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 Au25 core coated by a shell of multi-branched highly fluorinated thiols (SF27) resulting in almost 500 fluorine atoms, i.e., ([Au25(SF27)18]0). The cluster shows a switchable solubility in the fluorous phase. X-ray analysis and computational studies reveal the key role of both intracluster and intercluster F···F contacts in driving [Au25(SF27)18]0 crystal packing and stabilization, highlighting the ability of multi-branched fluorinated thiols to endow atomically precise nanoclusters with remarkable crystallogenic behavior.

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 1) and the DA reaction involving 1-methoxy-butadiene and cyano-ethylene (system 2) 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. The relative importance of these three domains varies along the reaction coordinate. In addition to the usual reactant-like and product-like covalent Lewis structures, ionic Lewis structures have non-negligible weights. In system 2, the electron-donor OCH3 on the diene and the electron-acceptor CN on the dienophile make more important the contributions of ionic Lewis structures that stabilize the transition state and determine the decrease of the reaction barrier with respect to system 1.

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-1. Two-state model calculations show that the results of the quantum dynamics are robust and intrinsic to the use of noise in the simulations.

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. The 2P absorption cross-sections predicted by the response theory are accounted for by considering just one intermediate state (S1) in the sum-over-states formulation. For the chromophore featuring the stronger acceptor, the energetic positions of the 1P- and 2P-active states prevent the exploitation of the theoretically predicted very high 2P activity due to the competing 1P absorption into the S1 state.

Effects of knot tightness at the molecular level.

Three 819 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 1H 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. Understanding the effects of tightening nanoscale knots may usefully inform the design of knotted and entangled molecular materials.

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. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.

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. An explicit, time-evolving model is applied, which is able to count all possible photo-excitations occurring during the photoemission process, showing that they evolve on a short time-scale, of about 10 fs. The method reveals itself to be a valid approach to reproduce photoemission spectra of polycyclic aromatic hydrocarbons (PAHs).

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.

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. Time-critical components are identified via profiling of an existing implementation and several different variants are tested involving the GPU at increasing levels of abstraction. A publicly available library supporting basic linear algebra operations on the GPU turns out to accelerate the computation approximately 50-fold with minor dependence on actual problem size. The performance gain does not compromise numerical accuracy and is of significant value for practical purposes.

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. On the basis of these quantum dynamics simulations, it is hypothesized that the ultrafast exciton energy transfer process, which in general gives rise to a delocalized exciton within these clusters, may contribute to the low efficiency of photolytic processes in water ice. It is proposed that exciton diffusion inherently competes with the nuclear dynamics that drives the photodissociation process in the repulsive S1 state on the sub-10 fs time scale.

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. With a laser excitation energy of 2.39 eV and a fluence of 1.5 mJ/cm(2), the most pronounced changes were observed in approximately 180 fs, a time similar to the temporal resolution of the technique. The presence of the laser field turns the electronic wavefunction into a wavepacket whose quantum dynamics governs the onset of the structural rearrangement. Density functional theory calculations with a quantum propagator that include the laser field show that the charge density of graphite expands between the layers in an ultrafast process of the order of approximately 10 fs. Calculations as a function of the field/fluence further show different values of the maximum bond order reached at the stationary state. The experimentally used value is at the crossover between two regimes. It is tempting to associate the second regime with the electron organization necessary to achieve ablation or melting. The application of the model demonstrates its potential for examining the dynamical nature of the charge density and chemical bonding as it forms.

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. The electron wave function dynamics accurately accounts for the previously proposed mechanism of transfer via the terminal methyl group of the flavin moiety present in the catalytic electron-donor cofactor, FADH(-), which also contains adenine. This latter moiety, which has often been assumed to be present mainly for structural reasons, instantaneously modifies the interaction between acceptor and donor by a variation of the electrostatic interactions so that the presence of its local atomic charges is necessary to trigger the transfer. In principle, knowledge of the details of the electron transfer dynamics and of the important role of polarization effects can be exploited to improve the efficiency of the repair mechanism in artificial systems.

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. This theoretical development enables us to study rapid photon-induced bond dissociation dynamics and demonstrates the partial breakdown of electronic coherence as well as electronic population trapping in the excited state when the molecular vibrations detune the system with respect to the applied field. The method offers a practical way to use on-the-fly dynamics for modeling light-molecule interactions that lead to interesting photochemical events.

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. The method is applied to wave functions calculated using the B3LYP (hybrid) density functional, with the STO-3G and the 6-31+G basis sets. The molecule undergoes full population inversion between the HOMO and the LUMO when the electric field is in resonance with the HOMO-LUMO energy gap. The magnitude of the electric field directly affects the rate at which electronic transitions occur and the rate at which charges move between lithium and hydrogen atoms. The method is used to model both monochromatic and bichromatic multiphoton effects in LiH. Monochromatic one-, two- and three-photon transitions occur between the HOMO, LUMO and two other virtual orbitals. There is evidence of both [1+2] direct and [1+1+1] stepwise multiphoton transitions. Bichromatically, two "laser" pulses are applied at different frequencies. Electronic transitions can be fine-tuned to occur via pre-specified pathways of virtual molecular orbitals.

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. Along the entire pathway, the intramolecular energy that stabilizes the single helices is slowly transformed into intermolecular energy that finally provides the necessary stabilization only near the end of the entwining process. Solvent or other chemical factors, such as the presence of ions, able to destabilize the full formation of the double helix may therefore drastically affect its formation.