energy effects of the protons as well as electron-proton correlation are shown to noticeably impact the density of states and band structures for these systems. These developments provide a foundation for the application of multicomponent DFT to a wide range of other extended condensed matter systems.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126936055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulating the charging of cylindrical electrolyte-filled pores with the modified Poisson-Nernst-Planck equations.","authors":"Jie Yang, Mathijs Janssen, Cheng Lian, R. van Roij","doi":"10.1063/5.0094553","DOIUrl":"https://doi.org/10.1063/5.0094553","url":null,"abstract":"Understanding how electrolyte-filled porous electrodes respond to an applied potential is important to many electrochemical technologies. Here, we consider a model supercapacitor of two blocking cylindrical pores on either side of a cylindrical electrolyte reservoir. A stepwise potential difference 2Φ between the pores drives ionic fluxes in the setup, which we study through the modified Poisson-Nernst-Planck equations, solved with finite elements. We focus our discussion on the dominant timescales with which the pores charge and how these timescales depend on three dimensionless numbers. Next to the dimensionless applied potential Φ, we consider the ratio R/Rb of the pore's resistance R to the bulk reservoir resistance Rb and the ratio rp/λ of the pore radius rp to the Debye length λ. We compare our data to theoretical predictions by Aslyamov and Janssen (Φ), Posey and Morozumi (R/Rb), and Henrique, Zuk, and Gupta (rp/λ). Through our numerical approach, we delineate the validity of these theories and the assumptions on which they were based.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127839466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasmon-driven oxidative coupling of aniline-derivative adsorbates: A comparative study of para-ethynylaniline and para-mercaptoaniline.","authors":"Kexun Chen, Hui Wang","doi":"10.1063/5.0094890","DOIUrl":"https://doi.org/10.1063/5.0094890","url":null,"abstract":"Plasmon-driven photocatalysis has emerged as a paradigm-shifting approach, based on which the energy of photons can be judiciously harnessed to trigger interfacial molecular transformations on metallic nanostructure surfaces in a regioselective manner with nanoscale precision. Over the past decade, the formation of aromatic azo compounds through plasmon-driven oxidative coupling of thiolated aniline-derivative adsorbates has become a testbed for developing detailed mechanistic understanding of plasmon-mediated photochemistry. Such photocatalytic bimolecular coupling reactions may occur not only between thiolated aniline-derivative adsorbates but also between their nonthiolated analogs. How the nonthiolated adsorbates behave differently from their thiolated counterparts during the plasmon-driven coupling reactions, however, remains largely unexplored. Here, we systematically compare an alkynylated aniline-derivative, para-ethynylaniline, to its thiolated counterpart, para-mercaptoaniline, in terms of their adsorption conformations, structural flexibility, photochemical reactivity, and transforming kinetics on Ag nanophotocatalyst surfaces. We employ surface-enhanced Raman scattering as an in situ spectroscopic tool to track the detailed structural evolution of the transforming molecular adsorbates in real time during the plasmon-driven coupling reactions. Rigorous analysis of the spectroscopic results, further aided by density functional theory calculations, lays an insightful knowledge foundation that enables us to elucidate how the alteration of the chemical nature of metal-adsorbate interactions profoundly influences the transforming behaviors of the molecular adsorbates during plasmon-driven photocatalytic reactions.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116676053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adiabatic electronic flux in molecules and in condensed matter.","authors":"R. Resta","doi":"10.1063/5.0087883","DOIUrl":"https://doi.org/10.1063/5.0087883","url":null,"abstract":"The theory of adiabatic electron transport in a correlated condensed-matter system is rooted in a seminal paper by Niu and Thouless [J. Phys. A: Math. Gen. 17, 2453 (1984)]; I adopt here an analogous logic in order to retrieve the known expression for the adiabatic electronic flux in a molecular system [L. A. Nafie, J. Chem. Phys. 79, 4950 (1983)]. Its derivation here is considerably simpler than those available in the current quantum-chemistry literature; it also explicitly identifies the adiabaticity parameter, in terms of which the adiabatic flux and the electron density are both exact to first order. It is shown that the continuity equation is conserved to the same order. For the sake of completeness, I also briefly outline the relevance of the macroscopic electronic flux to the physics of solids and liquids.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126675962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanoparticle cluster formation mechanisms elucidated via Markov state modeling: Attraction range effects, aggregation pathways, and counterintuitive transition rates.","authors":"Xi Yang, Zhong-yuan Lu","doi":"10.1063/5.0086110","DOIUrl":"https://doi.org/10.1063/5.0086110","url":null,"abstract":"Nanoparticle clusters are promising candidates for developing functional materials. However, it is still a challenging task to fabricate them in a predictable and controllable way, which requires investigation of the possible mechanisms underlying cluster formation at the nanoscale. By constructing Markov state models (MSMs) at the microstate level, we find that for highly dispersed particles to form a highly aggregated cluster, there are multiple coexisting pathways, which correspond to direct aggregation, or pathways that need to pass through partially aggregated, intermediate states. Varying the range of attraction between nanoparticles is found to significantly affect pathways. As the attraction range becomes narrower, compared to direct aggregation, some pathways that need to pass through partially aggregated intermediate states become more competitive. In addition, from MSMs constructed at the macrostate level, the aggregation rate is found to be counterintuitively lower with a lower free-energy barrier, which is also discussed.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116303252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracing the origin of heterogeneities in the local structure and very sluggish dynamics of [Cho][Gly] ionic liquid confined between rutile and graphite slit nanopores: A MD study.","authors":"Farzad Khorrami, M. H. Kowsari","doi":"10.1063/5.0092381","DOIUrl":"https://doi.org/10.1063/5.0092381","url":null,"abstract":"Atomistic-level understanding of the interfacial behavior of ionic liquids (ILs) confined in slit-like nanopores is of both fundamental and practical interest. Molecular dynamics (MD) is an efficient and robust approach to characterize the properties of confined systems in contrast with some limitations in direct experimental measurements at low-dimensions. In this research, MD simulations are used to study the biocompatible IL cholinium glycinate, [Cho][Gly], confined between two parallel plates of rutile or graphite, with the separation distance of 24 Å along the z-direction. As expected, both the microscopic local structure and dynamical behavior of the confined IL are very heterogeneous and depend effectively on the position of the ions to the pore walls. The ion z-density profile is used for segmentation of the inter-wall space into a central region and two outer layers. The behavior of ions in the central region is very similar to the bulk IL, while the behavior of the arranged ionic layers adjacent to the pore walls shows the clear deviation from the bulk IL due to confinement. In general, the confined IL shows a \"solid-like\" dynamics at T = 353 K, especially in the outer layers near the walls as well as in the z-direction. The presence of the \"IL-rutile wall\" electrostatic interaction and hydrogen bonding (H-bonding) causes a significant difference in the local structure and very sluggish dynamics of the IL adjacent to the rutile walls vs the graphite walls. Simulation reveals a significant decrease in the average number of key cation-anion H-bonds at the outer layers relative to the central regions of both confined systems. The recognized [Cho]+⋯[Gly]-⋯[Cho]+ bridge structure at the central region is lost in the vicinity of the rutile walls due to inaccessibility of the hydroxyl hydrogen atom, which forms a stable H-bond with the rutile oxygen site. However, another unprecedented [Gly]- bridge is confirmed and preserved near the graphite walls, and [Cho]+ cations prefer to stay parallel to the wall surface to form the van der Waals dispersion interactions with the uncharged graphite walls.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"5 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120916431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multiscale time-Laplace method to extract relaxation times from non-stationary dynamic light scattering signals.","authors":"François Liénard, É. Freyssingeas, P. Borgnat","doi":"10.1063/5.0088005","DOIUrl":"https://doi.org/10.1063/5.0088005","url":null,"abstract":"Dynamic Light Scattering (DLS) is a well-known technique to study the relaxation times of systems at equilibrium. In many soft matter systems, we actually have to consider non-equilibrium or non-stationary situations. We discuss here the principles, the signal processing techniques we developed, based on regularized inverse Laplace transform, sliding with time, and the light scattering signal acquisition, which enable us to use DLS experiments in this general situation. In this article, we show how to obtain such a time-Laplace analysis. We claim that this method can be adapted to numerous DLS experiments dealing with non-equilibrium systems so as to extract the non-stationary distribution of relaxation times. To prove that, we test this time-Laplace method on three different non-equilibrium processes or systems investigated by means of the DLS technique: the cooling kinetics of a colloidal particle solution, the sol-gel transition and the internal dynamics of a living cell nucleus.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131696700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bonding properties of molecular cerium oxides tuned by the 4f-block from ab initio perspective.","authors":"Ziyong Chen, J. Yang","doi":"10.1063/5.0090214","DOIUrl":"https://doi.org/10.1063/5.0090214","url":null,"abstract":"Probing chemical bonding in molecules containing lanthanide elements is of theoretical interest, yet it is computationally challenging because of the large valence space, relativistic effects, and considerable electron correlation. We report a high-level ab initio study that quantifies the many-body nature of Ce-O bonding with the coordination environment of the Ce center and particularly the roles of the 4f orbitals. The growing significance of the overlap between Ce 4f and O 2p orbitals with the increasing coordination of Ce atoms enhances Ce-O bond covalency and in return directs the molecular geometry. Upon partial reduction from neutral to anionic ceria, the excessive electrons populate the Ce-centered localized 4f orbital. The interplay between the admixture and localization of the 4f-block dually modulates bonding patterns of cerium oxide molecules, underlying the importance of many-body interactions between ligands and various lanthanide elements.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132384242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}