Harmonic analysis of large systems. II. Comparison of different protein models

A series of normal mode analyses of bovine pancreatic trypsin inhibitor (BPTI) has been performed. The results of modifying the long-range truncation of electrostatics, reducing the conformational space of the system (reduced basis normal mode analysis), and using different parameter sets and models for the potential function are reported. Both explicit (904 atoms) and polar hydrogen (580 atoms) representations of BPTI were examined and produced nearly identical normal mode vectors but slightly modified vibrational frequencies. The truncation methods—no cutoff, shift, and switch—were examined, and the use of a short switching function was found to alter harmonic motion greatly. A table relating the different cutoff methods to several previously published frequencies for BPTI indicates that the diversity of published lowest frequencies is due to the use of different electrostatic models rather than to inherent differences in the models or energy parameters. Examining reduced basis results demonstrates that a dihedral basis yields similar normal mode vectors, though the vibrational frequencies are shifted to higher values. The analysis of BPTI harmonic dynamics using a spherical harmonic reduced basis set yields significantly altered dynamics, indicating that BPTI is not well represented as a homogeneous object at low temperatures. © 1995 John Wiley & Sons, Inc.

1 This article is a U.S. Government work and, as such, is in the public domain in the United States of America.

     

Solid-phase synthesis using a new polyacrylic resin : Synthesis of the fragment 14–21 of the amino acid sequence of histone H4

The solid-phase synthesis of the octapeptide 1 AcGly-Ala-Lys-Arg-His-Arg-Lys-ValOMe, which represents the fragment 14-21 of the amino acid sequence of the chromosomal histone H4, as well as of the structurally related nonapeptide 2 AcGly-Ala-Lys-Leu-Arg-His-Arg-Lys-ValOMe, is described using a new polyacrylic resin containing a glycolamide ester linkage(resin-NHCO-CH₂-OCO-peptide) acting as a labile anchoring moiety between the resin and the peptide.After elongation of the polypeptide chain using classical protecting groups, i.e. t-butyloxycarbonyl for the α-NH₂ function, benzyloxycarbonyl, nitro and 2,4-dinitrophenyl groups for the side-chains of Lys, Arg and His respectively, both peptides 1 and 2 were obtained in good yields and with a high purity as shown by high-pressure liquid chromatography, by amino-acid analysis and by high-field proton NMR spectroscopy.This work demonstrates the ability of the newly introduced polyacrylic resin to act as a convenient support for solid-phase peptide synthesis.     

The reduction and hydrolysis of some 7,7-diethylpyrazolo[1,2-a]-pyridazine-6,8(7H)dione derivatives

The chemistry of several of the Diels-Alder adducts formed by the reaction of 4,4-diethylpyrazoline-3,5-dione ( 1 ) with conjugated dienes was studied with respect to reduction (hydride and catalytic) and reaction with base. Reaction of the 2,3-dimethyl-1,3-butadiene adduct with lithium aluminum hydride followed by hydrogenation gave 1,3,5,6,7,8-hexahydro-cis-endo-6,7-dimethyl-2,2-diethylpyrazolo[1,2-a]pyridazine ( 11 ). Attempted conversion of this compound to 3,3-diethyl-cis-7,8-dimethyl-1,5-diazacyclononane ( 12 ) gave instead a compound which has been tentatively identified as N-(2,3-dimethyl-4-aminobutyl)-2-ethyl-2-methylbutanaldimine ( 14 ). Lithium aluminum hydride reduction of 4,4-diethylpyrazolidine-3,5-dione ( 22 ) or the adducts formed from 1 and cyclopentadiene or 1,3-cyclohexadiene gave good yields of 4,4-diethylpyrazolidine ( 21 ). This later reduction gave a new and efficient synthetic route to the pyrazolidine ring system. Lithium aluminum hydride reduction of 5,6,7,8-tetrahydro-5,8-ethano-2,2-diethylpyrazolo[1,2-a]pyridazine-1,3(2H)dione ( 26 ) followed by hydrogenolysis led to a high yield of 4,4-diethyl-2,6-diazabicyclo[5.2.2]undecane ( 28 ) which is the first reported example of this ring system. Reaction of several of the adducts with ethanolic potassium hydroxide resulted in the opening of the five-membered ring.     

Alkylation of heme by the antimalarial drug artemisinin

The peroxide function of artemisinin has been activated by iron(II)-heme generated in situ from iron(III)-protoporphyrin-IX and glutathione, a biologically relevant reductant. In mild conditions, this reaction produced a high yield (85%) of heme derivatives alkylated at alpha-, beta-, and delta-meso positions by a C4-centered radical derived from artemisinin.     

Extended average energy perturbation calculation of the 2s2 and 2p21S resonance state energies of two-electron atoms

An extended average energy (EAE) calculation of the 2s² and 2p²¹S resonance state energies of two-electron atoms is carried out. We take the bare-nucleus hamiltonian as the initial approximation and treat the zeroth-order degeneracy by van Vleck perturbation theory, For both H^? and He the lower state energies agree quite well with experiment while the upper state is about 1–2 eV too high. Our remits for He are comparable in accuracy to those obtained by the 1/Z Hartree—Fock perturbation method. A brief concluding discussion of ways to improve the simple EAE technique is presented.     

Thermally stable silarylene-1,3,4-oxadiazole polymers

The effects of incorporating a p-phenylene- (or m-phenylene)-1,3,4-oxadiazole fragment into the backbone of poly[1,4-phenylene(diphenylsilyl)-1,4-phenylene-2,5-(1,3,4-oxadiazole)], which was developed by the authors, was investigated. Bis[(p-carbohydrazidophenyl)]diphenylsilane was copolymerized with dipentachlorophenyl terephthalate or isophthalate to produce the prepolymers poly[N-(p-diphenylsilylbenzoyl)-N′N″-(terephthaloyl)-N″′-(p-benzoyl)dihydrazide] and poly[N-(p-diphenylsilylbenzoyl)-N′,-N″-(isophthaloyl)-N″′-p-(benzoyl) dihydrazide], respectively. The polyhydrazides were converted by thermal dehydration into poly[1,4-phenylene(diphenylsilyl)-1,4-phenylene-(1,3,4-oxadiazole-2,5-diyl)-1,4-phenylene-2,5-(1,3,4-oxadiazole)] and poly[1,4-phenyl-ene(diphenylsilyl)-1,4-phenylene-(1,3,4-oxadiazole-2,5-diyl)-1,3,4-(oxadiazole)]. The new polymers were soluble in organic solvents. Films cast from these solutions exhibited good adhesion to glass and metal surfaces. Thermal analysis showed that the heat stability of all these polymers was about the same and that they were resistant to decomposition when heated in air to about 400°C. The results also indicated that these polymers were somewhat less heat-resistant than samples of poly-[1,4-phenylene(diphenylsilyl)-1,4-phenylene-2,5-]1,3,4-(oxadiazole) synthesized from bis(p-carbohydrazidophenyl)diphenylsilane and bis-(p-carbopentachlorophenoxy-phenyl)diphenylsilane.     

Concise synthesis of anhydrovinblastine from leurosine

[reaction: see text] The Cp(2)TiCl-mediated deoxygenation of leurosine (1) afforded anhydrovinblastine (4) in good yield. Furthermore, as the reaction proceeded via a carbon-centered radical intermediate, this transient was also trapped by a hydrogen-atom donor to afford selectively reduced alkaloid 10.