The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors

Summary Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and -electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3,5-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.     

Observation of the symmetry-forbidden 5sigmau-->ksigmau CS2 transition: a vibrationally driven photoionization resonance

Vibrationally resolved photoelectron spectroscopy and Schwinger calculations are used to characterize a new resonance phenomenon in the 5sigma(u)-->ksigma(u) photoionization of CS2. This resonant channel is symmetry forbidden, yet is observable because it is activated by the antisymmetric stretching vibration. In addition, we show that a Franck-Condon breakdown occurs even though the energy dependence of the cross section is insensitive to geometry changes, which is unprecedented in photoionization.     

Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

Quasibound continuum states in SiF4 (D2A1) photoionization: photoelectron-vibrational coupling

The authors report a fully vibrationally resolved photoelectron spectroscopy investigation of a nonplanar molecule studied over a range of excitation energies. Experimental results for all four fundamental vibrational modes are presented. In each case significant non-Franck-Condon effects are seen. The vibrational branching ratio for the totally symmetric mode nu1+ is found to be strongly affected by resonant excitation in the SiF4+ (D2A1) photoionization channel. This is shown to be the result of two distinct shape resonances, which for the first time have been both confirmed by theoretical calculations. Vibrationally resolved Schwinger photoionization calculations are used to understand the vibronic coupling for the photoelectrons, both using ab initio and harmonic vibrational wave functions.     

Molecular frame and recoil frame photoelectron angular distributions from dissociative photoionization of NO2

The authors report measured and computed molecular frame photoelectron angular distributions (MFPADs) and recoil frame photoelectron angular distributions (RFPADs) for the single photon ionization of the nonlinear molecule NO2 leading to the (1a2)-1 b 3A2 and (4a1)-1 3A1 states of NO2+. Experimentally, the RFPADs were obtained using the vector correlation approach applied to the dissociative photoionization (DPI) involving these molecular ionic states. The polar and azimuthal angle dependences of the photoelectron angular distributions are measured relative to the reference frame provided by the ion recoil axis and direction of polarization of the linearly polarized light. Experimental results are reported for the photon excitation energies hnu=14.4 and 22.0 eV. Theoretically the authors give expressions for both the MFPAD and the RFPAD. They show that the functional form in the recoil frame, where an average over the azimuthal dependence of the molecular fragments about the recoil direction is made, is identical to that they have earlier found for the DPI experiments performed on linear molecules. MFPADs were then computed using single-center expansion techniques within the fixed-nuclei frozen-core Hartree-Fock approximation. The computed cross sections for ionization to the (1a2)-1 b 3A2 state show a strong propensity for ionization with the polarization of the light perpendicular to the plane of the molecule, whereas the ionization to the (4a1)-1 3A1 state of the ion is of similar intensity for all orientations of the polarization of the light in the molecular frame. These qualitative features of the MFPAD are also evident in the RFPAD. The RFPAD for ionization leading to the (1a2)-1 b 3A2 state is strongly peaked in the perpendicular orientation, whereas the RFPAD for ionization leading to the (4a2)-1 3A1 state is much more nearly isotropic. Comparison between experimental and theoretical RFPADs indicates that the recoil angle for NO+ fragments is approximately 50 degrees relative to the symmetry axis of the initial C2v symmetry of the NO2 molecule in the ionization leading to the (1a2)-1 b 3A2 state and the recoil angle is approximately 120 degrees for the O+ fragment for ionization leading to the (4a1)-1 3A1 state.     

Computing the superexchange electronic factor of electron transfer theory using a grid‐based numerical method

We report a method for calculating the electronic factor in the superexchange rate equation of electron transfer theory; this method is a basis set independent, grid‐based numerical technique that utilizes fast Fourier transforms (FFTs) and a Lanczos recursion in a pseudospectral framework and is used to treat a three‐dimensional one‐electron model of the electronic factor. We compare eigenvalues calculated from the current method to eigenvalues from the literature for both one‐dimensional (1D) and three‐dimensional (3D) model problems and find that the current method provides excellent accuracy and efficiency. With respect to the superexchange electronic factor, we use model potentials to calculate the tunneling matrix elements with the present method to illustrate how the method can be used to address current issues in superexchange. In particular, we show how this method is useful in evaluating the effect of the bridge potential on the superexchange electronic factor when using repulsive‐core pseudopotentials to represent the bridge. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1262–1273, 2000     

Launching a particle on a ring: b2u-->ke2g ionization of C6F6

Evidence is presented demonstrating that an electron launched into the continuum is trapped in an unprecedented quasibound state, namely, one that extends through the backbone of the six-member carbon ring of C6F6. The mode specificity of the vibrational sensitivity to the electron trapping provides an experimental signature for this phenomenon, while adiabatic static model-exchange scattering calculations are used to map the wave function, which corroborate the interpretation.