International Reviews in Physical Chemistry最新文献

{"title":"Collisions of Rydberg atoms with neutral targets","authors":"F. Dunning, S. Buathong","doi":"10.1080/0144235X.2018.1512201","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1512201","url":null,"abstract":"ABSTRACT Atoms in highly excited Rydberg states possess physical characteristics quite unlike those associated with atoms in the ground or low-lying excited states. In particular, they are physically very large and are only very weakly bound. In consequence, collisions can lead to a wide variety of reaction processes many of which are unique to Rydberg species and have very large collision cross sections. In collisions with neutral targets, Rydberg atoms behave not as an atom but rather as a pair of well-separated independent scatterers, namely the core ion and the excited Rydberg electron. In the present article we discuss many of the different reactions that can occur when Rydberg atoms collide with neutral targets, focusing principally on reactions that are dominated by (binary) Rydberg electron-target interactions and include collisions with molecules that attach free low-energy electrons and with polar targets. In certain situations, however, interactions involving the Rydberg core ion are important. This is illustrated using as an example the destruction of ultralong-range Rydberg molecules excited in a cold dense gas.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"94 1","pages":"287 - 328"},"PeriodicalIF":6.1,"publicationDate":"2018-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80628410","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":"A twisted tale: measuring viscosity and temperature of microenvironments using molecular rotors","authors":"Aurimas Vyšniauskas, M. Kuimova","doi":"10.1080/0144235X.2018.1510461","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1510461","url":null,"abstract":"ABSTRACT Measuring viscosity and temperature on the microscale is a challening yet very important task, in materials sciences and in biology alike. In this perpsective we review and discuss fluorescent microviscosity sensors, termed ‘molecular rotors’, that offer a convenient way of measuring microscopic viscosity and sometimes may even be used to measure microscopic temperature in addition to viscosity. We discuss how temperature in combination with various solvent properties can affect microviscosity measurements and we review possible action mechanisms that make molecular rotors sensitive to multiple parameters of their environment. Overall, we reveal a complicated, yet exciting, behaviour of molecular rotors at different viscosity, temperature and solvent properties on the microscale and how this behaviour can be explained and exploited.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"263 1","pages":"259 - 285"},"PeriodicalIF":6.1,"publicationDate":"2018-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77190416","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":"Interconnections between dissociative electron attachment and electron-driven biological processes","authors":"S. Pshenichnyuk, A. Modelli, A. Komolov","doi":"10.1080/0144235X.2018.1461347","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1461347","url":null,"abstract":"Abstract Small molecular species present in mitochondria as, e.g. quinones and oxygen, can capture cellular electrons thus behaving as electron carriers or reactive species, supporting the fundamental process of respiration, and providing protection from pathogens. When xenobiotics penetrate living cells, their delicate redox balance can be altered by capture of cellular electrons to form temporary negative ions. The latter can give rise to the formation of reactive species via dissociative electron attachment (DEA), as observed under gas-phase or electrochemical conditions. DEA to isolated biorelevant molecules studied in vacuo with the support of in silico methods can serve as a model to predict the behaviour of these species in vivo under conditions of electron ‘leakage’ in the lipid-protein-cytosol media or in enzymatic active centres. The present review summarises the results of studies on the correlation between the biological activity of various classes of compounds and fragment species formed by DEA. The following classes of compounds are included into the present review: chlorinated organic pollutants, brominated ethers, captafol and 2,6-dichloroisonicotinic acid, atrazine and bromoxynil, non-steroidal anti-inflammatory drugs, natural polyphenolic compounds, anthralin, salicylic acid and related compounds, ascorbic acid, melatonin, tryptophan, indole and related compounds and some organic peroxides. Formation of temporary molecular anions and their decay are characterised using electron transmission spectroscopy (ETS) and DEA spectroscopy. Quantum-chemical calculations support the identification of the dissociation products. Cellular electron attachment to unnatural electron acceptors is likely to be the first step of cascade processes which constitute the molecular mechanisms of electron-driven biological processes. The fragment species detected with DEA are of importance for understanding the metabolism of xenobiotics, including side effects produced by drugs.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"48 1","pages":"125 - 170"},"PeriodicalIF":6.1,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73606176","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":"Advances in modelling switchable mechanically interlocked molecular architectures","authors":"Gloria Bazargan, K. Sohlberg","doi":"10.1080/0144235X.2018.1419042","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1419042","url":null,"abstract":"Abstract The development of switchable mechanically interlocked molecular architectures (MIMAs) is an active area of experimental and theoretical research because the environmental-responsiveness of these systems makes them desirable candidates for incorporation into molecular machines. Presented here is a review of the recent literature that reports theoretical and computational studies of these topologically complex systems. Modelling strategies that have been applied to switchable MIMAs are analysed and outstanding challenges to theory and computation are highlighted.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"36 1","pages":"1 - 82"},"PeriodicalIF":6.1,"publicationDate":"2018-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89654839","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 of doped superfluid liquid helium and nanodroplets","authors":"F. Ancilotto, M. Barranco, F. Coppens, J. Eloranta, N. Halberstadt, A. Hernando, D. Mateo, M. Pi","doi":"10.1080/0144235X.2017.1351672","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1351672","url":null,"abstract":"Abstract During the last decade, density function theory (DFT) in its static and dynamic time dependent forms, has emerged as a powerful tool to describe the structure and dynamics of doped liquid helium and droplets. In this review, we summarise the activity carried out in this field within the DFT framework since the publication of the previous review article on this subject [M. Barranco et al., J. Low Temp. Phys. 142, 1 (2006)]. Furthermore, a comprehensive presentation of the actual implementations of helium DFT is given, which have not been discussed in the individual articles or are scattered in the existing literature.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"4 1","pages":"621 - 707"},"PeriodicalIF":6.1,"publicationDate":"2017-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74255179","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":"Dynamic dipole polarizabilities of heteronuclear alkali dimers: optical response, trapping and control of ultracold molecules","authors":"R. Vexiau, D. Borsalino, M. Lepers, A. Orbán, M. Aymar, O. Dulieu, N. Bouloufa-Maafa","doi":"10.1080/0144235X.2017.1351821","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1351821","url":null,"abstract":"Abstract In this article we address the general approach for calculating dynamical dipole polarizabilities of small quantum systems, based on a sum-over-states formula involving in principle the entire energy spectrum of the system. We complement this method by a few-parameter model involving a limited number of effective transitions, allowing for a compact and accurate representation of both the isotropic and anisotropic components of the polarizability. We apply the method to the series of ten heteronuclear molecules composed of two of (Li,Na,K,Rb,Cs) alkali-metal atoms. We rely on both up-to-date spectroscopically-determined potential energy curves for the lowest electronic states, and on our systematic studies of these systems performed during the last decade for higher excited states and for permanent and transition dipole moments. Such a compilation is timely for the continuously growing researches on ultracold polar molecules. Indeed the knowledge of the dynamic dipole polarizabilities is crucial to model the optical response of molecules when trapped in optical lattices, and to determine optimal lattice frequencies ensuring optimal transfer to the absolute ground state of initially weakly-bound molecules. When they exist, we determine the so-called ‘magic frequencies’ where the ac-Stark shift and thus the viewed trap depth, is the same for both weakly-bound and ground-state molecules.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"18 1","pages":"709 - 750"},"PeriodicalIF":6.1,"publicationDate":"2017-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73157017","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 terahertz dynamics of simplest fluids probed by inelastic X-ray scattering","authors":"A. Cunsolo","doi":"10.1080/0144235X.2017.1331900","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1331900","url":null,"abstract":"Abstract More than two decades of inelastic X-ray scattering (IXS) studies on noble gases and alkali metals are reviewed to illustrate the advances they prompted in our understanding of the terahertz dynamics of simplest systems. The various literature results outline a remarkably coherent picture of common and distinctive behaviours of liquids and their crystalline counterparts. Furthermore, they draw a consistent and comprehensive picture of the evolution of collective modes at the crossover between the hydrodynamic and the single particle regime, their coupling with fast (sub-ps) relaxation processes and their gradual disappearance upon approaching microscopic scales. The gradual transition of the spectrum towards the single particle limit along with its coupling with collisional relaxations will be discussed in some detail. Finally, less understood emerging topics will be discussed as the occurrence of polyamorphic crossovers, the onset of non-hydrodynamic modes and quantum effects on the spectrum, as well as recent IXS results challenging our vision of the supercritical phase as an intrinsically homogeneous thermodynamic domain.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"40 1","pages":"433 - 539"},"PeriodicalIF":6.1,"publicationDate":"2017-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74711964","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 synthesis of large interstellar molecules","authors":"E. Herbst","doi":"10.1080/0144235X.2017.1293974","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1293974","url":null,"abstract":"This review is concerned with the formation of molecules in the interstellar medium (ISM), which is composed mainly of regions of gas and dust known as interstellar clouds, ranging in size from a few to 100’s of light years in extent. Upwards of 200 different molecules have been observed spectroscopically in these objects, with a significant fraction of them ‘large’ by astronomical standards; i.e. containing six or more atoms. Interstellar clouds are of interest to chemists because of the exotic molecules and chemistry that occur in these sources, while they are of interest to astronomers because these clouds are the only known birthplaces of new stars and extrasolar planets. The formation of stars and planets from portions of dense interstellar clouds is a complex evolutionary process with multiple stages dependent upon the mass of the collapsing object. For low-mass stars such as our sun, the process is reasonably well understood and proceeds through the following intermediate stages: cold dense cores, pre-stellar cores, hot cores, and protoplanetary discs. For high-mass stars, the process is significantly less well understood because these objects are rare and are formed through evolutionary stages that are short in duration, at least astronomically speaking. Molecules are found in all of these stages, in the gas phase and often in the solid phase, with the chemistry dependent upon the physical conditions and their history. Indeed, the many molecules detected have helped significantly to unravel much of the complexity involved in stellar and planetary formation. This review is divided into sections in which, following an introduction, we discuss the different types of chemical reactions that synthesise large molecules, starting with cold dense cores of temperature 10 K and gas density , and proceeding through the various stages of low-mass star formation through protoplanetary discs. Several other types of sources are discussed briefly. We then review some recent progress that has occurred within the last several years in improving our knowledge of the chemistry in this fast-growing and rapidly evolving field of research. We end with a brief discussion of the detailed chemical simulations employed to follow the chemistry in the various sources in the ISM.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"5 1","pages":"287 - 331"},"PeriodicalIF":6.1,"publicationDate":"2017-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88831750","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":"Clarification of nonadiabatic chemical dynamics by the Zhu-Nakamura theory of nonadiabatic transition: from tri-atomic systems to reactions in solutions","authors":"T. Ishida, S. Nanbu, Hiroki Nakamura","doi":"10.1080/0144235X.2017.1293399","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1293399","url":null,"abstract":"Abstract It is now confirmed that the Zhu–Nakamura (ZN) theory of nonadiabatic transition is useful to investigate various nonadiabatic chemical dynamics. The theory, being one-dimensional, presents a whole set of analytical formulas that enables us to treat the dynamics efficiently. It is also quite significant that classically forbidden transitions can be dealt with analytically. The theory can be combined with the trajectory surface hopping (TSH) method (ZN-TSH) and is demonstrated to be useful to clarify the dynamics of not only simple tri-atomic reactions but also large chemical systems. The whole set of analytical formulas directly applicable to practical systems is summarised and the applications to polyatomic systems are illustrated. Examples of polyatomic molecules are , , indolylmaleimide, cyclohexadiene (CHD), and retinal. The Fortran code for the whole set of ZN formulas is provided in Appendix for the convenience of a reader who is interested in using them. The ZN-TSH method can be combined with the QM/MM method to clarify reaction dynamics in the surrounding environment. This is named as ZN-QM/MM-TSH. The particle-mesh Ewald (PME) method can also be combined with ZN-TSH to clarify reaction dynamics in solutions. This is named as ZN-PME-TSH. Formulations of these methods are presented together with practical applications. Examples treated by ZN-QM/MM-TSH are photoisomerization dynamics of retinal chromophore embedded in the protein environment. The differences in the isomerization mechanisms between rhodopsin and isorhodopsin are made clear. The faster and more efficient isomerization of rhodopsin compared to isorhodopsin is nicely reproduced. Examples of reactions in solutions are photoisomerizations of retinal and CHD. The experimentally observed long life time of the excited state of retinal is reproduced and is found to be due to the long-range solvation effect. The solvent dependent branching ratios of CHD:hexatriene (HT) are clarified for the ethanol and hexane solvents by the ZN-PME-TSH method. Both ZN-QM/MM-TSH and ZN-PME-TSH are thus demonstrated to be promising methods to deal with a wide range of nonadiabatic dynamics in large chemical and biological systems.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"40 1","pages":"229 - 285"},"PeriodicalIF":6.1,"publicationDate":"2017-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80367661","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":"Identifying the structural and kinetic elements in protein large-amplitude conformational motions","authors":"J. Chu, Haw Yang","doi":"10.1080/0144235X.2017.1283885","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1283885","url":null,"abstract":"The importance of how a protein reconfigures its structure to achieve its function has long been appreciated; yet, the progress in our fundamental understanding of protein dynamics does not seem to be commensurate with the rapid advances in experimental techniques and ever increasing computational prowess. In this review, we attempt to look at this issue based on quantitative characterisations that go beyond simply determining the kinetics rates or only allowing qualitative statements about conformational states. We summarise the theoretical basis for determining from experimental data the kinetics and the structural elements of protein conformational dynamics. The two kinetics elements include the apparent potential of mean force and the intra-molecular diffusion coefficient along a coordinate defined by the pair of single-molecule Förster-type resonance energy transfer reporters that are chemically attached to the protein. We show that it is now possible to resolve the relative contributions of these two kinetics elements when discussing the physical origin of the protein’s conformation-reconfiguration rate changes due to mutation or interaction with chemical effectors or with other proteins. The structural element refers to the orthogonal conformational modes that give rise to the intrinsic conformational motions of the protein, and could allow a comparative study among proteins from different families. To achieve these, it is essential that experimental data be rigorously analysed and integrated with molecular simulations – which include molecular dynamics simulations, coarse-grained modelling, and enhanced sampling. In turn, the close interplay between computation and experiment through this new direction could accelerate the discovery of predictive models.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"54 1","pages":"185 - 227"},"PeriodicalIF":6.1,"publicationDate":"2017-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91211756","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}