Recent progress in protein 3D structure comparison

Quantitation of protein 3-D structure similarity is crucial in such fields as evolutionary studies, structural modeling and prediction of biological function. There are various approaches, many of which are tailored to specific problems. This review summarizes the recent developments in this field with particular interest in two main areas: i) improvements to and statistical interpretation of the root-man-square distance between equivalent atoms, rmsd; and ii) methods of protein structural classification based on geometrical features. Special attention is given to fast methods capable of analyzing large structural databases.     

Electron-transfer in molecular functional materials

We discuss electron-transfer processes that govern the physics of several materials or systems of interest for advanced applications. The discussion touches upon several topics, ranging from solvatochromism to solvent-induced symmetry breaking, from excitonic to cooperative effects in molecular crystals, from phase transitions to vibrational contributions to the dielectric constant in organic materials, from spectroscopy to molecular transport. In all these diverse systems electron transfer (ET) plays a major role and is discussed with reference to simple models for delocalized charges.     

Solid state spin densities in triplet-exciton TCNQ salts

The combination of molecular spin densities and of structural data is shown to provide a sensitive test for the fine structure splittings and principal axes of triplet spin excitons in organic ion-radical crystals, in support of weakly-perturbed molecular sites in these solids. The exchange pathway in Rb(TCNQ) and the occurrence of dimer radicals, with fractional charges, in several tetrameric (TCNQ)₄^2? stacks illustrate the comparisons afforded by computations of fine structure parameters for triplets states in the solid.     

Polarization and polarizability in extended one-dimensional organic materials

The modern theory of polarization in extended insulators is applied to one-dimensional models for conjugated polymers and charge transfer salts. Closed expressions for the dependence of the polarization on the site and bond energy alternations are presented for uncorrelated models, and results from exact real-space diagonalization are obtained for correlated models. Changes in polarization induced by lattice phonons or molecular vibrations are directly related to the intensity of infrared bands in the far and mid-IR, respectively. We model intensities by introducing linear electron-vibration coupling and show that coupling to delocalized electrons generates a combination band consisting of a lattice phonon and a molecular vibration. The displaced dipole operator is defined on a real-space basis allowing for the finite field calculation of linear polarizability in finite size systems with periodic boundary conditions. Size-consistency arguments are used to demonstrate that the resulting polarizability becomes exact in the thermodynamic limit, and numerical calculations demonstrate that this approach leads to reliable results that converge rapidly to the thermodynamic limit.     

The photoelectron spectrum of tetramethyldiazetine: The elucidation of ring size effects on azo group ionization potentials

The photoelectron spectrum of 3,3,4,4-tetramethyldiazetine (4-Me₄) has been measured. By comparison with the previously reported photoelectron spectra of 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline, 4-Me₄ has three resolved low energy ionization (8.87, 10.36, and 11.65 eV) with an anomalously low second ionization potential. MINDO/3-and ab initio STO-3G calculations on 3-, 4-, and 5-membered ring azo compounds (diazenes) have been carried out, and these allow definite conclusions about the order of n_?, n₊, and π ionization potentials to be made for the diazetine (n_? < N₊ < π) and for 3,3-dimethyldiazirine and 3,3,5,5-tetramethylpyrazoline(n_? < π n₊), in agreement with the predictions of Heilbronner. Ab initio STO-3G calculations on the nitrogen and alkyl fragments of the cyclic diazenes reveal the origin of ionization energy shifts with changes in ring size.     

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH₂)₂COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation. Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002     

Poly-N-vinylamides,complexation and conformational changes in aqueous solution

Interaction between small molecules (iodine and 1-anilinonaphthalene-8-sulphonate) and poly-N-methylacetamide (PVMA), poly-N-vinylcaprolactam (PVCL), poly-N-vinylpyrrolidone (PVP) and copolymers of N-vinyleaprolactam with N-vinylpyrrolidone (CP VCL-VP) and with N-vinyl-N-methylacetamide (VMA) were studied. All the polymers formed complexes with the small molecules. The stability constant for the complexes with the probe increases in the series PVMA < PVP < copolymer < PVCL indicating the essential role of hydrophobic interactions in the complex formation. With increasing temperature of aqueous solution from 18 to 33°, the constant decreased for PVP, PVMA and copolymers with low VCL content and increased for PVCL. A folding of PVC coils was observed over the temperature range, demonstrating a relationship between the conformational changes of macromolecules and the polymer complex formation. Addition of PVCL, PVMA and PVP to aqueous I₃^? solution brings about a shift of λ_max from 350 nm for free triiodide ions to 372, 367 and 364 nm respectively. It is explained by different dipole moments of the side substituents. The stability constant for the polymers and I₃^? was estimated as approx. 10⁵ M. The ability of the polymers to form complexes depends on chainlength. The greatest loss of the ability was observed for PVCL with $\text{M}{}_{\mathrm{n}}$ changing from 6 × 10³ to 2 × 10³. Interaction of the polymers with I₃^? is accompanied by a conformational shrinking of coils. In the case of the probe, forces of electrostatic repulsion between negative charges of sulphonate groups result in an unfolding of polimer coils.     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

Need and use of reference materials in a comprehensive countrywide monitoring of radionuclides

The reliability of measurement results is essential for forming a common database of a laboratory network, because a well-maintained and consistent database is the crucial point of countrywide monitoring. Reference materials are important tools in realizing some aspects of quality assurance; they are especially useful in harmonizing work within the network. Among usual types of reference materials in radio analytics solutions, matrix reference materials and some special reference objects are used. All classes of reference materials should be used depending on the purpose of the demonstration of quality, even in-house reference materials. Interlaboratory measurement comparison and performance evaluation programs play important quality assurance role in radio analytical laboratories. Fortunately, nowadays, the main task is to determine a very low radioactivity concentration in the environment; therefore, pre-concentration is necessary. Generally, the radionuclide bearing natural materials collected from sites where there had been sufficient time for natural processes to redistribute various chemically different species of radionuclides are more reliable reference materials than spiked materials—the main difference is the chemical bounding which is crucial from the point of view of the bioavailability. The need of reference material is summarized according to the intended use, like quality control, measurement validation, and instrument calibration.