Roger A. Klein

What is a hydrogen bond? Mutually consistent theoretical and experimental criteria for characterizing H-bonding interactions

The maturity of a science can be measured in terms of successively improved operational definitions of its terms of reference. From this perspective, the science of hydrogen bonding remains in a somewhat immature and unsettled state, reflecting current uncertainties in empirical diagnosis, theoretical origin, and formal definition of this important phenomenon. Authentic progress in the H-bonding sciences should therefore be accompanied by efforts to formulate improved quantitative criteria for identifying, characterizing, and delimiting the H-bonding phenomenon, consistent with best current understanding. The present paper proposes such criteria in a form that better summarizes current understanding of H-bonding and allows progressive refinements of its definition as improved theoretical and experimental methods become available.

Utilization of amino acids by Trypanosoma brucei in culture: L-threonine as a precursor for acetate

The amino acid compositions of several culture media have been analysed and compared. The utilization and excretion of amino acids and other metabolites have been followed during growth of Trypanosoma brucei S42 in a defined medium. All of the added L-threonine was metabolized by the cells, even when it was present at elevated concentrations. Glucose was consumed throughout the growth cycle: glutamine was consumed more rapidly than glutamic acid, which was itself used at about the same rate as proline. Threonine was cleaved to form glycine and acetate, both of which accumulated in the medium. Alanine and succinate were excreted together with a small amount of pyruvate, but these three products accounted for less than half of the glucose used. CO2 production from glucose was not measured, but insignificant amounts of CO2 were produced from threonine. Tetraethylthiuram disulphide blocked the cleavage of threonine and was a potent inhibitor of trypanosome growth.

Hydrogen peroxide metabolism in Trypanosoma brucei

Contrary to previous reports in the literature, bloodstream forms of the haemoflagellate protozoan Trypanosoma brucei brucei are not deficient in their ability to metabolize hydrogen peroxide, although they either lack or only possess the normal enzymes for H2O2 detoxification, catalase (EC 1.11.1.6) and glutathione peroxidase (EC 1.11.1.9), at extremely low levels. The hydrogen peroxide which is consumed appears to be reduced by NADPH derived from glucose via the pentose phosphate pathway. This process requires the newly discovered cofactor trypanothione.

Mass spectrometric localization of carbon-carbon double bonds: A critical review of recent methods

Abstract Current methods are reviewed for determining the position of double bonds in fatty acids, and other unsaturated organic compounds, using mass spectrometry. ‘On-site’ and ‘remote-site’ derivatization methods are described, and their advantages and disadvantages for mass spectrometric analysis discussed. Chemical transformation of double bonds by methoxylation, silyloxylation or deuteration, together with electron impact (EI), chemical ionization (CI) or collisionally induced decomposition (CID) techniques in combination with fast atom bombardment (FAB) or CI, are found to be most suitable for polyunsaturated fatty acids (PUFA): for the analysis of less unsaturated compounds on a submicrogram scale those methods are most promising which either do not involve derivatization of the double bonds, or give derivatives in quantitative yields. Effects of mass spectrometer geometry and operating conditions are also considered.

What is a hydrogen bond? Resonance covalency in the supramolecular domain

We address the broader conceptual and pedagogical implications of recent recommendations of the International Union of Pure and Applied Chemistry (IUPAC) concerning the re-definition of hydrogen bonding, drawing upon the recommended IUPAC statistical methodology of mutually correlated experimental and theoretical descriptors to operationally address the title question. Both direct and statistical lines of evidence point to the essential resonance covalency of H-bonding interactions, rather than the statistically insignificant “dipole–dipole” character that is persistently advocated in current textbooks. The revised conception of H-bonding is both supported by modern quantum chemical technology and consistent with the pre-quantal insights of G. N. Lewis and other bonding pioneers. We offer specific suggestions for how relatively minor changes in the usual discussion of Lewis-structural and resonance concepts—supported by modern web-based computational modeling tools—can readily accommodate this fundamental change of perspective.

Threonine catabolism in Trypanosoma brucei.

L-Threonine is catabolized by Trypanosoma brucei to give equimolar quantities of glycine and acetate. The pathway, which involves the two enzymes L-threonine dehydrogenase (EC 1.1.1.103) and aminoacetone synthase (acetyl-CoA:glycine C-acetyltransferase, EC 2.3.1.29) and subsequent hydrolysis of the acetyl-CoA, is most active in cultured trypanosomes but is also present in bloodstream forms. L-Threonine dehydrogenase from both culture and bloodstream forms of trypanosomes has an apparent molecular weight of between 28 000 and 38 000, and is sensitive to a wide range of sulphydryl reagents.

Spectroscopic investigations on the binding site of bovine hepatic fatty acid binding protein. Evidence for the existence of a single binding site for two fatty acid molecules

The hydrophobic region of the binding site of a bovine fatty acid binding protein (pI 7.0-FABP) has been characterized using fluorescence and circular dichroism (CD) spectroscopy. Blue-shifts of fluorescence emission maxima and increased lifetimes of naphthylamine dyes, anthroyloxy-fatty acids, pyrene nonanoic acid and trans-parinaric acid indicated a hydrophobic interaction with FABP. The fluorescence quenching of various anthroyloxy-fatty acids by iodide and acrylamide showed lower accessibility to the fluorophore linked to the carbon adjacent to the carbonyl group and towards the methyl end of the fatty acid. Binding stoichiometries were different for fatty acids and their bulky fluorescent analogues. trans-Parinaric acid when bound to FABP showed a complex induced CD-spectrum, which is explained by a close proximity of two ligands in the same binding site. Fluorescent derivatives of phosphatidylcholine with trans-parinaric acid and cholesteryl trans-parinarate did not bind to FABP. Thus, the binding site appears to be constructed for high affinity binding of long chain fatty acids.

Improved General Understanding of the Hydrogen‐Bonding Phenomena: A Reply

We believe that fair-minded readers will recognize that our “anti-electrostatic hydrogen bonding” (AEHB) article was prepared for a general chemical audience of Angewandte Chemie readers, building on “common parlance” rather than the imagined technical associations that Frenking and Caramori (FC) wish to assign them (else we would have properly cited such associations). In fact, there is little usage per se of natural bond orbital (NBO) analysis or related technical terminology in our work, except to exhibit obvious graphical similarities between NBO interactions in AEHB and conventional hydrogen-bonded species. Nothing approaching full-fledged NBO analysis (i.e., in the sense of chapters 1–6 of “Discovering Chemistry with Natural Bond Orbitals”; see below) was attempted or claimed in our work. Many of FC’s strongest remarks (viz., “Coulombic interactions are calculated...using hand-waiving arguments and a wrong equation”, “Pauli repulsion...is completely ignored”, “NBO calculations always suggest orbital interactions for explaining chemical phenomena”, “the NBO method is useless for elucidating the nature of chemical bonding because it affords only information about orbital interactions in a biased way,...”) are unsupported and fallacious, seemingly directed at some imagined parody of NBO analysis rather than what could be fairly inferred from our AEHB paper or the broader literature of NBO methods. Let us first summarize important points on which there appears to be substantial agreement. FC raise no substantive quibbles concerning our computational AEHB work, nor claim any previous anticipation of the surprising H-bonding in these high-energy complexes between like-charged ions. Furthermore, they express essential agreement with our basic assertion that H-bonding (like ordinary covalent bonding) cannot be reasonably understood in classical electrostatic terms, but instead derives from deeper aspects of Schrçdinger s quantum-mechanical wave equation (which different workers may prefer to express in different words). In agreement with our AEHB work and earlier papers on H bonding, FC express skepticism of the simplistic classical pointcharge formulas (and presumably the associated “dipole– dipole” conceptions) that are the basis of most current molecular dynamics simulations and classroom pedagogy of H-bonding. Hence, their sharp criticisms focus essentially on the NBO method itself, and how it differs in terminology and concepts from the particular “energy decomposition analysis” (EDA) method that the senior author has long advocated. To clarify the specific verbal associations that FC wish to attribute to “electrostatics” (or “elstat”) and other components of EDA-based labeling, we start from the basic EDA assumption, 9] that the interaction energy (DEint) of species “A” and “B” at separation R can be decomposed into simple additive contributions from electrostatic (DEelstat), Pauli exchange repulsion (DEPauli), and quantum-mechanical “orbital” interactions (DEorbital), namely Equation (1) [10]

MS and NMR analysis of the cross-reacting determinant glycan from Trypanosoma brucei brucei MITat 1.6 variant specific glycoprotein

The cross-reacting determinant glycan from Trypanosoma brucei brucei MITat 1.6 is known to contain galactose, mannose and non-acetylated glucosamine. The structural elucidation of this oligosaccharide has been impeded by an unusual non-glycosidic linkage to the peptide chain and a glycosidic linkage to inositol phosphate on either side of the oligosaccharide. Using two different approaches for the isolation of the glycan, namely hydrolysis to give the oligosaccharide directly or pronase digestion to yield the glycan-containing C-terminal glycophosphopeptide, the structure of this glycan was elucidated by mass spectrometry and 1H-NMR spectroscopy. There was evidence of heterogeneity in the glycan residue.

Do rodent and human brains have different N-glycosylation patterns?

Abstract A large number of studies on the structure of Nglycosidically linked oligosaccharides from glycoproteins of different organs and/or different species have been carried out in the past using various combinations of techniques such as monosaccharide analysis, permethylation, peracteylation, exoglycosidase sequencing, normal and reversed phase HPLC, mass spectrometry and nuclear magnetic resonance spectroscopy. Although it is widely accepted that the processing of Nglycans in the ER and Golgi of mammalian cells follows the same principal metabolic rules, analyses have revealed that the glycosylation pattern of a particular protein may differ depending on the cell type in which it is expressed. Nglycans from brain glycoproteins have been shown to include a variety of hybrid and complextype structures with structural features that are not so commonly found on glycoproteins from other organs and which have, therefore, been classified as brainspecific. Comparison of the Nglycans of glycoproteins from homogenates of rat, mouse and human brains confirm that, in general, glycoproteins from human brain show a similar profile of brainspecific Nglycans as glycoproteins from mouse and rat brain.