Pub Date : 2017-03-09DOI: 10.1080/0144235X.2017.1293399
T. Ishida, S. Nanbu, Hiroki Nakamura
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.
{"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}
Pub Date : 2017-03-09DOI: 10.1080/0144235X.2017.1283885
J. Chu, Haw Yang
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.
{"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}
Pub Date : 2017-02-06DOI: 10.1080/0144235X.2017.1256604
R. Moran, D. Dawson, S. Ashbrook
Abstract Although the solid state is typically characterised by inherent periodicity, many interesting physical and chemical properties of solids arise from a variation in this, i.e. changes in the nature of the atom occupying a particular site in a crystal structure or variation in the position of an atom (or group of atoms) in different parts of a structure, or variation as a function of time. This lack of long-range order poses significant challenges, not just for the characterisation of the structure of disordered materials, but also simply for its description. The sensitivity of nuclear magnetic resonance (NMR) spectroscopy to the local, atomic-scale environment, without the requirement for long-range order, makes it a powerful tool for the study of disorder in the solid state. Information on the number and type(s) of coordinating atoms or through-space and through-bond connectivity between atomic species enables the construction of a detailed picture of the structure. After a brief description of the background theory of NMR spectroscopy, and the experimental methods employed, we will describe the effects of disorder on NMR spectra and the use of calculations to help interpret experimental measurements. We will then review a range of applications to different types of disordered materials, including oxides and ceramics, minerals, porous materials, biomaterials, energy materials, pharmaceuticals, polymers and glasses. We will discuss the most successful approaches for studying different materials, and illustrate the type of information available and the structural insight gained.
{"title":"Exploiting NMR spectroscopy for the study of disorder in solids","authors":"R. Moran, D. Dawson, S. Ashbrook","doi":"10.1080/0144235X.2017.1256604","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1256604","url":null,"abstract":"Abstract Although the solid state is typically characterised by inherent periodicity, many interesting physical and chemical properties of solids arise from a variation in this, i.e. changes in the nature of the atom occupying a particular site in a crystal structure or variation in the position of an atom (or group of atoms) in different parts of a structure, or variation as a function of time. This lack of long-range order poses significant challenges, not just for the characterisation of the structure of disordered materials, but also simply for its description. The sensitivity of nuclear magnetic resonance (NMR) spectroscopy to the local, atomic-scale environment, without the requirement for long-range order, makes it a powerful tool for the study of disorder in the solid state. Information on the number and type(s) of coordinating atoms or through-space and through-bond connectivity between atomic species enables the construction of a detailed picture of the structure. After a brief description of the background theory of NMR spectroscopy, and the experimental methods employed, we will describe the effects of disorder on NMR spectra and the use of calculations to help interpret experimental measurements. We will then review a range of applications to different types of disordered materials, including oxides and ceramics, minerals, porous materials, biomaterials, energy materials, pharmaceuticals, polymers and glasses. We will discuss the most successful approaches for studying different materials, and illustrate the type of information available and the structural insight gained.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"1396 1","pages":"115 - 39"},"PeriodicalIF":6.1,"publicationDate":"2017-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81219605","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}
Pub Date : 2017-02-06DOI: 10.1080/0144235X.2017.1276726
C. Hutchison, J. V. van Thor
Abstract Ultrafast X-ray crystallography of the photoactive yellow protein with femtosecond delays using an X-ray free electron laser has successfully probed the dynamics of an early Franck-Condon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The sub-picosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additional to photoisomerisation that is considered to proceed through activated barrier crossing, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate X-ray free electron laser instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence.
{"title":"Populations and coherence in femtosecond time resolved X-ray crystallography of the photoactive yellow protein","authors":"C. Hutchison, J. V. van Thor","doi":"10.1080/0144235X.2017.1276726","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1276726","url":null,"abstract":"Abstract Ultrafast X-ray crystallography of the photoactive yellow protein with femtosecond delays using an X-ray free electron laser has successfully probed the dynamics of an early Franck-Condon species. The femtosecond pump-probe application of protein crystallography represents a new experimental regime that provides an X-ray structural probe for coherent processes that were previously accessible primarily using ultrafast spectroscopy. We address how the optical regime of the visible pump, that is necessary to successfully resolve ultrafast structural differences, affects the motions that are measured using the technique. The sub-picosecond photochemical dynamics in PYP involves evolution of a mixture of electronic ground and excited state populations. Additional to photoisomerisation that is considered to proceed through activated barrier crossing, within the dephasing time structural motion include vibrational coherence arising from excited states, the ground state and a ground state intermediate under experimental conditions used for ultrafast crystallography. Intense optical pulses are required to convert population levels in PYP crystals that allow detection by X-ray crystallography, but the compromise currently needed for the optical bandwidth and power has consequences with regard to the contributions to the motions that are experimentally measured with femtosecond delays. We briefly review the ultrafast spectroscopy literature of the primary photoreactions of PYP and discuss relevant physical models taken from coherent control and femtosecond coherence spectroscopy literature that address both the population transfer as well as the vibrational coherences. We apply linear response theory, with the additional use of a high power approximation, of on-resonance impulsive vibrational coherence in the ground state and the non-impulsive coherence in the excited state and discuss experimental approaches to manipulate the coherence contributions. The results are generalised and extended to discuss the future capabilities of high repetition rate X-ray free electron laser instruments providing enhanced sensitivity to perform the crystallographic equivalent of an impulsive Raman measurement of vibrational coherence.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"6 1","pages":"117 - 143"},"PeriodicalIF":6.1,"publicationDate":"2017-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83415163","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}
Pub Date : 2017-02-06DOI: 10.1080/0144235X.2016.1253244
F. McBride, A. Hodgson
Abstract Water and its fragments are present on metal surfaces under all but the most extreme conditions, acting both as a reactive species and as a ligand in ways that have yet to be fully explored. This review focuses on experimental studies of the chemical species and hydrogen bonding structures that form in the first layer adsorbed on a metal surface. The development of non-invasive probes that avoid dissociating water, or disrupting fragile bonding structures, now allows experiments to distinguish between different structural models for water and its fragments at the surface, allowing us to test the accuracy of modern structural calculations and provide a better picture of how the metal surface influences the structures and chemical species present. We start by describing the behaviour of Pt(1 1 1), whose redox chemistry is important in electrochemical fuel cells and has been studied in detail, providing a good reference system against which to discuss the effect changing the surface symmetry and metal reactivity has on the interface structure. Evidence for the presence and the role of hydroxyl and hydrated ‘hydronium’ species is described and we discuss the outlook for future experiments and identify some questions that remain to be resolved.
{"title":"Water and its partially dissociated fragments at metal surfaces","authors":"F. McBride, A. Hodgson","doi":"10.1080/0144235X.2016.1253244","DOIUrl":"https://doi.org/10.1080/0144235X.2016.1253244","url":null,"abstract":"Abstract Water and its fragments are present on metal surfaces under all but the most extreme conditions, acting both as a reactive species and as a ligand in ways that have yet to be fully explored. This review focuses on experimental studies of the chemical species and hydrogen bonding structures that form in the first layer adsorbed on a metal surface. The development of non-invasive probes that avoid dissociating water, or disrupting fragile bonding structures, now allows experiments to distinguish between different structural models for water and its fragments at the surface, allowing us to test the accuracy of modern structural calculations and provide a better picture of how the metal surface influences the structures and chemical species present. We start by describing the behaviour of Pt(1 1 1), whose redox chemistry is important in electrochemical fuel cells and has been studied in detail, providing a good reference system against which to discuss the effect changing the surface symmetry and metal reactivity has on the interface structure. Evidence for the presence and the role of hydroxyl and hydrated ‘hydronium’ species is described and we discuss the outlook for future experiments and identify some questions that remain to be resolved.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"52 5 1","pages":"1 - 38"},"PeriodicalIF":6.1,"publicationDate":"2017-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79717791","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}
Pub Date : 2017-02-06DOI: 10.1080/0144235X.2017.1283844
S. Price, James D Fletcher, F. E. Gossan, M. Parkes
Abstract This review discusses the recent developments in our understanding of the electron transfer and bond-forming reactions of small atomic and molecular dications in the gas-phase. A summary of the properties of isolated dications is presented, followed by a review of the major experimental techniques used to probe dicationic reactivity. Electron transfer reactions of dications with neutral species are then discussed, including recent rationalisations of this class of reactivity using simple electrostatic models. Our current understanding of the reactions of dications with neutral atoms and molecules which result in the formation of new chemical bonds is then presented. This part of the account is built around three case studies, including some new results on the bond-forming reactions of with CH4. Moving beyond dicationic species, the account then discusses recent results concerning the bond-forming reactivity of tricationic atoms and small molecules. This section includes the mechanistic conclusions drawn from the first results involving the coincident detection of all three positively charged species generated from the reaction of a molecular trication: + O2 → SO+ + CS+ + O+. The review concludes with some thoughts concerning the future development of the field.
{"title":"Bimolecular reactions of the dications and trications of atoms and small molecules in the gas-phase","authors":"S. Price, James D Fletcher, F. E. Gossan, M. Parkes","doi":"10.1080/0144235X.2017.1283844","DOIUrl":"https://doi.org/10.1080/0144235X.2017.1283844","url":null,"abstract":"Abstract This review discusses the recent developments in our understanding of the electron transfer and bond-forming reactions of small atomic and molecular dications in the gas-phase. A summary of the properties of isolated dications is presented, followed by a review of the major experimental techniques used to probe dicationic reactivity. Electron transfer reactions of dications with neutral species are then discussed, including recent rationalisations of this class of reactivity using simple electrostatic models. Our current understanding of the reactions of dications with neutral atoms and molecules which result in the formation of new chemical bonds is then presented. This part of the account is built around three case studies, including some new results on the bond-forming reactions of with CH4. Moving beyond dicationic species, the account then discusses recent results concerning the bond-forming reactivity of tricationic atoms and small molecules. This section includes the mechanistic conclusions drawn from the first results involving the coincident detection of all three positively charged species generated from the reaction of a molecular trication: + O2 → SO+ + CS+ + O+. The review concludes with some thoughts concerning the future development of the field.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"67 1","pages":"145 - 183"},"PeriodicalIF":6.1,"publicationDate":"2017-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89039170","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}
Pub Date : 2016-10-01DOI: 10.1080/0144235X.2016.1229331
K. Schwing, M. Gerhards
The well-known correlation between structure and functionality has motivated generations of scientists to intensively investigate the structural behaviour of peptide and protein systems, e.g. their folding, their aggregation reactions or the process of molecular recognition. A variety of environmental effects on peptide structures occur among them the influence of solvent molecules or aggregation partners; a further decisive factor is the amino acid sequence. Thus a bottom-up approach comprises the investigation of isolated peptide systems, increasing in size, as well as a successive introduction of potential aggregation partners. For this purpose mass and isomer selective combined IR/UV investigations in a molecular expansion represent ideal experiments to analyse intrinsic structural properties of peptides and aggregates. Against this background the presented review article illustrates general aspects of peptide structure, spectroscopic methods and experimental set-ups in the first part. This overview is followed by a summary of the current results in this field of research including a more detailed discussion of our work but also selected findings of other groups.
{"title":"Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition","authors":"K. Schwing, M. Gerhards","doi":"10.1080/0144235X.2016.1229331","DOIUrl":"https://doi.org/10.1080/0144235X.2016.1229331","url":null,"abstract":"The well-known correlation between structure and functionality has motivated generations of scientists to intensively investigate the structural behaviour of peptide and protein systems, e.g. their folding, their aggregation reactions or the process of molecular recognition. A variety of environmental effects on peptide structures occur among them the influence of solvent molecules or aggregation partners; a further decisive factor is the amino acid sequence. Thus a bottom-up approach comprises the investigation of isolated peptide systems, increasing in size, as well as a successive introduction of potential aggregation partners. For this purpose mass and isomer selective combined IR/UV investigations in a molecular expansion represent ideal experiments to analyse intrinsic structural properties of peptides and aggregates. Against this background the presented review article illustrates general aspects of peptide structure, spectroscopic methods and experimental set-ups in the first part. This overview is followed by a summary of the current results in this field of research including a more detailed discussion of our work but also selected findings of other groups.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"2 1","pages":"569 - 677"},"PeriodicalIF":6.1,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87268232","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}
Pub Date : 2016-10-01DOI: 10.1080/0144235X.2016.1239335
T. Michaels, A. Dear, T. Knowles
The formation of elongated supra-molecular structures from protein building blocks generates functional intracellular filaments, but this process is also at the heart of many neurodegenerative conditions including Alzheimer’s and Parkinson’s diseases, where it occurs in an uncontrolled manner. When observed at appropriate concentration and time scales, the chemical kinetics of filamentous protein self-assembly exhibits the remarkable property of self-similarity: the dynamics appears similar as the observation scale changes. We discuss here how this property leads to crucial simplifications of the fundamental laws governing protein filament formation and the emergence of scaling laws that provide the basis for connecting microscopic events with macroscopic realisations of such processes. In particular, we review recent developments in the modelling of linear protein self-assembly phenomena in the light of the concepts of dimensional analysis and physical self-similarity. We show how these tools and concepts can be used to elucidate the nature of the scaling laws for filamentous protein self-assembly, which illuminate the ultimately simple mathematical and physical principles underlying this seemingly highly complex phenomenon, and are expected to guide further developments in the field of linear self-assembly.
{"title":"Scaling and dimensionality in the chemical kinetics of protein filament formation","authors":"T. Michaels, A. Dear, T. Knowles","doi":"10.1080/0144235X.2016.1239335","DOIUrl":"https://doi.org/10.1080/0144235X.2016.1239335","url":null,"abstract":"The formation of elongated supra-molecular structures from protein building blocks generates functional intracellular filaments, but this process is also at the heart of many neurodegenerative conditions including Alzheimer’s and Parkinson’s diseases, where it occurs in an uncontrolled manner. When observed at appropriate concentration and time scales, the chemical kinetics of filamentous protein self-assembly exhibits the remarkable property of self-similarity: the dynamics appears similar as the observation scale changes. We discuss here how this property leads to crucial simplifications of the fundamental laws governing protein filament formation and the emergence of scaling laws that provide the basis for connecting microscopic events with macroscopic realisations of such processes. In particular, we review recent developments in the modelling of linear protein self-assembly phenomena in the light of the concepts of dimensional analysis and physical self-similarity. We show how these tools and concepts can be used to elucidate the nature of the scaling laws for filamentous protein self-assembly, which illuminate the ultimately simple mathematical and physical principles underlying this seemingly highly complex phenomenon, and are expected to guide further developments in the field of linear self-assembly.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"65 1","pages":"679 - 703"},"PeriodicalIF":6.1,"publicationDate":"2016-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91149219","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}
Pub Date : 2016-09-13DOI: 10.1080/0144235X.2016.1220774
Shirong Bai, R. T. Skodje
A new representation for chemical kinetics based on a sum over histories formulation is discussed. The description of the time-dependent chemistry of a reaction network is provided by chemical pathways defined at a molecular level. Using this methodology, the quantitative time evolution of the kinetics is described by enumerating the most important pathways followed by a chemical moiety such as a tagged atom. An explicit formula for the pathway probabilities is derived which takes the form of an integral over a time-ordered product. This expression has a simple and computationally efficient Monte Carlo representation which permits the method to be applied to a wide range of problems. For small reaction networks, the chemical pathways can be enumerated using graph theoretic methods. More complicated networks can be explored using random walks computed from a stochastic algorithm. The workings of the method are illustrated using a simple network of 20 chemical species which react via first-order kinetics. The application of the sum over histories representation to problems in surface catalysis and hydrogen combustion provide more realistic applications.
{"title":"The sum over histories representation for chemical kinetics: a quantitative theory based on chemical pathways","authors":"Shirong Bai, R. T. Skodje","doi":"10.1080/0144235X.2016.1220774","DOIUrl":"https://doi.org/10.1080/0144235X.2016.1220774","url":null,"abstract":"A new representation for chemical kinetics based on a sum over histories formulation is discussed. The description of the time-dependent chemistry of a reaction network is provided by chemical pathways defined at a molecular level. Using this methodology, the quantitative time evolution of the kinetics is described by enumerating the most important pathways followed by a chemical moiety such as a tagged atom. An explicit formula for the pathway probabilities is derived which takes the form of an integral over a time-ordered product. This expression has a simple and computationally efficient Monte Carlo representation which permits the method to be applied to a wide range of problems. For small reaction networks, the chemical pathways can be enumerated using graph theoretic methods. More complicated networks can be explored using random walks computed from a stochastic algorithm. The workings of the method are illustrated using a simple network of 20 chemical species which react via first-order kinetics. The application of the sum over histories representation to problems in surface catalysis and hydrogen combustion provide more realistic applications.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"77 1","pages":"539 - 567"},"PeriodicalIF":6.1,"publicationDate":"2016-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85912329","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}
Pub Date : 2016-08-08DOI: 10.1080/0144235X.2016.1203522
Cate S. Anstöter, J. Bull, J. Verlet
The recently developed method of frequency-, angle-, and time-resolved photoelectron imaging (FAT-PI) applied to the study of the dynamics of resonances of open-shell anions is reviewed. The basic principles of the method and its experimental realisation are outlined. The dynamics of a number of radical quinone anions is then considered. Firstly, we show for para-benzoquinone how frequency- and angle-resolved photoelectron imaging provides finger-prints of the dynamics of resonances and then how time-resolved photoelectron imaging yields deep mechanistic insight into the relaxation dynamics of the resonances. The effect of chemical substitutions of the para-quinone electrophore on the dynamics of resonances is discussed. Increasing the conjugation leads to a greatly enhanced ability for resonances to decay to the ground electronic state of the radical anion. Using time-resolved photoelectron spectroscopy, it is shown that the dynamics are facilitated by a bound valence state of the anion. The addition of electron donating methoxy groups leads to a reduced ability to access the ground state compared to para-benzoquinone. Both time-resolved dynamics and calculations provide a rationale for these observations. We consider the benefits and limitations of FAT-PI and its complementarity to 2D electron spectroscopy.
{"title":"Ultrafast dynamics of temporary anions probed through the prism of photodetachment","authors":"Cate S. Anstöter, J. Bull, J. Verlet","doi":"10.1080/0144235X.2016.1203522","DOIUrl":"https://doi.org/10.1080/0144235X.2016.1203522","url":null,"abstract":"The recently developed method of frequency-, angle-, and time-resolved photoelectron imaging (FAT-PI) applied to the study of the dynamics of resonances of open-shell anions is reviewed. The basic principles of the method and its experimental realisation are outlined. The dynamics of a number of radical quinone anions is then considered. Firstly, we show for para-benzoquinone how frequency- and angle-resolved photoelectron imaging provides finger-prints of the dynamics of resonances and then how time-resolved photoelectron imaging yields deep mechanistic insight into the relaxation dynamics of the resonances. The effect of chemical substitutions of the para-quinone electrophore on the dynamics of resonances is discussed. Increasing the conjugation leads to a greatly enhanced ability for resonances to decay to the ground electronic state of the radical anion. Using time-resolved photoelectron spectroscopy, it is shown that the dynamics are facilitated by a bound valence state of the anion. The addition of electron donating methoxy groups leads to a reduced ability to access the ground state compared to para-benzoquinone. Both time-resolved dynamics and calculations provide a rationale for these observations. We consider the benefits and limitations of FAT-PI and its complementarity to 2D electron spectroscopy.","PeriodicalId":54932,"journal":{"name":"International Reviews in Physical Chemistry","volume":"339 1","pages":"509 - 538"},"PeriodicalIF":6.1,"publicationDate":"2016-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80729896","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}
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