Temperature weighted histogram analysis method, replica exchange, and transition paths

We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to determine the potential of mean force in the transition region between a minor alpha-helical population and the major beta-hairpin population and identify a possible transition path between them along which the peptide retains a significant amount of secondary structure. This observation provides new insights into a possible mechanism of formation of beta-sheet secondary structures in proteins. We developed a novel Bayesian statistical uncertainty estimation method for any quantity derived from WHAM and used it to validate the calculated potential of mean force. The feasibility of estimating regions of the potential of mean force with unfavorable free energy at room temperature by T-WHAM analysis of replica exchange simulations was further tested on a system that can be solved analytically and presented some of the same challenges found in more complex chemical systems.     

The synthesis and characterization of α- and β-1, 1-diiodo-3,4-benzo-1-telluracyclopentane,C8H8Tel2

Elemental Tellurium reacts with α,α′-dichloro-o-xylene and NaI in 2-methoxyethanol to form 1,1-diiodo-3,4-benzo-1-telluracyclopentane in 83% yield. C₈H₈TeI₂ is molecular in acetone, methylene chloride and methyl ethyl ketone, but ionic in DMF. Two crystalline modifications of the compound have been isolated from 2-methoxyethanol. The yellow-orange or α form is monoclini?, space group P2₁/c; the orange-red or β form is also monoclinic, space group I2/c. Infrared, optical and mass spectral data, along with solution UV, NMR, molecular weight and conductivity data, suggest that the two crystalline modifications are plymorphs, possibly differing in the degree and type of heavy atom interaction. In 2-methoxyethanol the β form undergoes a solution phase transformation to the stable α form. Both forms are thermochromic.     

PHOTOREDUCTION OF SOME NITROBIPHENYL ETHER HERBICIDES TO NITRO RADICAL ANIONS BY β-CAROTENE AND RELATED COMPOUNDS

Abstract —The nitrobiphenyl ether herbicides; 4-nitrobiphenyl ether, bifenox, nitrofen, acifluorfen, acifluorfen-methyl, acifluorfen-ethyl, and oxyfluorfen were reduced to their corresponding nitro radical anions by visible light in the presence of β-carotene, lycopene, retinol, retinal, retinoic acid and retinyl acetate in anaerobic solutions at high pH. It was more difficult to obtain spectra of bifenox, nitrofen and oxyfluorfen than acifluorfen derivatives, probably due to their poor solubilities. In neutral solutions the steady-state concentration of the nitro radical anions was low due to their faster rate of dispropor-tionation and the poor solubility of β-carotene. In the presence of retinal, the nitro radical anion of acifluorfen was produced at pH 7.4. Compounds containing conjugated double bonds such as crotonaldehyde and 2.4-hexadienal also reduced acifluorfen and its derivatives to their respective nitro radical anions in the presence of light. Ubiquinone-50 which does not contain conjugated double bonds in the side chain did not reduce acifluorfen under similar conditions.     

Substituenteneffekte auf azido-tetrazolo-gleichgewichte elektronische und sterische effekte bei s-triazolo[4,3-c]tetrazolo[1,5-a]pyrimidinen1

The azido tetrazolo valence isomerism of twenty 9-methyl-s-triazolo[4,3-c]tetrazolo[1,5-a]pyrimidines with different substituents at position 5 has been studied by means of ¹H NMR spectroscopy. All the compounds have been found to be tetrazoles in the solid state and in (CD₃)₂SO solution; in CF₃COOH azido and tetrazolo isomers are in equilibrium. From equilibrium constants K and thermodynamic data determined it is concluded that in this series K depends on both electronic effects and steric requirements of the 5-substituents. A linear relation between K and σ was found for 5-arylderivatives because ΔS° keeps approximately constant and the substituent mainly operates on ΔH°.     

The isomerization of optically-active propargyl alcohols to terminal acetylenes.

The isomerization of optically-active secondary propargyl alcohols, RCHOHCC(CH₂)_nCH₃, to terminal acetylenic alcohols, RCHOH(CH₂)_n+1 C=CH, by potassium 3-aminopropylamide (KAPA) proceeds without loss of configuration at the hydroxy center.     

Synthesis of mixed metal decaosmium carbido clusters: The X-ray structures of the monoanions [Os10C(CO)24Cu(NCMe)]− and [Os10C(CO)24AuPPh3]−

The high nuclearity mixed metal cluster monoanions [Os₁₀C(CO)₂₄Cu(NCMe)]^? (I) and [Os₁₀C(CO)₂₄AuPPh₃]^? (II) have been obtained by reaction of the carbido-dianion [Os₁₀C(CO)₂₄]^2? (III) with one equivalent of [Cu(NCMe)₄] [BF₄] and Ph₃PAuCl, respectively, in CH₂Cl₂. X-ray analysis of the [PPh₃Me]⁺ salts of I and II show that the Cu and Au ligands have added to capping tetrahedra of the dianion III in μ₃- and μ₂-bridging positions, respectively.     

Synthesis of some heterocyclic systems from nucleophilic substitution reactions with η6-o-dichlorobenzene-η5-cyclopentadienyliron hexafluorophosphate

A method for the synthesis of heterocylic systems related to 9,10-dihydroanthracene with two hetero-atoms at the 9,10-positions is described. It involves the nucleophilic substitution reaction of η⁶-o-dichlorobenzene-η⁵-cyclopentadienyliron hexafluorophosphate with two nucleophilic groups (OH, SH and/or NH₂) located in the 1,2-positions of a benzene ring to give a cyclopentadienyliron complexed heterocycle. Upon pyrolytic sublimation of the complex, the free heterocyclic compound is then obtained.     

Effects of alkali metal halide salts on the hydrogen bond network of liquid water

Measurements of the oxygen K-edge X-ray absorption spectrum (XAS) of aqueous sodium halide solutions demonstrate that ions significantly perturb the electronic structure of adjacent water molecules. The addition of halide salts to water engenders an increase in the preedge intensity and a decrease in the postedge intensity of the XAS, analogous to those observed when increasing the temperature of pure water. The main-edge feature exhibits unique behavior and becomes more intense when salt is added. Density functional theory calculations of the XAS indicate that the observed red shift of the water transitions as a function of salt concentration arises from a strong, direct perturbation of the unoccupied molecular orbitals on water by anions, and does not require significant distortion of the hydrogen bond network beyond the first solvation shell. This contrasts the temperature-dependent spectral variations, which result primarily from intensity changes of specific transitions due to geometric rearrangement of the hydrogen bond network.     

Sterically Congested Phosphite Ligands: Synthesis,crystallographic characterization,and observation of unprecedented eight-Bond 31P,31P coupling in the 31P-NMR spectra

The synthesis and characterization of 2-{1-{3,5-bis(1,1-dimethylethyl)-2-{[2,4,8,10-tetrakis(1,1-dimethylethyl)dibenzo[d,f][1,3,2]dioxaphosphepin-6-yl]oxy}phenyl}ethyl}-4,6-bis(1,1-dimethylethyl)phenyl diphenyl phosphite ( 6 ) is described. In the ³¹P-NMR spectrum (¹H-decoupled) of 6 , an unprecedented eight-bond P,P coupling of J = 72.8 Hz is observed. In the X-ray crystal structure of 6 , an intramolecular P–P distance of 3.67 Å is found, which is within the sum of the van-der-Waals radii of the P-atoms. The observed intramolecular P–P distance suggests that a through-space coupling mechanism is operative. The solid-state conformation of 6 is compared to the conformation obtained by semi-empirical MO geometry optimizations (PM3 method). The calculated geometry suggests that the solid-state structure is near a true energy minimum, but that crystal-packing forces decrease the intramolecular P–P distance in the solid state. In the absence of crystal-packing forces, however, the collisional and vibrational energy available in solution may lead to the population of states with a shortened intramolecular P–P distance in 6 . The proximity of the P-atoms in 6 is due to restricted conformational freedom resulting from steric congestion within the molecule. The free energy of activation (ΔG* = 10.2 and 10.8 kcal/mol for unequal populations of exchanging conformers) for ring inversion of the dibenzo[d,f][1,3,2]dioxaphosphepin ring in 6 is determined by variable-temperature ³¹P-NMR spectroscopy. Semi-empirical MO calculation on model compounds suggest that the structure of the transition state for ring inversion has the two aryl rings and O-atoms in a common plane, with the P-atom lying above this plane.     

Rhodopsin reconstituted into a planar-supported lipid bilayer retains photoactivity after cross-linking polymerization of lipid monomers

Transmembrane proteins (TMPs), particularly ion channels and receptors, play key roles in transport and signal transduction. Many of these proteins are pharmacologically important and therefore targets for drug discovery. TMPs can be reconstituted in planar-supported lipid bilayers (PSLBs), which has led to development of TMP-based biosensors and biochips. However, PSLBs composed of natural lipids lack the high stability desired for many technological applications. One strategy is to use synthetic lipid monomers that can be polymerized to form robust bilayers. A key question is how lipid polymerization affects TMP structure and activity. In this study, we have examined the effects of UV polymerization of bis-Sorbylphosphatidylcholine (bis-SorbPC) on the photoactivation of reconstituted bovine rhodopsin (Rho), a model G-protein-coupled receptor. Plasmon-waveguide resonance spectroscopy (PWR) was used to compare the degree of Rho incorporation and activation in fluid and poly(lipid) PSLBs. The results show that reconstitution of Rho into a supported lipid bilayer composed only of bis-SorbPC, followed by photoinduced lipid cross-linking, does not measurably diminish protein function.