Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Franck-Condon picture of incoherent neutron scattering.

ABSTRACT: A spectroscopic interpretation of incoherent neutron scattering experiments is presented which is based on Franck-Condon-type probabilities for scattering-induced transitions between quantum states of the target. The resulting expressions for the scattering functions enable an energy landscape-oriented analysis of neutron scattering spectra as well as a physical interpretation of Van Hove's space-time correlation functions in the quantum regime that accounts for the scattering kinematics. They suggest moreover a combined analysis of quasielastic and elastic scattering that become inseparable for complex systems with slow power-law relaxation.

SUBMITTER: Kneller GR

PROVIDER: S-EPMC6156675 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Franck-Condon picture of incoherent neutron scattering.

Kneller Gerald R GR

Proceedings of the National Academy of Sciences of the United States of America 20180830 38

A spectroscopic interpretation of incoherent neutron scattering experiments is presented which is based on Franck-Condon-type probabilities for scattering-induced transitions between quantum states of the target. The resulting expressions for the scattering functions enable an energy landscape-oriented analysis of neutron scattering spectra as well as a physical interpretation of Van Hove's space-time correlation functions in the quantum regime that accounts for the scattering kinematics. They s ...[more]

PMID: 30166450

Similar Datasets

Dynamics Properties of Photosynthetic Microorganisms Probed by Incoherent Neutron Scattering.

Project description:Studies on the dynamical properties of photosynthetic membranes of land plants and purple bacteria have been previously performed by neutron spectroscopy, revealing a tight coupling between specific photochemical reactions and macromolecular dynamics. Here, we probed the intrinsic dynamics of biotechnologically useful mutants of the green alga Chlamydomonas reinhardtii by incoherent neutron scattering coupled with prompt chlorophyll fluorescence experiments. We brought to light that single amino acid replacements in the plastoquinone (PQ)-binding niche of the photosystem II D1 protein impair electron transport (ET) efficiency between quinones and confer increased flexibility to the host membranes, expanding to the entire cells. Hence, a more flexible environment in the PQ-binding niche has been associated to a less efficient ET. A similar function/dynamics relationship was also demonstrated in Rhodobacter sphaeroides reaction centers having inhibited ET, indicating that flexibility at the quinones region plays a crucial role in evolutionarily distant organisms. Instead, a different functional/dynamical correlation was observed in algal mutants hosting a single amino acid replacement residing in a D1 domain far from the PQ-binding niche. Noteworthy, this mutant displayed the highest degree of flexibility, and besides having a nativelike ET efficiency in physiological conditions, it acquired novel, to our knowledge, phenotypic traits enabling it to preserve a high maximal quantum yield of photosystem II photochemistry in extreme habitats. Overall, in the nanosecond timescale, the degree of the observed flexibility is related to the mutation site; in the picosecond timescale, we highlighted the presence of a more pronounced dynamic heterogeneity in all mutants compared to the native cells, which could be related to a marked chemically heterogeneous environment.

| S-EPMC6506642 | biostudies-literature

Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering.

Project description:Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.

| S-EPMC6451406 | biostudies-literature

General Time Dependent Approach to Vibronic Spectroscopy Including Franck-Condon, Herzberg-Teller, and Duschinsky Effects.

Project description:An effective time-dependent (TD) approach to compute vibrationally resolved optical spectra from first principles is presented for the computation of one-photon electronic spectra induced by either electric or magnetic transition dipoles or by their mutual interaction, namely absorption, emission, and circular dichroism. Particular care has been devoted to generality, modularity, and numerical stability including all the contributions that play a role at the harmonic level of approximation, namely Franck-Condon, Herzberg-Teller, and Dushinsky (i.e., mode mixing) effects. The implementation shares the same general framework of our previous time-independent (TI) model, thus allowing an effective integration between both approaches with the consequent enhancement of their respective strengths (e.g., spectrum completeness and straightforward account of temperature effects for the TD route versus band resolution and assignment for the TI route) using a single set of starting data. Implementation of both models in the same general computer program allows comprehensive studies using several levels of electronic structure description together with effective account of environmental effects by atomistic and/or continuum models of different sophistication. A few medium-size molecules (furan, phenyl radical, anthracene, dimethyloxirane, coumarin 339) have been studied in order to fully validate the approach.

| S-EPMC6485600 | biostudies-literature

How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?

Project description:Incoherent neutron scattering (INS) is one of the useful experimental methods for studying protein dynamics at the pico-nanosecond timescale. At this timescale, protein dynamics is highly coupled with hydration, which is observed as protein dynamical transition (PDT). INS is very sensitive to hydrogen atomic dynamics because of the large incoherent scattering cross section of hydrogen atom, and thus, the INS of a hydrated protein provides overall dynamic information about the protein, including hydration water. Separation of hydration water dynamics is essential for understanding hydration-related protein dynamics. H2O/D2O exchange is an effective method in the context of INS experiments for observing the dynamics of protein and hydration water separately. Neutron scattering is directly related to the van Hove space-time correlation function, which can be calculated quantitatively by performing molecular dynamics (MD) simulations. Diffusion and hydrogen bond dynamics of hydration water can be analyzed by performing MD simulation. MD simulation is useful for analyzing the dynamic coupling mechanism in hydration-related protein dynamics from the viewpoint of interpreting INS data because PDT is induced by hydration. In the present work, we demonstrate the methodological advantages of the H2O/D2O exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water.

| S-EPMC6975894 | biostudies-literature

Excited State Frequencies of Chlorophyll f and Chlorophyll a and Evaluation of Displacement through Franck-Condon Progression Calculations.

Project description:We present ground and excited state frequency calculations of the recently discovered extremely red-shifted chlorophyll f. We discuss the experimentally available vibrational mode assignments of chlorophyll f and chlorophyll a which are characterised by particularly large downshifts of 13¹-keto mode in the excited state. The accuracy of excited state frequencies and their displacements are evaluated by the construction of Franck-Condon (FC) and Herzberg-Teller (HT) progressions at the CAM-B3LYP/6-31G(d) level. Results show that while CAM-B3LYP results are improved relative to B3LYP calculations, the displacements and downshifts of high-frequency modes are underestimated still, and that the progressions calculated for low temperature are dominated by low-frequency modes rather than fingerprint modes that are Resonant Raman active.

| S-EPMC6479460 | biostudies-literature

Interference between Franck-Condon and Herzberg-Teller Terms in the Condensed-Phase Molecular Spectra of Metal-Based Tetrapyrrole Derivatives.

Project description:The commonly used Franck-Condon (FC) approximation is inadequate for explaining the electronic spectra of compounds that possess vibrations with substantial Herzberg-Teller (HT) couplings. Metal-based tetrapyrrole derivatives, which are ubiquitous natural pigments, often exhibit prominent HT activity. In this paper, we compare the condensed phase spectra of zinc-tetraphenylporphyrin (ZnTPP) and zinc-phthalocyanine (ZnPc), which exhibit vastly different spectral features in spite of sharing a common tetrapyrrole backbone. The absorption and emission spectra of ZnTPP are characterized by a lack of mirror symmetry and nontrivial temperature dependence. In contrast, mirror symmetry is restored, and the nontrivial temperature-dependent features disappear in ZnPc. We attribute these differences to FC-HT interference, which is less pronounced in ZnPc because of a larger FC component in the dipole moment that leads to FC-dominated transitions. A single minimalistic FC-HT vibronic model reproduces all the experimental spectral features of these molecules. These observations suggest that FC-HT interference is highly susceptible to chemical modification.

| S-EPMC9393888 | biostudies-literature

Reassignment of the Photoelectron Spectrum of Methylketene Using a Hybrid Model of Harmonic and Anharmonic Oscillators to Compute Franck-Condon Factors.

Project description:We constructed a hybrid model of harmonic and anharmonic oscillators to compute Franck-Condon factors and interpret the photoelectron spectrum of methylketene. The equilibrium structures of methylketene and its cation were optimized, and then, the harmonic and anharmonic vibrational frequencies were computed using the B3LYP, PBE0, APFD, and ωB97XD approaches of the density functional theory. The photoelectron spectrum of methylketene was simulated by computing the Franck-Condon factors with both the harmonic and hybrid models. The adiabatic ionization energy of methylketene was computed by using the CCSD(T) approach extrapolating to the complete basis set limit. The simulated photoelectron spectra are consistent with those from the experiment for both the harmonic and hybrid models. However, the error in band positions is reduced by using the hybrid model. The computed adiabatic ionization energies of methylketene are in agreement with the experiment, with the smallest error being 0.017 eV. Our interpretation based on the theoretical spectrum led to the reassignment of the experimental photoelectron spectrum of methylketene.

| S-EPMC10637627 | biostudies-literature

Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering.

Project description:The temperature dependence of the dynamics of mesophilic and thermophilic dihydrofolate reductase is examined using elastic incoherent neutron scattering. It is demonstrated that the distribution of atomic displacement amplitudes can be derived from the elastic scattering data by assuming a (Weibull) functional form that resembles distributions seen in molecular dynamics simulations. The thermophilic enzyme has a significantly broader distribution than its mesophilic counterpart. Furthermore, although the rate of increase with temperature of the atomic mean-square displacements extracted from the dynamic structure factor is found to be comparable for both enzymes, the amplitudes are found to be slightly larger for the thermophilic enzyme. Therefore, these results imply that the thermophilic enzyme is the more flexible of the two.

| S-EPMC2397366 | biostudies-literature

Protein Backbone and Average Particle Dynamics in Reconstituted Discoidal and Spherical HDL Probed by Hydrogen Deuterium Exchange and Elastic Incoherent Neutron Scattering.

Project description:Lipoproteins are supramolecular assemblies of proteins and lipids with dynamic characteristics critically linked to their biological functions as plasma lipid transporters and lipid exchangers. Among them, spherical high-density lipoproteins are the most abundant forms of high-density lipoprotein (HDL) in human plasma, active participants in reverse cholesterol transport, and associated with reduced development of atherosclerosis. Here, we employed elastic incoherent neutron scattering (EINS) and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to determine the average particle dynamics and protein backbone local mobility of physiologically competent discoidal and spherical HDL particles reconstituted with human apolipoprotein A-I (apoA-I). Our EINS measurements indicated that discoidal HDL was more dynamic than spherical HDL at ambient temperatures, in agreement with their lipid-protein composition. Combining small-angle neutron scattering (SANS) with contrast variation and MS cross-linking, we showed earlier that the most likely organization of the three apolipoprotein A-I (apoA-I) chains in spherical HDL is a combination of a hairpin monomer and a helical antiparallel dimer. Here, we corroborated those findings with kinetic studies, employing hydrogen-deuterium exchange mass spectrometry (HDX-MS). Many overlapping apoA-I digested peptides exhibited bimodal HDX kinetics behavior, suggesting that apoA-I regions with the same amino acid composition located on different apoA-I chains had different conformations and/or interaction environments.

| S-EPMC7022587 | biostudies-literature

Softness of atherogenic lipoproteins: a comparison of very low density lipoprotein (VLDL) and low density lipoprotein (LDL) using elastic incoherent neutron scattering (EINS).

Project description:Apolipoprotein B100 (apoB100)-containing plasma lipoproteins (LDL and VLDL) supply tissues and cells with cholesterol and fat. During lipolytic conversion from VLDL to LDL the size and chemical composition of the particles change, but the apoB100 molecule remains bound to the lipids and regulates the receptor mediated uptake. The molecular physical parameters which control lipoprotein remodeling and enable particle stabilization by apoB100 are largely unknown. Here, we have compared the molecular dynamics and elasticities of VLDL and LDL derived by elastic neutron scattering temperature scans. We have determined thermal motions, dynamical transitions, and molecular fluctuations, which reflect the temperature-dependent motional coupling between lipid and protein. Our results revealed that lipoprotein particles are extremely soft and flexible. We found substantial differences in the molecular resiliences of lipoproteins, especially at higher temperatures. These discrepancies not only can be explained in terms of lipid composition and mobility but also suggest that apoB100 displays different dynamics dependent on the lipoprotein it is bound to. Hence, we suppose that the inherent conformational flexibility of apoB100 permits particle stabilization upon lipid exchange, whereas the dynamic coupling between protein and lipids might be a key determinant for lipoprotein conversion and atherogenicity.

| S-EPMC3173844 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data