Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

The potentials of mean force of 21 heterodimers of the molecules modeling hydrophobic amino acid side chains: ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), methyl propyl sulfide (for methionine), and indole (for tryptophane) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay-Berne term to represent effective van der Waals interactions and the cavity term proposed in our earlier work were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, are well represented by the analytical expressions for all systems; large deviations between the MD-determined PMF and the analytical approximations are observed for pairs involving the least spheroidal solutes: ethylbenzene, indole, and methyl propyl sulfide at short distances at which the PMF is high and, consequently, these regions are rarely visited. When data from the PMF within only 10 kcal/mol above the global minimum are considered, the standard deviation between the MD-determined and the fitted PMF is from 0.25 to 0.55 kcal/mol (the relative standard deviation being from 4% to 8%); it is larger for pairs involving nonspherical solute molecules. The free energies of contact computed from the PMF surfaces are well correlated with those determined from protein-crystal data with a slope close to that relating the free energies of transfer of amino acids (from water to n-octanol) to the average contact free energies determined from protein-crystal data. These observations justify future use of the determined potentials in coarse-grained protein-folding simulations.     

Thioperoxy derivative generated by UV-induced transformation of N-hydroxypyridine-2(1H)-thione isolated in low-temperature matrixes

Photochemical transformations of N-hydroxypyridine-2(1H)-thione and its deuterated isotopologue were studied using the matrix-isolation technique. Low-temperature Ar and N2 matrixes containing monomers of this compound were irradiated with continuous-wave near-UV light. Photogeneration of two products was observed in these experiments. The relative population of these photogenerated species was found to be dependent on the wavelength of the UV light used for irradiation. By comparison of the IR spectra of the photoproducts with the spectra simulated theoretically at the DFT(B3LYP)/6-311++G(d, p) level, the final and the intermediate products were identified as rotameric forms of 2-hydroxysulfanyl-pyridine. This is the first report on generation of this thioperoxy derivative of pyridine. The mechanism of photogeneration of 2-hydroxysulfanyl-pyridine involves a photoinduced cleavage of the N-O bond in N-hydroxypyridine-2(1H)-thione, generation of the .OH radical weakly bound with the remaining pyridylthiyl radical, and recombination of these two radicals by formation of the new -S-O- bond. A theoretical model supporting this interpretation was constructed on the basis of approximate coupled cluster (CC2) calculations of the potential energy surfaces of the ground and first excited singlet electronic states of the system. After electronic excitation of the monomeric N-hydroxypyridine-2(1H)-thione, the molecule evolves to the conical intersection with the potential energy surface of the ground state and then to the global minimum corresponding to 2-hydroxysulfanyl-pyridine.     

Contributions to photodoping in oxygen-deficient YBa2Cu3Ox films

We report our studies on the superconducting and normal-state properties of metallic thin films ( 52 K) exposed to long-term white-light illumination (photodoping). It was observed that the effects of photoexcitation strongly depended on the temperature at which the photodoping was performed. At low temperatures, both the Hall mobility and the Hall number were photoenhanced, whereas, at temperatures slightly below room temperature, the Hall mobility initially showed an abrupt increase followed by a long-term decrease, and the Hall number increased even stronger than at low temperatures. The enhancement of the film's superconducting transition temperature T_c, caused by photodoping, exhibited the same temperature dependence as the enhancement of the Hall number, being largest ( 2.6 K) at high temperatures. From the asynchronous behavior of the Hall quantities, we conclude that both the photoassisted oxygen ordering and charge transfer mechanisms contribute to photodoping. The relative contributions of both mechanisms and, thus, the electronic properties of the photoexcited state are strongly temperature dependent. Studies of the relaxation of the photoexcited state at 290 K showed an unexpectedly short relaxation time of the Hall mobility after termination of the illumination. The relaxation saturated somewhat below the initial, undoped value, similarly to the decrease of the Hall mobility, observed upon long illumination. These latter findings give evidence for a competition between the oxygen ordering and thermal disordering processes during and after the photoexcitation in the high-temperature range. Received: 13 October 1997 / Accepted: 19 November 1997     

Concerted and stepwise proton-coupled electron transfers in aquo/hydroxo complex couples in water: oxidative electrochemistry of [Os(II)(bpy)(2)(py)(OH(2))](2+)

Successive oxidation of transition metal(II) aqua complexes (M(II)OH(2) to M(III)OH) is a domain in which proton-coupled electron transfer reactions are extremely common. The mechanism of these PCET reactions-concerted or stepwise-is an important issue in the understanding and design of natural or artificial systems catalyzing the formation of dioxygen by four-electron oxidation of water. Concerted proton-coupled electron transfer from an aqua metal(II) to a hydroxo metal(III) complex requires the close proximity of a proton-accepting group with a pK value between those of the aqua complexes. Otherwise, stepwise electron-proton or proton-electron pathways involving high-energy intermediates are followed. Concerted proton-electron pathways involving water as proton-acceptor or proton-donor group are inefficient. Cyclic voltammetry of the title complex in buffered aqueous solution and re-examination of previous results for the same complex attached to an electrode surface are used to establish these conclusions, which provide a starting point on the route to higher degrees of oxidation, such as those involved in the catalysis of water oxidation.     

Photoisomerizations of N4-hydroxycytosines

A series of N4-hydroxycytosines, unsubstituted or substituted with methyl groups at N3 or C5 atoms of the heterocyclic ring, was studied using the matrix-isolation method. Depending on the absence or presence of the methyl substituent at N3 or C5 atoms (or at both of them) the syn or anti form of the compounds (or a mixture of both forms) was trapped from the gas phase into a low-temperature matrix. Upon UV (lambda > 295 nm) irradiation of the matrixes the syn --> anti as well as the anti --> syn photoisomerization reactions were observed. The syn and anti isomers of N4-hydroxycytosines were identified by comparing their experimental IR spectra with the theoretical spectra calculated at the DFT(B3LYP)/6-31G(d,p) level. For the majority of the studied compounds, the UV induced reactions led to a photostationary state. The position of the final photostationary state was found to be a sensitive function of weak interactions of a studied N4-hydroxycytosine with the matrix environment: solid argon or solid nitrogen. However, not all of the studied photoisomerizations led to a classical photostationary state. For some of the investigated N4-hydroxycytosines, the position of the photostationary state was shifted very strongly in favor of the photoproduct, whereas for some others the position was shifted so strongly in favor of the starting isomer that no photoisomerization was observed. These experimental findings were elucidated by theoretical investigations of the potential energy surfaces of the ground (S0) and first excited (S1) electronic states of N4-hydroxycytosine. The crucial result of these calculations (carried out at the CASSCF level) was the localization of a conical intersection between S0 and S1 at a structure with perpendicular orientation of the hydroxylimino group with respect to the heterocyclic ring.     

Investigation of structural and electronic properties of β- HgS: Molecular dynamics simulations

The pressure induced phase transition of β-HgS is studied using an ab initio molecular dynamics simulation. The structural phase transformation from the zinc-blende structure to the NaCl-type structure (space group $Fm\overline{3}m$) and from this structure to CsCl-type structure ($Pm\overline{3}m$) with the application of hydrostatic pressure is predicted. Additionally, the electronic properties of HgS and various physical properties such as the lattice constants, the bulk modulus and the pressure derivative of the bulk modulus are revealed. Furthermore, these phase transitions are obtained using the total energy and enthalpy calculations. According to these calculations these transformations are occurring at about 20?GPa and 28?GPa for $F\overline{4}3m$ →$Fm\overline{3}m$ and $Fm\overline{3}m$ →$Pm\overline{3}m$, respectively.