THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

The Weighted Histogram Analysis Method (WHAM), an extension of Ferrenberg and Swendsen's Multiple Histogram Technique, has been applied for the first time on complex biomolecular Hamiltonians. The method is presented here as an extension of the Umbrella Sampling method for free-energy and Potential of Mean Force calculations. This algorithm possesses the following advantages over methods that are currently employed: (1) It provides a built-in estimate of sampling errors thereby yielding objective estimates of the optimal location and length of additional simulations needed to achieve a desired level of precision; (2) it yields the “best” value of free energies by taking into account all the simulations so as to minimize the statistical errors; (3) in addition to optimizing the links between simulations, it also allows multiple overlaps of probability distributions for obtaining better estimates of the free-energy differences. By recasting the Ferrenberg–Swendsen Multiple Histogram equations in a form suitable for molecular mechanics type Hamiltonians, we have demonstrated the feasibility and robustness of this method by applying it to a test problem of the generation of the Potential of Mean Force profile of the pseudorotation phase angle of the sugar ring in deoxyadenosine. © 1992 by John Wiley & Sons, Inc.     

Non-aqueous cerimetric determination of thioureas

Ammonium hexanitratocerate (in acetonitrile) solution has been used as an oxidimetric reagent for the visual and potentiometric determination of thiourea and its alkyl derivatives in acetonitrile medium. The thioureas are oxidized to their corresponding disulphides. The method is simple, accurate, reliable and widely applicable.     

Supramolecular peptide helix from a novel double turn forming peptide containing a β-amino acid

A single-crystal X-ray diffraction study of the terminally protected tetrapeptide Boc-β-Ala-Aib-Leu-Aib-OMe 1 (Aib: α-aminoisobutyric acid; β-Ala: β-Alanine) reveals that it adopts a new type of double turn structure which self-associates to form a unique supramolecular helix through intermolecular hydrogen bonds. Scanning electron microscopic studies show that peptide 1 exhibits amyloid-like fibrillar morphology in the solid state.     

Use of a Water-in-Oil Microemulsion as Mobile Phase in Complexation TLC of Amino Acids on Silica Layers Impregnated with Metal Cations

JPC – Journal of Planar Chromatography – Modern TLC - A water-in-oil microemulsion has been used for the first time as a mobile phase in thin-layer chromatography of amino acids. A new...     

Physico-mechanical and free volume behaviour of guar gum filled polyurethane/polyacrylonitrile biodegradable composites

A series of different weight ratios of guar gum viz. 5, 10, 20 and 30 were incorporated into polyurethane/polyacrylonitrile (PU/PAN, 50/50) semi interpenetrating polymer networks (SIPNs) using polyethylene glycol-400, 4,4′-diphenyl methane diisocyanate, acrylonitrile, benzoyl peroxide and new metallic catalyst. The obtained polymer composites were subjected to biodegradation studies using specific fungi Aspergillus niger. The composites are characterized for physico-mechanical properties like density and tensile behaviour of the specimens before and after biodegradation. The positron annihilation lifetime spectroscopy (PALS) was used to monitor the content of free volume before and after biodegradation. The extent of degradation was examined by change in tensile behaviour and surface morphology. The influences of fungi on mechanical and morphological behaviour of filled IPNs are found to be interesting. The free volume changes in the composite systems correlates well with the mechanical properties.     

Furan ring oxidation strategy for the synthesis of macrosphelides A and B

By using the convenient protocol for conversion of 2-substituted furans into 4-oxo-2-alkenoic acids ((i) NBS, (ii) NaClO(2)), macrosphelide B (2) was synthesized from furyl alcohol 5 (>98% ee) and acid 6 (99% ee). The protocol was first applied to the PMB ether of 5 to afford acid 13b. On the other hand, DCC condensation of acid 6 with 5 gave 16 after deprotection of the TBS group. Condensation was again carried out between 13b and 16 to furnish the key ketone 17, which upon reduction with Zn(BH(4))(2) afforded anti alcohol 18 stereoselectively (15:1). After protection/deprotection steps, the furan 18 was converted to seco acid 3 by using the furan oxidation protocol mentioned above, and lactonization of 3 with Cl(3)C(6)H(2)COCl, Et(3)N, and DMAP afforded 22 (MOM ether of 2), which upon deprotection with TFA produced 2. Transformation of 22 to macrosphelide A (1) was then investigated. Although the chelation-controlled reduction of 22 should afford the desired anti alcohol 24, Zn(BH(4))(2) at <-90 degrees C gave a 2 approximately 1:1 mixture of anti/syn alcohols. On the contrary, reduction with NaBH(4) in MeOH at -15 degrees C produced the syn isomer 23 with >10:1 diastereoselectivity. Mitsunobu inversion of the resulting C(14)-hydroxyl group and deprotection of the MOM group with TFA afforded 1. Similarly, reduction of 2 with NaBH(4) afforded the C(14)-epimer of 1 stereoselectively. The observed stereoselectivity in the reductions of 22 and 2 could be explained on the basis of computer-assisted calculation, which showed presence of the low-energy conformers responsible for the stereoselective reduction. In addition, conversion of 2 to 1 was established, for the first time.     

Antistatic applications of conducting polyaniline

A method is described to impart flexibility and mechanical strength to conducting polyaniline by polymerizing aniline on fabrics and on cellulose papers. The study indicates that these conducting fabrics offer 16–18 dB of shielding effectiveness for the control of electromagnetic interference (EMI) up to a frequency of 10³ MHz.     

THE PHOTOREACTIVITY OF PYRIMIDINE-PURINE SEQUENCES IN SOME DEOXYDINUCLEOSIDE MONOPHOSPHATES AND ALTERNATING DNA COPOLYMERS

Abstract— A reversed-phase HPLC system has been developed which separates the common nucleo-bases from the 6-methylimidazo[4,5- b ]pyridin-5-one (6-MIP) produced on acid hydrolysis of a thymine-adenine photoadduct (TA*) that is formed between adjacent thymine and adenine bases in UV-irradiated polydeoxyribonucleotides. By measuring the relative amounts of adenine and 6-MIP in acid hydrolysates, this system has been used to investigate how polynucleotide conformation affects the yield of TA* in poly(dA-dT) irradiated at 254 nm. The photoreactivity of other pyrimidine-purine sequences has been examined with the deoxydinucleoside monophosphates d(TpI) and d(m⁵CpA) and with the alternating DNA copolymers poly(dA-dU), poly(dI-dC), poly(dG-dC) and poly(dA-dC).poly(dG-dT). Samples were irradiated at 254 nm in aqueous solution and in ice, and at wavelengths >290 nm with acetone as photosensitizer. A photoproduct resembling TA*, and giving 6-MIP on acid hydrolysis, was isolated from d(TpI) irradiated at 254 nm in solution or in ice; d(m⁵CpA) was comparatively unreactive. Acid hydrolysates of the irradiated DNA copolymers were screened by HPLC and by TLC and paper electrophoresis, for the presence of imidazo[4,5- b ]pyridin-5-one, 6-MIP, or other species attributable to specific photoproduct formation. By this criterion, however, none of the copolymers showed evidence of significant photoreactivity in either their single- or double-stranded conformational states. The formation of mixed pyrimidine-purine photoadducts in DNA is therefore probably restricted to T-A doublets.     

NMR spectroscopic study of the inclusion complex of desloratadine with β-cyclodextrin in solution

Desloratadine (DES) is an antihistamine used in the treatment of allergies and chronic urticaria. ¹H NMR spectroscopic study of varying ratios of DES and β-Cyclodextrin (β-CD) in D₂O suggests the formation of a 1:1 inclusion complex formed by the penetration of Cl-substituted aromatic ring into the β-CD cavity. The stoichiometry and binding constant of the complex were determined by Scott’s method.     

Development of Odorless Thiols and Sulfides and Their Applications to Organic Synthesis

Summary. Development of new odorless thiols (dodecanethiol, 4-n-heptylphenylmethanethiol, 4-trimethylsilylphenylmethanethiol, 4-trimethylsilylbenzenethiol) and an odorless sulfide (1-methylsulfanyldodecane) and their applications to dealkylation, Michael addition, Swern oxidation, and Corey-Kim oxidation are described.