The Journal of chemical physics最新文献

{"title":"Deuteron magnetic resonance study of glyceline deep eutectic solvents: Selective detection of choline and glycerol dynamics.","authors":"Yannik Hinz, R. Böhmer","doi":"10.1063/5.0088290","DOIUrl":"https://doi.org/10.1063/5.0088290","url":null,"abstract":"Glyceline, a green solvent considered for various electrochemical applications, represents a multi-component glass former. Viewed from this perspective, the choline cation and the hydrogen bond donor glycerol, the two major constituents forming this deep eutectic solvent, were studied using nuclear magnetic resonance in a selective manner by means of suitably deuteron-labeled isotopologues. Carried out from far above to far below the glass transition temperature, measurements and analyses of the spin-lattice and spin-spin relaxation times reveal that the reorientational dynamics of the components, i.e., of glycerol as well as of chain deuterated choline chloride are slightly different. Possible implications of this finding regarding the hydrogen-bonding pattern in glyceline are discussed. Furthermore, the deuterated methyl groups in choline chloride are exploited as sensitive probes of glyceline's supercooled and glassy states. Apart from spin relaxometry, a detailed line shape analysis of the CD3 spectra yields valuable insights into the broad intermolecular and intramolecular energy barrier distributions present in this binary mixture.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"67 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124359872","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":"Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes.","authors":"F. C. Freitas, Michelli Maldonado, A. B. Oliveira Junior, J. Onuchic, R. J. Oliveira","doi":"10.1063/5.0083875","DOIUrl":"https://doi.org/10.1063/5.0083875","url":null,"abstract":"Biotin-labeled proteins are widely used as tools to study protein-protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130052570","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":"The onset of solidification: From interface formation to the Stefan regime.","authors":"A. Belozerov, Y. Shikhmurzaev","doi":"10.1063/5.0084044","DOIUrl":"https://doi.org/10.1063/5.0084044","url":null,"abstract":"The onset of a solidification process is considered in a situation where the free surface of a warm liquid is touched by a sufficiently cold solid. The process is analyzed in terms of a model that takes into account the formation of a liquid-solid interface as the two media are brought in contact and then the appearance of the solidified liquid as a third bulk phase. As is shown, the temperature at the liquid-solid interface and then at the solidification front evolves in a non-monotone way, and when the solidification front appears and starts to move, its velocity is not a function of its temperature. The classical Stefan regime of solidification appears as a limit as the temperature at the solidification front evolves toward the melting temperature.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"147 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115829483","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":"Modeling colloidal interactions that predict equilibrium and non-equilibrium states.","authors":"Brian K. Ryu, Scott M Fenton, Tuan T D Nguyen, M. Helgeson, R. Zia","doi":"10.1063/5.0086650","DOIUrl":"https://doi.org/10.1063/5.0086650","url":null,"abstract":"Modulating the interaction potential between colloids suspended in a fluid can trigger equilibrium phase transitions as well as the formation of non-equilibrium \"arrested states,\" such as gels and glasses. Faithful representation of such interactions is essential for using simulation to interrogate the microscopic details of non-equilibrium behavior and for extrapolating observations to new regions of phase space that are difficult to explore in experiments. Although the extended law of corresponding states predicts equilibrium phases for systems with short-ranged interactions, it proves inadequate for equilibrium predictions of systems with longer-ranged interactions and for predicting non-equilibrium phenomena in systems with either short- or long-ranged interactions. These shortcomings highlight the need for new approaches to represent and disambiguate interaction potentials that replicate both equilibrium and non-equilibrium phase behavior. In this work, we use experiments and simulations to study a system with long-ranged thermoresponsive colloidal interactions and explore whether a resolution to this challenge can be found in regions of the phase diagram where temporal effects influence material state. We demonstrate that the conditions for non-equilibrium arrest by colloidal gelation are sensitive to both the shape of the interaction potential and the thermal quench rate. We exploit this sensitivity to propose a kinetics-based algorithm to extract distinct arrest conditions for candidate potentials that accurately selects between potentials that differ in shape but share the same predicted equilibrium structure. The algorithm selects the candidate that best matches the non-equilibrium behavior between simulation and experiments. Because non-equilibrium behavior in simulation is encoded entirely by the interparticle potential, the results are agnostic to the particular mechanism(s) by which arrest occurs, and so we expect our method to apply to a range of arrested states, including gels and glasses. Beyond its utility in constructing models, the method reveals that each potential has a quantitatively distinct arrest line, providing insight into how the shape of longer-ranged potentials influences the conditions for colloidal gelation.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"126 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131635199","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":"Adsorption of C2-C5 alcohols on ice: A grand canonical Monte Carlo simulation study.","authors":"J. Joliat, S. Picaud, A. Patt, P. Jedlovszky","doi":"10.1063/5.0096013","DOIUrl":"https://doi.org/10.1063/5.0096013","url":null,"abstract":"In this paper, we report grand canonical Monte Carlo simulations performed to characterize the adsorption of four linear alcohol molecules, comprising between two and five carbon atoms (namely, ethanol, n-propanol, n-butanol, and n-pentanol) on crystalline ice in a temperature range typical of the Earth's troposphere. The adsorption details analyzed at 228 K show that, at low coverage of the ice surface, the polar head of the adsorbed molecules tends to optimize its hydrogen bonding with the surrounding water, whereas the aliphatic chain lies more or less parallel to the ice surface. With increasing coverage, the lateral interactions between the adsorbed alcohol molecules lead to the reorientation of the aliphatic chains that tend to become perpendicular to the surface; the adsorbed molecules pointing thus their terminal methyl group up to the gas phase. When compared to the experimental data, the simulated and measured isotherms show a very good agreement, although a small temperature shift between simulations and experiments could be inferred from simulations at various temperatures. In addition, this agreement appears to be better for ethanol and n-propanol than for n-butanol and n-pentanol, especially at the highest pressures investigated, pointing to a possible slight underestimation of the lateral interactions between the largest alcohol molecules by the interaction potential model used. Nevertheless, the global accuracy of the approach used, as tested under tropospheric conditions, opens the way for its use in modeling studies also relevant to another (e.g., astrophysical) context.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"156 22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130879773","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":"Composition-dependent sign inversion of the Soret coefficient of SiO2 in binary borosilicate melts.","authors":"M. Shimizu, Kenzo Sato, Kento Nakashima, T. Kiyosawa, J. Matsuoka, Y. Shimotsuma, K. Miura","doi":"10.1063/5.0090939","DOIUrl":"https://doi.org/10.1063/5.0090939","url":null,"abstract":"Using a laser-induced local-heating experiment combined with temperature analysis, we observed the composition-dependent sign inversion of the Soret coefficient of SiO2 in binary silicate melts, which was successfully explained by a modified Kempers model used for describing the Soret effect in oxide melts. In particular, the diffusion of SiO2 to the cold side under a temperature gradient, which is an anomaly in silicate melts, was observed in the SiO2-poor compositions. The theoretical model indicates that the thermodynamic mixing properties of oxides, partial molar enthalpy of mixing, and partial molar volume are the dominant factors for determining the migration direction of the SiO2 component under a temperature gradient.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123911351","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":"Dielectric constant of aqueous solutions of proteins and organic polymers from molecular dynamics simulations.","authors":"Susanne Liese, Alexander Schlaich, R. Netz","doi":"10.1063/5.0089397","DOIUrl":"https://doi.org/10.1063/5.0089397","url":null,"abstract":"The dielectric constant of water/oligomer mixtures, spanning the range from pure water to pure oligomeric melts, is investigated using molecular dynamics (MD) simulations. As prototypical water-soluble organic substances, we consider neutral poly-glycine, poly-ethylene glycol, and charged monomeric propionic acid. As the water content is reduced, the dielectric constant decreases but does not follow an ideal mixing behavior. The deviations from ideal mixing originate primarily in the non-linear relation between the oligomer mass fraction and collective polarization effects. We find that the dielectric constant is dominated by water polarization, even if the oligomer mass fraction exceeds 50%. By a double extrapolation of the MD simulation results to the limit of vanishing water fraction and to the limit of infinite oligomeric chain length, we estimate the orientational contribution to the dielectric constant of the pure polymeric melts. By this procedure, we obtain ɛ = 17 ± 2 for polyglycine and ɛ = 1 ± 0.3 for polyethylene glycol. The large difference is rationalized by polarization correlations of glycine units. Interestingly, we find constant temperature simulations to outperform replica exchange simulations in terms of equilibration speed.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126278273","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":"The rate of thermodynamic cost against adiabatic and nonadiabatic fluctuations of a single gene circuit in Drosophila embryos.","authors":"Kun Zhang, A. F. Ramos, Erkang Wang, Jin Wang","doi":"10.1063/5.0091710","DOIUrl":"https://doi.org/10.1063/5.0091710","url":null,"abstract":"We study the stochastic dynamics of the externally regulating gene circuit as an example of an eve-skipped gene stripe in the development of Drosophila. Three gene regulation regimes are considered: an adiabatic phase when the switching rate of the gene from the OFF to ON state is faster than the rate of mRNA degradation; a nonadiabatic phase when the switching rate from the OFF to ON state is slower than that of the mRNA degradation; and a bursting phase when the gene switching is fast and transcription is very fast, while the ON state probability is very low. We found that the rate of thermodynamic cost quantified by the entropy production rate can suppress the fluctuations of the gene circuit. A higher (lower) rate of thermodynamic cost leads to reduced (increased) fluctuations in the number of gene products in the adiabatic (nonadiabatic) regime. We also found that higher thermodynamic cost is often required to sustain the emergence of more gene states and, therefore, more heterogeneity coming from genetic mutations or epigenetics. We also study the stability of the gene state using the mean first passage time from one state to another. We found the monotonic decrease in time, i.e., in the stability of the state, in the transition from the nonadiabatic to adiabatic regimes. Therefore, as the higher rate of thermodynamic cost suppresses the fluctuations, higher stability requires higher thermodynamics cost to maintain.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"156 22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130948615","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 unified approach for calculating free energies of liquid and defective crystals based on thermodynamic integration.","authors":"Jinping Luo, Chenyang Zhou, Qihang Li, Lijun Liu","doi":"10.1063/5.0095638","DOIUrl":"https://doi.org/10.1063/5.0095638","url":null,"abstract":"Free energy calculation is fundamentally important in the research of physics, chemistry, and materials. Thermodynamic integration is the most common way to estimate free energies. In the research, we proposed a unified approach using atomic simulations to calculate the free energies of liquid and defective crystals. The new approach is based on thermodynamic integration using two alchemical pathways. Softcore potentials are developed for three-body interatomic potentials to realize the alchemical pathways. Employing the new approach, the free energy of the liquid can be calculated without requiring another reference system. The free energy of the defective crystal can be calculated directly at high temperatures. It avoids the singularity at the integration endpoint caused by the defect diffusion, which is a serious problem in the widely used Einstein crystal method. In addition, the new approach can capture the whole free energy of the defective crystal including the contribution of anharmonic and configurational entropy, which are particularly important at high temperatures. The new method is simple yet effective and can be extended to different materials and more complex liquid and defective crystal systems.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"156 21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128675868","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":"Correlated rotational excitations in NO-CO inelastic collisions.","authors":"Guoqiang Tang, Matthieu Besemer, J. Onvlee, T. Karman, A. van der Avoird, G. Groenenboom, S. V. D. van de Meerakker","doi":"10.1063/5.0092561","DOIUrl":"https://doi.org/10.1063/5.0092561","url":null,"abstract":"We present a joint experimental and theoretical study of rotationally inelastic collisions between NO (X2Π1/2, ν = 0, j = 1/2, f) radicals and CO (X1Σ+, ν = 0, j = 0) molecules at a collision energy of 220 cm-1. State-to-state scattering images for excitation of NO radicals into various final states were measured with high resolution by combining the Stark deceleration and velocity map imaging techniques. The high image resolution afforded the observation of correlated rotational excitations of NO-CO pairs, which revealed a number of striking scattering phenomena. The so-called \"parity-pair\" transitions in NO are found to have similar differential cross sections, independent of the concurrent excitation of CO, extending this well-known effect for collisions between NO and rare gas atoms into the realm of bimolecular collisions. Forward scattering is found for collisions that induce a large amount of rotational energy transfer (in either NO, CO, or both), which require low impact parameters to induce sufficient energy transfer. This observation is interpreted in terms of the recently discovered hard collision glory scattering mechanism, which predicts the forward bending of initially backward receding trajectories if the energy uptake in the collision is substantial in relation to the collision energy. The experimental results are in good agreement with the predictions from coupled-channels quantum scattering calculations based on an ab initio NO-CO potential energy surface.","PeriodicalId":446961,"journal":{"name":"The Journal of chemical physics","volume":"235 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123735270","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}