Analysis of Colubroidea snake venoms by liquid chromatography with mass spectrometry: evolutionary and toxinological implications

The evolution of the venomous function of snakes and the diversification of the toxins has been of tremendous research interest and considerable debate. It has become recently evident that the evolution of the toxins in the advanced snakes (Colubroidea) predated the evolution of the advanced, front-fanged delivery mechanisms. Historically, the venoms of snakes lacking front-fanged venom-delivery systems (conventionally grouped into the paraphyletic family Colubridae) have been largely neglected. In this study we used liquid chromatography with mass spectrometry (LC/MS) to analyze a large number of venoms from a wide array of species representing the major advanced snake clades Atractaspididae, Colubrinae, Elapidae, Homalopsinae, Natricinae, Psammophiinae, Pseudoxyrhophiinae, Xenodontinae, and Viperidae. We also present the first sequences of toxins from Azemiops feae as well as additional toxin sequences from the Colubrinae. The large body of data on molecular masses and retention times thus assembled demonstrates a hitherto unsuspected diversity of toxins in all lineages, having implications ranging from clinical management of envenomings to venom evolution to the use of isolated toxins as leads for drug design and development. Although definitive assignment of a toxin to a protein family can only be done through demonstrated structural studies such as N-terminal sequencing, the molecular mass data complemented by LC retention information, presented here, do permit formulation of reasonable hypotheses concerning snake venom evolution and potential clinical effects to a degree not possible till now, and some hypotheses of this kind are proposed here. The data will also be useful in biodiscovery.     

A mass spectrometry study of XCO+, X=Si, Ge: is SiCO+ a main group carbonyl? Comments on the bonding in ground state SiCO and the

The cation [Si,C,O]+ has been generated by 1) the electron ionisation (EI) of tetramethoxysilane and 2) chemical ionisation (CI) of a mixture of silane and carbon monoxide. Collisional activation (CA) experiments performed for mass-selected [Si,C,O]+, generated by using both methods, indicate that the structure is not inserted OSiC+; however, a definitive structural assignment as Si(+)-CO, Si(+)-OC or some cyclic variant is impossible based on these results alone. Neutralisation-reionisation (+NR+) experiments for EI-generated [Si,C,O]+ reveal a small peak corresponding to SiC+, but no detectable SiO+ signal, and thus establishes the existence of the Si(+)-CO isomer. CCSD(T)@B3LYP calculations employing a triple-zeta basis set have been used to explore the doublet and quartet potential-energy surfaces of the cation, as well as some important neutral states. The results suggest that both Si(+)-CO and Si(+)-OC isomers are feasible; however, the global minimum is 2 pi SiCO+. Isomeric 2 pi SiOC+ is 12.1 kcal mol-1 less stable than 2 pi SiCO+, and all quartet isomers are much higher in energy. The corresponding neutrals Si-CO and Si-OC are also feasible, but the lowest energy Si-OC isomer (3A") is bound by only 1.5 kcal mol-1. We attribute most, if not all, of the recovery signal in the +NR+ experiment to SiCO+ survivor ions. The nature of the bonding in the lowest energy isomers of Si(+)-(CO,OC) is interpreted with the aid of natural bond order analyses, and the ground state bonding of SiCO+ is discussed in relation to classical analogues such as metal carbonyls and ketenes.     

Design of surface active soluble peptide molecules at the air/water interface

Surface active molecules collect at interfaces and have the potential to be used for water evaporation reduction. The objective of this work is to design surface active soluble peptides that collect at the air/water interface using molecular simulations. Rotational isomeric state Monte Carlo (RISMC) sampling together with a solvation model that we recently invented, the AAD solvation model [Gu, C.; Lustig, S.; Trout, B. J. Phys. Chem. B 2006, 110 (3), 1476-1484] was applied to calculate the adsorption free energy of the peptide molecule at the air/water interface. The results were validated by both molecular dynamics simulations with an explicit solvent model and surface tension measurements on synthesized peptides. It was demonstrated that this approach is able to give a reasonable prediction of surface activity with an approximately 50% hit rate in terms of designed surface active molecules actually being surface active. The relationship between the chemical composition and the surface morphology is also discussed.     

10‐Step Asymmetric Total Synthesis and Stereochemical Elucidation of (+)‐Dragmacidin D

The asymmetric synthesis of dragmacidin D ( 1 ) was completed in 10 steps. Its sole stereocenter was set by using direct asymmetric alkylation enabled by a C₂‐symmetric tetramine and lithium N‐(trimethylsilyl)‐tert‐butylamide as the enolization reagent. A central Larock indole synthesis was employed in a convergent assembly of the heterocyclic subunits. The stereochemical evidence from this work strongly supports the predicted S configuration at the 6′′′ position, which is consistent with other members of the dragmacidin family of natural products.     

Spectrophotometric determination of copper after adsorption of its 1-phenyl-4,4,6-trimethyl(1H, 4H)-pyrimidine-2-thiol complex onto microcrystalline naphthalene

A selective Spectrophotometric method has been developed for the trace determination of copper after adsorption of its 1-phenyl-4,4,6-trimethyl(1H, 4H)-pyrimidine-2-thiol (PTPT) complex onto microcrystalline naphthalene. The complex is quantitatively adsorbed on naphthalene in the pH range 7.5–11.5, separated by filtration, dissolved in dimethylformamide (DMF) and determined spectrophotometrically at 400 nm. Beer's law is obeyed in the concentration range 2.5–37.5 g of copper in 10 ml of DMF. The molar absorptivity and Sandell's sensitivity are 1.30 × 10⁴1 · mol^–1 · cm^–1 and 0.0048g cm^–2, respectively. Ten replicate analyses of a solution containing 20.0 g of copper gave a mean absorbance of 0.410 with a relative standard deviation of 0.91 %. The interferences of various ions have been studied and the method has been validated by the determination of copper in various standard reference materials, beers, wines, human hair, goat liver and environmental samples.On leave from St. Stephen's College, Delhi 110 007, India     

Highly conformationally constrained halogenated 6-spiroepoxypenicillins as probes for the bioactive side-chain conformation of benzylpenicillin

Summary The halogenated 6-spiroepoxypenicillins are a series of novel semisynthetic-lactam compounds with highly conformationally restricted side chains incorporating an epoxide. Their biological activity profiles depend crucially on the configuration at position C-3 of that epoxide. In derivatives with aromatic-containing side chains, e.g., anilide, the 3R-compounds possess notable Gram-positive antibacterial activity and potent-lactamase inhibitory properties. The comparable 3S-compounds are antibacterially inactive, but retain-lactamase inhibitory activity.Using the molecular simulation programs COSMIC and ASTRAL, we attempted to map a putative, lipophilic accessory binding site on the PBPs that must interact with the side-chain aromatic residue. Comparative computer-assisted modelling of the 3R, and 3S-anilides, along with benzylpenicillin, indicated that the available conformational space at room temperature for the side chains of the 3R and the 3S-anilides was mutually exclusive. The conformational space for the more flexible benzylpenicillin could accommodate the side chains ofboth the constrained penicillin derivatives. By a combination of van der Waals surface calculations and a pharmacophoric distance approach, closely coincident conformers of the 3R-anilide and benzylpenicillin were identified. These conformers must be related to the antibacterial, bioactive conformer for the classical-lactam antibiotics. From these proposed bioactive conformations, a model for the binding of benzylpenicillin to the PBPs relating the three-dimensional arrangement of a putative lipophilic S₂-subsite, specific for the side-chain aromatic moiety, and the 3-carboxylate functionality is presented.This work has been reported in preliminary form at the 4th Royal Society of Chemistry International Symposium on Recent Advances in the Chemistry of-lactam Antibiotics, Churchill College, Cambridge, U.K., 3–6 July 1988.     

Low temperature carbene-to-carbene homologations

Since alkynes have higher symmetry than olefins, it is not easy to infer the mechanism of a triplet carbene’s addition to an alkyne by traditional product analysis studies. Specifically, no stereochemical information which might offer insight into the carbene’s spin state can be extracted from the cyclopropene products. In 1971, Hendrick, Baron, and Jones showed that diphenylcarbene reacts with terminal alkynes in solution to produce indenes via a “self-trapping” vinylcarbene. They also examined the diphenylcarbene reaction with disubstituted alkynes and found at most trace amounts of the “self-trapping” indene product. In this work, we report the direct observation by organic matrix EPR of the vinylcarbenes generated from triplet fluorenylidene and terminal alkynes. Our efforts to confirm the identities of these intermediates by independent synthesis, intermolecular trapping, and an intramolecular “self-trapping” method-halogen-migration-are also recounted. These findings are among the few instances in which fluorenylidene undergoes carbon-carbon bond formation rather than atom abstraction reactions in a low-temperature matrix, and in which the biradical adduct of a triplet carbene and a π-bonded substrate can be directly observed.     

Steric effects on nascent vibrational distributions of the HCN product produced in CN radical reactions with ethane, propane and chloroform

Time-resolved IR emission spectroscopy (TRIES) has been used to study infrared emission in the 3400–3100 cm⁻¹ region from HCN molecules produced when CN radicals abstract a hydrogen atom from ethane, propane, and chloroform. From these observations the nascent vibrational distributions of the HCN produced were derived. The nascent vibrational population distributions of the product HCN in all of the reactions are non-statistical and inverted in both the pure CH stretch (00p) and CH stretch—bend (0np) series.