Dynamics of proton transfer in bacteriorhodopsin

Proton transfer in bacteriorhodopsin from the cytoplasm to the extracellular side is initiated from protonated asp96 in the cytoplasmic region toward the deprotonated Schiff base. This occurs in the transition from the photocycle late M state to the N state. To investigate this proton-transfer process, a quantum mechanics/molecular mechanics (QM/MM) model is constructed from the bacteriorhodopsin E204Q mutant crystal structure. Three residues, asp96, asp85, and thr89, as well as most of the retinal chromophore and the Schiff base link of lys216 are treated quantum mechanically and connected to the remaining classical protein through linker atom hydrogens. Structural transformation in the M state results in the formation of a water channel between the Schiff base and asp96. Since a part of this channel is lined with hydrophobic residues, there has been a question on the mechanism of proton transfer in a hydrophobic channel. Ab initio dynamics using the CHARMM/GAMESS methodology is used to simulate the transfer of the proton through a partially hydrophobic channel. Once sufficient water molecules are added to the channel to allow the formation of a single chain of waters from asp96 to the Schiff base, the transfer occurs as a fast (less than a picosecond) concerted event irrespective of the protonation state of asp85. Dynamic transfer of the proton from asp96 to the nearest water initiates the organization of a strongly bonded water chain conducive to the transfer of the proton to the Schiff base nitrogen.     

A Mild Isomerization Reaction for β,γ‐Unsaturated Ketone to α,β‐Unsaturated Ketone

A series of β,γ‐unsaturated ketones were isomerized to their corresponding α,β‐unsaturated ketones by the introduction of DABCO in iPrOH at room temperature. The endo‐cyclic double bond (β,γ‐position) on ketone was rearranged to exo‐cyclic double bond (α,β‐position) under the reaction conditions.     

Capillary electrophoresis of cardiolipin with on-line dye interaction and spectrophotometric detection

Cardiolipin is an important phospholipid present in the mitochondrial inner membrane. It plays a key function in mitochondrial respiration by interacting with many enzymes or cofactors related to oxidative phosphorylation complexes. We have determined the concentration of cardiolipin using on-line 10-N-nonyl acridine orange (NAO) dye interaction capillary electrophoresis (CE) and spectrophotometric detection with a sample throughput of 3 min. In addition to the presence of 0.1 mM NAO, the background electrolyte (BGE) composition has been set at 80% methanol-10% acetonitrile-10% H(2)O (all v/v) to provide both good solubility and the maximum absorbance enhancement at 497 nm for the NAO-cardiolipin complex as compared to NAO alone. Sample consumption for each injection is about 57 nL. A calibration curve is established from 0.5 microM to 0.1 mM with R (2) = 0.9912 with a detection limit of 0.05 microM for cardiolipin. In a blind study, actual mitochondrial cell membrane samples in the microL range before or after UV light exposure were analyzed using the CE method. Cardiolipin concentration decreased in the different parts of the membrane sample upon UV photolysis of the cells. Support for the theory that UV light can induce cardiolipin translocation from the inner membrane (IM) to the outer membrane (OM) was indicated by a significant percentage increase of cardiolipin (as measured by the cardiolipin in the OM as compared to the sum total in the OM and IM) from 30.7 +/- 2.4% before UV light photolysis to 38.3 +/- 2.2% after UV irradiation.     

Experimental and theoretical studies of rate coefficients for the reaction O(3P)+CH3OH at high temperatures

Rate coefficients of the reaction O((3)P) + CH(3)OH in the temperature range of 835-1777 K were determined using a diaphragmless shock tube. O atoms were generated by photolysis of SO(2) with a KrF excimer laser at 248 nm or an ArF excimer laser at 193 nm; their concentrations were monitored via atomic resonance absorption excited by emission from a microwave-discharged mixture of O(2) and He. The rate coefficients determined for the temperature range can be represented by the Arrhenius equation, k(T) = (2.29 +/- 0.18) x 10(-10) exp[-(4210 +/- 100)T] cm(3) molecule(-1) s(-1); unless otherwise noted, all the listed errors represent one standard deviation in fitting. Combination of these and previous data at lower temperature shows a non-Arrhenius behavior described as the three-parameter equation, k(T) = (2.74 +/- 0.07) x 10(-18)T(2.25 +/- 0.13) exp[-(1500 +/- 90)T] cm(3)molecule(-1) s(-1). Theoretical calculations at the Becke-3-Lee-Yang-Parr (B3LYP)6-311 + G(3df,2p) level locate three transition states. Based on the energies computed with coupled clusters singles, doubles (triples) [CCSD(T)]/6-311 + G(3df,2p)B3LYP6-311 + G(3df,2p), the rate coefficients predicted with canonical variational transition state theory with small curvature tunneling corrections agree satisfactorily with the experimental observations. The branching ratios of two accessible reaction channels forming OH + CH(2)OH (1a) and OH + CH(3)O (1b) are predicted to vary strongly with temperature. At 300 K, reaction (1a) dominates, whereas reaction (1b) becomes more important than reaction (1a) above 1700 K.     

Structure and electronic structure of polyacene

It is shown that infinite long polyacene chains may have three energetically close but structurally distinct isomers (a symmetrical, sym, form and two lower symmetry forms: one with double bonds in a trans and another isomer with double bonds in a cis pattern). The energetics is based on solid state MNDO theory. We discuss that the symmetrical form has a substantial energy gap E_g in the Hartree–Fock approach owing to exact exchange terms, which are nonlocal. Broken symmetry Hartree–Fock (HF ) solutions for polyacene are also described. An angularly distorted structure suggested earlier on Jahn–Teller grounds is found to be energetically not favorable.     

AuCl(3)-catalyzed benzannulation: synthesis of naphthyl ketone derivatives from o-alkynylbenzaldehydes with alkynes

The reaction of o-alkynylbenzaldehydes 1 and alkynes 2 in the presence of a catalytic amount of AuCl3 in (CH2Cl)2 at 80 degrees C gave naphthyl ketone products in high yields. The AuCl3-catalyzed formal [4 + 2] benzannulation proceeds most probably through the coordination of the triple bond of 1 to AuCl3, the formation of benzo[c]pyrylium auric ate complex via the nucleophilic addition of the carbonyl oxygen atom, the Diels-Alder addition of alkynes 2 to the auric ate complex, and subsequent bond rearrangement. Similarly, the AuCl3-catalyzed reactions of o-alkynylacetophenone and o-alkynylbenzophenone with phenylacetylene afforded the corresponding naphthyl ketone products in good yields.     

Dry etching of InGaP and AlInP in CH4/H2/Ar

Electron cyclotron resonance (ECR) plasma etching with additional rf-biasing produces etch rates 2,500 A/min for InGaP and AlInP in CH₄/H₂/Ar. These rates are an order of magnitude or much higher than for reactive ion etching conditions (RIE) carried out in the same reactor. N₂ addition to CH₄/H₂/Ar can enhance the InGaP etch rates at low flow rates, while at higher concentrations it provides an etch-stop reaction. The InGaP and AlInP etched under ECR conditions have somewhat rougher morphologies and different stoichiometries up to 200 Å from the sur face relative to the RIE samples.     

Asymmetric Synthesis of Calyculin C. 2. Synthesis of the C(26)-C(37) Fragment and Model Wittig Couplings

We report our synthesis of the C(26)-C(37) fragment of serine/threonine protein phosphatase PP1 and PP2A inhibitor calyculin C (1). Outlined in this paper are synthetic approaches to the two components based on disconnection at the C(33)-N(3) amide bond. We report the successful synthesis of the C(33)-C(37) aza-sugar derived from D-lyxose which was coupled onto a C(26)-C(32) aminooxazole originating from L-pyroglutamic acid. Elaboration of the resulting amide to a fully deprotected C(26)-C(37) fragment of calyculin C completed our synthesis. This provided an appropriate phosphonium salt for use in a Wittig olefination for joining both halves of the natural product.