Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory.

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.

Theoretical Rationalization of the Emission Properties of Prototypical Cu(I)-Phenanthroline Complexes.

The excited state properties of transition metal complexes have become a central focus of research owing to a wide range of possible applications that seek to exploit their luminescence properties. Herein, we use density functional theory (DFT), time-dependent DFT (TDDFT), classical and quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations to provide a full understanding on the role of the geometric and electronic structure, spin-orbit coupling, singlet-triplet gap and the solvent environment on the emission properties of nine prototypical copper(I)-phenanthroline complexes. Our calculations reveal clear trends in the electronic properties that are strongly correlated to the luminescence properties, allowing us to rationalize the role of specific structural modifications. The MD simulations show, in agreement with recent experimental observations, that the lifetime shortening of the excited triplet state in donor solvents (acetonitrile) is not due to the formation of an exciplex. Instead, the solute-solvent interaction is transient and arises from solvent structures that are similar to the ones already present in the ground state. These results based on a subset of the prototypical mononuclear Cu(I) complexes shed general insight into these complexes that may be exploited for development of mononuclear Cu(I) complexes for applications as, for example, emitters in third generation OLEDs.

A quantum dynamics study of the ultrafast relaxation in a prototypical Cu(I)-phenanthroline.

The ultrafast nonadiabatic dynamics of a prototypical Cu(I)-phenanthroline complex, [Cu(dmp)2](+) (dmp = 2,9-dimethyl-1,10-phenanthroline), initiated after photoexcitation into the optically bright metal-to-ligand charge-transfer (MLCT) state (S3) is investigated using quantum nuclear dynamics. In agreement with recent experimental conclusions, we find that the system undergoes rapid (∼100 fs) internal conversion from S3 into the S2 and S1 states at or near the Franck-Condon (FC) geometry. This is preceded by a dynamic component with a time constant of ∼400 fs, which corresponds to the flattening of the ligands associated with the pseudo Jahn-Teller distortion. Importantly, our simulations demonstrate that this latter aspect is in competition with subpicosecond intersystem crossing (ISC). The mechanism for ISC is shown to be a dynamic effect, in the sense that it arises from the system traversing the pseudo Jahn-Teller coordinate where the singlet and triplet states become degenerate, leading to efficient crossing. These first-principles quantum dynamics simulations, in conjunction with recent experiments, allow us to clearly resolve the mechanistic details of the ultrafast dynamics within [Cu(dmp)2](+), which have been disputed in the literature.

X-ray spectroscopic study of solvent effects on the ferrous and ferric hexacyanide anions.

We present an Fe Kα resonant inelastic X-ray scattering (RIXS) and X-ray emission (XES) study of ferrous and ferric hexacyanide dissolved in water and ethylene glycol. We observe that transitions below the absorption edge show that the solvent has a distinct effect on the valence electronic structure. In addition, both the RIXS and XES spectra show a stabilization of the 2p levels when dissolved in water. Using molecular dynamics simulations, we propose that this effect arises from the hydrogen-bonding interactions between the complex and nearby solvent molecules. This withdraws electron density from the ligands, stabilizing the complex but also causing a slight increase in π-backbonding.

X-ray absorption spectroscopy of ground and excited rhenium-carbonyl-diimine complexes: evidence for a two-center electron transfer.

Steady-state and picosecond time-resolved X-ray absorption spectroscopy is used to study the ground and lowest triplet states of [ReX(CO)(3)(bpy)](n+), X = Etpy (n = 1), Cl, or Br (n = 0). We demonstrate that the transient spectra at both the Re L(3)- and Br K-edges show the emergence of a pre-edge feature, absent in the ground-state spectrum, which is associated with the electron hole created in the highest occupied molecular orbital following photoexcitation. Importantly, these features have the same dynamics, confirming previous predictions that the low-lying excited states of these complexes involve a two-center charge transfer from both the Re and the ligand, X. We also demonstrate that the DFT optimized ground and excited structures allow us to reproduce the experimental XANES and EXAFS spectra. The ground-state structural refinement shows that the Br atom contributes very little to the latter, whereas the Re-C-O scattering paths are dominant due to the so-called focusing effect. For the excited-state spectrum, the Re-X bond undergoes one of the largest changes but still remains a weak contribution to the photoinduced changes of the EXAFS spectrum.

Solvent-induced luminescence quenching: static and time-resolved X-ray absorption spectroscopy of a copper(I) phenanthroline complex.

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) ([Cu(dmp)2](+); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photoluminescence spectra in dichloromethane and acetonitrile are also presented and show a shift to longer wavelengths for the latter, which points to a stronger stabilization of the excited complex. The fine structure features of the static and transient X-ray spectra allow an unambiguous assignment of the electronic and geometric structure of the molecule in both its ground and excited (3)MLCT states. Importantly, the transient spectra are remarkably similar for both solvents, and the spectral changes can be rationalized using the optimized ground- and excited-state structures of the complex. The proposed assignment of the lifetime shortening of the excited state in donor solvents (acetonitrile) to a metal-centered exciplex is not corroborated here. Molecular dynamics simulations confirm the lack of complexation; however, in both solvents the molecules come close to the metal but undergo rapid exchange with the bulk. The shortening of the lifetime of the title complex and nine additional related complexes can be rationalized by the decrease in the (3)MLCT energy. Deviations from this trend may be explained by means of the effects of the dihedral angle between the ligand planes, the solvent, and the (3)MLCT-(1)MLCT energy gap.

A wavelet analysis for the X-ray absorption spectra of molecules.

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rhenium diimine complex, [ReX(CO)(3)(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.

Photoemission and photoionization time delays and rates.

Ionization and, in particular, ionization through the interaction with light play an important role in fundamental processes in physics, chemistry, and biology. In recent years, we have seen tremendous advances in our ability to measure the dynamics of photo-induced ionization in various systems in the gas, liquid, or solid phase. In this review, we will define the parameters used for quantifying these dynamics. We give a brief overview of some of the most important ionization processes and how to resolve the associated time delays and rates. With regard to time delays, we ask the question: how long does it take to remove an electron from an atom, molecule, or solid? With regard to rates, we ask the question: how many electrons are emitted in a given unit of time? We present state-of-the-art results on ionization and photoemission time delays and rates. Our review starts with the simplest physical systems: the attosecond dynamics of single-photon and tunnel ionization of atoms in the gas phase. We then extend the discussion to molecular gases and ionization of liquid targets. Finally, we present the measurements of ionization delays in femto- and attosecond photoemission from the solid-vacuum interface.

Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG).

We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational families with collisional cross-sections of 93.8 and 96.8 Å(2). After separation, each family is independently analyzed by acquiring the infrared predissociation spectrum of the H(2)-tagged molecules. The ion mobility and spectroscopic data combined with density functional theory (DFT) based molecular dynamics simulations confirm the presence of one major conformer per family, which arises from cis/trans isomerization about the proline residue. We induce isomerization between the two conformers by using collisional activation in the drift tube and monitor the evolution of the ion distribution with ion mobility and infrared spectroscopy. While the cis-proline species is the preferred gas-phase structure, its relative population is smaller than that of the trans-proline species in the initial ion mobility drift distribution. This suggests that a portion of the trans-proline ion population is kinetically trapped as a higher energy conformer and may retain structural elements from solution.

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

Caspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/molecular mechanics Car-Parrinello study of key steps of the enzymatic reaction for a representative member of this family, caspase-3. The hydrolysis of the acyl-enzyme complex is described at the density functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calculations show that the attack of the hydrolytic water molecule implies an activation free energy of ca. DeltaF(A) approximately equal 19 +/- 4 kcal/mol in good agreement with experimental data and leads to a previously unrecognized gem-diol intermediate that can readily (DeltaF(A) approximately equal 5 +/- 3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well-characterized cysteine proteases (papains and cathepsins) and may help design novel transition-state analog inhibitors.

[The fetlock tunnel syndrome in horses: literature review and retrospective study]. / Das Fesseltunnelsyndrom beim Pferd: Literaturübersicht und retrospektive Untersuchung.

The annular ligament constriction is characterized by a disproportion between the available space and the contents within the fetlock tunnel. The main symptoms are a persisting lameness, distention of the tendon sheath, a typical "notch" when the fetlock is viewed from the side and a hyperflexion pain in the fetlock. The surgical treatment consists of the transection of the fetlock annular ligament. The conservative management can be considered as a independent therapy or as a preparation for a subsequent desmotomy. The medical records of 75 horses suffering from fetlock tunnel syndrome presented at the Veterinary Surgery Clinic of the University of Zurich were studied. 39 horses with 41 affected limbs were reexamined clinically and ultrasonographically. 70% of the surgical cases and 82% of the conservatively treated cases were judged to be sound. Altogether it can be said that the surgical case group had a success rate of 62% while the conservatively treated group showed a success rate of 58%.

Photooxidation and photoaquation of iron hexacyanide in aqueous solution: A picosecond X-ray absorption study.

We present a picosecond Fe K-edge absorption study of photoexcited ferrous and ferric hexacyanide in water under 355 and 266 nm excitation. Following 355 nm excitation, the transient spectra for the ferrous and ferric complexes exhibit a red shift of the edge reflecting an increased electron density at the Fe atom. For the former, an enhanced pre-edge transition is also observed. These observations are attributed to the aquated [Fe(CN)5OH2](3-) species, based on quantum chemical calculations which also provide structural parameters. Upon 266 nm excitation of the ferric complex, a transient reminiscent of the aquated species is observed (appearance of a pre-edge feature and red shift of the edge) but it is different from that obtained under 355 nm excitation. This points to a new reaction channel occurring through an intermediate state lying between these two excitation energies. Finally, 266 nm excitation of the ferrous species is dominated by the photooxidation channel with formation of the ferric complex as main photoproduct. However, we observe an additional minor photoproduct, which is identical to the 266 nm generated photoproduct of the ferric species, suggesting that under our experimental conditions, the pump pulse photooxidises the ferrous complex and re-excites the primary ferric photoproduct.

A closer look into G protein coupled receptor activation: X-ray crystallography and long-scale molecular dynamics simulations.

G protein coupled receptors (GPCRs) are a large eukaryotic protein family of transmembrane receptors that react to a signal coming from the extracellular environment to generate an intracellular response through the activation of a signal transduction pathway mediated by a heterotrimeric G protein. Their diversity, dictated by the multiplicity of stimuli to which they respond and by the variety of intracellular signalling pathways they activate, make them one of the most prominent families of validated pharmacological targets in biomedicine. In recent years, major breakthroughs in structure determination of GPCRs have given new stimuli to the exploration of the biology of these proteins, providing a structural basis to understand the molecular origin of GPCR mechanisms of action. Based on the information coming from these structural studies, a number of recent in silico investigations used molecular dynamics (MD) simulations to contribute to our knowledge of GPCRs. In this review, we will focus on investigations that, taking advantage of the tremendous progress in both hardware and software, made testable hypotheses that have been validated by subsequent structural studies. These stateof- the-art molecular simulations highlight the potential of microsecond MD simulations as a valuable tool in GPCR structural biology and biophysics.

Molecular dynamics studies of caspase-3.

Caspase-3 is a fundamental target for pharmaceutical interventions against a variety of diseases involving disregulated apoptosis. The enzyme is active as a dimer with two symmetry-related active sites, each featuring a Cys-His catalytic dyad and a selectivity loop, which recognizes the characteristic DEVD pattern of the substrate. Here, a molecular dynamics study of the enzyme in complex with two pentapeptide substrates DEVDG is presented, which provides a characterization of the dynamic properties of the active form in aqueous solution. The mobility of the substrate and that of the catalytic residues are rather low indicating a distinct preorganization effect of the Michaelis complex. An essential mode analysis permits us to identify coupled motions between the two monomers. In particular, it is found that the motions of the two active site loops are correlated and tend to steer the substrate toward the reactive center, suggesting that dimerization has a distinct effect on the dynamic properties of the active site regions. The selectivity loop of one monomer turns out to be correlated with the N-terminal region of the p12 subunit of the other monomer, an interaction that is also found to play a fundamental role in the electrostatic stabilization of the quaternary structure. To further characterize the specific influence of dimerization on the enzyme essential motions, a molecular dynamics analysis is also performed on the isolated monomer.

Cis-trans isomerization in triply-bonded ditungsten complexes: a multitude of possible pathways.

We have investigated different possible mechanisms for the cis-trans isomerization in triply bonded ditungsten complexes with stoichiometry W(2)Cl(4)(NHEt)(2)(PMe(3))(2) using static density functional calculations as well as Car-Parrinello simulations. Our studies reveal an unexpected richness of possible reaction pathways that include both unimolecular and bimolecular mechanisms. Among the possible routes that have been identified are processes involving successive dissociation/reassociation of phosphine ligands, intramolecular chloride hopping, intertungsten phosphine exchange as well as numerous combinations of these basic reaction types. All pathways involve maximal activation barriers of less than 35 kcal/mol and include phosphine concentration dependent and independent routes. The energetically most favorable phosphine-dependent pathway is based on the dissociation/reassociation of phosphine ligands. This path is characterized by a maximal dissociation barrier of 18 kcal/mol. The fastest alternative unimolecular route (with a maximal activation barrier of 24 kcal/mol) is based on a direct exchange of phosphine between the two metallic coordination centers. All the identified pathways, with the exception of a previously proposed internal flip mechanism that can be ruled out on energetic grounds, are competitive and may contribute in various combinations to the overall reaction rate. The identified isomerization mechanisms are fully consistent with the experimentally observed 3-state-kinetics and the dependence of the overall reaction rate on the excess concentration of phosphine which is demonstrated with a simplified kinetic model of the process.

Three- and four-center trans effects in triply bonded ditungsten complexes: an ab initio molecular dynamics study of compounds with stoichiometry W2Cl4(NHEt)2(PMe3)2.

We have performed ab initio molecular dynamics simulations based on density functional theory to characterize the structural, electronic, and dynamic properties of the three major isomeric forms of the title compound. In agreement with experimental results, calculations with two different parametrizations of the exchange-correlation functional (BLYP and BP) both indicate the cis-C2 form as the most stable isomer. The relative energies of the different forms are, however, small (less than approximately 1-2 kcal/mol), and the three compounds show overall very similar ground-state properties. Larger differences exist in their finite temperature behavior, which is dominated by the facile dissociation of one or both phosphine ligands. The calculated activation energies for phosphine dissociation differ clearly for the trans and the cis isomers and vary in the order trans << cis-C2 less than approximately cis-Ci. Analysis of the electronic structure of the transition states shows that the difference in activation energy between cis and trans isomers can be rationalized in terms of a classic trans effect caused by a molecular orbital spanning the three atomic centers N-W-P. The subtle difference between the two cis isomers, on the other hand, is likely due to an analogous four-center trans effect N-W-W-P which is mediated via metal-metal orbitals and involves ligands on both tungsten atoms.

A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations.

A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low molecular weight analog of the active site was performed with dynamical density functional and mixed quantum-classical calculations. This combined approach enables a direct comparison of the properties of the biomimetic and the natural systems throughout the course of the catalytic reaction. In both cases, five essential forms of the catalytic cycle have been investigated: the resting state in its semi-reduced (catalytically inactive) and its oxidized (catalytically active) form, A(semi) and A(ox), respectively; a protonated intermediate B; the transition state for the rate-determining hydrogen abstraction step C, and its product D. For A and B the electronic properties of the biomimetic compound are qualitatively very similar to the ones of the natural target. However, in agreement with the experimentally observed difference in catalytic activity, the calculated activation energy for the hydrogen abstraction step is distinctly lower for GOase (16 kcal/mol) than for the mimetic compound (21 kcal/mol). The enzymatic transition state is stabilized by a delocalization of the unpaired spin density over the sulfur-modified equatorial tyrosine Tyr272, an effect that for geometric reasons is essentially absent in the biomimetic compound. Further differences between the mimic and its natural target concern the structure of the product of the abstraction step, which is characterized by a weakly coordinated aldehyde complex for the latter and a tightly bound linear complex for the former.

Biosynthesis of riboflavin: cloning, sequencing, and expression of the gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of Escherichia coli.

3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. The gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of Escherichia coli has been cloned and sequenced. The gene codes for a protein of 217 amino acid residues with a calculated molecular mass of 23,349.6 Da. The enzyme was purified to near homogeneity from a recombinant E. coli strain and had a specific activity of 1,700 nmol mg-1 h-1. The N-terminal amino acid sequence and the amino acid composition of the protein were in agreement with the deduced sequence. The molecular mass as determined by ion spray mass spectrometry was 23,351 +/- 2 Da, which is in agreement with the predicted mass. The previously reported loci htrP, "luxH-like," and ribB at 66 min of the E. coli chromosome are all identical to the gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase, but their role had not been hitherto determined. Sequence homology indicates that gene luxH of Vibrio harveyi and the central open reading frame of the Bacillus subtilis riboflavin operon code for 3,4-dihydroxy-2-butanone 4-phosphate synthase.

[Euphyllin retard and "exercise-induced" asthma]. / Euphyllin retard und "exercise-induced" Asthma.

In a double blind crossover experiment the protective effect of theophylline slow-releasing coated tablets (Euphyllin retard) on exercise-induced asthma has been compared with that of a placebo. Sixteen patients with bronchial asthma (mean age 23 years, range 16-49 years) who were selected in a preliminary test exhibited an FEV1 decrease greater than 15% 10 minutes after an exhausting 6 minute run on the treadmill. Euphyllin retard and placebo were given 6 hours before the exercise test. Venous blood was sampled 6 hours prior to and immediately before exercise in order to determine the plasma concentrations of theophylline by a tritium radioimmunoassay method. FEV1 was measured prior to and immediately after exercise, 10 and 20 minutes later and after a final orciprenaline inhalation. A group of 9 patients (group 1) has plasma concentrations of theophylline lower than 6.2 microgram/ml (4.8 +/- 0.9 microgram/ml), and a group of 7 patients (group 2) had concentrations higher than 10.0 microgram/ml (13.8 +/- 3.3 microgram/ml). Compared with placebo, a protective effect of Euphyllin retard could be observed in group 2 only (p < 0.025). In group 1 the asthma protection was indistinguishable form that of placebo. Hence, plasma concentrations higher than 10 microgram/ml appear to be required to protect asthmatics from exercise-induced asthma. Although in some patients an effective concentration can be achieved by the recommended dose of one tablet of Euphyllin retard (350 mg aminophylline) every 12 hours, the importance of measuring plasma concentrations must be emphasized in view of the variable absorption and elimination of theophylline. Side effects may occur at concentrations higher than 15 microgram/ml.