Annual review of physical chemistry最新文献

No longer viewed as a passive consequence of cellular activities, membrane curvature-the physical shape of the cell membrane-is now recognized as an active constituent of biological processes. Nanoscale topographies on extracellular matrices or substrate surfaces impart well-defined membrane curvatures on the plasma membrane. This review examines biological events occurring at the nano-bio interface, the physical interface between the cell membrane and surface nanotopography, which activates intracellular signaling by recruiting curvature-sensing proteins. We encompass a wide range of biological processes at the nano-bio interface, including cell adhesion, endocytosis, glycocalyx redistribution, regulation of mechanosensitive ion channels, cell migration, and differentiation. Despite the diversity of processes, we call attention to the critical role of membrane curvature in each process. We particularly highlight studies that elucidate molecular mechanisms involving curvature-sensing proteins with the hope of providing comprehensive insights into this rapidly advancing area of research.

The unique properties of ionic liquids (ILs) result from the tunable mélange of Coulomb interactions, hydrogen bonding, and dispersion interactions among the constituent ions. In hydroxy-functionalized ILs, local and directional hydrogen bonds (H-bonds) lead to the anticipated formation of ion pairs but also to the elusive formation of cationic clusters. Here, we review how hydrogen-bonding motifs in the bulk liquid and gas phase of hydroxy-functionalized ILs shed light on the general nature of hydrogen bonding. Infrared spectroscopy, nuclear magnetic resonance, neutron diffraction, and molecular dynamics simulations provide information about the structure, strength, and dynamics of cationic clusters in the bulk liquid ILs. Cryogenic ion vibrational predissociation (CIVP) spectroscopy along with density functional theory calculations has established a clear picture about the specific contacts within isolated H-bonded cationic clusters formed in the gas phase. This information from experiment, simulation, and theory provides a fundamental understanding of hydrogen bonding between the ions in ILs.

In this review, we explore the electrostatic environment of the interface between a solid and dilute electrolyte solution, with an emphasis on the electric field profiles that these systems produce. We review the theoretical formalism that connects electrostatic potential profiles, electric field profiles, and charge density fields. This formalism has served as the basis for our understanding of interfacial electric fields and their influences on microscopic chemical and physical processes. Comparing various traditional models of interfacial electrostatics to the results of molecular dynamics (MD) simulation yields mutually inconsistent descriptions of the interfacial electric field profile. We present MD simulation results demonstrating that the average electric field profiles experienced by particles at the interface differ from the properties of traditional models and from the fields derived from the mean charge density of atomistic simulations. Furthermore, these experienced electric field profiles are species-dependent. Based on these results, we assert that a single unifying electrostatic potential profile-the gradient of which defines a single unifying electric field profile-cannot correctly predict the electrostatic forces that act on species at the interface.

How long thread-like eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which reproduce contact maps that measure the probabilities that two loci are in spatial contact, have predicted the 3D structures of interphase chromosomes. Data-driven approaches, using contact maps as input, predict that mitotic helical chromosomes are characterized by a switch in handedness, referred to as perversion. By using experimentally derived effective interactions between chromatin loci in simulations, structures of conventional and inverted nuclei have been accurately predicted. Polymer theory and simulations show that the dynamics of individual loci in chromatin exhibit subdiffusive behavior but the diffusion exponents are broadly distributed, which accords well with experiments. Although coarse-grained models are successful, many challenging problems remain, which require the creation of new experimental and computational tools to understand genome biology.

Attosecond science requires a substantial rethinking of how to make measurements on very short timescales; how to acquire the necessary equipment, technology, and personnel; and how to build a set of laboratories for such experiments. This entails a rejuvenation of the author in many respects, in the laboratory itself, with regard to students and postdocs, and in generating funding for research. It also brings up questions of what it means to do attosecond science, and the discovery of the power of X-ray spectroscopy itself, which complements the short timescales addressed. The lessons learned, expressed in the meanderings of this autobiographical article, may be of benefit to others who try to reinvent themselves.

Recent theoretical and algorithmic developments have improved the accuracy with which path integral dynamics methods can include nuclear quantum effects in simulations of condensed-phase vibrational spectra. Such methods are now understood to be approximations to the delocalized classical Matsubara dynamics of smooth Feynman paths, which dominate the dynamics of systems such as liquid water at room temperature. Focusing mainly on simulations of liquid water and hexagonal ice, we explain how the recently developed quasicentroid molecular dynamics (QCMD), fast-QCMD, and temperature-elevated path integral coarse-graining simulations (Te PIGS) methods generate classical dynamics on potentials of mean force obtained by averaging over quantum thermal fluctuations. These new methods give very close agreement with one another, and the Te PIGS method has recently yielded excellent agreement with experimentally measured vibrational spectra for liquid water, ice, and the liquid-air interface. We also discuss the limitations of such methods.

Low-resolution coarse-grained (CG) models provide remarkable computational and conceptual advantages for simulating soft materials. In principle, bottom-up CG models can reproduce all structural and thermodynamic properties of atomically detailed models that can be observed at the resolution of the CG model. This review discusses recent progress in developing theory and computational methods for achieving this promise. We first briefly review variational approaches for parameterizing interaction potentials and their relationship to machine learning methods. We then discuss recent approaches for simultaneously improving both the transferability and thermodynamic properties of bottom-up models by rigorously addressing the density and temperature dependence of these potentials. We also briefly discuss exciting progress in modeling high-resolution observables with low-resolution CG models. More generally, we highlight the essential role of the bottom-up framework not only for fundamentally understanding the limitations of prior CG models but also for developing robust computational methods that resolve these limitations in practice.

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

Water-metal oxide interfaces are central to many phenomena and applications, ranging from material corrosion and dissolution to photoelectrochemistry and bioengineering. In particular, the discovery of photocatalytic water splitting on TiO₂ has motivated intensive studies of water-TiO₂ interfaces for decades. So far, a broad understanding of the interaction of water vapor with several TiO₂ surfaces has been obtained. However, much less is known about liquid water-TiO₂ interfaces, which are more relevant to many practical applications. Probing these complex systems at the molecular level is experimentally challenging and is sometimes possible only through computational studies. This review summarizes recent advances in the atomistic understanding, mostly through computational simulations, of the structure and dynamics of interfacial water on TiO₂ surfaces. The main focus is on the nature, molecular or dissociated, of water in direct contact with low-index defect-free crystalline surfaces. The hydroxyls resulting from water dissociation are essential in the photooxidation of water and critically affect the surface chemistry of TiO_2.

The phase state of aerosol particles can impact numerous atmospheric processes, including new particle growth, heterogeneous chemistry, cloud condensation nucleus formation, and ice nucleation. In this article, the phase transitions of inorganic, organic, and organic/inorganic aerosol particles are discussed, with particular focus on liquid-liquid phase separation (LLPS). The physical chemistry that determines whether LLPS occurs, at what relative humidity it occurs, and the resultant particle morphology is explained using both theoretical and experimental methods. The known impacts of LLPS on aerosol processes in the atmosphere are discussed. Finally, potential evidence for LLPS from field and chamber studies is presented. By understanding the physical chemistry of the phase transitions of aerosol particles, we will acquire a better understanding of aerosol processes, which in turn impact human health and climate.