International Reviews in Physical Chemistry最新文献

{"title":"Anion photoelectron spectroscopy of protein chromophores","authors":"Alice Henley, H. Fielding","doi":"10.1080/0144235X.2018.1548807","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1548807","url":null,"abstract":"ABSTRACT Photoactive proteins that efficiently and selectively transfer light energy into a physical response are ubiquitous in nature. The small molecule chromophores that lie at the heart of these processes often exist as closed-shell anions following deprotonation in proton-transfer reactions. This review highlights the important role that anion photoelectron spectroscopy, combined with computational chemistry calculations, is playing in improving our understanding of the electronic structure and relaxation dynamics of these protein chromophores. We discuss key aspects of anion photoelectron spectroscopy. We then review recent anion photoelectron spectroscopy studies of the deprotonated chromophore anions found in green fluorescent protein (GFP), photoactive yellow protein (PYP) and the deprotonated luciferin anion found in the luciferase enzyme.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2019-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84825921","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 quantum nature of hydrogen","authors":"W. Fang, Ji Chen, Yexin Feng, Xin-Zheng Li, A. Michaelides","doi":"10.1080/0144235X.2019.1558623","DOIUrl":"https://doi.org/10.1080/0144235X.2019.1558623","url":null,"abstract":"ABSTRACT Hydrogen is the most abundant element. It is also the most quantum, in the sense that quantum tunnelling, quantum delocalisation, and zero-point motion can be important. For practical reasons, most computer simulations of materials have not taken such effects into account, rather they have treated nuclei as classical particles. However, thanks to methodological developments over the last few decades, nuclear quantum effects can now be treated in complex materials. Here we discuss our studies on the role nuclear quantum effects play in hydrogen containing systems. We give examples of how the quantum nature of the nuclei has a significant impact on the location of the boundaries between phases in high pressure condensed hydrogen. We show how nuclear quantum effects facilitate the dissociative adsorption of molecular hydrogen on solid surfaces and the diffusion of atomic hydrogen across surfaces. Finally, we discuss how nuclear quantum effects alter the strength and structure of hydrogen bonds, including those in DNA. Overall, these studies demonstrate that nuclear quantum effects can manifest in different, interesting, and non-intuitive ways. Whilst historically it has been difficult to know in advance what influence nuclear quantum effects will have, some of the important conceptual foundations have now started to emerge.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84827877","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 TDDVR approach for molecular photoexcitation, molecule–surface and triatomic reactive scattering processes","authors":"Souvik Mandal, Sandip Ghosh, Subhankar Sardar, S. Adhikari","doi":"10.1080/0144235X.2018.1548103","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1548103","url":null,"abstract":"ABSTRACT The Time Dependent Discrete Variable Representation (TDDVR) method was initiated by Adhikari and Billing considering time dependent Gauss-Hermite basis functions, where all the parameters were assumed to be time dependent. Adhikari et al. had reformulated the TDDVR approach considering the width parameter as time independent, whereas the equation of motion for time dependent parameters (center of wave packet and its momentum) are derived from Dirac-Frenkel variational principle. Such a method is computationally efficient due to its inherent parallelizable nature to perform multistate (electronic) multidimensional (vibrational) quantum dynamics for well-converged results within reasonably fast computation time, where the complexity of the Hamiltonian is not a matter of concern. Its parallel version is computationally efficient as compared to other quantum dynamical method like the multiconfiguration time dependent Hartree (MCTDH). The parallelized version of this method has also been employed to different complex dynamical systems to calculate transition probabilities, tunnelling probabilities, inelastic surface scattering, bi-molecular reactive scattering and photoexcitation. We have also made use of TDDVR methodology successfully to different diatom (H2/D2)-metal surface (Cu/Ni) scattering processes and triatomic reaction dynamics by using 3D time dependent wave packet approach in hyperspherical coordinates to calculate state-to-state reaction probabilities of D+H2 reaction for J=0 case.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73798904","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":"Cold ion spectroscopy for structural identifications of biomolecules","authors":"O. Boyarkin","doi":"10.1080/0144235X.2018.1547453","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1547453","url":null,"abstract":"ABSTRACT Over the last decade, the spectroscopy of cryogenically cold ions isolated in the gas phase has been developed as a new tool for structural elucidations of biological molecules. Cooling allows for vibrational resolution in UV and IR spectra of small to midsize peptides, enabling different multi-laser techniques of conformer-specific spectroscopy. In conjunction with quantum chemistry calculations, IR spectra of single conformers allows for solving their intrinsic geometries. Here, we briefly review some fundamental and technical aspects of the cold-ion spectroscopy (CIS) approach and illustrate its application for protonated peptides, carbohydrates and for non-covalent complexes of biomolecules. The challenges and limitations of CIS in view of its relevance to life-science studies are critically assessed. Finally, we discuss and illustrate some approaches of CIS for the analytical identification of biomolecules, in particular the recently developed method of 2D UV-MS fingerprinting, which combines CIS with high-resolution mass spectrometry.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91164288","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":"Aqueous charge injection: solvation bonding dynamics, molecular nonbond interactions, and extraordinary solute capabilities","authors":"Chang Q. Sun","doi":"10.1080/0144235X.2018.1544446","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1544446","url":null,"abstract":"ABSTRACT Aqueous charge injection in forms of electrons, protons, lone pairs, ions, and molecular dipoles by solvation is ubiquitously important to our health and life. Pursuing fine-resolution detection and consistent insight into solvation dynamics and solute capabilities has become an increasingly active subject. This treatise shows that charge injection by solvation mediates the O:H–O bonding network and properties of a solution through O:H formation, H↔H fragilization, O:⇔:O compression, electrostatic polarization, H2O dipolar shielding, solute–solute interaction, and undercoordinated H–O bond contraction. A combination of the hydrogen bond (O:H–O or HB with ‘:’ being the electron lone pairs of oxygen) cooperativity notion and the differential phonon spectrometrics (DPS) has enabled quantitative information on the following: (i) the number fraction and phonon stiffness of HBs transiting from the mode of ordinary water to hydration; (ii) solute–solvent and solute–solute molecular nonbond interactions; and (iii) interdependence of skin stress, solution viscosity, molecular diffusivity, solvation thermodynamics, and critical pressures and temperatures for phase transitions. An examination of solvation dynamics has clarified the following: (i) the excessive protons create the H↔H or anti-HB point breaker to disrupt the acidic solution network and surface stress. (ii) The excessive lone pairs generate the O:⇔:O or super–HB point compressor to shorten the O:H nonbond but lengthen the H–O bond in H2O2 and basic solutions; yet, bond-order-deficiency shortens and stiffens the H–O bond due H2O2 and OH− solutes. (iii) Ions serve each as a charge center that aligns, clusters, stretches, and polarizes their neighboring HBs to form hydration shells. (iv) Solvation of alcohols, aldehydes, complex salts, carboxylic and formic acids, glycine, and sugars distorts the solute–solvent interface structures with the involvement of the anti-HB or the super-HB. Extending the knowledge and strategies to catalysis, solution–protein, drug–cell, liquid–solid, colloid–matrix interactions and molecular crystals would be even more fascinating and rewarding.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76480213","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":"Theoretical methods for the rotation–vibration spectra of triatomic molecules: distributed Gaussian functions compared with hyperspherical coordinates","authors":"M. Márquez-Mijares, O. Roncero, P. Villarreal, T. González-Lezana","doi":"10.1080/0144235X.2018.1514187","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1514187","url":null,"abstract":"ABSTRACT An approximate variational method based in the use of distributed Gaussian functions (DGF) and bond-length coordinates has been applied to study the rotation–vibration spectra of different triatomic molecules. In addition, an approach which employs hyperspherical coordinates and a basis set of hyperspherical harmonics constitutes a valid benchmark to test its capabilities. This work describes the technical details of both methods to provide the energies and symmetry of the corresponding rovibrational states and reviews their application to three different systems: For Ar and Ne the DGF technique exhibits a particularly good performance, but some limitations are observed for a more demanding scenario such as the H ion. The possible origin of these deficiencies are also discussed in detail.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82037610","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":"Ring-polymer instanton theory","authors":"Jeremy O. Richardson","doi":"10.1080/0144235X.2018.1472353","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1472353","url":null,"abstract":"Abstract Instanton theory provides a simple description of a quantum tunnelling process in terms of an optimal tunnelling pathway. The theory is rigorously based on quantum mechanics principles and is derived from a semiclassical approximation to the path-integral formulation. In multidimensional systems, the optimal tunnelling pathway is generally different from the minimum-energy pathway and is seen to ‘cut the corner’ around the transition state. A ring-polymer formulation of instanton theory leads to a practical computational method for applying the theory to describe, simulate and predict quantum tunnelling effects in complex molecular systems. It can be used to compute either the rate of a tunnelling process leading to a chemical reaction or the tunnelling splitting pattern of a molecular cluster. In this review, we introduce a unification of the theory’s derivation and discuss recent improvements to the numerical implementation.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78348912","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":"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":null,"pages":null},"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":"Roaming signature in photodissociation of carbonyl compounds","authors":"K. Lin, Po-Yu Tsai, Meng-Hsuan Chao, M. Nakamura, T. Kasai, A. Lombardi, F. Palazzetti, V. Aquilanti","doi":"10.1080/0144235X.2018.1488951","DOIUrl":"https://doi.org/10.1080/0144235X.2018.1488951","url":null,"abstract":"ABSTRACT An alternative to the transition state (TS) pathway, the roaming route, which bypasses the minimum energy path but produces the same molecular products, was recently found in photodissociation dynamics. This account describes signatures of roaming in photodissociation of the carbonyl compounds, specifically methyl formate and aliphatic aldehydes. Methyl formate was promoted to the excited state, followed by internal conversion via a conical intersection. Then, the energetic precursor dissociated to fragments which proceeded along either TS or roaming path. In contrast to the lack of a roaming saddle point found in methyl formate, the structure of the roaming saddle point for each of a series of aliphatic aldehydes comprises two moieties that are weakly bound at a distance. As its size increases, the energy difference between the TS barrier and the roaming saddle point increases and the roaming pathway becomes increasingly dominant. Experimentally, the rotational-level dependence of the roaming route was measured with ion imaging, while the vibrational-state dependence was observed with time-resolved Fourier-transform infrared emission spectroscopy. The roaming signature was verified theoretically by quasi-classical trajectory (QCT) calculations. As an alternative to the QCT method, a multi-center impulsive model was developed to simulate the roaming scalar and vector properties.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2018-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81474468","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":null,"pages":null},"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}