Kinematic effects associated with molecular frames in structural isomerization dynamics of clusters

Kinematic effects associated with movements of molecular frames, which specify instantaneous orientation of molecules, is investigated in structural isomerization dynamics of a triatomic cluster whose total angular momentum is zero. The principal-axis frame is employed to introduce the so-called principal-axis hyperspherical coordinates, with which the mechanism of structural isomerization dynamics of the cluster is systematically analyzed. A force called "democratic centrifugal force" is extracted from the associated kinematics. This force arises from an intrinsic non-Euclidean metric in the internal space and has an effect of distorting the triatomic cluster to a collapsed shape and of trapping the system around collinear transition states. The latter effect is particularly important in that the kinematics effectively makes a basin at the saddle (transition state) on the potential surface. Based on this framework, we study the effect of the gauge field associated with the Eckart frame in internal space, which has not been carefully examined in the conventional reaction rate theories. Numerical comparison between the dynamics with and without the gauge field has revealed that this field has an effect to suppress the rate of isomerization reaction to a considerable amount. Thus a theory neglecting this effect will significantly overestimate the rate of isomerization. We show the physical origin of this suppressing effect.     

Gyration-radius dynamics in structural transitions of atomic clusters

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.     

Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside

The transition path sampling (TPS) method is a powerful approach to study chemical reactions or transitional properties on complex potential energy landscapes. One of the main advantages of the method over potential of mean force methods is that reaction rates can be directly accessed without knowledge of the exact reaction coordinate. We have investigated the complementary nature of these two differing approaches, comparing transition path sampling with the weighted histogram analysis method to study a conformational change in a small model system. In this case study, the transition paths for a transition between two rotational conformers of a model disaccharide molecule, methyl beta-D-maltoside, were compared with a free energy surface constrained by the two commonly used glycosidic (phi,psi) torsional angles. The TPS method revealed a reaction channel that was not apparent from the potential of mean force method, and the suitability of phi and psi as reaction coordinates to describe the isomerization in vacuo was confirmed by examination of the transition path ensemble. Using both transition state theory and transition path sampling methods, the transition rate was estimated. We have estimated a characteristic time between transitions of approximately 160 ns for this rare isomerization event between the two conformations of the carbohydrate. We conclude that transition path sampling can extract subtle information about the dynamics not apparent from the potential of mean force method. However, in calculating the reaction rate, the transition path sampling method required 27.5 times the computational effort than was needed by the potential of mean force method.     

Multiple barriers in forced rupture of protein complexes

Curvatures in the most probable rupture force (f(?)) versus log-loading rate (log?r(f)) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple barriers or a single barrier with force-dependent transition state. Here, we provide a criterion to select one scenario over another. If the rupture dynamics occurs by crossing a single barrier in a physical free energy profile describing unbinding, the exponent ν, from (1 - f(?)∕f(c))(1∕ν) ～ (log?r(f)) with f(c) being a critical force in the absence of force, is restricted to 0.5 ≤ ν ≤ 1. For biotin-ligand complexes and leukocyte-associated antigen-1 bound to intercellular adhesion molecules, which display large curvature in the DFS data, fits to experimental data yield ν < 0.5, suggesting that if ligand unbinding is assumed to proceed along one-dimensional pulling coordinate, the dynamics should occur in a energy landscape with multiple-barriers.     

Small-amplitude protein conformational dynamics: Second-order analytic relation between cartesian coordinates and dihedral angles

An analytic expression for protein atomic displacements in Cartesian coordinate space (CCS) against small changes in dihedral angles is derived. To study time-dependent dynamics of a native protein molecule in CCS from dynamics in the internal coordinate space (ICS), it is necessary to convert small changes of internal coordinate variables to Cartesian coordinate variables. When we are interested in molecular motion, six degrees of freedom for translational and rotational motion of the molecule must be eliminated in this conversion, and this conversion is achieved by requiring the Eckart condition to hold. In this article, only dihedral angles are treated as independent internal variables (i.e., bond angles and bond lengths are fixed), and Cartesian coordinates of atoms are given analytically by a second-order Taylor expansion in terms of small deviations of variable dihedral angles. Coefficients of the first-order terms are collected in the K matrix obtained previously by Noguti and Go (1983) (see ref. 2). Coefficients of the second-order terms, which are for the first time derived here, are associated with the (newly termed) L matrix. The effect of including the resulting quadratic terms is compared against the precise numerical treatment using the Eckart condition. A normal mode analysis (NMA) in the dihedral angle space (DAS) of the protein bovine pancreatic trypsin inhibitor (BPTI) has been performed to calculate shift of mean atomic positions and mean square fluctuations around the mean positions. The analysis shows that the second-order terms involving the L matrix have significant contributions to atomic fluctuations at room temperature. This indicates that NMA in CCS involves significant errors when applied for such large molecules as proteins. These errors can be avoided by carrying out NMA in DAS and by considering terms up to second order in the conversion of atomic motion from DAS to CCS. © 1995 by John Wiley & Sons, Inc.     

Riemannian three dimensional molecular spaces

A simple manipulation of the first order density function permits to define a curved 3D Riemannian coordinate set, which can substitute the usual flat 3D Cartesian space, where atoms and molecules are supposed to exist. Several simple models are discussed. Gaussian type orbitals generate a space division with positive and negative curvatures, the later one being near the centre of the functions; contrarily Slater type orbitals provide a positive curvature everywhere.     

Intramolecular electron transfer in bis(methylene) adamantyl radical cation: a case study of diabatic trapping

Our characterization of the potential energy surface for electron transfer (ET) in the bis(methylene)adamantane (BMA) model radical cation shows that the surface topology is prone to diabatic trapping (competition between ET and upward hops to the excited state). The general conditions for this phenomenon have been derived. The surface is centered around a conical intersection, and diabatic trapping occurs because one of the branching space coordinates (coordinates that lift the degeneracy at first order) corresponds to a vector of small length. For BMA, this coordinate is an antisymmetric breathing mode of the rigid carbon framework. Other modes (including methylene torsions and pyramidalizations) may lift the degeneracy at second-order but do not affect the energy gap at the intersection region effectively. The resulting topology is similar to that of an (n - 1) dimensional seam (where n is the number of nuclear degrees of freedom of the molecule) that cannot be avoided along the reaction coordinate, thus favoring recrossing to the upper surface. This analysis is extended by ab initio semiclassical dynamics using an Ehrenfest and a trajectory surface hopping algorithm implemented at the CASSCF level. Examination of the trajectories shows that there is no single mode that controls the diabatic trap, in agreement with the condition that there is no predominant degeneracy-lifting coordinate. Thus the reactivity depends on a combination of small effects, where presumably higher-order effects come into play. This should be the general behavior of dynamics at a diabatic trapping situation.     

Molecular dynamics integration meets standard theory of molecular vibrations

An iterative SISM (split integration symplectic method) for molecular dynamics (MD) integration is described. This work explores an alternative for the internal coordinate system prediction in the SISM introduced by JaneZic et al. (J. Chem. Phys. 2005, 122, 174101). The SISM, which employs a standard theory of molecular vibrations, analytically resolves the internal high-frequency molecular vibrations. This is accomplished by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The Eckart frame, which is usually used in the standard theory of molecular vibrations as an internal coordinate system of a molecule, is adopted to be used within the framework of the second order generalized leapfrog scheme. In the presented MD integrator the internal coordinate frame at the end of the integration step is predicted halfway through the integration step using a predictor-corrector type iterative approach thus ensuring the method's time reversibility. The iterative SISM, which is applicable to any system of molecules with one equilibrium configuration, was applied here to perform all-atom MD simulations of liquid CO2 and SO2. The simulation results indicate that for the same level of accuracy, this algorithm allows significantly longer integration time steps than the standard second-order leapfrog Verlet (LFV) method.     

Constrained dynamics of localized excitations causes a non-equilibrium phase transition in an atomistic model of glass formers

Recent progress has demonstrated that trajectory space for both kinetically constrained lattice models and atomistic models can be partitioned into a liquid-like and an inactive basin with a non-equilibrium phase transition separating these behaviors. Recent work has also established that excitations in atomistic models have statistics and dynamics like those in a specific class of kinetically constrained models. But it has not been known whether the non-equilibrium phase transitions occurring in the two classes of models have similar origins. Here, we show that the origin is indeed similar. In particular, we show that the number of excitations identified in an atomistic model serves as the order parameter for the inactive-active phase transition for that model. In this way, we show that the mechanism by which excitations are correlated in an atomistic model - by dynamical facilitation - is the mechanism from which the active-inactive phase transition emerges. We study properties of the inactive phase and show that it is amorphous lacking long-range order. We also discuss the choice of dynamical order parameters.     

Molecular dynamics in triglycine sulphate by cold neutron spectroscopy

Molecular dynamics of the ferroelectric compound triglycine sulphate (TGS) was studied by quasi-elastic neutron scattering. From among the three glycine molecules forming the unit cell the non-planar GI molecule is responsible for the polarisation which occurs in crystal and for the order–disorder ferroelectric phase transition at T_c = 49 °C. This molecule also shows a complex dynamics much faster than that performed by the other glycine molecules. The key group of this molecule is the amino group that, on one hand, seems to be responsible for the phase transition and, on the other hand, performs motional processes spread on a wide time scale. These motions have been detailed studied by means of different energy resolution windows within the quasi-elastic scattering range. We found that the dynamics of this group develops in a restricted spatial volume and consists in a faster rotational diffusion around the molecular axis of the group and a slower flipping dynamics between two symmetrical positions on both sides of a mirror plane containing the molecular axis of GI molecule.     

Vibronic dynamics of I(2) trapped in amorphous ice: coherent following of cage relaxation

Four-wave mixing measurements are carried out on I(2)-doped ice, prepared by quench condensing the premixed vapor at 128 K. Coherent vibrational dynamics is observed in two distinct ensembles. The first is ascribed to trapping in asymmetric polar cages in which, as in water, the valence absorption of the molecule is blueshifted by 3500 cm(-1), predissociation of the B state is complete upon the first extension of the molecular bond, and the vibrational frequency in the ground state (observed through coherent anti-Stokes Raman scattering) is reduced by 6.5%. The effect is ascribed to polarization of the molecule. The implied local field and the ionicity of the molecule are extracted, to conclude that the molecule is oxygen bonded to one water molecule on one side and hydrogen bonded on the other side. The second ensemble is characterized by the transient grating signal, which shows coherent vibrational dynamics on the B state. The small predissociation rate in this site suggests a symmetric cage in which the local electric field undergoes effective cancellation; and consistent with this, the extracted blueshift of the valence transition in this site (approximately 1500 cm(-1)) coincides with that observed in clathrate hydrates of iodine. Remarkably, in this site, the vibrational period of the B state packet coherently stretches from an initial value of 245 fs to 325 fs in the course of five oscillations (1.3 ps), indicative of vibrationally adiabatic following of the cage expansion. The dynamics is characteristic of a molecule trapped in a tight symmetric cage, with a soft cage coordinate that relaxes without eliciting elastic response. Enclathration in low-density amorphous ice is concluded.     

Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers

Conventional molecular dynamics simulations of macromolecules require long computational times because the most interesting motions are very slow compared to the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is, with bond lengths, bond angles, and torsions as independent variables, gives a theoretical possibility of eliminating all uninteresting fast degrees of freedom from the system. This article presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived that are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations of a 56 residue globular protein. For the first time it was possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of amino acids, that is, with fixed bond lengths, bond angles, and rigid aromatic groups, the characteristic step size is 4 fs, which is 2 times higher than with fixed bond lengths only. The step size can be increased up to 11 fs when rotation of hydrogen atoms is suppressed. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1354–1364, 1997     

Ab initio calculations of the ultraviolet resonance Raman spectra of uracil

An equation been derived to calculate, ab initio, the frequencies and intensities of a resonant Raman spectrum from the transform theory of resonance Raman scattering. This equation has been used to calculate the intensities of the ultraviolet resonance Raman spectra from the first π-π* excited state of uracil and 1,3-dideuterouracil. The protocol for this calculation is as follows: (1) The force constant matrix elements in Cartesian coordinate space, the vibrational frequencies, and the minimum energy ground and excited state geometries of the molecule are calculated ab initio using the molecular orbital program Gaussian 92, (2) the force constants in Cartesian coordinates are transformed into force constants in the space of a set of 3N – 6 nonredundant symmetrized internal coordinates, (3) the G matrix is constructed from the energy minimized ground state Cartesian coordinates and the GFL = LΛ eigenvalue equation is solved in internal coordinate space, (4) the elements of the L and L^?1 matrices are calculated, (5) the changes in all of the internal coordinates in going from the ground to the excited state are calculated, and (6) these results are used in combination with the transform theory of resonance Raman scattering to calculate the relative intensities of each of the 3N – 6 vibrations as a function of the exciting laser frequency. There are no adjustable parameters in this calculation, which reproduces the experimental frequencies and intensities with remarkable fidelity. This indicates that the Dushinsky rotation of the modes in the excited state of these molecules is not important and that the simplest form of the transform theory is adequate. © 1995 John Wiley & Sons, Inc.     

Curvature modulates the self-assembly of amphiphilic molecules

In this work, we used lattice Monte Carlo simulations and theoretical model calculations to show how the self-assembly of adsorbed amphiphilic molecules is affected by the local curvature of solid surfaces. It is found that, beyond a critical curvature value, solid surface geometry governs the spatial ordering of aggregates and may induce the morphological transitions. The simulation results show how the curvature of solid surfaces modulates the distribution of aggregates: the anisotropy in local curvature along and perpendicular to the cylindrical surfaces tends to generate orientationally ordered cylindrical micelles. To account for the morphological transitions induced by the local curvature of solid surfaces, we constructed a theoretical model which includes the Helfrich bending energy, the deformation energy of aggregates induced by solid surfaces, and the adsorption energy. The model calculations indicate that on highly curved solid surfaces the bending energy for bilayer structure sharply increases with surface curvature, which in turn induces the morphological transition from bilayer to cylindrical structure. Our results suggest that the local curvature provides a means of controlling the spatial organization of amphiphilic molecules.     

Non-linear dynamics of the photodissociation of nitrous oxide: equilibrium points, periodic orbits, and transition states

The diffuse vibrational bands, observed in the ultraviolet photodissociation spectrum of nitrous oxide by exciting the molecule in the first (1)A' state, have recently been attributed to resonances localized mainly in the NN stretch and bend degrees of freedom. To further investigate the origin of this localization, fundamental families of periodic orbits emanating from several stationary points of the (1)A' potential energy surface and bifurcations of them are computed. We demonstrate that center-saddle bifurcations of periodic orbits are the main mechanism for creating stable regions in phase space that can support the partial trapping of the wave packet, and thus they explain the observed spectra. A non-linear mechanical methodology, which involves the calculation of equilibria, periodic orbits, and transition states in normal form coordinates, is applied for an in detail exploration of phase space. The fingerprints of the phase space structures in the quantum world are identified by solving the time dependent Schro?dinger equation and calculating autocorrelation functions. This demonstrates that different reaction channels could be controlled if exact knowledge of the phase space structure is available to guide the initial excitation of the molecule.     

The Non‐Ergodic Nature of Internal Conversion

The absorption of light by molecules can induce ultrafast dynamics and coupling of electronic and nuclear vibrational motion. The ultrafast nature in many cases rests on the importance of several potential energy surfaces in guiding the nuclear motion—a concept of central importance in many aspects of chemical reaction dynamics. This Minireview focuses on the non‐ergodic nature of internal conversion, that is, on the concept that the nuclear dynamics only sample a reduced phase space, potentially resulting in localization of the dynamics in real space. A series of results that highlight the nonstatistical nature of the excited‐state deactivation process is presented. The examples are categorized into four groups. 1) Localization of the energy in one degree of freedom in S₂→S₁ transitions, in which the transition is either determined by the time spent in the S₂→S₁ coupling region or by the time it takes to reach it. 2) Localization of energy into a single reactive mode, which is dictated by the internal conversion process. 3) Initiation of the internal conversion by activation of a single complex motion, which then specifically couples to a reactive mode. 4) Nonstatistical internal conversion as a tool to accomplish biomolecular stability. Herein, the discussion on nonstatistical internal conversion in DNA as a mechanism to eliminate electronic excitation energy is extended to include molecules with an S?S bond as a model of the disulfide bridge in peptides. All of these examples are summed up in Kasha’s rule. For systems with multiple degrees of freedom it will be possible to locate an appropriate motion somewhere in phase space that will take the wavepacket to the coupling region and facilitate an ultrafast transition to S₁. Once at S₁, the momentum of the wavepacket is lost and the only options left are the statistical processes of reaction or light emission.     

MOLECULAR AGGREGATION IN LIPID-WATER DISPERSION PHASES

Polar lipids from aqueous liquid-crystalline phases which are the basis for the understanding of their functionality in technical applications. The structural characteristics of these phases and the relation between chemical structure of lipid molecules and their phase properties are reviewed. Special attention is given to new results on cubic phases, the most complex of lipid-water phases. The lipid bilayer is curved in space so that there are no selfintersections. There are two water-channel systems separated by the bilayer. The characteristic feature of the cubic phases is that the lipid bilayer has zero average curvature in all points.     

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators

New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The translation and rotation of a molecule are treated as vibrational motions with the vibrational frequency zero. All types of motion are thus described in terms of the normal coordinates. The method's time reversibility requirement was used to determine the equations of motion for internal coordinate system of a molecule. The calculation of long-range forces is performed numerically within the generalized second-order leap-frog scheme, in the same way as in standard second-order symplectic methods. The new methods for integrating classical equations of motion using normal mode analysis allow us to use a long integration step and are applicable to any system of molecules with one equilibrium configuration.