Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.     

Correlation of observed and model vibrational frequencies for aqueous organic acids: UV resonance Raman spectra and molecular orbital calculations of benzoic, salicylic, and phthalic acids

The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the pK(a)'s for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10(-4)M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.     

Molecular order and disorder of surfactants in clay nanocomposites

Disorder of intercalated surfactant molecules in clay minerals causes gradual swelling, rather than commonly assumed swelling in discrete steps.     

Ueber die Untersuchung von Drogen und den daraus hergestellten K?rpern

Ohne Zusammenfassung     

Hysteresis in clay swelling induced by hydrogen bonding: accurate prediction of swelling states

We perform grand-canonical molecular simulations to study the molecular mechanism of clay swelling hysteresis as a function of the relative humidity. In particular, we focus on the transition from the one- to the two-layer hydrate and the influence of three types of counterions (Li+, Na+, and K+). Our results cover the experimental relative humidity region where swelling and shrinking usually occur. We show that the thermodynamic origin of swelling hysteresis is a free-energy barrier separating the layered hydrates. This free-energy barrier is dominated by breaking and formation of hydrogen bonds between and within water layers. This network of water molecules is similar for all counterions, but the positions of these counterions depend upon their size. The relatively large K+ counterions show more affinity for clay surface adsorption, which increases the free-energy barrier and inhibits swelling. On the other hand, the relatively small Li+ counterions are quite well-accommodated in the water network, and thereby, they can form a new swelling state with a basal spacing of approximately 13.5 A. This new swelling state is an alternative explanation for the widely accepted simultaneous occurrence of two or more swelling phases.     

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AM1 atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino- s -triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, m 1.4, m 6.4 and 0.0 kcal/mol for PCB14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of m 5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM+ force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and m 0.7 (PPDDT) kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by m 3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.