Unsteady axisymmetric stagnation flow on a circular cylinder

Unsteady, axisymmetric stagnation flow about a circular cylinderis examined when the far-field flow is a periodic function oftime with a fixed time average and an oscillatory part of prescribedamplitude and frequency. Solutions are computed for arbitraryvalues of the Reynolds number, quantifying the effects of surfacecurvature, and a frequency parameter based on the period ofthe far-field flow. It is found that solutions remain regularand periodic provided that the far-field amplitude lies belowa critical value. Above this value, solutions terminate in afinite-time singularity. The blow-up time is delayed by increasingthe curvature of the surface. These results are corroboratedby asymptotic predictions valid in the limits of small and largeamplitude and frequency. For large Reynolds number, the problemreduces to the two-dimensional stagnation-point flow againsta plane wall studied by previous authors.     

The structure of the enzyme-substrate complex of the phosphodiesterase catalytic domain with cyclic diguanosine monophosphate

A three-dimensional, all-atom structure of the enzyme-substrate complex of the phosphodiesterase catalytic domain with diguanosine monophosphate was constructed based on the results of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations.     

Polyethylene glycol matrix reduces the rates of photochemical and thermal release of nitric oxide from S-nitroso-N-acetylcysteine

S -nitrosothiols have many biological activities and may act as nitric oxide (NO) carriers and donors, prolonging NO half-life in vivo. In spite of their great potential as therapeutic agents, most S -nitrosothiols are too unstable to isolate. We have shown that the S -nitroso adduct of N -acetylcysteine (SNAC) can be synthesized directly in aqueous and polyethylene glycol (PEG) 400 matrix by using a reactive gaseous (NO/O₂) mixture. Spectral monitoring of the S–N bond cleavage showed that SNAC, synthesized by this method, is relatively stable in nonbuf-fered aqueous solution at 25°C in the dark and that its stability is greatly increased in PEG matrix, resulting in a 28-fold decrease in its initial rate of thermal decomposition. Irradiation with UV light (λ= 333 nm) accelerated the rate of decomposition of SNAC to NO in both matrices, indicating that SNAC may find use for the photogeneration of NO. The quantum yield for SNAC decomposition decreased from 0.65 ± 0.15 in aqueous solution to 0.047 ± 0.005 in PEG 400 matrix. This increased stability in PEG matrix was assigned to a cage effect promoted by the PEG microenvironment that increases the rate of geminated radical pair recombination in the homolytic S–N bond cleavage process. This effect allowed for the storage of SNAC in PEG at −20°C in the dark for more than 10 weeks with negligible decomposition. Such stabilization may represent a viable option for the synthesis, storage and handling of S -nitrosothiol solutions for biomedical applications.     

Supercomputer technologies for structural-kinetic study of mechanisms of enzyme catalysis: A quantum-chemical description of aspartoacylase catalysis

The results of modeling of the complete catalytic cycle of aspartoacylase-catalyzed N-acetylaspartate hydrolysis by the combined quantum mechanics/molecular mechanics method and with the use of umbrella sampling replica-exchange molecular dynamics simulations are reported. It has been shown that the decrease in the high-energy barriers of rate-limiting stages is achieved through the preceding equilibrium stages, such as proton transfer and conformational changes. General features of the catalytic behavior of enzymes have been formulated.     

Quantum chemical modeling of components of dye-sensitized solar cells

Ab initio approaches of quantum chemistry, including the fragment molecular orbital (FMO) method, as well as the multiconfigurational quasidegenerate perturbation theory (XMCQDPT2) and time-dependent density functional theory (TD DFT) were applied to compute optical spectra of a polyene dye molecule on the surface of titanium dioxide.     

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase‐2 (MMP‐2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all‐atom three‐dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace‐Gln‐Gly～Ile‐Ala‐Gly‐Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four‐step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C? N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate‐limiting step in MMP‐2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations. © 2015 Wiley Periodicals, Inc.     

Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases

Structural Chemistry - In this work, we focus on some structural aspects of enzyme catalysis by modeling effects of the electrostatic potential created by the solvation water shells on properties...     

Structure and dynamics of photoactivatable adenylyl cyclase

Russian Chemical Bulletin - The full-atom 3D model of the dimer of the photoregulated adenylyl cyclase is constructed. It contains a molecule of flavin mononucleotide chromophore in the...