The quantitative measurement of rotational motion of the subfragment-1 region of myosin by saturation transfer epr spectroscopy.

According to current models of muscle contraction (Huxley, H. E., Science 164: 1356-1366 [1969]), motion of flexible myosin crossbridges is essential to the contractile cycle. Using a spin-label analog of iodoacetamide bound to the subfragment No. 1 (S1) region of myosin, we have obtained rotational correlation times (tau 2) for this region of the molecule with the ultimate goal of making quantitative measurements of the motion of the crossbridges under conditions comparable to those in living, contracting muscle. We used the newly developed technique of saturation transfer electron paramagnetic resonance spectroscopy (Hyde, J.S., and Thomas, D.D., Ann. N.Y. Acad Sci. 22:680-692 [1973]), which is uniquely sensitive to rotational motion in the range of 10(-7)-10(-3) sec. Our results indicate that the spin label is rigidly bound to S1 (tau 2 for isolated S1 is 2 X 10(-7) sec) and that the motion of the label reflects the motion of the S1 region of myosin. the value of tau 2 for the S1 segment of myosin is less than twice that for isolated S1, while the molecular weights differ by a factor of 4, indicating flexibility of myosin in agreement with the conclusions of Mendelson et al. (Biochemistry 12:2250-2255 [1973]). Adding F-actin increses tau 2 in either myosin or isolated S1 by a factor of mearly 103, indicating rigid immobilization of S1 by actin. Formation of myosin filaments (at an ionic strength of 0.15 or less) increses tau 2 by a factor of 10-30, depending on the ionic strength, indicating a decrease of the rotational mobility of S1 in these agregates. The remaining motion is at least a factor of 10 faster than would be expected for the filament itself, suggesting motion of the S1 region independent of the filament backbone but slower than in a single molecule. F-actin has a strong immobilizing effect on labeled S1 in myosin filaments (in 0.137 M KC1), but the immobilization is less complete than that observed when F-actin is added to labeled myosin monomers (in 0.5 M KC1). A spin-label analog of maleimide, attached to the SH-2 thiol groups of S1, is immobilized to a much lesser extent by F-actin than is the label on SH-1 groups. The maleimide label also was attached directly to F-actin and was sufficiently immobilized to suggest rigid binding to actin.     

State-to-state photodissociation of carbonyl sulfide (nu2=0,1/JlM). II. The effect of initial bending on coherence of S(1D2) polarization

Photodissociation studies using ion imaging are reported, measuring the coherence of the polarization of the S((1)D(2)) fragment from the photolysis of single-quantum state-selected carbonyl sulfide (OCS) at 223 and 230 nm. A hexapole state-selector focuses a molecular beam of OCS parent molecules in the ground state (nu2=0mid R:JM=10) or in the first excited bending state (nu2=1mid R:JlM=111). At 230 nm photolysis the Im[a1 (1)(parallel, perpendicular)] moment for the fast S(1D2) channel increases by about 50% when the initial OCS parent state changes from the vibrationless ground state to the first excited bending state. No dependence on the initial bending state is found for photolysis at 223 nm. We observe separate rings in the slow channel of the velocity distribution of S(1D2) correlating to single CO(J) rotational states. The additional available energy for photolysis at 223 nm is found to be channeled mostly into the CO(J) rotational motion. An improved value for the OC-S bond energy D0=4.292 eV is reported.     

Extended model free approach to analyze correlation functions of multidomain proteins in the presence of motional coupling

Interdomain motion in proteins plays an important role in biomolecular interaction. Its presence also complicates interpretation of many spectroscopy measurements. Nuclear magnetic resonance (NMR) study of domain dynamics relies on knowledge of its rotational correlation function. The extended model free (EMF) approach has been implemented to analyze coupled domain and overall motions for calmodulin, a dual-domain protein; however, the validity of EMF treatment in coupled motion has not been tested. We performed stochastic simulations on a dual-vector system employing two simple restraints to drive hydrodynamics and domain coupling: (1) both unitary vectors diffuse randomly on the surface of a sphere and (2) vectors are correlated through user-defined intervector potential. The resulting correlation curve can be adequately fit with either a single- or double-exponential decay function. The latter is consistent with the EMF treatment. The derived order parameters S (2) range from about 0.4 to 1, while the motion separation, the ratio of overall and domain motion time scales (tau m/tau s), ranges from 1 to 4. A complete overlap between time scales occurs when S (2) is less than 0.4, and the correlation function effectively behaves as a single-exponential. The S (2) values are consistent with theoretical predictions from the given potential function, differing by no more than 0.03, suggesting EMF to be a generally valid approach. In addition, from the dependence of S (2) on tau m/tau s obtained from simulation, we found a cosine potential, favoring extended conformers, as opposed to the normally assumed cone potential, reached a better agreement to experimental data.     

Rotational spectrum and inversion motions in the neon-dimethyl sulfide complex

The rotational spectra of the (20)Ne and (22)Ne isotopomers of the Ne-dimethyl sulfide (DMS) rare gas dimer have been measured by Fourier transform microwave spectroscopy. MP2/6-311++G(2d,2p) calculations, and the experimental spectroscopic data, suggest a structure of C(s) symmetry in which the Ne atom lies above the heavy atom plane of the DMS (in the sigma(v) plane which bisects the CSC angle). Experimental rotational constants are consistent with a S...Ne distance of 3.943(6) Angstroms and a (cm...S...Ne) angle of 63.2(6) degrees (where cm is the center of mass of DMS). A motion of the Ne atom from one side of the DMS to the other gives rise to inversion splittings of around 3 MHz in the c-type transitions. An ab initio potential energy surface calculation has allowed examination of several possible tunneling pathways, and suggests a barrier of between 20 and 40 cm(-1) for the inversion motion, depending on the tunneling pathway taken by the Ne. Dipole moment measurements are consistent with both the experimental and ab initio structures.     

Unveiling the nonadiabatic rotational excitation process in a symmetric-top molecule induced by two intense laser pulses

We experimentally investigate the nonadiabatic rotational excitation process of a symmetric-top molecule, benzene, in the electronic ground state irradiated by intense nonresonant ultrafast laser fields. The initial rotational-state distribution was restricted mostly to the five lowest levels with different nuclear spin modifications by an extensive adiabatic cooling with the rotational temperature well below 1 K, and distributions after the interaction with a femtosecond double-pulse pair (3-5 TW/cm(2) each with 160 fs duration) with time delays were probed in a quantum-state resolved manner by employing resonant enhanced multiphoton ionization via the S(1) ← S(0) 6(0) (1) vibronic transition. Populations of 10 rotational levels with J ranging from 0 to 4 and K from 0 to 3 were examined to show an oscillatory dependence on the time delay between the two pulses. Fourier analysis of the beat signals provides the coupling strengths between the constituent levels of the rotational wave packets created by the nonadiabatic excitation. These data are in good agreement with the results from quantum mechanical calculations, evidencing stepwise excitation pathways in the wave packet creation with ΔJ = 2 in the K = 0 stack while ΔJ = 1 and 2 in the K > 0 stacks.     

Role of the direct reaction H2S + SO2 in the homogeneous Claus reaction

Quantum chemical methods at the Gaussian-2 and -3 levels of theory have been used to investigate the reactions between H(2)S, SO(2), and S(2)O such as might occur in the front-end furnace of the Claus process. The direct reaction between H(2)S and SO(2) occurs via a 5-centered transition state with an initial barrier of approximately 135 kJ mol(-1) and an overall barrier of approximately 153 kJ mol(-1) to produce S(2)O and H(2)O. We indicate approximate values here because there are a number of isomers in the reaction pathway that have barriers slightly different from those quoted. The presence of a water molecule lowers this by approximately 60 kJ mol(-1), but the van der Waals complex required for catalysis by water is thermodynamically unfavorable under the conditions in the Claus reactor. The direct reaction between H(2)S and S(2)O can occur via two possible pathways; the analogous reaction to H(2)S + SO(2) has an initial barrier of approximately 117 kJ mol(-1) and an overall barrier of approximately 126 kJ mol(-1) producing S(3) and H(2)O, and a pathway with a 6-centred transition state has a barrier of approximately 111 kJ mol(-1), producing HSSSOH. Rate constants, including a QRRK analysis of intermediate stabilization, are reported for the kinetic scheme proposed here.     

Internal rotational motion of the chloromethyl group of the jet-cooled benzyl chloride molecule

The mass-resolved resonance enhanced two-photon ionization spectra of jet-cooled benzyl chloride were measured. Some low-frequency vibronic bands around the S1-S0 origin band were assigned to transitions of the internal rotational mode of the chloromethyl group. The internal rotational motion was analyzed by using the one-dimensional free rotor approximation. The conformation in the S1 state was found to be that in which the C-Cl bond lies in orthogonal to the benzene plane. For the species with m/e 126, the transition energy of the internal rotational bands corresponded well to the potential energy values of V2 = 1900 cm(-1) and V4 = 30 cm(-1) in the S1 state and the reduced rotational constant B values 0.50 and 0.47 cm(-1) in the S0 and S1 states, respectively. The B values obtained for the chlorine isotopomer (m/e 128) were slightly different. The S1 potential barrier height was found to be about 3 times larger than that for the S0 state. Molecular orbital calculations suggest that the difference between energies of the HOMO and LUMO with respect to the rotation of the chloromethyl group correspond approximately to the potential energy curve obtained for the S1 state.     

Probing highly efficient photoisomerization of a bridged azobenzene by a combination of CASPT2//CASSCF calculation with semiclassical dynamics simulation

Mechanism of phototriggered isomerization of azobenzene and its derivatives is of broad interest. In this paper, the S(0) and S(1) potential energy surfaces of the ethylene-bridged azobenzene (1) that was recently reported to have highly efficient photoisomerization were determined by ab initio electronic structure calculations at different levels and further investigated by a semiclassical dynamics simulation. Unlike azobenzene, the cis isomer of 1 was found to be more stable than the trans isomer, consistent with the experimental observation. The thermal isomerization between cis and trans isomers proceeds via an inversion mechanism with a high barrier. Interestingly, only one minimum-energy conical intersection was determined between the S(0) and S(1) states (CI) for both cis → trans and trans → cis photoisomerization processes and confirmed to act as the S(1) → S(0) decay funnel. The S(1) state lifetime is ～30 fs for the trans isomer, while that for the cis isomer is much longer, due to a redistribution of the initial excitation energies. The S(1) relaxation dynamics investigated here provides a good account for the higher efficiency observed experimentally for the trans → cis photoisomerization than the reverse process. Once the system decays to the S(0) state via CI, formation of the trans product occurs as the downhill motion on the S(0) surface, while formation of the cis isomer needs to overcome small barriers on the pathways of the azo-moiety isomerization and rotation of the phenyl ring. These features support the larger experimental quantum yield for the cis → trans photoisomerization than the trans → cis process.     

Ultrafast nonradiative decay of electronically excited States of malachite green: ab initio calculations

We have investigated the nonradiative deactivation process of malachite green in the singlet excited states, S(1) and S(2), by high-level ab initio quantum chemical calculations using the CASPT2//CASCF approach. The deactivation pathways connecting the Franck-Condon region and conical intersection regions are identified. The initial population in the S(1) state is on a flat surface and the relaxation involves a rotation of phenyl rings, which leads the molecule to reach the conical intersection between the S(1) and S(0) states, where it efficiently decays back to the ground state. There exists a small barrier connecting the Franck-Condon and conical intersection regions on the S(1) potential energy surface. The decay mechanism from the S(2) state also involves the twisting motion of phenyl rings. In contrast to the excitation to the S(1) state, the initial population is on a downhill ramp potential and the barrierless relaxation through the rotation of substituted phenyl rings is expected. During the course of relaxation, the molecule switches to the S(1) state at the conical intersection between S(2) and S(1), and then it decays back to the ground state through the intersection between S(1) and S(0). In relaxation from both S(1) and S(2), large distortion of phenyl rings is required for the ultrafast nonradiative decay to the ground state.     

Vibronic structure in the S1-S0 transition of jet-cooled dibenzofuran

Fluorescence excitation spectra of dibenzofuran in a supersonic jet are observed and the vibronic structure is analyzed for the S(1) (1)A(1) (pipi) and S(0) states. An observation of the rotational envelopes reveals that the band is a B-type band. However, it is shown that most of the strong vibronic bands are A-type bands. The intensity arises from vibronic coupling with the S(2) (1)B(2) state. We find a broad emission in the dispersed fluorescence spectrum for the excitation of the high vibrational levels in the S(1) state. This indicates that intramolecular vibrational redistribution (IVR) occurs efficiently in the isolated dibenzofuran molecule.     

Characteristic behavior of short-term dynamics in reorientation for Gay-Berne particles near the nematic-isotropic phase transition temperature

A specific transition behavior was found in the tumbling motion near the nematic-isotropic phase boundary using molecular dynamics simulations of the Gay-Berne mesogenic model under isobaric conditions at a reduced pressure P* of 2.0. The relaxation time for the motion obtained from the second-rank orientational time correlation function and the rotational diffusion coefficient showed a clear jump at the nematic-isotropic phase transition temperature. Regardless of the temperature dependence of the relaxation time, the change in the rotational diffusion coefficient evaluated from the orientational order parameters and the relaxation time agreed qualitatively with that of real mesogens. The rotational viscosity coefficients gamma(1) and gamma(2) were obtained from the simulation data for the relaxation time for the short-term dynamics and for the rotational diffusion coefficients. gamma(1) was proportional to (2), where is the second-rank orientational parameter. Furthermore, the rotational behavior of the model was compared with that of the Debye approximation in the isotropic phase.     

Excited state hydrogen transfer in fluorophenol.ammonia clusters studied by two-color REMPI spectroscopy

Two-color (1 + 1') REMPI mass spectra of o-, m- and p-fluorophenol.ammonia (1 ration) clusters were measured with a long delay time between excitation and ionization lasers. The appearance of NH(4)(NH(3))(n-1)(+) with 100 ns delay after exciting the S(1) state is a strong indication of generation of long-lived species via S(1). In analogy with the phenol.ammonia clusters, we conclude that an excited state hydrogen transfer reaction occurs in o-, m- and p-fluorophenol.ammonia clusters. The S(1)-S(0) transition of o-, m- and p-fluorophenol.ammonia (1 : 1) clusters were measured by the (1 + 1') REMPI spectra, while larger (1 ration) cluster (n = 2-4) were observed by monitoring the long-lived NH(4)(NH(3))(n-1) clusters action spectra. The vibronic structures of m- and p-fluorophenol.ammonia clusters are assigned based on vibrational calculations in S(0). The o-fluorophenol.ammonia (1 : 1) cluster shows an anharmonic progression that is analyzed by a one-dimensional internal rotational motion of the ammonia molecule. The interaction between the ammonia molecule and the fluorine atom, and its change upon electronic excitation are suggested. The broad action spectra observed for the o-fluorophenol.ammonia (1 : n) cluster (n>== 2) suggest the excited state hydrogen transfer is faster than in m- and p-fluorophenol.ammonia clusters. The different reaction rates between o-, m- and p-fluorophenol.ammonia clusters are found from comparison between the REMPI and action spectra.     

Quantitative (upsilon, N, Ka) product state distributions near the triplet threshold for the reaction H2CO --> H + HCO measured by Rydberg tagging and laser-induced fluorescence

In this paper, we report quantitative product state distributions for the photolysis of H2CO --> H + HCO in the triplet threshold region, specifically for several rotational states in the 2(2)4(3) and 2(3)4(1) H2CO vibrational states that lie in this region. We have combined the strengths of two complementary techniques, laser-induced fluorescence for fine resolution and H atom Rydberg tagging for the overall distribution, to quantify the upsilon, N, and Ka distributions of the HCO photofragment formed via the singlet and triplet dissociation mechanisms. Both techniques are in quantitative agreement where they overlap and provide calibration or benchmarks that permit extension of the results beyond that possible by each technique on its own. In general agreement with previous studies, broad N and Ka distributions are attributed to reaction on the S0 surface, while narrower distributions are associated with reaction on T1. The broad N and Ka distributions are modeled well by phase space theory. The narrower N and Ka distributions are in good agreement with previous quasi-classical trajectory calculations on the T1 surface. The two techniques are combined to provide quantitative vibrational populations for each initial H2CO vibrational state. For dissociation via the 2(3)4(1) state, the average product vibrational energy (15% of E(avail)) was found to be about half of the rotational energy (30% of E(avail)), independent of the initial H2CO rotational state, irrespective of the singlet or triplet mechanism. For dissociation via the 2(2)4(3) state, the rotational excitation remained about 30% of E(avail), but the vibrational excitation was reduced.     

An investigation of water dynamics in binary mixtures of water and dimethyl sulfoxide

The motion of water molecules in mixtures of water and d6-dimethyl sulfoxide (DMSO) has been explored through molecular dynamics (MD) simulations using the SPC/E water model (J. Chem. Phys. 1987, 91, 6269) and the P2 DMSO model (J. Chem. Phys. 1993, 98, 8160). We evaluate the self-intermediate scattering functions, FS(Q,t), which are related by a Fourier transform to the incoherent structure factors, S(Q,omega), measured in quasielastic neutron scattering (QNS) experiments. We compare our results to recent QNS experiments on these mixtures reported by Bordallo et al. (J. Chem. Phys. 2004, 121, 12457). In addition to comparing the MD data to the experimental signals, which correspond to a convolution of S(Q,omega) with a resolution function, we examine the rotational and translational components of FS(Q,t) and investigate to what extent simulation results for the single-molecule dynamics follow the dynamical models that are used in the analysis of the experimental data. We find that the agreement between the experimental signal and the MD data is quite good and that the portion of FS(Q,t) due to translational dynamics is well represented by the jump-diffusion model. The model parameters and their composition dependence are in reasonable agreement with experiment, exhibiting similar trends in water mobility with composition. Specifically, we find that water motion is less hindered in water-rich and water-poor mixtures than it is near equimolar composition. We find that the extent of coupling between rotational and translational motion contributing to FS(Q,t) increases as the equimolar composition of the mixture is approached. Thus, the decoupling approximation, which is used to extract information on rotational relaxation from QNS spectra at higher momentum transfer (Q) values, becomes less accurate than that in water-rich or DMSO-rich mixtures. We also find that rotational relaxation deviates quite strongly from the isotropic rotational diffusion model. We explore this issue further by investigating the behavior of orientational time correlations for different unit vectors and corresponding to Legendre polynomials of orders 1-4. We find that the rotational time correlations of water molecules behave in a way that is more consistent with the extended jump rotation model recently proposed by Laage and Hynes (Science 2006, 311, 832).     

Intrachain energy migration to weak charge-transfer state in polyfluorene end-capped with naphthalimide derivative

Polyfluorene end-capped with N-(2-benzothiazole)-1,8-naphthalimide (PF-BNI) is a highly fluorescent material with fluorescence emission modulated by solvent polarity. Its low energy excited state is assigned as a mixed configuration state between the singlet S(1) of the fluorene backbone (F) with the charge transfer (CT) of the end group BNI. The triexponential fluorescence decays of PF-BNI were associated with fast energy migration to form an intrachain charge-transfer (ICCT) state, polyfluorene backbone decay, and ICCT deactivation. Time-resolved fluorescence anisotropy exhibited biexponential relaxation with a fast component of 12-16 ps in addition to a slow one in the range 0.8-1.4 ns depending on the solvent, showing that depolarization occurs from two different processes: energy migration to form the ICCT state and slow rotational diffusion motion of end segments at a longer time. Results from femtosecond transient absorption measurements agreed with anisotropy decay and showed a decay component of about 16 ps at 605 nm in PF-BNI ascribed to the conversion of S(1) to the ICCT excited state. From the ratio of asymptotic and initial amplitudes of the transient absorption measurement, the efficiency of intrachain ICCT formation is estimated in 0.5, which means that, on average, half of the excited state formed in a BNI-(F)(n)-BNI chain with n = 32 is converted to its low energy intrachain charge-transfer (ICCT) state.     

Approximation of contacts for calculating the velocity of the thermal motion of rodlike molecules in narrow slitlike pores

Expressions for calculating the thermal velocities of the motion of rodlike molecules in slitlike pores were obtained within the framework of a lattice gas model valid over a wide range of fluid densities (from rarefied gases to liquids) and temperatures, including the critical region. The translational and rotational motion of molecules was described using the transition-state theory for nonideal reaction systems, which takes into account the effect of the neighboring molecules on the activation barrier height. The local distributions of the components of the mixture under equilibrium conditions were calculated by describing lateral interactions in the approximation of isolated contacts. The equations of the model reflect the fact that the distributions of the components in the direction perpendicular to the pore walls (due to the effect of adsorption forces) and along the pore axis (if capillary condensation occurs) exhibit a strong anisotropy.     

Differential cross sections and product energy distributions for the C(3P)+OH(X 2Pi)-->CO(X 1Sigma+)+H(2S) reaction using a quasiclassical trajectory method

Quasiclassical trajectory calculations have been carried out for the C((3)P)+OH(X (2)Pi)-->CO(X (1)Sigma(+))+H((2)S) reaction using a recent ab initio potential energy surface for the ground electronic state X (2)A(') of COH. Differential cross sections (DCSs), and product vibrational, rotational and translational distributions have been determined for a wide range of collision energies (0.001-1 eV). The role of excitations (rotation or vibration) of the OH reactant on these quantities has been investigated. Product vibrational, rotational, and translational distributions are found to be almost independent on the rovibrational state of OH, whereas DCSs show a weak dependence on the initial rotational state of OH. We also analyze the results using a study based on the lifetime of the intermediate complex and on the kinematic constraint associated with the mass combination.     

Coupling of translational and rotational motion in chiral liquids in electromagnetic and circularly polarised electric fields

Non-equilibrium molecular dynamics simulations of R and S enantiomers of 1,1-chlorofluoroethane, both for pure liquids and racemic mixtures, have been performed at 298 K in the absence and presence of both electromagnetic (e/m) and circularly polarised electric (CP) fields of varying frequency (100-2200 GHz) and intensity (0.025-0.2 V ?(-1) (rms)). Significant non-thermal field effects were noted in the coupling of rotational and translational motion; for instance, in microwave and far-infrared (MW/IR) e/m fields, marked increases in rotational and translational diffusion vis-à-vis the zero-field case took place at 0.025-0.1 V ?(-1) (rms), with a reduction in translational diffusion vis-à-vis the zero-field case above 0.1 V ?(-1) (rms) above 100 GHz. This was due to enhanced direct coupling of rotational motion with the more intense e/m field at the ideal intrinsic rotational coupling frequency (approximately 700 GHz) leading to such rapidly oscillating rotational motion that extent of translational motion was effectively reduced. In the case of CP fields, rotational and translational diffusion was also enhanced for all intensities, particularly at approximately 700 GHz. For both MW/IR and CP fields, non-linear field effects were evident above around 0.1 V ?(-1) (rms) intensity, in terms of enhancements in translational and rotational motion. Simulation of 90-10 mol. % liquid mixtures of a Lennard-Jones solvent with R and S enantiomer-solutes in MW/IR and CP fields led to more limited promotion of rotational and translational diffusion, due primarily to increased frictional effects. For both e/m and CP fields, examination of the laboratory- and inertial-frame auto- and cross-correlation functions of velocity and angular velocity demonstrated the development of explicit coupling with the external fields at the applied frequencies, especially so in the more intense fields where nonlinear effects come into play. For racemic mixtures, elements of the laboratory- and inertial-frame velocity and angular velocity were found to couple with each other to a lesser extent.