Anisotropic pseudorotation of the photoexcited triplet state of fullerene C60 in molecular glasses studied by pulse EPR

Spin-polarized echo-detected electron paramagnetic resonance (EPR) spectra and the transversal relaxation rate T2(-1) of the photoexcited triplet state of fullerene C60 molecules were studied in o-terphenyl, 1-methylnaphthalene, and decalin glassy matrices. The model is composed of a fast (correlation time approximately 10(-12) s) pseudorotation of (3)C60 in a local anisotropic potential created by interaction of the fullerene molecule with the surrounding matrix molecules. In simulations, this potential is assumed to be axially symmetric around some axis of a preferable orientation in a matrix cage. The fitted value of the potential was found to depend on the type of glass and to decrease monotonically with a temperature increase. A sharp increase of the T2(-1) temperature dependence was found near 240 K in glassy o-terphenyl and near 100 K in glassy 1-methylnaphthalene and decalin. This increase probably is related to the influence on the pseudorotation of the onset of large-amplitude vibrational molecular motions (dynamical transition in glass) that are known for glasses from neutron scattering and molecular dynamics studies. The obtained results suggest that molecular and spin dynamics of the triplet fullerene are extremely sensitive to molecular motions in glassy materials.     

Rotational dynamics and polymerization of C60 in C60-cubane crystals: a molecular dynamics study

We report classical and tight-binding molecular dynamics simulations of the C(60) fullerene and cubane molecular crystal in order to investigate the intermolecular dynamics and polymerization processes. Our results show that, for 200 and 400 K, cubane molecules remain basically fixed, presenting only thermal vibrations, while C(60) fullerenes show rotational motions. Fullerenes perform "free" rotational motions at short times (approximately < 1 ps), small amplitude hindered rotational motions (librations) at intermediate times, and rotational diffusive dynamics at long times (approximately > 10 ps). The mechanisms underlying these dynamics are presented. Random copolymerizations among cubanes and fullerenes were observed when temperature is increased, leading to the formation of a disordered structure. Changes in the radial distribution function and electronic density of states indicate the coexistence of amorphous and crystalline phases. The different conformational phases that cubanes and fullerenes undergo during the copolymerization process are discussed.     

Laser spectroscopic visualization of hydrogen bond motions in liquid water

Ultrafast pump-probe experiments are described permitting a visualization of molecular motions in diluted HDO/D₂O solutions. The experiments were realized in the mid-infrared spectral region with a time resolution of 150 fs. They were interpreted by a careful theoretical analysis, based on the correlation function approach of statistical mechanics. Combining experiment and theory, stretching motions of the OHO bonds as well as HDO rotations were ‘filmed’ in real time. It was found that molecular rotations are the principal agent of hydrogen bond breaking and making in water. Recent literatures covering the subject, including molecular dynamics simulations, are reviewed in detail.     

Conformational properties of penicillins: quantum chemical calculations and molecular dynamics simulations of benzylpenicillin

Herein, we present theoretical results on the conformational properties of benzylpenicillin, which are characterized by means of quantum chemical calculations (MP2/6-31G* and B3LYP/6-31G*) and classical molecular dynamics simulations (5 ns) both in the gas phase and in aqueous solution. In the gas phase, the benzylpenicillin conformer in which the thiazolidine ring has the carboxylate group oriented axially is the most favored one. Both intramolecular CH. O and dispersion interactions contribute to stabilize the axial conformer with respect to the equatorial one. In aqueous solution, a molecular dynamics simulation predicts a relative population of the axial:equatorial conformers of 0.70:0.30 in consonance with NMR experimental data. Overall, the quantum chemical calculations as well as the simulations give insight into substituent effects, the conformational dynamics of benzylpenicillin, the frequency of ring-puckering motions, and the correlation of side chain and ring-puckering motions.     

Simulating the formation of sodium:electron tight-contact pairs: watching the solvation of atoms in liquids one molecule at a time

The motions of solvent molecules during a chemical transformation often dictate both the dynamics and the outcome of solution-phase reactions. However, a microscopic picture of solvation dynamics is often obscured by the concerted motions of numerous solvent molecules that make up a condensed-phase environment. In this study, we use mixed quantum/classical molecular dynamics simulations to furnish the molecular details of the solvation dynamics that leads to the formation of a sodium cation-solvated electron contact pair, (Na(+), e(-)), in liquid tetrahydrofuran following electron photodetachment from sodide (Na(-)). Our simulations reveal that the dominant solvent response is comprised of a series of discrete solvent molecular events that work sequentially to build up a shell of coordinating THF oxygen sites around the sodium cation end of the contact pair. With the solvent response described in terms of the sequential motion of single molecules, we are then able to compare the calculated transient absorption spectroscopy of the sodium species to experiment, providing a clear microscopic interpretation of ultrafast pump-probe experiments on this system. Our findings suggest that for solute-solvent interactions similar to the ones present in our study, the solvation dynamics is best understood as a series of kinetic events consisting of reactions between chemically distinct local structures in which key solvent molecules must be considered to be part of the identity of the reacting species.     

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 ?) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.     

Conformational dynamics of the cytochrome P450 BM3/N-palmitoylglycine complex: the proposed "proximal-distal" transition probed by temperature-jump spectroscopy

The ferric spin state equilibrium of the heme iron was analyzed in wild-type cytochrome P450 BM3 and its F87G mutant by using temperature (T)-jump relaxation spectroscopy in combination with static equilibrium experiments. No relaxation process was measurable in the substrate-free enzyme indicating a relaxation process with a rate constant>10,000 s(-1). In contrast, a slow spin state transition process was observed in the N-palmitoylglycine (NPG)-bound enzyme species. This transition occurred with an observed rate constant (298 K) of approximately 800 s(-1) in the wild-type, and approximately 2500 s(-1) in the F87G mutant, suggesting a significant contribution of the phenylalanine side chain to a reaction step rate limiting the actual spin state transition. These findings are discussed in terms of an equilibrium between different binding modes of the substrate, including a position 7.5 A away from the heme iron ("distal") and the catalytically relevant "proximal" binding site, and are in accordance with results from X-ray crystallography, NMR studies, and molecular dynamics simulations.     

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

Nonspherical cages in inclusion compounds can result in non‐uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO₂ molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO₂ guests in terms of a polar angle θ and azimuth angle ? and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO₂ sI clathrate. The experimental ¹³C NMR lineshapes of CO₂ guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the ¹³C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.     

Hydrogen motions in the alpha-relaxation regime of poly(vinyl ethylene): a molecular dynamics simulation and neutron scattering study

The hydrogen motion in poly(vinyl ethylene) (1,2-polybutadiene) in the alpha-relaxation regime has been studied by combining neutron spin echo (NSE) measurements on a fully protonated sample and fully atomistic molecular dynamics simulations. The almost perfect agreement between experiment and simulation results validates the simulated cell. A crossover from Gaussian to non-Gaussian behavior is observed for the intermediate scattering function obtained from both NSE measurements and simulations. This crossover takes place at unusually low Q values, well below the first maximum of the static structure factor. Such anomalous deviation from Gaussian behavior can be explained by the intrinsic dynamic heterogeneity arising from the differences in the dynamics of the different protons in this system. Side group hydrogens show a markedly higher mobility than main chain protons. Taking advantage of the simulations we have investigated the dynamic features of all different types of hydrogens in the sample. Considering each kind of proton in an isolated way, deviations from Gaussian behavior are also found. These can be rationalized in the framework of a simple picture based on the existence of a distribution of discrete jumps underlying the atomic motions in the alpha process.     

(1)H relaxation dispersion in solutions of nitroxide radicals: Effects of hyperfine interactions with (14)N and (15)N nuclei

(1)H relaxation dispersion of decalin and glycerol solutions of nitroxide radicals, 4-oxo-TEMPO-d(16)-(15)N and 4-oxo-TEMPO-d(16)-(14)N was measured in the frequency range of 10 kHz-20 MHz (for (1)H) using STELAR Field Cycling spectrometer. The purpose of the studies is to reveal how the spin dynamics of the free electron of the nitroxide radical affects the proton spin relaxation of the solvent molecules, depending on dynamical properties of the solvent. Combining the results for both solvents, the range of translational diffusion coefficients, 10(-9)-10(-11) m(2)∕s, was covered (these values refer to the relative diffusion of the solvent and solute molecules). The data were analyzed in terms of relaxation formulas including the isotropic part of the electron spin - nitrogen spin hyperfine coupling (for the case of (14)N and (15)N) and therefore valid for an arbitrary magnetic field. The influence of the hyperfine coupling on (1)H relaxation of solvent molecules depending on frequency and time-scale of the translational dynamics was discussed in detail. Special attention was given to the effect of isotope substitution ((14)N∕(15)N). In parallel, the influence of rotational dynamics on the inter-molecular (radical - solvent) electron spin - proton spin dipole-dipole coupling (which is the relaxation mechanism of solvent protons) was investigated. The rotational dynamics is of importance as the interacting spins are not placed in the molecular centers. It was demonstrated that the role of the isotropic hyperfine coupling increases for slower dynamics, but it is of importance already in the fast motion range (10(-9)m(2)∕s). The isotope effects is small, however clearly visible; the (1)H relaxation rate for the case of (15)N is larger (in the range of lower frequencies) than for (14)N. It was shown that when the diffusion coefficient decreases below 5 × 10(-11) m(2)∕s electron spin relaxation becomes of importance and its role becomes progressively more significant when the dynamics slows done. As far as the influence of the rotational dynamics is concerned, it was show that this process is of importance not only in the range of higher frequencies (like for diamagnetic solutions) but also at low and intermediate frequencies.     

A study of the vibrational motions of water in an aqueous CaCl2 solution

A detailed analysis of the vibrational motions of water in a 1.1 M aqueous CaCl₂ solution is presented on the basis of molecular dynamics computer simulations. Autocorrelation functions corresponding to approximate normal coordinates are constructed and evaluated separately for the hydration water of the ions and for the bulk water of the solution. Approximate lifetimes for the intramolecular motions are estimated. The theoretical results are compared with experimental ones from IR spectroscopy of water-base complexes.     

A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics

A suite of (2)H-based spin relaxation NMR experiments is presented for the measurement of molecular dynamics in a site-specific manner in uniformly (13)C, randomly fractionally deuterated ( approximately 50%) RNA molecules. The experiments quantify (2)H R(1) and R(2) relaxation rates that can subsequently be analyzed to obtain information about dynamics on a pico- to nanosecond time scale. Sensitivity permitting, the consistency of the data can be evaluated by measuring all five rates that are accessible for a spin 1 particle and establishing that the rates obey relations that are predicted from theory. The utility of the methodology is demonstrated with studies of the dynamics of a 14-mer RNA containing the UUCG tetraloop at temperatures of 25 and 5 degrees C. The high quality of the data, even at 5 degrees C, suggests that the experiments will be of use for the study of RNA molecules that are as large as 30 nucleotides.     

Development and validation of an integrated computational approach for the modeling of cw-ESR spectra of free radicals in solution: p-(methylthio)phenyl nitronylnitroxide in toluene as a case study

In this work we address the interpretation, via an ab initio integrated computational approach, of continuous wave electron spin resonance (cw-ESR) spectra of p-(methylthio)phenyl nitronylnitroxide (MTPNN) dissolved in toluene. Our approach is based on the determination of the spin Hamiltonian, averaged with respect to fast vibrational motions, with magnetic tensor parameters (Zeeman and hyperfine tensors) characterized by quantum mechanical density functional calculations. The system is then described by a stochastic Liouville equation, with inclusion of diffusive rotational dynamics. Parametrization of diffusion rotational tensor is provided by a hydrodynamic model. Cw-ESR spectra of MTPNN are simulated for a wide range of temperatures (155-292 K) with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems.     

Temperature dependence of NMR order parameters and protein dynamics

The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the temperature dependence of internal motions of the backbone amide moieties of HP36. The potential of mean force (PMF) for the N-H bond vector, determined from the constrained simulations, is found to be temperature dependent. A simple analytical expression is derived that describes the temperature dependence of the PMF. The parameters of this model are obtained from the PMF, from the unconstrained molecular dynamics simulations, or from experimental values of the generalized order parameter. The results provide a linkage between experimental and theoretical measures of the temperature dependence of protein motions.     

First-principles molecular dynamics evaluation of thermal effects on the NMR (1)J(Li,C) spin-spin coupling

Car-Parrinello (CP) molecular dynamics were applied to sample conformations of various models of organolithium aggregates which are chosen to estimate (1)J(Li,C) NMR coupling constants. The results show that the deviations from the values computed using static (optimized) geometries are small provided no large-amplitude motions occur within the timescale of the simulations. In the case of the vinyllithium dimer, for which rotation of the vinyl chain is observed, this approach allows analysis of the various contributions to the experimentally measured constants. For the trisolvated methyllithium monomer, partial decoordination of solvating dimethyl ether is observed and results in a significant shift of (1)J(Li,C). All these results highlight that a varied physicochemical machinery is hidden behind general empirical formulas, such as the Bauer-Winchester-Schleyer rule used experimentally.     

Modeling the effects of structure and dynamics of the nitroxide side chain on the ESR spectra of spin-labeled proteins

In the companion paper (J. Phys. Chem. B 2006, 110, jp0629487), a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface-exposed alpha-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated within the framework of the Stochastic Liouville equation (SLE) methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side chain of the R2 spin label, only a few noninterconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights that can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral line shapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin-labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches.     

Rotamer libraries of spin labelled cysteines for protein studies

Studies of structure and dynamics of proteins using site-directed spin labelling rely on explicit modelling of spin label conformations. The large computational effort associated with such modelling with molecular dynamics (MD) simulations can be avoided by a rotamer library approach based on a coarse-grained representation of the conformational space of the spin label. We show here that libraries of about 200 rotamers, obtained by iterative projection of a long MD trajectory of the free spin label onto a set of canonical dihedral angles, provide a representation of the underlying trajectory adequate for EPR distance measurements. Rotamer analysis was performed on selected X-ray structures of spin labelled T4 lysozyme mutants to characterize the spin label rotamer ensemble on a single protein site. Furthermore, predictions based on the rotamer library approach are shown to be in nearly quantitative agreement with electron paramagnetic resonance (EPR) distance data on the Na(+)/H(+) antiporter NhaA and on the light-harvesting complex LHCII whose structures are known from independent cryo electron microscopy and X-ray studies, respectively. Suggestions for the selection of labelling sites in proteins are given, limitations of the approach discussed, and requirements for further development are outlined.     

Charge controlled changes in the cluster and spin dynamics of Sc3N@C80(CF3)2: the flexible spin density distribution and its impact on ESR spectra

Cluster and spin dynamics of a Sc(3)N@C(80)(CF(3))(2) derivative are studied by DFT in different charge states, from -3 to +1. For the neutral Sc(3)N@C(80)(CF(3))(2), static DFT computations of many cluster conformers as well as Born-Oppenheimer molecular dynamics (BOMD) show that addition of two CF(3) groups to Sc(3)N@C(80) significantly changes dynamics of the Sc(3)N cluster: instead of free rotation as in Sc(3)N@C(80), the cluster in Sc(3)N@C(80)(CF(3))(2) exhibits only hindered motions. Similar cluster dynamics is found in the mono- and trianions of Sc(3)N@C(80)(CF(3))(2), while free rotation of the cluster is found in the cation. In the radical species, motions of the cluster dramatically change spin-density distribution. Spin populations of the metal atoms and the carbon cage are followed along the BOMD trajectories to reveal the details of the spin-flow. (45)Sc ESR hyperfine coupling constants integrated over BOMD trajectories are found to be substantially different from the results of static DFT computations, which emphasizes that cluster dynamics should be taken into account for reliable predictions of spectroscopic properties.     

A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein

A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.