Deconstructing the excited-state dynamics of β-carotene in solution

The femtosecond to nanosecond dynamics of the all-trans β-carotene carotenoid dissolved in 3-methylpentane is characterized and dissected with excitation-wavelength and temperature-dependent ultrafast dispersed transient absorption signals. The kinetics measured after red-edge (490 nm) and blue-edge (400 nm) excitation were contrasted under fluid solvent (298 K) and rigid glass (77 K) conditions. In all four measured data sets, the S* population kinetics was resolved prompting the development of a modified multicompartment model. The temperature-dependent and excitation wavelength-dependent S* quantum yield is ascribed to a competition of population surmounting a weak (55 cm(-1)) energy barrier on the S(2) state to favor S(1) generation and rapid internal conversion that favors S* generation. When cooled from room temperature to 77 K, the S* decay time scale shifted significantly from 30 to 400 ps, which is ascribed to small-scale structural relaxation with a 115 cm(-1) energy barrier. For the first time under low-energy excitation conditions, the triplet state is observed and confirmed to not originate from S* or S(1), but from S(2). The interconnectivity of the S* and S(1) populations is discussed, and no observed population flow is resolved between S* and S(1). Comparison of samples obtained from different laboratories with different purity levels demonstrates that sample contamination is not the primary origin of the S* state.     

Why does the intermolecular dynamics of liquid biphenyl so closely resemble that of liquid benzene? Molecular dynamics simulation of the optical-Kerr-effect spectra

The combination of optical-Kerr-effect (OKE) spectroscopy and molecular dynamics simulations has provided us with a newfound ability to delve into the librational dynamics of liquids, revealing, in the process, some surprising commonalities among aromatic liquids. Benzene and biphenyl, for example, have remarkably similar OKE spectra despite marked differences in their shapes, sizes, and moments of inertia--and even more chemically distinct aromatics tend to have noticeable similarities in their spectra. We explore this universality by using a molecular dynamics simulation to investigate the librational dynamics of molten biphenyl and to predict its OKE spectrum, comparing the results with our previous calculations for liquid benzene. We suggest that the impressive level of quantitative agreement between these two liquids is largely a reflection of the fact that librations in these and other aromatic liquids act as torsional oscillations with oscillator frequencies selected from the liquid's librational bands. Since these bands are centered about the librational Einstein frequencies, the quantitative similarities between the liquids are essentially reflections of the near identities of their Einstein frequencies. Why then are the Einstein frequencies themselves so insensitive to molecular details? We show that, for nearly planar molecules, mean-square torques and moments of inertia tend to scale with molecular dimensions in much the same way. We demonstrate that this near cancellation provides both a quantitative explanation of the close relationship between benzene and biphenyl and a more general perspective on the similarities seen in the ultrafast dynamics of aromatic liquids.     

Experimental study of the director pattern dynamics in the vicinity of the Fréedericksz twist geometry

We present an experimental study of the transient periodic structures appearing in the nematic director field in the magnetically induced reorientation of the director in the vicinity of the twist Fréedericksz geometry. Thin nematic samples (50?µm thick) were exposed to magnetic fields of variable intensity and orientation relative to the surface aligning direction of the sample. The director reorientation was induced by a rapid rotation of the sample in the static magnetic field producing a misalignment between the director and the magnetic field. The director field was optically monitored during the reorientation process and the transient periodic structures were characterized. Two types of periodic structures could be identified, namely bands and walls. Walls grow from bands close to the twist Fréedericksz geometry. The time dependence of the wave length and inclination of the periodic structures was obtained as a function of the magnetic field intensity and orientation relative to the surface aligning direction of the sample. The results for the bands are compared with the predictions of a model that we specifically developed to account for the non-orthogonal field orientations. It is seen that our model can account rather well for the experimental results considering that it uses only the field rotation time as adjustable parameter. All other model parameters are known.     

On the study of nonlinear dynamics of complex chemical reaction systems

When driven far from equilibrium,nonlinear chemical reactions often show a variety of self-organization behavior,including chemical oscillations,waves,chaos and patterns[1].Recently,the study of such nonlinear phenomena in‘complex’systems,such as the li…     

Molecular dynamics and the structure of macrocycles —Solvent acetonitrile interactions

Microwave complex permittivities,* = -J, are reported in the 1–90 GHz frequency range for the macrocycles 18-crown-6 (18C6) and 15C5 added to acetonitrile in stoichiometric proportions, in the solvent CCl₄ at 25°C. Digitized infrared spectra of the CN stretch ₂ vibration of acetonitrile for the same systems are reported in the 2300–2200 cm^–1 spectral region. The macrocycle 12C4 added to CH₃CN has also been investigated in the infrared. Both the dielectric relaxation and infrared results are interpreted in terms of macrocycle-acetonitrile interactions, probably involving a methyl-hydrogen to ethereal-oxygen interaction. These interactions with CH₃CN diminish in strength according to the sequence: 18C6 > 15C5 > 12C4.This paper is dedicated to the memory of the late Dr C. J. Pedersen.     

Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.     

Forces,stresses and the (thermo?) dynamics of active matter

The statistical mechanics and microhydrodynamics of active matter systems have been studied intensively during the past several years, by various soft matter physicists, chemists, engineers, and biologists around the world. Recent attention has focused on the fascinating nonequilibrium behaviors of active matter that cannot be observed in equilibrium thermodynamic systems, such as spontaneous collective motion and swarming. Even minimal kinetic models of active Brownian particles exhibit self-assembly that resembles a gas–liquid phase separation from classical equilibrium systems. Self-propulsion allows active systems to generate internal stresses that enable them to control and direct their own behavior and that of their surroundings. In this review, we discuss the forces that govern the motion of active Brownian microswimmers, the stress (or pressure) they generate, and the implication of these concepts on their collective behavior. We focus on recent work involving the unique “swim pressure” exerted by active systems and discuss how this perspective may be the basic underlying physical mechanism responsible for self-assembly and pattern formation in all active matter. We discuss the utility of the swim pressure concept to quantify the forces, stresses, and the (thermo?) dynamics of active matter.     

Quantum dynamics of the S+OH→SO+H reaction

First accurate quantum mechanical scattering calculations have been carried out for the S((3)P)+OH(X?(2)Π)→SO(X?(3)Σ(-))+H((2)S) reaction using a recent ab initio potential energy surface for the ground electronic state, X?(2)A("), of HSO. Total and state-to-state reaction probabilities for a total angular momentum J=0 have been determined for collision energies up to 0.5 eV. A rate constant has been calculated by means of the J-shifting approach in the 10-400 K temperature range. Vibrational and rotational product distributions show no specific behavior and are consistent with a mixture of direct and indirect reaction mechanisms.     

Molecular dynamics simulation of the equilibrium liquid–vapor interphase with solidification

The equilibrium structure of the finite, interphase interfacial region that exists between a liquid film and a bulk vapor is resolved by molecular dynamics simulation. Argon systems are considered for a temperature range that extends below the melting point. Physically consistent procedures are developed to define the boundaries between the interphase and the liquid and vapor phases. The procedures involve counting of neighboring molecules and comparing the results with boundary criteria that permit the boundaries to be precisely established. Two-dimensional radial distribution functions at the liquid and vapor boundaries and within the interphase region demonstrate the physical consistency of the boundary criteria and the state of transition within the region. The method developed for interphase boundary definitions can be extended to nonequilibrium systems. Spatial profiles of macroscopic properties across the interphase region are presented. A number of interfacial thermodynamic properties and profile curve-fit parameters are tabulated, including evaporation/condensation coefficients determined from molecular flux statistics. The evaporation/condensation coefficients away from the melting point compare more favorably with transition state theory than those of previous simulations. Near the melting point, transition theory approximations are less valid and the present results differ from the theory. The effects of film substrate wetting on evaporation/condensation coefficients are also presented.     

Low-temperature dynamics in amorphous polymers and low-molecular-weight glasses--what is the difference?

Numerous experiments have shown that the low-temperature dynamics of a wide variety of disordered solids is qualitatively universal. However, most of these results were obtained with ensemble-averaging techniques which hide the local parameters of the dynamic processes. We used single-molecule (SM) spectroscopy for direct observation of the dynamic processes in disordered solids with different internal structure and chemical composition. The surprising result is that the dynamics of low-molecular-weight glasses and short-chain polymers does not follow, on a microscopic level, the current concept of low-temperature glass dynamics. An extra contribution to the dynamics was detected causing irreproducible jumps and drifts of the SM spectra on timescales between milliseconds and minutes. In most matrices consisting of small molecules and oligomers, the spectral dynamics was so fast that SM spectra could hardly or not at all be recorded and only irregular fluorescence flares were observed. These results provide new mechanistic insight into the behavior of glasses in general: At low temperatures, the local dynamics of disordered solids is not universal but depends on the structure and chemical composition of the material.     

Ultrafast dynamics of aniline in the 294-234 nm excitation range: the role of the πσ∗ state

The ultrafast relaxation of jet-cooled aniline was followed by time-resolved ionization, after excitation in the 294-234 interval. The studied range of energy covers the absorption of the two bright ππ? excitations, S(1) and S(3), and the almost dark S(2) (πσ?) state. The employed probe wavelengths permit to identify different ultrafast time constants related with the coupling of the involved electronic surfaces. A τ(1) = 165 ± 30 fs lifetime is attributed to dynamics along the S(2) (πσ?) repulsive surface. Other relaxation channels as the S(1)→S(0) and S(3)→S(1) internal conversion are also identified and characterized. The work provides a general view of the photophysics of aniline, particularly regarding the role of the πσ? state. This state appears as minor dissipation process due to the ineffective coupling with the bright S(1) and S(3) states, being the S(1)→S(0) internal conversion the main non-radiative process in the full studied energy range. Additionally, the influence of the off-resonance adiabatic excitation of higher energy electronic states, particularly S(3), is also observed and discussed.     

The amino terminus of cGMP-dependent protein kinase Iβ increases the dynamics of the protein's cGMP-binding pockets

The type I cGMP-dependent protein kinases play critical roles in regulating vascular tone, platelet activation and synaptic plasticity. PKG I α and PKG Iβ differ in their first ~100 amino acids giving each isoform unique dimerization and autoinhibitory domains with identical cGMP-binding pockets and catalytic domains. The N-terminal leucine zipper and autoinhibitory domains have been shown to mediate isoform specific affinity for cGMP. PKG Iα has a >10 fold higher affinity for cGMP than PKG Iβ, and PKG Iβ that is missing its leucine zipper has a three-fold decreased affinity for cGMP. The exact mechanism through which the N-terminus of PKG alters cGMP-affinity is unknown. In the present study, we have used deuterium exchange mass spectrometry to study how PKG Iβ's N-terminus affects the conformation and dynamics of its cGMP-binding pockets. We found that the N-terminus increases the rate of deuterium exchange throughout the cGMP-binding domain. Our results suggest that the N-terminus shifts the conformational dynamics of the binding pockets, leading to an "open" conformation that has an increased affinity for cGMP.     

Deuteron dynamics in the γ phase of titanium deuterides as probed by NMR

Titanium deuterides TiD _x (x = 1.92, 1.98, 2.0) and the Ti_0.95Zr_0.05D_1.76 alloy were studied by ²H NMR in magnetic fields of 4.69 and 7.04 T in the temperature range 120–500 K. The correlation coefficients of deuteron self-diffusion calculated from the temperature dependence of the line width were described by the Arrhenius equation. The activation energies E _a and preexponential factors were determined. For the Ti_0.95Zr_0.05D_1.76 alloy, the line width was found to depend on the magnetic field, which was explained by the fact that deuterons are in different environments formed by titanium and zirconium atoms.     

Role of alkylated residues in the tetrapeptide self-assembly—A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.     

Topological phase transitions in the vibration–rotation dynamics of an isolated molecule

A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluoromethyl substituents shows for both compounds the most pronounced evidence of the anomeric effect, as expressed as hyperconjugative delocalization of the nitrogen lone pair, in structures with the substituent in the axial position and the N–H bond in the equatorial position. This structure is the lowest-energy structure in the fluoro case but not in the trifluoromethyl case where there is an increased axial penalty associated with the CF₃ group. The anomeric effect is characterized via geometrical evidence, natural bond orbital analysis, electrostatic effects, and energetic criteria. Computational results from a variety of levels of theory are presented including CCSD(T) with complete basis set extrapolation, B2PLYP-D, ωB97XD, B97-D, M06-2X, B3LYP, and MP2 allowing for a comparison of performance. The CCSD(T)/CBS results are very well represented by either B2PLYP-D or ωB97XD with moderate to large basis sets (aug-cc-pVTZ or aug-cc-pVDZ). Hyperconjugation, electrostatic effects, and steric effects play a role in the relative energetic ordering of the isomers considered.     

A molecular dynamics study of the thermal response of crystalline cellulose Iβ

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose Iβ. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose Iβ at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475–500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30° and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.     

HDX-ESI-MS reveals enhanced conformational dynamics of the amyloidogenic protein β 2-microglobulin upon release from the MHC-1

The light chain of the major histocompatibility complex class 1 (MHC-1), the protein β ₂-microglobulin (β ₂m), has amyloidogenic properties that arise only upon its dissociation from the MHC-1. Here hydrogen/deuterium exchange electrospray ionization mass spectrometry (HDX-ESI-MS) has been used to compare the solution dynamics of β ₂m in its MHC-1 bound state compared with those of β ₂m as a free monomer. The capability of tandem mass spectrometry to dissociate the MHC-1 into its individual constituents in the gas phase following deuterium incorporation in solution has permitted the direct observation of the exchange properties of MHC-1 bound β ₂m for the first time. The HDX-ESI-MS data show clearly that the H→D exchange of MHC-1 bound β ₂m follows EX2 kinetics and that about 20 protons remain protected from exchange after 17 days. Free from the MHC-1, monomeric β ₂m exhibits significantly different HDX behavior, which encompasses both EX1 and EX2 kinetics. The EX2 kinetics indicate a tenfold increase in the rate of exchange compared with MHC-1 bound β ₂m, with just 10 protons remaining protected from EX2 exchange and therefore exchanging only via the EX1 mechanism. The EX1 kinetics observed for unbound β ₂m are consistent with unfolding of its exchange-protected core with a t_1/2 of 68 min (pH 7, 37° C). Thus, upon dissociation from the stabilizing influence of the MHC-1, free β ₂m becomes highly dynamic and undergoes unfolding transitions that result in an aggregation-competent protein.     

Quasi-classical trajectory study of the dynamics of the Cl + CH4→ HCl + CH3 reaction

We present an on-the-fly classical trajectory study of the Cl + CH(4)→ HCl + CH(3) reaction using a specific reaction parameter (SRP) AM1 Hamiltonian that was previously optimized for the Cl + ethane reaction [S. J. Greaves et al., J. Phys Chem A, 2008, 112, 9387]. The SRP-AM1 Hamiltonian is shown to be a good model for the potential energy surface of the title reaction. Calculated differential cross sections, obtained from trajectories propagated with the SRP-AM1 Hamiltonian compare favourably with experimental results for this system. Analysis of the vibrational modes of the methyl radical shows different scattering distributions for ground and vibrationally excited products.     

Molecular dynamics simulation study on zwitterionic structure to maintain the normal conformations of Glutathione

Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".     

Mechanistic and dual-level direct dynamics studies on the reaction Cl + CH2FCl

Theoretical investigations are carried out on the reaction Cl + CH₂FCl by means of direct dynamics method. The minimum energy path (MEP) is obtained at the MP2/6-311G(d, p) level. The energetic information is further improved by single-point energy calculations using QCISD(T)/6-311++G(d, p) method. The kinetics of this reaction are calculated by canonical variational transition state theory incorporating with the small-curvature tunneling correction over a wide temperature range of 220–3,000 K, and rate constant expression are found to be k(T) = 1.48 × 10^?17 T ^2.04exp(?913.91/T). For the title reaction, H-abstraction reaction channel is the major channel at the lower temperatures. At higher temperatures, the contribution of Cl-abstraction reaction channel should be taken into account.