The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom-up investigation

The geometry of surrounding water molecules on the side chain of glycine, alanine, α-aminoisobutyric acid, α-aminobutyric acid, valine, and related hydrocarbons has been analyzed combining bottom-up and quantum chemical methodologies. To minimize the cavity size and to prevent water-water hydrogen bonding loss, the water molecules adopt a shape, resembling the one found in crystal structure of gas clathrate hydrates, with water molecules tangentially oriented to the surface of hydrophobic side chain. The cage is directly hydrogen bonded to the backbone's polar groups, thus hydration shells around hydrophobic and hydrophilic groups are folded together in amphiphilic molecules. The hydrophobe enclathration implies a substantial freedom degree reduction which makes it entropically disfavored. This disadvantageous entropic contribution is partially compensated by the favorable van der Waals interactions with guest in stabilizing clathrate hydrate formation. The water shell around the side chain relates intimately with the side-chain rotational isomerism. Present data are correlated with the experimental determined populations of the three rotamers, yielding promising results for both α-aminobutyric acid and valine.     

Investigation of some 2,3-didehydro amino acids by fast ion bombardment,chemical ionization and mass-selected collision-induced dissociation mass spectrometry

Four 2,3-didehydro amino acids were investigated by fast ion bombardment (FIB) and ammonia chemical ionization (NH₃-CI) mass Spectrometry. The protonated molecules formed by the two techniques were mass selected and their respective collision-induced dissociations (CIDs) in the translational energy range 5–200 eV (in the laboratory frame of reference) were investigated. No obvious quantitative differences between the FIB and NH₃-CI mass spectra of the (E)- and (Z)-isomers were observed. Different internal excitation of the protonated molecules formed by the two techniques and the role of CID data in clarifying this particular observation are discussed.     

Investigation of the interaction of HCl and three amino acids,HEPES, MOPSO and glycine,by EMF measurements

Ionic interaction in the three systems Hcl-HEPES (N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid), HCl-MOPSO (3-(N-Morpholino)-2-hydroxypropanesulfonic acid), and HCl-glycine have been studied in terms of their mutual influence on the respective activity coefficients of each component. Activity coefficients for each component of the three systems are calculated from emf measurements of solutions containing HCl and the amino acid in a H₂/solution/AgCl,Ag cell at 25°C. The first dissociation constant of HEPES at 25°C has also been determined using emf and pH titration measurements.     

Lipophilicity determination of some fully protected peptides and amino acids

Summary The lipophilicity of 21 fully protected peptides and amino acids was determined by reversed-phase thin-layer chromatography. The R_M values decreased linearly with growing methanol concentration of the eluent. The sequence and conformation of molecular substructures did not significantly influence the lipophilicity. The presence of salt and ammonia in the eluent had a negligible impact on retention; the effect of the pH value was also low. In the presence of 1M and 2M acetic acid the retention of each compound considerably decreased. Acetic acid also changed markedly the selectivity. Our data suggest that the acetic acid has a preponderant role in changing the retention and selectivity of fully protected peptides and amino acids in reversedphase thin-layer chromatography.     

Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids

Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds.     

Effect of some amino acids and peptides on silicic acid polymerization

The polymerization of silicic acid in aqueous solutions at different pH was followed by the colorimetric molybdosilicate method. The role of four amino acids (serine, lysine, proline and aspartic acid) and the corresponding homopeptides was studied. All four amino acids behave the same way and favor the condensation of silicic acid. Peptides exhibit a stronger catalytic effect than amino acids but they appear to behave in very different ways depending on the nature of side-groups and pH. Poly-lysine and poly-proline for instance lead to the precipitation of solid phases containing both silica and peptides. The role of these biomolecules on the polymerization of silicic acid is discussed in terms of electrostatic interactions, hydrogen bonds and solubility.     

13C isotope effects on 1H chemical shifts: NMR spectral analysis of 13C‐labelled D‐glucose and some 13C‐labelled amino acids

The one‐ and two‐bond ¹³C isotope shifts, typically ?1.5 to ?2.5 ppb and ?0.7 ppb respectively, in non‐cyclic aliphatic systems and up to ?4.4 ppb and ?1.0 ppb in glucose cause effects that need to be taken into account in the adaptive NMR spectral library‐based quantification of the isotopomer mixtures. In this work, NMR spectral analyses of some ¹³C‐labelled amino acids, D ‐glucose and other small compounds were performed in order to obtain rules for prediction of the ¹³C isotope effects on ¹H chemical shifts. It is proposed that using the additivity rules, the isotope effects can be predicted with a sufficient accuracy for amino acid isotopomer applications. For glucose the effects were found strongly non‐additive. The complete spectral analysis of fully ¹³C‐labelled D ‐glucose made it also possible to assign the exocyclic proton signals of the glucose. Copyright © 2009 John Wiley & Sons, Ltd.     

Reactivity of some sulphur- and non-sulphur-containing amino acids towards water soluble colloidal MnO<Subscript>2</Subscript>. A kinetic study

Kinetic data for the oxidation of glutathione (reduced, GSH), cysteine, glycine and glutamic acid by colloidal manganese dioxide, (MnO₂) _n are reported. Colloidal MnO₂, oxidized glutathione to disulphide (glutathione, oxidized), was reduced to manganese (II). Glycine and glutamic acid (structural units of glutathione) are not oxidized by colloidal MnO₂, but the other structural unit, cysteine, is also oxidized by the same oxidant under similar experimental conditions. This is interpreted in terms of the rate-determining colloidal MnO₂-S bonded intermediate. The reactivity of GSH towards colloidal MnO₂ is very much higher than cysteine. Kinetics of oxidation of GSH and cysteine by colloidal MnO₂ were performed spectrophotometrically as a function of [GSH], [cysteine], colloidal [(MnO₂) _n ], [HClO₄], temperature and trapping agents sodium fluoride and manganese (II) (reduction product of colloidal MnO₂). The purpose of this work was to study the role of –NH₂, –COOH, –SH groups present in the carbon chain of the above amino acids. It was found that the reactivity of –SH group is higher than –NH₂ and –COOH groups. The mechanisms, involving a colloidal MnO₂ complex with GSH and cysteine, are proposed. The complexes decompose in a rate-determining step, leading to the formation of free radical and manganese (III), which is also an intermediate. The dimerization of radicals takes place in a subsequent fast step to yield the products.     

Kinetics and mechanism of oxidation of some basic amino acids with bromamine-T

Kinetics of oxidative decarboxylation of arginine, glutamine, histidine and lysine by bromamine-T (BAT) was investigated in acid and alkaline media at 30° and 20° fespectively. The form of the rate law at low concentrations of HClO₄ has been worked out. Proton inventory studies in H₂O-D₂O mixtures with Arg as a probe have been made. The rate increases in the order: His > Lys > Arg > Glu - NH₂. In alkaline media, the rate shows a first order dependence on [BAT]₀ and is fractional in [S] and [OH].p-Toluene sulphonamide retards the rate. Mechanisms proposed are consistent with the experimental rate laws.     

Synthesis,characterization, equilibrium studies,and biological activity of complexes involving copper(II), 2-aminomethylthiophenyl-4-bromosalicylaldehyde Schiff base,and selected amino acids

Ternary complexes of copper(II) with 2-aminomethylthiophenyl-4-bromosalicylaldehyde (ATS) and some amino acids have been isolated and characterized by elemental analyses, IR, magnetic moment, molar conductance, UV–vis, mass spectra, and ESR. The proposed general formulas of the prepared complexes are [Cu(ATS)(AA)]·nH₂O (where AA?=?glycine, alanine, and valine). The low molar conductance values suggest the non-electrolytic nature of the complexes. IR spectra show that ATS is coordinated to copper in a bidentate manner through azomethine-N and phenolic-OH. The amino acids also are monobasic bidentate ligands via amino and ionized carboxylate groups. The magnetic and spectral data indicate the square-planar geometry of Cu(II) complexes. The geometry of the Cu(II) complexes has been fully optimized using parameterized PM3 semiempirical method. The Cu–N bond length is longer than that of Cu–O in the isolated complexes. Also, information is obtained from calculations of molecular parameters for all complexes including net dipole moment of the metal complexes, values of binding energy, and lipophilicity value (log P). The antimicrobial activity studies indicate significant inhibitory activity of complex 3 against the selected types of bacteria. The mixed ligand complexes have also been studied in solution state. Protonation constants of ATS and amino acids were determined by potentiometric titration in 50% (v/v) DMSO–water solution at ionic strength of 0.1?M NaCl. ATS has two protonation constants. The binary and ternary complexes of copper(II) involving ATS and some selected amino acids (glycine, alanine, and valine) were examined. Copper(II) forms [Cu(ATS)], [Cu(ATS)₂], [Cu(AA)], [Cu(AA)₂], and [Cu(ATS)(AA)] complexes. The ternary complexes are formed in a simultaneous mechanism.     

Investigation of the amino acids glycine, proline, and methionine by photoemission spectroscopy

The valence and core level photoelectron spectra of glycine, proline, and methionine in the gas phase have been investigated by VUV and soft X-ray radiation. The outer valence band photoemission spectra are similar to previously reported He I spectra, although relative peak intensities are different due to the different photon energy. We extended the spectral range to include the inner valence region. The carbon, nitrogen, and oxygen 1s as well as the sulfur 2p core level spectra of these amino acids have been measured and the states identified. Valence band spectra of proline have been recorded as a function of temperature, and they provide information about the relative populations of the lowest energy conformers.     

Synthesis of amino acid derivative Schiff base copper(II) complexes by microwave and wet mechanochemical methods

As resource- and time-saving and environmentally friendly synthetic methods than conventional one in a solution, microwave, and wet mechanochemical synthesis are tested for l-amino acid derivative Schiff base copper(II) complexes. Herein, we systematically compared efficiency (low-temperature, time, and yield (if possible to detect)) for both conventional solution method and microwave or mechanochemical methods. The wet mechanochemical synthesis promoted fast reaction (typically 20 ​min by mechanochemical vs 4 ​h by conventional) by a little amount of solvent for preparations of amino acid derivative Schiff base copper(II) complexes. New crystal structure of a five-coordinated square pyramidal copper(II) complex as one of the products of microwave method was also reported.     

Benzophenone Schiff bases of glycine derivatives: Versatile starting materials for the synthesis of amino acids and their derivatives

This review focuses on the introduction and early development, in solution, of phase-transfer catalyzed (PTC) reactions to afford racemic or enantioenriched natural and unnatural amino acids. To form monosubstituted amino acids alkylation reactions are performed on the benzophenone Schiff base of glycine. For α,α-disubstituted amino acids the activated intermediate is an aldimine derivative of the monosubstituted amino acid. Enantioenriched products are produced by organocatalysis using derivatives of Cinchona alkaloids as the phase-transfer catalyst. Selectivity for monoalkylatation and lack of product racemization depend on the acidities of the glycine imines, and dialkylated products are formed from aldimine esters of monoalkyl amino acids. The racemic and catalytic enantioselective reactions of a cationic glycine equivalent with organoboranes, organometallics and malonate anion are discussed as are other reactions of these versatile Schiff bases derivatives.     

A three-dimensional chemical phase pharmacophore mapping,QSAR modelling and electronic feature analysis of benzofuran salicylic acid derivatives as LYP inhibitors

Lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, has a critical negative regulatory role in T-cell antigen receptor (TCR) and emerged as a promising drug target for human autoimmune diseases. A five-point pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic ring features was generated for a series of benzofuran salicylic acid derivatives as LYP inhibitors in order to elucidate their anti-autoimmune activity. The generated pharmacophore yielded a significant 3D-QSAR model with r² of 0.9146 for a training set of 27 compounds. The model also showed excellent predictive power with Q² of 0.7068 for a test set of eight compounds. The investigation of the 3D-QSAR model has revealed the structural insights which could lead to more potent analogues. The most active and inactive compounds were further subjected to electronic structure analysis using density functional theory (DFT) at B3LYP/3?21^?G level to support the 3D-QSAR predictions. The results obtained from this study are expected to be useful in the proficient design and development of benzofuran salicylic acid derivatives as inhibitors of LYP.     

叶酸与氨基酸相互作用的荧光光谱

在模拟动物生理条件下,利用荧光光谱法在分子水平上研究了叶酸同色氨酸、酪氨酸、苯丙氨酸的相互作用;根据双对数方程求出了不同温度下两者反应的结合常数和结合位点数.结果表明:叶酸能导致氨基酸的荧光猝灭,三种氨基酸的猝灭机制均为静态猝灭;从相应的热力学参数可知,色氨酸和酪氨酸与叶酸之间的主要作用力为疏水作用力,而苯丙氨酸与叶酸之间的主要作用力为氢键和范德华力.     

Synthesis of N,N-dimethyl-2,4-dinitro-5-fluorobenzylamine and its reactions with amino acids and peptides

A practical synthesis is described for N,N-dimethyl-2,4-dinitro-5-fluorobenzylamine (DMDNFB) and its -d₆ analog as an alternative Sanger's reagent (DNFB), for purposes of amino acid derivatization detectable by positive mode electrospray ionization mass spectrometry. DMDNFB is comparable to DNFB in its efficiency to derivatize amino acids and peptides. Various DMDNP (d₀/d₆) derivatives of (modified) lysine were synthesized to evaluate the potential use of isotope-edited LC-ESI-MS as a tool for structural definition of the posttranslational modification of protein-based lysines.     

关于氨基酸结构与RNA中碱基密码间关系的探讨

探讨了氨基酸结构与ＲＮＡ中碱基三字密码间的关系,找到了与决定氨基酸相应碱基三字码的主要因素,指出决定氨基酸三字码的第１,２个码的碱基的亲水性要与氨基酸的亲水性相匹配,强亲水性的碱基与强亲水性的氨基酸相应;第２个码的碱基的亲水性是决定其亲水性的主要因素,而第１个码的碱基亲水必屯有相当的影响,每种氨基酸的碱基三字码个数的多少,以及三字码中第３个码为何种碱基,都与氨基酸的化学结构密切相关,特别是与Ｒ（Ｒ