Quantum study of the absorption spectroscopy of bis(triarylamine) radical cations

Absorption spectra of bridged triarylamine radical cations are calculated quantum mechanically which extends our previous classical analysis (Lambert et al. J. Phys. Chem. A 2004, 108, 6474). A comparison between spectra determined within a diabatic and an adiabatic representation shows that under certain circumstances deviations occur. It is found that the latter are mainly caused by the Condon approximation for the dipole moments. The inclusion of vibrational degrees of freedom leads to an excellent agreement with experiment.     

Atomistic insights into rhodopsin activation from a dynamic model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.     

Sterically bulky tris(triazolyl)borate ligands as water-soluble analogues of tris(pyrazolyl)borate

The recently synthesized 3-tert-butyl-5-methyl-1,2,4-triazole reacted with KBH4 to give the new potassium tris(3-tert-butyl-5-methyl-1,2,4-triazolyl)borate K(Ttz(tBu,Me)) ligand. Ttz(tBu,Me) formed a four-coordinate (Ttz(tBu,Me))CoCl complex and five-coordinate (Ttz(tBu,Me))CoNO3 and (Ttz(tBu,Me))ZnOAc complexes. When these complexes were compared to their Tp(tBu,Me) analogues, it was found that Ttz(tBu,Me) resulted in negligible steric differences. K(Ttz(tBu,Me)) is more water-soluble than K(Tp(tBu,Me)), so bulky tris(triazolyl)borate ligands should lead to functional models for enzyme active sites in an aqueous environment and the creation of water-soluble analogues of Tp catalysts.     

Random-phase-approximation-based correlation energy functionals: benchmark results for atoms

The random phase approximation for the correlation energy functional of the density functional theory has recently attracted renewed interest. Formulated in terms of the Kohn-Sham orbitals and eigenvalues, it promises to resolve some of the fundamental limitations of the local density and generalized gradient approximations, as, for instance, their inability to account for dispersion forces. First results for atoms, however, indicate that the random phase approximation overestimates correlation effects as much as the orbital-dependent functional obtained by a second order perturbation expansion on the basis of the Kohn-Sham Hamiltonian. In this contribution, three simple extensions of the random phase approximation are examined; (a) its augmentation by a local density approximation for short-range correlation, (b) its combination with the second order exchange term, and (c) its combination with a partial resummation of the perturbation series including the second order exchange. It is found that the ground state and correlation energies as well as the ionization potentials resulting from the extensions (a) and (c) for closed subshell atoms are clearly superior to those obtained with the unmodified random phase approximation. Quite some effort is made to ensure highly converged data, so that the results may serve as benchmark data. The numerical techniques developed in this context, in particular, for the inherent frequency integration, should also be useful for applications of random phase approximation-type functionals to more complex systems.     

The influence of surface states on in-plane-gated structures

A model for in-plane-gated structures is proposed, taking into account surface currents and surface charges. The lateral band structures and barrier heights are calculated self-consistently for different bias voltages utilizing this new model. Accumulated negative surface charges lead to a strongly increased depletion length at the positively biased side of the lateral barriers. Most of the applied bias drops in this depleted region and does not affect the barrier height. We have found good agreement between these theoretical results and experimentally determined barrier heights and depletion lengths obtained from temperature-dependent current measurements and optical-beam-induced current measurements.     

Imaging and manipulation of biological structures with the AFM

Many biologists have dreamt of physically touching and manipulating the biomolecules they were investigating. With the invention of the atomic force microscope (AFM), this dream has come true. Here, recent applications of the AFM to image and to manipulate biological systems at the nanometer scale are reviewed. Macromolecular biological assemblies as well as individual biomolecules can be subjected to controlled nanomanipulation. Examples of AFM application in imaging and nanomanipulation include the extraction of chromosomal DNA for genetic analysis, the disruption of antibody--antigen bonds, the dissection of biological membranes, the nanodissection of protein complexes, and the controlled modulation of protein conformations. Also reviewed is the novel combination of single molecule imaging and force spectroscopy which allows biomolecules to be imaged, and inter- and intramolecular forces to be measured. Future application of these nanotechniques will reveal new information on the structure, function and assembly of biomolecules.