Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

A Theoretical Investigation of the Ni(II)-Catalyzed Hydrovinylation of Styrene

We report a detailed and full computational investigation on the hydrovinylation reaction of styrene with the Ni(II)-phospholane catalytic system, which was originally presumed to proceed through a cationic mechanism involving a nickel hydride intermediate. The following general features emerge from this study on a specific catalyst complex that was found to give quantitative yield and moderate selectivity: (a) the activation barrier for the initiation (18.8 kcal/mol) is higher than that for the reaction due to a low-lying square-planar pentenyl chelate intermediate originating from a Ni(II)-allyl catalyst precursor. Consequently there is an induction period for the catalysis; (b) the exit of product from the catalyst is via a β-H-transfer step instead of the usual β-H elimination pathway, which has a very high activation energy due to a trans effect of the phospholane ligand; (c) the turnover-limiting and enantio- determining transition state is also the β-H-transfer; (d) because of the absence of a hydride intermediate, the unwanted isomerization of the product is prevented; (e) since the enantio-discrimination is decided at the H-transfer stage itself, the configuration of the product in a catalytic cycle influences the enantioselectivity in the subsequent cycle; (f) the trans effect of the sole strong ligand in the d8 square-planar Ni(II), the stability of the η3-benzyl intermediate, and the availability of three coordination sites enable regioselective hydrovinylation over the possible oligomerization/polymerization of the olefin substrates and linear hydrovinylation. This work has also confirmed the previously recognized role of the hemilabile group at various stages in the mechanism.

Structures of mannose-6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: implications for catalytic mechanism

Mannose-6-phosphate isomerase (MPI) catalyzes the inter-conversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism. Isomerization involves acid/base catalysis with proton transfer between the C1 and C2 atoms of the substrate. His99, Lys132, His131 and Asp270 are close to the substrate and are likely to be the residues involved in proton transfer. The interactions observed at the active site suggest that the ring-opening step is probably catalyzed by His99 and Asp270. An active-site loop consisting of residues 130-133 undergoes conformational changes upon substrate binding. Zn2+ binding induces structural order in the loop consisting of residues 50-54. The metal atom appears to play a role in substrate binding and is probably also important for maintaining the architecture of the active site. Isomerization probably follows the previously suggested cis-enediol mechanism.

beta.-Turn conformation of N-acetyl-L-prolylglycyl-L-phenylalanine. Crystal structure and solution studies

Pro-Gly segments in peptides and proteins are prone to adopt the 0-turn conformation. This paper reports experimental data for the presence of this conformation in a linear tripeptide N-acetyl-L-prolylglycyl-L-phenylalanineb oth in the solid state and in solution. X-ray diffraction data on the tripeptide crystal show that it exists in the type I1 0-turn conformation. CD and proton NMR data show that this conformation persists in trifluoroethanol and methanol solutions in equilibrium with the nonhydrogen-bonded structures. Isomerization around the acetyl-prolyl bond is seen to take place in dimethyl sulfoxide solutions of the tripeptide.

Novel photoisomerization of spirodienones

Spironaphthalenones of the type (Image ) have been demonstrated to undergo isomerization to (Image ) upon UV irradiation.

Epigallocatechin gallate is a slow-tight binding inhibitor of enoyl-ACP reductase from Plasmodium falciparum

Epigallocatechin gallate (EGCG) is known to have numerous pharmacological properties. In the present study, we have shown that EGCG inhibits enoyl–acyl carrier protein reductase of Plasmodium falciparum (PfENR) by following a two-step, slow, tight-binding inhibition mechanism. The association/isomerization rate constant (k5) of the reversible and loose PfENR–EGCG binary complex to a tight [PfENR–EGCG]* or EI* complex was calculated to be 4.0 × 10−2 s−1. The low dissociation rate constant (k6) of the [PfENR–EGCG]* complex confirms the tight-binding nature of EGCG. EGCG inhibited PfENR with the overall inhibition constant (Ki*) of 7.0 ± 0.8 nM. Further, we also studied the effect of triclosan on the inhibitory activity of EGCG. Triclosan lowered the k6 of the EI* complex by 100 times, lowering the overall Ki* of EGCG to 97.5 ± 12.5 pM. The results support EGCG as a promising candidate for the development of tea catechin based antimalarial drugs.

Studies in oxasteroids—I : Synthesis of 3-cyano-3-methyl-7-methoxychroman-4-one and the structure of an “abnormal” product

A synthesis of 3-cyano-3-methyl-7-methoxychroman-4-one is reported. The structure of an “abnormal” product obtained during isomerization (III) with potassium t-butoxide in t-butanol, followed by alkylation with methyl iodide has been proved to be 3-t-butoxy-2-cyano- 2-mehthyl-2′,4′-dimethoxypropiophenone (IVa).

Comparison of promoter-specific events during transcription initiation in mycobacteria

DNA protein interactions that occur during transcription initiation play an important role in regulating gene expression. To initiate transcription, RNA polymerase (RNAP) binds to promoters in a sequence-specific fashion. This is followed by a series of steps governed by the equilibrium binding and kinetic rate constants, which in turn determine the overall efficiency of the transcription process. We present here the first detailed kinetic analysis of promoter RNAP interactions during transcription initiation in the sigma(A)-dependent promoters P-rrnAPCL1, P-rrnB and P-gyr of Mycobacterium smegmatis. The promoters show comparable equilibrium binding affinity but differ significantly in open complex formation, kinetics of isomerization and promoter clearance. Furthermore, the two rrn promoters exhibit varied kinetic properties during transcription initiation and appear to be subjected to different modes of regulation. In addition to distinct kinetic patterns, each one of the housekeeping promoters studied has its own rate-limiting step in the initiation pathway, indicating the differences in their regulation.

Organometallic chemistry of diphosphazanes *1: VIII. Synthesis, spectroscopic studies and crystal structure of fac-[Mo(CO)3(MeCN)Ph2PN(iPr)P(Ph)(DMP)], and its reactions with tertiary phosphines

The reaction of fac-[Mo(CO)3(MeCN)3] with the unsymmetrical diphosphazane Ph2PN(iPr)P(Ph)(DMP) (L) gives the complex fac-[Mo(CO)3(MeCN)(L)] (2) in almost quantitative yield. The structure of the complex has been determined by an X-ray diffraction study. The compound reacts with PR3 (where R = Ph, OPh) to give fac-[Mo(CO)3(PR3)(L)] (3a, 4a), which undergoes an intramolecular isomerization to afford mer-[Mo(CO)3(PR3)(L)] (3b, 4b). Synthesis of cis-[Mo(CO)4(L)] (1) and fac-[MO(CO)3L] (2a) and their spectroscopic data are also reported.

Isomerisation of 1-methylene-2-methyl-2-(2-oxopropyl)-cyclohexanes to 2-methylene-1-methyl-1-(2-oxopropyl)-cyclohexanes by ene and retro-ene reaction

Thermal activation of the normal Claisen products, the enones 4 7 and 14 in the presence of a catalytic amount of propionic acid generated the isomeric enones 6 9 and 15 via the sequential intramolecular ene-reaction of the enol tautomer followed by 1,5-hydrogen transfer (or retro ene-reaction) of the resultant acetyl cyclopropane intermediate. conversion of the enones 9 and 15 into the corresponding cyclohexenones 10 and 16 established the structures of the rearrangement products.

Photochemistry of benzylidene-d,l-piperitones in solution and the melt phase

The solution- and melt-phase photochemistry of four trans-benzylidene-d,l-piperitones (1) has been investigated under a variety of conditions. The 1 undergo trans reversible cis isomerization to establish a quasi photostationary state. Further irradiation leads to 2 via oxidative ring closure. Conspicuously absent are dimers (obtained upon irradiation of the neat crystals) and the plausible Norrish Type II photoproducts, 3. Although 1c yields 2c, no evidence for the alternative cyclization route to 2a (requiring loss of HCl) has been observed. Rationalizations for the transformations are presented. The structure of 2b has been determined unambiguously from X-ray crystallographic analysis.

Organometallic Chemistry of Diphosphazanes. 11. Reactions of fac-[Mo(CO)3(MeCN){.eta.2-Ph2PN(Pri)PPh(DMP)}] (DMP = 3,5-Dimethyl-1-Pyrazolyl) with Diphosphazanes and Diphosphinoalkanes and Oxidative Addition with Iodine

The use of fac-[Mo(CO)(3)(MeCN)(eta(2)-L(1))] (1a) {L(1) = Ph(2)PN(Pr-i)PPh(DMP)}(2) as a precursor to metalloligands and bimetallic, heterotrimetallic, and heptacoordinated complexes is reported. The reaction of 1a with diphosphazane, dppa, or a diphosphinoalkane such as dppm or dppe yields the fac-eta(1)-diphosphine substituted metalloligands, fac-[Mo(CO)(3)(eta(2)-L(1))(eta(1)-PXP)] {PXP = dppa (2), dppm (3), and dppe (4)}. These undergo isomerization to yield the corresponding mer-diphosphine complexes (5-7). Oxidation of the uncoordinated phosphorus atom of the mer-eta(1)-dppm-substituted complex eventually provides mer-[Mo(CO)(3)-(eta(2)-L(1)){eta(1)-Ph(2)PCH(2)P(O)Ph(2)}](8). The structure of the latter complex has been confirmed by single crystal X-ray diffraction {triclinic system, P ($) over bar 1; a = 11.994(3), b = 14.807(2), c = 15.855(3) Angstrom; alpha = 114.24(1), beta = 91.35(2), and gamma = 98.95(1)degrees; Z = 2, 4014 data (F-0 > 5 sigma(F-0)), R = 0.066, R(W) = 0.069}. Treatment of the dppe metalloligand 7 with [PtCl2(COD)] yields the heterotrimetallic complex cis-[PtCl2{mer-[Mo(CO)(3)(eta(2)-L(1))(eta(1)-dppe]}(2)] (9). Attempts to prepare a related trimetallic complex with the dppm-containing metalloligand were unsuccessful; only the tetracarbonyl complex cis-[Mo(CO)(4)(eta(2)-L(1))] (1b) and cis-[PtCl2(eta(2)-dppm)] were obtained. Reaction of la with dppe in the ratio 2:1 yields the mer-mer dinuclear complex [{mer-[Mo(CO)(3)(eta(2)-L(1))]}(2)(mu-dppe)] (10) bridged by dppe. Oxidation of 1a with iodine yields the Mo(II) heptacoordinated complex [MoI2(CO)(2)(eta(3)-L(1))] (11) with tridentate PPN coordination. The same Mo(II) complex 11 is also obtained by the direct oxidation of the tetracarbonyl complex cis-[Mo(CO)(4)(eta(2)-L(1))] (1b) with iodine. The structure of 11 has been confirmed by X-ray diffraction studies {monoclinic system, Cc; a = 10.471(2), b = 19.305(3), c = 17.325(3) Angstrom; beta = 95.47(2)degrees; Z = 4, 3153 data (F-0 > 5 sigma(F-0)), R = 0.049, R(W) = 0.051}. This complex exhibits an unusual capped-trigonal prismatic geometry around the metal. A similar heptacoordinated complex 12 with a chiral diphosphazane ligand {L(3) = (S,R)-P(h)2PN-(*CHMePh)*PPh(DMP)} has also been synthesized.

Transformation of dehydroepiandrosterone and pregnenolone by Mucor piriformis

The mode of transformation of dehydroepiandrosterone (I, 3 beta-hydroxyandrost-5-en-17-one) and pregnenolone (II, 3 beta-hydroxypregn-5-en-20-one) was studied using Mucor piriformis. Biotransformation products formed from I were 3 beta,17 beta-dihydroxyandrost-5-ene (Ia), 3 beta-hydroxyandrost-5-ene-7,17-dione (Ib), 3 beta,17 beta-dihydroxyandrost-5-en-7-one (Ic), 3 beta,7 alpha-dihydroxyandrost-5-en-17-one (Id) and 3 beta,7 alpha,17 beta-trihydroxyandrost-5-ene (Ie). Biotransformation products formed from compound II were 3 beta,7 alpha-dihydroxypregn-5-en-20-one (IIa) and 3 beta,7 alpha,11 alpha-trihydroxypregn-5-en-20-one (IIb). The organism did not carry out isomerization of the 5-en-3 beta-ol to a 4-en-3-one system in the steroid molecules tested. In addition, it failed to carry out 14 alpha-hydroxylation possibly because of the lack of a 4-en-3-one system in I and II, and stereospecific hydroxylation at the C-7 position in I and II.

Wavepacket dynamical studies on trans-azobenzene: absorption spectrum and resonance Raman excitation profiles of the n??* transition

Time-dependent wavepacket propagation techniques have been used to calculate the absorption spectrum and the resonance Raman excitation profiles of the n-pi* transition in azobenzene. A comparison of both the calculated absorption spectrum and excitation profiles with experiment has been made. From an analysis of the data, it is concluded that the Raman intensities are mainly due to resonance from the n-pi* transition and not from the pre-resonance of the pi-pi* transition, as reported earlier. We find that the isomerization pathway is through the inversion mechanism rather than by rotation. This is the first direct spectroscopic evidence for the isomerization pathway in trans-azobenzene.

Chemistry of dihydrogen complexes containing only phosphorus co-ligands

A series of new dicationic dihydrogen complexes of ruthenium of the type cis-[(dppm)(2)Ru(eta(2)-H-2)(L)][BF4](2) (dppm = Ph2PCH2PPh2; L = phosphite) have been prepared by protonating the precursor hydride complexes cis-[(dPPM)(2)Ru(H)(L)][BF4] using HBF4.Et2O. The precursor hydride complexes have been obtained from trans-[(dppm)(2)Ru(H)(L)][BF4][(L = phospfiite) via a rare acid-catalysed isomerization reaction in six coordinate species. The trans-[(dppm)(2)Ru(H)(L)][BF4] complexes (L = phosphine) upon protonation gave the isomerized derivatives, however, further addition of acid resulted in a five-coordinate species, [(dppm)(2)RuCl](+) presumably via an intermediate phosphine dihydrogen complex. The electronic as well as the steric properties of the co-ligands seem to strongly influence the structure-reactivity behaviour of this series of complexes.