On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract

The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges on the atoms in the hydrophilic site as methanol.     

Identification of hydrogen selenide and other volatile selenols by derivatization with 1-fluoro-2,4-dinitrobenzene

A procedure is described for the trapping and identification of hydrogen selenide and methyl selenol ( CH3SeH ). The volatile selenols were generated by reducing selenious acid or dimethyldiselenide with Zn dust and hydrochloric acid under a stream of nitrogen and passing into a trapping solution composed of 50 mM 1-fluoro-2,4-dinitrobenzene plus 83 mM sodium bicarbonate in 67% dimethylformamide:33% water. The selenols react rapidly to form stable dinitrophenyl (DNP) selenoethers that can be extracted into benzene; these are easily identified by TLC, HPLC, or mass spectrometry. Hydrogen selenide is trapped in 90-99% yield, primarily as the di-DNP- monoselenide with a trace of di-DNP- diselenide .     

Helix packing of leucine-rich peptides: a parallel leucine ladder in the structure of Boc-Aib-Leu-Aib-Aib-Leu-Leu-Leu-Aib-Leu-Aib-OMe.

The packing of peptide helices in crystals of the leucine-rich decapeptide Boc-Aib-Leu-Aib-Aib-Leu-Leu-Leu-Aib-Leu-Aib-OMe provides an example of ladder-like leucylleucyl interactions between neighboring molecules. The peptide molecule forms a helix with five 5----1 hydrogen bonds and two 4----1 hydrogen bonds near the C terminus. Three head-to-tail NH ... O = C hydrogen bonds between helices form continuous columns of helices in the crystal. The helicial columns associate in an antiparallel fashion, except for the association of Leu ... Leu side chains, which occurs along the diagonal of the cell where the peptide helices are parallel. The peptide, with formula C56H102N10O13, crystallizes in space group P2(1)2(1)2(1) with Z = 4 and cell parameters a = 16.774(3) A, b = 20.032(3) A and c = 20.117(3) A; overall agreement factor R = 10.7% for 2014 data with magnitude of F(obs) greater than 3 sigma (F); resolution 1.0 A.     

Backbone side-chain interactions in peptides

IR, ¹H-NMR and X-ray experiments have been carried out on dipeptides with the Pro-Asp and Pro-Asn sequences protected on both ends by amide groups. The Pro-Asp dipeptide was investigated for the carboxylic, methyl ester and carboxylate forms of the Asp residue.In solution, all dipeptides are found to accommodate almost exclusively the I-turn conformation stabilized by an interaction between the Asp or Asn-NH and CO bonds. The I-turn percentage roughly parallels the basicity of the Asp or Asn side substituent, and decreases from Asp^- to Asn, and to Asp or Asp (OMe).The I-turn, stabilized by the interaction involving the Asp-CO site, is retained in the crystal structure of the Pro-Asp(OMe) dipeptide. The Pro-Asp and Pro-Asn dipeptides assume a II-turn conformation in the solid state and the polar Asp or Asn side-groups are involved in a complex network of intermolecular interactions.     

Copper ions and hydrogen peroxide form hypochlorite from NaCl thereby mimicking myeloperoxidase

Sea urchins have elaborated multiple defenses to assure monospermic fertilization. In this work, we have concentrated on a study of the mechanism(s) by which hydrogen peroxide (H₂O₂) prevents polyspermy in Arbacia punctulata. We found that it is not H₂O₂ but probably hypochlorous acid/hypochlorite (HOCl/OCl^?) derived from H₂O₂ that is toxic to the supernumerary sperm. The spermicidal activity of H₂O₂ is potentiated by at least one order of magnitude by cupric ions (Cu²⁺). This increased toxicity is not due to the formation of hydroxyl radicals (·OH) because ·OH scavengers did not counteract the activity of Cu²⁺. More-over, substitution of Cu²⁺ by ferrous ions (Fe²⁺), which are known to cause formation of ·OH from H₂O₂, had no effect on fertilization even at 10²?10³ times higher concentrations. In contrast, 3-amino-1,2,4-triazole (AT), an HOCl/OCl^? scavenger, totally reversed the toxic effects of Cu²⁺. Furthermore, we found that HOCl/OCl^? is generated in solutions of H₂O₂ and Cu²⁺ in the presence of 0.5 M NaCl and that its accumulation is abolished by AT. Thus it is possible that the antifertility properties of copper are due to its ability to mediate formation of HOCl/OCl^?. HOCl/OCl^? generated by Cu²⁺ from H₂O₂ and Cl^?, a low concentration of exogenously added HOCl/OCl^?, or increased concentrations of H₂O₂ has similar inhibitory effects on the fertilization process in sea urchins. Therefore, we suggest that polyspermy is prevented by the action of a myeloperoxidase that affects the formation of HOCl/OCl^? from the Cl^? present in sea water through reaction with H₂O₂ generated by the newly fertilized egg.     

One- and two-dimensional NMR spectral analysis of the consequences of single amino acid replacements in proteins

The traditional approach of using homologous sequences to elucidate the role of specific amino acid residues in protein structure and function becomes more meaningful as the number of differences is minimized, with the limit being alteration of a single residue. For small proteins in solution, NMR spectroscopy offers a means of obtaining detailed information about each residue and its response to a given change in the protein sequence. Extraction of this information has been aided by recent progress in spectrometer technology (higher magnetic fields, more sensitive signal detection, more sophisticated computers) and experimental strategies (new NMR pulse sequences including multiple-quantum and two-dimensional NMR methods). The set of avian ovomucoid third domains, which consists of the third domain proper plus a short leader (connecting peptide) and has a maximum of 56 amino acid residues, offers an attractive system for developing experimental methods for investigating sequence-structure and structure-function relationships in proteins. Our NMR results provide examples of sequence effects on pKa' values, average conformation, and internal motion of amino acid side chains.     

Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons

A method to be used for experimental studies of protein folding introduced by Schmid and Baldwin (J. Mol. Biol. 135: 199-215, 1979), which is based on the competition between amide hydrogen exchange and protein refolding, was extended by using rapid mixing techniques and 1H NMR to provide site-resolved kinetic information on the early phases of protein structure acquisition. In this method, a protonated solution of the unfolded protein is rapidly mixed with a deuterated buffer solution at conditions assuring protein refolding in the mixture. This simultaneously initiates the exchange of unprotected amide protons with solvent deuterium and the refolding of protein segments which can protect amide groups from further exchange. After variable reaction times the amide proton exchange is quenched while folding to the native form continues to completion. By using 1H NMR, the extent of exchange at individual amide sites is then measured in the refolded protein. Competition experiments at variable reaction times or variable pH indicate the time at which each amide group is protected in the refolding process. This technique was applied to the basic pancreatic trypsin inhibitor, for which sequence-specific assignments of the amide proton NMR lines had previously been obtained. For eight individual amide protons located in the beta-sheet and the C-terminal alpha-helix of this protein, apparent refolding rates in the range from 15 s-1 to 60 s-1 were observed. These rates are on the time scale of the fast folding phase observed with optical probes.     

A chemiluminescent method for measurement of activated oxygen forms in biological fluids and homogenates

A chemiluminescent method for measuring the concentration of activated oxygen species (O₂² and H₂O₂) is described. Its main features are: high sensitivity (10^?9 M H₂O₂), its applicability to systems with high optical absorbance in the visible spectral region, a wide linear dynamic range, and the possibility for recording the kinetics of the processes, in which activated oxygen species are involved.     

Detection of Myoglobin-Derived Radicals On Reaction of Metmyoglobin With Hydrogen Peroxide and Other Peroxidic Compounds

The reaction of metmyoglobin with equimolar concentrations of hydrogen peroxide has been studied using both electron spin resonance (e.s.r.) and optical spectroscopy. Using the former technique a strong anisotropic e.s.r. signal is observed, in the presence of the spin trap DMPO, which decays relatively rapidly. This previously unobserved signal, which is also observed on reaction of metmyoglobin with a number of other powerful oxidants (peracetic acid, 3-chloroperoxybenzoic acid, monoperoxyphthalic acid, iodosyl benzene, ¹BuOOH and cumene hydroperoxide) is assigned to a slowly-tumbling, metmyoglobin-derived, spin adduct. The parameters of this signal (a_N 1. 45, a_H 0.83 mT) are consistent with the trapped radical having a heteroatom centre; this is believed to be oxygen. The concentration of this species is not affected by compounds such as 2-deoxyribose, mannitol and phenylalanine which are all efficient hydroxyl radical scavengers, demonstrating that the formation of this radical is not due to reaction of “free” HO· generated by breakdown of H₂O₂, by released iron ions. The concentration of this species is however decreased by desferal, ascorbate, Trolox C, salicylate and, to a lesser extent, linoleic acid; with the first three of these compounds further substrate-derived radicals are also observed. Examination of similar reaction systems (though in the absence of DMPO) by optical spectroscopy shows that the myoglobin (IV) species is formed and that this species behaves in a somewhat different manner with these added compounds. These results suggest that the radical trapped in the e.s.r. experiments is a myoglobin-derived species, probably a tyrosine peroxyl radical, arising from oxidative damage to the globin moiety.

The diminution of both the e.s.r. signal of the spin adduct and the optical absorption of the myoglobin (IV) species in the presence of linoleic acid suggests that these myoglobin-derived species can initiate oxidative damage but that this process can be ameliorated by the presence of a number of water-soluble compounds such as ascorbate, Trolox C, desferal and salicylate.