Structure,dynamics, and solvation in a disordered metal–organic coordination polymer: a multiscale study

Metal–organic coordination polymers are a growing class of technologically-important materials in which transition metal ions are connected by multitopic organic chelators to form a 3-D network structure. While the structures of many highly-ordered metal–organic frameworks have been determined, far less structural information is available about the more common disordered materials. Our study combines pair distribution function analysis from total X-ray scattering, ab initio quantum mechanical calculations, and all-atom molecular dynamics to explore the structure and dynamics of a poorly-ordered branched coordination polymer. The polymer structure is highly flexible and dynamic, and is dramatically affected by its solvation state, a finding with far-reaching implications for the incorporation of coordination polymers into nanocomposite materials.     

Classical aspects emerging from local control of energy and particle transfer in molecules

The question in how far classical mechanics can be used to describe coherent control processes in molecules is addressed within the framework of local control theory. Therefore, quantum and classical calculations are compared for a model proton transfer process and also for the multi-photon infrared dissociation of the HOD molecule. It is shown that control fields can be derived classically as long as wave packet dispersion is not too large. This hints at further applications which might be helpful to devise control fields for complex molecular systems being present in biological processes.     

Proton dynamics in an extended array of hydrogen bonds: normal coordinates, proton transfer and macroscopic quantum entanglement in the ground state

After a brief introduction to neutron scattering techniques, illustrated with the scattering function for harmonic oscillators, some new aspects of proton dynamics in the KHCO₃ crystal are presented. The full scattering function for the proton modes measured on single crystals provides a graphic view of proton dynamics. Vibrational states are fully characterized with three quantum numbers. The effective oscillator mass of 1 amu confirms the decoupling of protons from the lattice. Combining infrared, Raman and inelastic neutron scattering techniques, the double minimum potential for the transfer of a single proton along hydrogen bonds is totally determined. Elastic neutron scattering techniques probe dynamics in the fully degenerate ground state. Quantum entanglement arising from normal coordinates gives rise to quantum interference. With diffraction techniques, the dynamical structure arising from large-scale quantum coherence is observed as ridges of intensity, well separated from Bragg's peaks. The vibrational wave function in the ground state must be regarded as a superposition of non-factorable macroscopic wave function.     

Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state

Intramolecular charge transfer (ICT) of gaseous π-conjugated oligo-phenyleneethynylenes (OPE) induced by a homogeneous applied electric field has been theoretically investigated using a combined approach integrating molecular dynamics (MD) simulations and Perturbed Matrix Method calculations. In line with recent investigations, our results indicate the peculiar role of conformational transitions on OPE electronic properties which reflects on a strong temperature effect on ICT. Electron transfer reactions inducing chemical alteration on OPE, also taken into account in this study, revealed extremely important for explaining non-linear ICT effects and probably plays a central role in the mechanisms underlying molecular transport junctions. Our study further points out the necessity of using MD-based approach for modelling molecular electronics, even when relatively rigid molecular systems are concerned.     

Car–Parrinello molecular dynamics on the SN2 reaction Cl+CH3Br in water

The results of the analysis of ab initio molecular dynamics simulations of the transition state of a bimolecular nuclear substitution reaction in water are discussed and a lower limit for the life-time of the hydrogen bonded interactions between the halogens and the surrounding water molecules is estimated. A new function is introduced to compute a lower estimate of the H-bond life-time and compared with the results of the traditional one.     

Modeling,docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.

Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid–protein interactions, indicating some future applications of ns-LTP-mediated transport.     

Quantum control of a chiral molecular motor driven by femtosecond laser pulses: Mechanisms of regular and reverse rotations

Rotational mechanisms of a chiral molecular motor driven by femtosecond laser pulses were investigated on the basis of results of a quantum control simulation. A chiral molecule, (R)-2-methyl-cyclopenta-2,4-dienecarboaldehyde, was treated as a molecular motor within a one-dimensional model. It was assumed that the motor is fixed on a surface and driven in the low temperature limit. Electric fields of femtosecond laser pulses driving both regular rotation of the molecular motor with a plus angular momentum and reverse rotation with a minus one were designed by using a global control method. The mechanism of the regular rotation is similar to that obtained by a conventional pump–dump pulse method: the direction of rotation is the same as that of the initial wave packet propagation on the potential surface of the first singlet (nπ^*) excited state S₁. A new control mechanism has been proposed for the reverse rotation that cannot be driven by a simple pump–dump pulse method. In this mechanism, a coherent Stokes pulse creates a wave packet localized on the ground state potential surface in the right hand side. The wave packet has a negative angular momentum to drive reverse rotation at an early time.     

Non-adiabatic molecular dynamics with quantum solvent effects

Three novel approaches extending quantum-classical non-adiabatic (NA) molecular dynamics (MD) to include quantum effects of solvent environments are described. In a standard NA-MD the solute subsystem is treated quantum mechanically, while the larger solvent part of a system is treated classically. The three novel approaches presented here are based on the Bohmian formulation of quantum mechanics, the stochastic Schrödinger equation for the evolution of open quantum systems and the quantized Hamilton dynamics generalization of classical mechanics. The approaches extend the standard NA-MD to incorporate the following quantum effects of the solvent. (1) Branching, i.e. the ability of solvent quantum wave packets to split and follow asymptotically diverging trajectories correlated with different quantum states of the solute. (2) Decoherence, i.e. loss of quantum interference within the solute subsystem induced by the diverging solvent trajectories. (3) Zero point energy that contributes to NA coupling and must be preserved during the energy exchange between solvent and solute degrees of freedom. The Bohmian quantum-classical mechanics, stochastic mean-field and quantized mean-field approximations incorporate the quantum solvent effects into the standard quantum-classical NA-MD in a straightforward and efficient way that can be easily applied to quantum dynamics of condensed phase chemical systems.     

The occurrence of electron transfer in aromatic nitration: dynamical aspects

Electron transfer (ET) from toluene to the nitronium ion in the region of van der Waals intermolecular distances has been investigated by a quantum dynamical analysis performed on potential-energy surfaces computed at the ab initio multireference configuration interaction level. The results show that ET is very fast, occurring on a timescale of a few picoseconds. This has important implications for the mechanism of aromatic nitration: the ET path can compete efficiently with the direct attack of the nitronium ion to the aromatic substrate to yield the Wheland intermediate and that could explain some unsettled points in the mechanism of aromatic nitration. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 12 May 2000     

Nonperturbative quantum simulation of time-resolved nonlinear spectra: Methodology and application to electron transfer reactions in the condensed phase

A quantum dynamical method is presented to accurately simulate time-resolved nonlinear spectra for complex molecular systems. The method combines the nonpertubative approach to describe nonlinear optical signals with the multilayer multiconfiguration time-dependent Hartree theory to calculate the laser-induced polarization for the overall field–matter system. A specific nonlinear optical signal is obtained by Fourier decomposition of the overall polarization. The performance of the method is demonstrated by applications to photoinduced ultrafast electron transfer reactions in mixed-valence compounds and at dye–semiconductor interfaces.     

离子液体的量化计算及分子动力学模拟研究进展

离子液体是由有机阳离子和无机/有机阴离子构成的盐类,一般在室温或接近于室温下呈液态,因此常被称为室温离子液体(RTIL).依据不同的划分标准,离子液体有多种分类方式:根据年代的不同可将离子液体分为第一代、第二代及第三代离子液体,例如:烷基咪唑和烷基吡啶的金属卤化物盐等[1];根据阳离子的不同可将离子液体分为季鏻     

Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ∼0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of −3.6 kcal/mol, located at 15–16 Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8–5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and chloroform.     

Use of Electron-Density Plots in Applied Quantum Chemistry

The uses in applied quantum chemistry of computer-produced three-dimensional diagrams of electron-density distributions are discussed. The two major catagories of such diagrams are contrasted; and advantages are described for plots showing as the third dimension the point-by-point electron density in a cross-sectional cut (corresponding to the other two dimensions) through a molecule. Examples are presented to show how these plots may be used (1) to assess the adequacies of a given mathematical representation employed in the calculation of a wavefunction, (2) to clarify the interrelationship between an individual molecular orbital and the atomic orbitals of the constituent atoms, as well as (3) to explain the canonical set of molecular orbitals of any selected molecule. Furthermore these plots serve(4) to demonstrate clearly a replication of key characteristics between certain molecular orbitals in different molecules. These examples are accompanied by others which indicate how the electron-density plots may be used(5) to understand and clarify accepted chemical dogma. Finally, the possibility is discussed of employing quantum calculations on a wider scale so as to be of value in the more practical aspects of chemistry.     

Molecular dynamics simulation of dual amino-functionalized imidazolium-based ionic liquids

In this work, the all-atom (AA) force fields were set up for three kinds of dual amino-functionalized imidazolium-based ionic liquids (ILs), composed by cations with different alkyl chain length and amino acid anion [Gly]⁻. The force field was based on our previous work and the default parameters were developed in this study. Molecular dynamics simulations were performed. Validation was carried out by comparing simulation densities with experimental data, and good agreement was obtained. Molar volume and heat capacity at constant pressure were predicted. Mean square displacements for these ILs were computed and these ILs were proved to move very slowly. It may be caused by hydrogen-bonded network between ions and the terminal azyl. To depict the microscopic structures of the ILs, many types of radial distribution functions were investigated. It is interesting to find that not only the cation and anion, but also the anions themselves will form hydrogen bonds.     

Recent progress in probing atomic and molecular quantum coherence with scanning tunneling microscopy

Quantum coherent physics and chemistry concern the creation and manipulation of an excited-state manifold that contains the superposition and entanglement of multiple quantum levels. Electromagnetic waves such as light and microwave can be used to generate and probe different quantum coherent phenomena. The recent advances in scanning tunneling microscopy (STM) techniques including ultrafast laser coupled STM and electron spin resonance STM combine electromagnetic excitation with tunneling electron detection, bringing the investigation of quantum coherence down to the atomic and molecular level. Here, we survey the latest STM studies of different quantum coherent phenomena covering molecular vibration, electron transfer, surface plasmon resonance, phonon, spin oscillation, and electronic transition, and discuss the state and promise of characterizing and manipulating quantum coherence at the atomic or molecular scale.     

Modeling of peptides containing D-amino acids: implications on cyclization

Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclizes in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated α_L rotamers even when simulations were performed at a higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L-amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular dynamics simulations of the Hras‐GTP complex and the Hras‐GDP complex

We study the structures of the Hras‐GTP complex and the Hras‐GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras‐GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg²⁺. Our simulations show that the averaged structure differences between the Hras‐GTP complex and Hras‐GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α2 ‐ helix of Hras‐GDP is shorter than the α2 ‐ helix of Hras‐GTP. The averaged number of water molecules in the first hydration sphere in Hras‐GDP complex is larger than that in Hras‐GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras‐GTP and in Hras‐GDP. In Hras‐GDP complex, β‐phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras‐GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc.     

Quantum two-state dynamics driven by stationary non-Markovian discrete noise: Exact results

We consider the problem of stochastic averaging of a quantum two-state dynamics driven by non-Markovian, discrete noises of the continuous time random walk type (multistate renewal processes). The emphasis is put on the proper averaging over the stationary noise realizations corresponding, e.g., to a stationary environment. A two-state non-Markovian process with an arbitrary non-exponential distribution of residence times (RTDs) in its states with a finite mean residence time provides a paradigm. For the case of a two-state quantum relaxation caused by such a classical stochastic field we obtain the explicit exact, analytical expression for the averaged Laplace-transformed relaxation dynamics. In the limit of Markovian noise (implying an exponential RTD), all previously known results are recovered. We exemplify new more general results for the case of non-Markovian noise with a biexponential RTD. The averaged, real-time relaxation dynamics is obtained in this case by numerically exact solving of a resulting algebraic polynomial problem. Moreover, the case of manifest non-Markovian noise with an infinite range of temporal autocorrelation (which in principle is not accessible to any kind of perturbative treatment) is studied, both analytically (asymptotic long-time dynamics) and numerically (by a precise numerical inversion of the Laplace-transformed averaged quantum relaxation).