Experimental and computational studies of the recognition of amino acids by galactosyl-imine and -amine derivatives: an attempt to understand the lectin-carbohydrate interactions

A galactosyl-naphthyl-imine-based derivative, 1-(beta-D-galactopyranosyl-1'-deoxy-1'-iminomethyl)-2-hydroxynaphthalene (GNI), and a galactosyl-naphthyl-amine-based derivative, 1-(galactopyranosyl-1'-deoxy-1'-aminomethyl)-2-hydroxynaphthalene (GNA), possessing an ONO binding core were studied for their recognition of naturally occurring amino acids using fluorescence and absorption spectroscopy, and the corresponding association constants were derived for the complexes formed. The complexes formed between GNI/GNA and amino acids were supported by electrospray ionization mass spectrometry (ESI/MS). The structures of the complexes were optimized by computational studies using density functional theory, and stabilization energies were computed for the complexes to substantiate the interactions present between GNI/GNA and amino acid. The interactions were found to be primarily hydrogen bonding in nature. These interactions are reminiscent of those present in the lectin-carbohydrate and glycosidase substrate. Thus, the carbohydrate moiety present in GNI shows high specificity toward the -COOH group of the amino acid, which may be relevant to such interactions present between the carbohydrates and the polypeptides.     

Characterization of new-layered Cr(III)-doped chlorocadmiumphosphate, Cd(HPO4)Cl·[H3N(CH2)6NH3]0.5 crystal by EPR and optical studies

Cr(III)-doped Cd(HPO₄)Cl·[H₃N(CH₂)₆NH₃]_0.5, a new-layered cadmium phosphate, is synthesized in acidic condition at room temperature. EPR and optical studies are carried out at room temperature. Polycrystalline EPR spectrum reveals the presence of two sites of Cr(III) ions in this layered phosphate lattice with zero-field splitting values of 24.24 and 7.65 mT, indicating that Cr(III) ions are in distorted octahedral sites. The optical absorption spectrum of the sample indicates near octahedral symmetry for the dopant ions. Crystal field, inter-electronic and bonding parameters are evaluated by collaborating EPR and optical data. The evaluated parameters suggest the mode of entry of Cr(III) ion into the layered phosphate as interstitial site, and bonding between the metal and ligand is partially covalent.     

Two carbamoyl‐substituted di­hydro­pyrimidines: potential mimics of di­hydro­pyridine calcium channel blockers

The structures of two conformationally similar 1,4‐di­hydro­pyrimidines with a novel carbamoyl substitution, viz. 6‐methyl‐5‐(N‐methyl­carbamoyl)‐4‐phenyl‐1,2,3,4‐tetrahydro­py­rimidine‐2‐thione monohydrate, C₁₃H₁₅N₃OS·H₂O, (I), and 4‐(4‐chloro­phenyl)‐6‐methyl‐5‐(N‐methyl­carbamoyl)‐1,2,3,4‐tetra­hydro­pyrimidine‐2‐thione monohydrate, C₁₃H₁₄ClN₃OS·H₂O, (II), exhibit the structural features of 1,4‐di­hydro­pyridine calcium channel blockers. In both structures, the pyrimidine ring adopts a flattened boat conformation and the carbamoyl side chain is in an extended conformation with an anticlinal orientation. The phenyl ring occupies a pseudo‐axial position with respect to the pyrimidine ring in these structures. Both compounds crystallize with one mol­ecule of water, which participates in a two‐dimensional hydrogen‐bonding network. The mol­ecules are linked into dimers by N—H·S hydrogen bonds in both structures.     

Enantioselective Nitroso‐Diels–Alder Reaction and Its Application for the Synthesis of (−)‐Peracetylated Conduramine A‐1

Cu^I‐catalyzed enantioselective nitroso‐Diels–Alder reactions (NDA reactions) of 2‐nitrosopyridine with various dienes are presented. The [CuPF₆(MeCN)₄]/Walphos‐CF₃ catalyst system is best suited to catalyze the NDA reaction of various dienes by using 2‐nitrosopyridine as a dienophile. In most of the cases studied, cycloadducts are obtained in quantitative yield with very good to excellent enantioselectivities. Based on DFT calculations, a model to explain the stereochemical outcome of the NDA reaction is presented. Finally, an efficient short synthesis of (?)‐peracetylated conduramine A‐1 by applying the enantioselective NDA reaction as a key step is described.     

Lenalidomide,an antineoplastic drug,and its hemihydrate

The crystal structures of lenalidomide [systematic name: (RS)‐3‐(4‐amino‐1‐oxoisoindolin‐2‐yl)piperidine‐2,6‐dione], C₁₃H₁₃N₃O₃, (I), an antineoplastic drug, and its hemihydrate, C₁₃H₁₃N₃O₃·0.5H₂O, (II), have been determined by single‐crystal X‐ray diffraction analysis. The overall conformation of the molecule defined by the orientation of the two ring portions, viz. pyridinedione and isoindolinone, is twisted in both structures. The influence of the self‐complementary pyridinedione ring is seen in the crystal packing of both structures through its involvement in forming hydrogen‐bonded dimers, although alternate dione O atoms are utilized. An extensive series of N—H...O hydrogen bonds link the dimers into two‐dimensional supramolecular arrays built up from infinite chains. The water molecule in (II) has a cohesive function, connecting three lenalidomide molecules by hydrogen bonds. The significance of this study lies in the analysis of the interactions in these structures and the aggregations occurring via hydrogen bonds in the hydrated and dehydrated crystalline forms of the title compound.     

Critically indecomposable graphs

An undirected graph G=(V,E) with a specific subset X⊂V is called X-critical if G and G(X), induced subgraph on X, are indecomposable but G(V−{w}) is decomposable for every w∈V−X. This is a generalization of critically indecomposable graphs studied by Schmerl and Trotter [J.H. Schmerl, W.T. Trotter, Critically indecomposable partially ordered sets, graphs, tournaments and other binary relational structures, Discrete Mathematics 113 (1993) 191-205] and Bonizzoni [P. Bonizzoni, Primitive 2-structures with the (n−2)-property, Theoretical Computer Science 132 (1994) 151-178], who deal with the case where X is empty.We present several structural results for this class of graphs and show that in every X-critical graph the vertices of V−X can be partitioned into pairs (a₁,b₁),(a₂,b₂),…,(a_m,b_m) such that G(V−{a_j1,b_j1,…,a_jk,b_jk}) is also an X-critical graph for arbitrary set of indices {j₁,…,j_k}. These vertex pairs are called commutative elimination sequence. If G is an arbitrary indecomposable graph with an indecomposable induced subgraph G(X), then the above result establishes the existence of an indecomposability preserving sequence of vertex pairs (x₁,y₁),…,(x_t,y_t) such that x_i,y_i∈V−X. As an application of the commutative elimination sequence of an X-critical graph we present algorithms to extend a 3-coloring (similarly, 1-factor) of G(X) to entire G.     

Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as approximately Nx with the number of monomers. We find two distinct exponents depending on the generations, x=0.47 for G1-G3 and x=0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G+1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.     

Quantification of clopidogrel in human plasma by sensitive liquid chromatography/tandem mass spectrometry

A simple, sensitive and rapid high-performance liquid chromatography/positive electrospray ionization tandem mass spectrometry method was developed and validated for the assay of clopidogrel in human plasma. Following liquid-liquid extraction, the analytes were separated using an isocratic mobile phase on a reversed-phase column and analyzed by mass spectrometry in the multiple reaction monitoring mode using the respective [M+H](+) ions, m/z 322/212 for clopidogrel and m/z 264/154 for the internal standard. The assay exhibited a linear dynamic range of 5-6000 pg/mL for clopidogrel in human plasma. The lower limit of quantification was 5 pg/mL with a relative standard deviation of less than 8%. Acceptable precision and accuracy were obtained for concentrations over the standard curve range. A run time of 2.5 min for each sample made it possible to analyze more than 400 human plasma samples per day. The validated method has been successfully used to analyze human plasma samples for application in pharmacokinetic, bioavailability or bioequivalence studies.     

Electrospray ionisation mass spectral studies on hydrolysed products of sulfur mustards

Off-site detection of the hydrolysed products of sulfur mustards in aqueous samples is an important task in the verification of Chemical Weapons Convention (CWC)-related chemicals. The hydrolysed products of sulfur mustards are studied under positive and negative electrospray ionisation (ESI) conditions using an additive with a view to detecting them at trace levels. In the presence of cations (Li(+), Na(+), K(+) and NH(4) (+)), the positive ion ESI mass spectra of all the compounds include the corresponding cationised species; however, only the [M+NH(4)](+) ions form [M+H](+) ions upon decomposition. The tandem mass (MS/MS) spectra of [M+H](+) ions from all the hydrolysed products of the sulfur mustard homologues were distinct and allowed these compounds to be characterised unambiguously. Similarly, the negative ion ESI mass spectra of all the compounds show prominent adducts with added anions (F(-), Cl(-), Br(-), and I(-)), but the [M-H](-) ion can only be generated by decomposition of an [M+F](-) ion. The MS/MS spectra of the [M-H](-) ions from all the compounds result in a common product ion at m/z 77. A precursor ion scan of m/z 77 is shown to be useful in the rapid screening of these compounds in aqueous samples at trace levels, even in the presence of complex masking agents, without the use of time-consuming sample preparation and chromatography steps. An MS/MS method developed to measure the detection limits of the hydrolysed products of sulfur mustards found these to be in the range of 10-500 ppb.     

Simultaneous quantification of atorvastatin and active metabolites in human plasma by liquid chromatography-tandem mass spectrometry using rosuvastatin as internal standard

A simple, sensitive, selective and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantification of atorvastatin and its active metabolites ortho-hydroxyatorvastatin and para-hydroxyatorvastatin in human plasma using rosuvastatin as internal standard (IS). Following simple liquid-liquid extraction, the analytes were separated using an isocratic mobile phase on a reversed-phase C18 column and analyzed by MS in the multiple reaction monitoring mode using the respective [M+H]+ ions, m/z 559/440 for atorvastatin, m/z 575/466 for ortho-hydroxyatorvastatin, m/z 575/440 for para-hydroxyatorvastatin and m/z 482/258 for the IS. The assay exhibited a linear dynamic range of 0.1-20 ng/mL for atorvastatin and its two metabolites in human plasma. The lower limit of quantification was 100 pg/mL with a relative standard deviation of less than 8%. Acceptable precision and accuracy were obtained for concentrations over the standard curve range. The average absolute recoveries of atorvastatin, ortho-hydroxyatorvastatin, para-hydroxyatorvastatin and the IS from spiked plasma samples were 54.2 +/- 3.2, 50.1 +/- 3.8, 65.2 +/- 3.6 and 71.7 +/- 2.7%, respectively. A run time of 2.5 min for each sample made it possible to analyze more than 300 human plasma samples per day. The validated method has been successfully used to analyze human plasma samples for application in pharmacokinetic, bioavailability or bioequivalence studies.