MiMiC: A high-performance framework for multiscale molecular dynamics simulations.

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach based on a multiple-program multiple-data (MPMD) paradigm, serving as an intermediary responsible for fast data exchange and interactions between the subsystems. The main goal of MiMiC is to avoid interfering with the underlying parallelization of the external programs, including the operability on hybrid architectures (e.

High-resolution crystal structure of a 20 kDa superfluorinated gold nanocluster.

Crystallization of atomically precise nanoclusters is gaining increasing attention, due to the opportunity of elucidating both intracluster and intercluster packing modes, and exploiting the functionality of the resulting highly pure crystallized materials. Herein, we report the design and single-crystal X-ray structure of a superfluorinated 20 kDa gold nanocluster, with an Au core coated by a shell of multi-branched highly fluorinated thiols (SF) resulting in almost 500 fluorine atoms, i.e.

Electron Dynamics with Explicit-Time Density Functional Theory of the [4+2] Diels-Alder Reaction.

The prototype Diels-Alder (DA) reaction between butadiene and ethene (system ) and the DA reaction involving 1-methoxy-butadiene and cyano-ethylene (system ) are investigated with an explicit-time-dependent Density Functional Theory approach. Bond orders and atomic net charges obtained in the dynamics at the transition state geometry and along the reaction coordinate toward reactants are used to provide a picture of the process in terms of VB/Lewis resonance structures that contribute to a resonance hybrid. The entire dynamics can be divided into different domains (reactant-like, product-like, and transition state domains) where different Lewis resonance structures contribute with different weights.

White and Colored Noises as Driving Forces of Electron Transfer: The Photolyase Repair Mechanism as a Test Case.

We introduce a model to investigate electron transfer where the explicit temporal propagation of the electronic wave function is modified by white and colored noises. Atomic energies are perturbed randomly to determine an electron transfer where the periodic electronic oscillations are greatly smothered and the transfer rates can reach up to the experimental time scale. Application to the photolyase enzyme that repairs the DNA lesions shows that the optimal conditions to reproduce the experimental lifetime are equivalent to a red or Brownian noise acting every 80 fs, that is, of ∼400 cm.

One- and two-photon absorption properties of quadrupolar thiophene-based dyes with acceptors of varying strengths.

The one-photon (1P) and two-photon (2P) absorption properties of three quadrupolar dyes, featuring thiophene as a donor and acceptors of varying strengths, are determined by a combination of experimental and computational methods employing the density functional theory (DFT). The emission shifts in different solvents are well reproduced by time-dependent DFT calculations with the linear response and state specific approaches in the framework of the polarizable continuum model. The calculations show that the energies of both 1P- and 2P-active states decrease with an increase of the strength of the acceptor.

Effects of knot tightness at the molecular level.

Three 8 knots in closed-loop strands of different lengths (∼20, 23, and 26 nm) were used to experimentally assess the consequences of knot tightness at the molecular level. Through the use of H NMR, diffusion-ordered spectroscopy (DOSY), circular dichroism (CD), collision-induced dissociation mass spectrometry (CID-MS) and molecular dynamics (MD) simulations on the different-sized knots, we find that the structure, dynamics, and reactivity of the molecular chains are dramatically affected by the tightness of the knotting. The tautness of entanglement causes differences in conformation, enhances the expression of topological chirality, weakens covalent bonds, inhibits decomplexation events, and changes absorption properties.

Structural determinants in the bulk heterojunction.

Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer.

Time-dependent quantum simulation of coronene photoemission spectra.

Photoelectron spectroscopy is usually described by a simple equation that relates the binding energy of the photoemitted electron, Ebinding, its kinetic energy, Ekinetic, the energy of the ionizing photon, Ephoton, and the work function of the spectrometer, ϕ, Ebinding = Ephoton - Ekinetic - ϕ. Behind this equation there is an extremely rich physics, which we describe here using as an example a relatively simple conjugated molecule, namely coronene. The theoretical analysis of valence band and C1s core level photoemission spectra showed that multiple excitations play an important role in determining the intensities of the final spectrum.

Imaging, photophysical properties and DFT calculations of manganese blue (barium manganate(VI) sulphate)--a modern pigment.

Manganese blue is a synthetic barium manganate(VI) sulphate compound that was produced from 1935 to the 1990s and was used both as a blue pigment in works of art and by conservators in the restoration of paintings. The photophysical properties of the compound are described as well as the setup needed to record the spatial distribution of the pigment in works of art.

Excitation Energy Transfer and Low-Efficiency Photolytic Splitting of Water Ice by Vacuum UV Light.

Experimental estimates of photolytic efficiency (yield per photon) for photodissociation and photodesorption from water ice range from about 10(-3) to 10(-1). However, in the case of photodissociation of water in the gas phase, it is close to unity. Exciton dynamics carried out by a quantum mechanical time-dependent propagator shows that in the eight most stable water hexamers, the excitation diffuses away from the initially excited molecule within a few femtoseconds.

GPU-accelerated computation of electron transfer.

Electron transfer is a fundamental process that can be studied with the help of computer simulation. The underlying quantum mechanical description renders the problem a computationally intensive application. In this study, we probe the graphics processing unit (GPU) for suitability to this type of problem.

Quantum study of laser-induced initial activation of graphite-to-diamond conversion.

Recently (Science 2009, 325, 181), femtosecond-resolved electron energy loss spectroscopy (FEELS) was used to map the structural changes of graphite upon laser irradiation, revealing the change from sp(2) to sp(3), i.e., diamond-like, hybridization.

What is adenine doing in photolyase?

The short answer to the title question is that it acts as an electrostatic bouncer that shoves the charge flow from flavin toward the DNA lesion that photolyase repairs. This explanation is provided by an explicit time-dependent quantum mechanical approach, which is used to investigate the electron transfer process that triggers the repair mechanism. The transfer occurs from the flavin photolyase cofactor to the cyclobutane ring of DNA, previously formed by light-induced cycloaddition of adjacent pyrimidine bases.

On-the-fly, electric-field-driven, coupled electron-nuclear dynamics.

An on-the-fly, electric field driven, coupled electron-nuclear dynamics approach is developed and applied to model the photodissociation of water in the A((1)B1) excited state. In this method, a quantum propagator evolves the photon-induced electronic dynamics in the ultrafast time scale, and a quasi-classical surface hopping approach describes the nuclear dynamics in the slower time scale. In addition, strong system-field interactions are explicitly included in the electronic propagator.

Mono- and bichromatic electron dynamics: LiH, a test case.

This paper describes an electron dynamics method where the time dependence of an external oscillating electric field is the perturbing part of the Hamiltonian. Application of the electric field induces charge movement inside the molecule and electronic transitions between the molecular orbitals. The test system is the neutral LiH molecule.

Pyridinedicarboxamide strands form double helices via an activated slippage mechanism.

The intertwining process of two strands of oligo-pyridinecarboxamides to form a double helix (Nature 2000, 407, 720) is found to consist of a series of discrete steps, where the tail of one of the strands proceeds inside the other single helix in an eddy-like process. While a plethora of minima can be located along the pathway, they exist only for a few, well-defined supramolecular arrangements of the two molecules. The initial transition state for the introduction of one molecule in the pitch of the other has the largest barrier and is therefore the rate-determining step of an activated slippage mechanism, which is characterized by a series of roller-coasting hills.