The inclusion of electrostatic hydration energies in molecular mechanics calculations

Summary The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.     

THE 'OPSIN SHIFT' IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS

Abstract— The difference (in cm⁻¹) in absorption maxima between the protonated Schiff base of retinals and the pigment derived therefrom has been defined as the opsin shift. It represents the influence of the opsin binding site on the chromophore. The analysis of the opsin shifts of a series of dihydrobacteriorhodopsins has led to the external point-charge model, which in addition to a counter anion near the Schiff base ammonium, carries another negative charge in the vicinity of the β-ionone ring. This is in striking contrast to the external point-charge model proposed earlier for the bovine visual pigment. The absorption maxima of rhodopsins formed from bromo- and phenyl retinals support the two models. A retinal carrying a photoaffinity label has yielded a nonbleachable bacteriorhodopsin.     

Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.     

Einige bestrahlungsexperimente mit 2, 1-Benzisothiazolen

Some Irradiation Experiments with 2, 1-Benzisothiazoles 2, 1-Benzisothiazole ( 1 ) on irradiation with a mercury high-pressure lamp in benzene/diethylamine yields, after acetylation, 2-acetylamino-benzaldehyde ( 3 ; Scheme 1). Similarly, irradiation of 3-chloro-2, 1-benzisothiazole ( 2 ) in benzene/diethylamine leads to a mixture of 3-dimethylamino-2, 1-benzisothiazole ( 6a ) and N, N-diethyl-thioanthranilamide ( 7a ; Scheme 2). Benzisothiazole 6a , on irradiation, is not transformed into 7a . On the other hand, when 2 is irradiated in methanol a mixture of 3-methoxy-2, 1-benzisothiazole ( 4a ) and methyl anthranilate ( 5a ; Scheme 2) is obtained. In this case, 4a on irradiation in methanol or ethanol also yields 5a . No exchange of the methoxy group in 4a is observed when the irradiation is performed in ethanolic solution. Thus, 2, 1-benzisothiazoles 1 , 2 and 4a react photochemically by N,S-bond cleavage and hydrogen-atom abstraction from the solvent (Scheme 3). 3-Chloro-2, 1-benzisothiazole ( 2 ) shows a second photoreaction, i.e. nucleophilic exchange of the chloro substituent by methanol or diethyl amine. The latter reaction can also be observed thermally, e.g. in boiling methanol in the presence of methoxide ions.     

Toward the development of new photolabile protecting groups that can rapidly release bioactive compounds upon photolysis with visible light

The synthesis and characterization of a new photolabile protecting group (caging group) for carboxylic acids, the 2-(dimethylamino)-5-nitrophenyl (DANP) group, is described. This compound has a major absorption band in the visible wavelength region with a maximum near 400 nm (epsilon400 = 9077 M(-1) cm(-1) at pH 7.4 and 21 degrees C). The caging group is attached through an ester linkage to the carboxyl functionality of beta-alanine, which activates the inhibitory glycine receptor in the mammalian central nervous system. Such caged compounds play an important role in transient kinetic investigations of fast cellular processes. Upon photolysis of DANP-caged beta-alanine, the caging group is released within 5 micros. Quantum yields of 0.03 and 0.002 were obtained in the UV region (308 and 360 nm) and the visible region (450 nm), respectively. Laser-pulse photolysis experiments, using 337 or 360 nm light, were performed with the caged compound equilibrated with HEK 293 cells transiently transfected with cDNA encoding the alpha1 homomeric, wild-type glycine receptor. The experiments demonstrated that neither DANP-caged beta-alanine nor its byproducts inhibit or activate the glycine receptors on the cell surface. Under physiological conditions, the DANP-caged beta-alanine is water-soluble and stable and can be used for transient kinetic measurements.     

Pd-catalyzed asymmetric allylic alkylation. A short route to the cyclopentyl core of viridenomycin

A palladium-catalyzed asymmetric allylic alkylation effects a dynamic kinetic asymmetric transformation of racemic isoprene monoepoxide and a surrogate for Nazarov's reagent in which a quaternary center is created with exellent ee. The resultant adduct allows easy access to a substrate for ring-closing metathesis to form a cyclopentenone and sets the stage for an 11-step synthesis of the cyclopentyl core of the antibiotic antitumor agent viridenomycin. [reaction: see text]     

Lipophilicity in PK design: methyl, ethyl, futile

Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume of distribution. However, more lipophilic compounds also become more vulnerable to P450 metabolism, leading to higher clearance. Molecular size and hydrogen bonding capacity are two other properties often considered as important for membrane permeation and pharmacokinetics. Interrelationships among these physicochemical properties are discussed. Increasing size (molecular weight) often gives higher potency, but inevitably also leads to either higher lipophilicity, and hence poorer dissolution/solubility, or to more hydrogen bonding capacity, which limits oral absorption. Differences in optimal properties between gastrointestinal absorption and uptake into the brain are addressed. Special attention is given to the desired lipophilicity of CNS drugs. In examples using -blockers, Ca channel antagonists and peptidic renin inhibitors we will demonstrate how potency and pharmacokinetic properties need to be balanced.     

Porous nanocomposites of zirconium dioxide and silicate

Highly porous nanocomposites of zirconium dioxide and silicate are synthesised in an aqueous system from an inorganic salt of zirconium; the nanacomposites, with tailorable pore structures, exhibit superior performance as catalyst supports.     

Asymmetric Michael addition of glycine imines via quaternary ammonium ion catalysis

The asymmetric Michael addition of glycine imine esters to simple α,β-unsaturated ketones via PTC is investigated. It is found that by employing 1 mol % of a chiral quaternary ammonium salt, derived from α-methylnaphthylamine in conjunction with Cs₂CO₃, high enantioselectivities can be obtained in conjugate additions involving simple alkylvinylketones.