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.     

Identification of unusual (modified and non-encoded) amino acid residues in peptides by combinations of high-performance liquid chromatography and high-performance capillary electrophoresis with matrix-assisted laser desorption ionization time-of-flight mass spectrometry

The techniques for micro-level analysis of some widespread unusual amino acids (phosphorylated and hydroxylated ones) as well as of some genetically non-encoded amino acids were developed for their subsequent identification in the peptide and protein amino acid sequence by narrow-bore column high-performance liquid chromatography (10 pmol of the sample), high-performance capillary electrophoresis (1–10 pmol), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (1–10 pmol), and automatic protein gas phase sequencing (1–50 pmol).     

Conformational studies of the linear homooligomers of a glucose-derived furanoid sugar amino acid

Conformational analysis of the linear tetramer of the glucose-derived furanoid sugar amino acid 1 by NMR and constrained molecular dynamics studies revealed that the fully protected tetramer 2a has a well-defined structure in CDCl₃ with repeating β-turns, each involving a 10-membered ring structure with intramolecular hydrogen bonds between NH_i → CO_i−2. Its deprotected versions 2b and 2c showed aggregation in organic solvents with structures similar to that of 2a.     

Performance and selectivity of polymeric pseudostationary phases for the electrokinetic separation of amino acid derivatives and peptides

Two polymeric pseudostationary phases, one an acrylamide polymer and the second a siloxane polymer, have been investigated for the separation of naphthalene-2,3-dicarboxaldehyde (NDA)-derivatized amino acids and small peptides. The dervatized amino acids were detected by UV absorbance and laser-induced fluorescence (LIF) detection. The polymers provided very high efficiency and good selectivity for the separation of the amino acids. The separation selectivity using the polymers was significantly different from that of SDS micelles, and there were subtle differences in selectivities between the polymers. Although very good detection limits were obtained with LIF detection, a significant background signal was observed when the polymers were not washed to remove fluorescent impurities. The polymers did not separate the peptides very well. It is postulated that the fixed covalent structure of the polymers prevents them from interacting strongly or efficiently with the peptides, which are large in relation to the analytes typically separated by electrokinetic chromatography using polymers.     

Conformational studies of 3,4-dideoxy furanoid sugar amino acid containing analogs of the receptor binding inhibitor of vasoactive intestinal peptide

Conformational analysis of vasoactive intestinal peptide (VIP) receptor binding inhibitor Leu¹-Met²-Tyr³-Pro⁴-Thr⁵-Tyr⁶-Leu⁷-Lys⁸1 by various NMR techniques and constrained molecular dynamics (MD) simulation studies revealed that the molecule had a turn structure involving its Tyr³-Pro⁴-Thr⁵-Tyr⁶ moiety with intramolecular hydrogen bond between Tyr⁶NH→Tyr³CO. In order to mimic the structure of 1, peptidomimetic analogs 2-4 were synthesized using conformationally constrained scaffolds of 3,4-dideoxy furanoid sugar amino acids (2S,5R)-ddSaa1 5 and its enantiomer (2R,5S)-ddSaa2 6. All these analogs displayed well defined three-dimensional structures akin to that found in 1. Peptides 2 and 3, which differed only in the sugar amino acid stereochemistry, show propensity of structures with identical intramolecular hydrogen bonds between ThrNH→MetCO. A similar structure with a hydrogen bond between TyrNH→MetCO was observed in 4.     

Molecular pair potential of chiral amino acid amphiphile in Langmuir monolayers on the basis of an atomistic model

In the present work, the pair potential of enantiomeric N-palmitoyl aspartic acid amphiphile monolayer at the air/water interface is calculated based on an atomistic model. The molecular structure and partial charges are calculated using two semi empirical (PM3, AM1) and one empirical (Gasteiger and Marcili) methods. A distance-dependent dielectric function is used to represent the interfacial dielectric constant at the aqueous subphase. The present study indicates that a pair of molecules have favorable interaction at specific ranges of mutual orientations. Other orientations are favorable but at larger separations. Favorable electrostatic interaction at a specific combination of orientation and short separations of the head groups significantly contribute to the total energy. The curvature of the domain boundary is suggested to be driven by the favorable arrangement which is dependent on the pair potential of molecules. The use of charges obtained by the PM3 and GM do not lead to a significant variation of the orientation-dependent features, while the AM1 predicts higher partial charges and interactions are stronger than the former two methods. However, orientation-dependent features remain the same. The variations in the LJ parameters and charges indicate that the conclusions made are insensitive to the choice of parameters. The mutual favorable interaction predicted by calculation agree with the handedness of curvature of domains.     

Analysis of the binding sites with NL-101 to amino acids and peptides by HPLC/MS/MS

Collision-induced dissociation experiment demonstrated that under the same collision energy, different fragmentation pattern could help distinguish the accurate location of amino acids-NL adducts.     

Long‐term thermal stability of fluorescent dye used for chiral amino acid analysis on future spaceflight missions

Future spaceflight missions focused on life detection will carry with them new, state‐of‐the‐art instrumentation capable of highly selective and sensitive organic analysis. CE–LIF is an ideal candidate for such a mission due to its high separation efficiency and low LODs. One perceived risk of utilizing this technique on a future mission is the stability of the chemical reagents in the spaceflight environment. Here, we present an investigation of the thermal stability of the fluorescent dye (5‐carboxyfluorescein succinimidyl ester) used for amino acid analysis. The dye was stored at 4, 25, and 60°C for 1 month, 6 months, 1 year, and 2 years. When stored at 4°C for 2 years, 25°C for 6 months, or 60°C for 1 month there was no effect on CE‐LIF assay performance due to dye degradation. Beyond these time points, while the dye degradation begins to interfere with the analysis, it is still possible to perform the analysis and achieve the majority of amino acid biosignature science goals described in the science definition team report for the potential Europa Lander mission. This work indicates that thermal control of the dye at ≤4°C will be needed during transit on future spaceflight missions to maintain dye stability.     

Equilibrium investigation of complex formation reactions involving copper(II), nitrilo-tris(methyl phosphonic acid) and amino acids,peptides or DNA constitutents. The kinetics,mechanism and correlation of rates with complex stability for metal ion promoted hydrolysis of glycine methyl ester

The complex formation reactions of [Cu(NTP)(OH₂)]^4? (NTP?=?nitrilo-tris(methyl phosphonic acid)) with some selected bio-relevant ligands containing different functional groups, are investigated. Stoichiometry and stability constants for the complexes formed are reported. The results show that the ternary complexes are formed in a stepwise mechanism whereby NTP binds to copper(II), followed by coordination of amino acid, peptide or DNA. Copper(II) is found to form Cu(NTP)H _n species with n?=?0, 1, 2 or 3. The concentration distribution of the various complex species has been evaluated. The kinetics of base hydrolysis of glycine methyl ester in the presence of copper(II)-NTP complex is studied in aqueous solution at different temperatures. It is proposed that the catalysis of GlyOMe ester occurs by attack of OH^? ion on the uncoordinated carbonyl carbon atom of the ester group. Activation parameters for the base hydrolysis of the complex [Cu(NTP)NH₂CH₂CO₂Me]^4? are, ΔH^±?=?9.5?±?0.3?kJ?mol^?1 and ΔS^±?=??179.3?±?0.9?J?K^?1?mol^?1. These show that catalysis is due to a substantial lowering of ΔH^±.     

Enantioseparation of various amino acid derivatives on a quinine based chiral anion-exchange selector at variable temperature conditions. Influence of structural parameters of the analytes on the apparent retention and enantioseparation characteristics

The influence of temperature on the performance of an enantioselective anion-exchange type chiral selector (SO) was systematically investigated. The resolution of the enantiomers of 23 N-acylated amino acids (selectands, SAs) on a covalently immobilized quinine tert.-butylcarbamate chiral stationary phase (CSP) was studied under linear chromatographic conditions over a temperature range of 0–85 °C with hydro–organic buffers (pH_a 6.0) as mobile phases. The apparent enantioseparation factors increased considerably at low column temperatures, indicating that enthalpic contributions are the dominating thermodynamic driving force for chiral recognition for all investigated SAs. Retention factors gave non-linear van’t Hoff plots, while the corresponding apparent enantioseparation factors showed linear van’t Hoff behavior. Correlations between magnitude and sign of the relative thermodynamic parameters of enantioselective adsorption (ΔΔG, ΔΔH and ΔΔS) and specific structural features of the analytes, i.e., steric and electronic nature of the various side chains and the N-acyl groups, are discussed with the aim to rationalize their possible contributions to the overall chiral recognition.     

Chiral discrimination in biliverdin (S)-amino acids,II: Structural variations of the amino acid functional groups

The Biliverdin-(S)-amino acid derivatives2–21 have been synthesized, and are subject to a thorough c. d. and u. v.-vis. electronic absorption analysis in the bilatriene chromophoric region. It is shown that the extent of chiral discrimination of the bilatriene helices is particularly sensitive towards structural variations of the amino acids bound to the propionic side chains. Thus, a pronounced decrease of chiral induction occurs if hydrogen bonding between one of the two essential coordination sites of the amino acid entity and the bilatriene backbone is disturbed. Accordingly, derivatives of (S)-amino acidt-butyl esters (3,5,7,16 and17) andN-substituted (S)-amino acids (8–10, 20 and21) generally display weak c. d. spectra. If additional polar groups are present in bis(amino acid) derivatives mutual interferences of the adjacent side chains must be taken into account. The attenuations of -values observed for the bis(serine) and bis(aspartic acid) compounds14 and15 thus are mainly due to intramolecular interchain interactions. The results provide evidence in support of the proposed mechanism of chiral discrimination in biliverdin amino acids.Dedicated to Prof. Dr.Kurt L. Komarek on the occasion of his 60th birthday.     

Surface-grafting onto aramid powder: reaction of acyl chloride groups on the surface with functional polymers having terminal hydroxyl or amino groups

The surface-grafting of polymers onto aramid, poly(p-phenylene terephthalamide), powder surface by the reaction of acyl chloride groups on the surface with functional polymers having terminal hydroxyl and amino groups was investigated. The introduction of acyl chloride groups onto the aramid powder surface was achieved by the reaction of the aramid powder with adipoyl dichloride: the acyl chloride group content of the surface was estimated to be 1.14 mmol/g (0.17 mmol/m²) by elemental analysis. It was found that by the reaction of acyl chloride groups on the surface with functional polymers, such as terminal diol-type poly(propylene oxide) (PPG) and terminal diamine-type poly(dimethylsiloxane) (SDA), these polymers were grafted onto the aramid powder surface; the percentage of surface grafting of PPG and SDA onto the aramid powder was 16.7 and 22.4%, respectively. The thermogravimetric curve of PPG surface-grafted aramid powder exhibited an initial weight loss at about 250°C and a second weight loss at about 500°C. This indicated that the grafting of PPG is limited to the powder surface. The wettability of the aramid powder surface turned from hydrophobic to hydrophilic by the surface-grafting of PPG onto the surface.     

Synthesis and properties of poly(phenylacetylenes) having two polar groups or one cyclic polar group on the phenyl ring

Phenylacetylene (PA) derivatives having two polar groups (ester, 2a – d ; amide, 4) or one cyclic polar group (imide, 5a – c ) were polymerized using (nbd)Rh⁺[(η⁶‐C₆H₅)B^?(C₆H₅)₃] catalyst to afford high molecular weight polymers (～1 × 10⁶ – 4 × 10⁶). The hydrolysis of ester‐containing poly(PA), poly( 2a) , provided poly(3,4‐dicarboxyPA) [poly ( 3 )], which could not be obtained directly by the polymerization of the corresponding monomer. The solubility properties of the present polymers were different from those of poly(PA) having no polar group; that is, poly( 2a )–poly( 2d ) dissolved in ethyl acetate and poly( 4 ) dissolved in N,N‐dimethylformamide, while poly(PA) was insoluble in such solvents. Ester‐group‐containing polymers [poly( 2a )–poly( 2d )] afforded free‐standing membranes by casting from THF solutions. The membrane of poly( 2a ) showed high carbon dioxide permselectivity against nitrogen (PCO₂/PN₂ = 62). © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5943–5953, 2006     

Impact of amines as co-modifiers on the enantioseparation of various amino acid derivatives on a tert-butyl carbamoylated quinine-based chiral stationary phase

A tert-butyl carbamoylated quinine-based chiral stationary phase (CSP) for direct enantiomer separation of various natural and unnatural amino acid derivatives was studied. The influence of functional groups in the amino acid side chains upon the enantioseparation is discussed with the aim of realizing contributions to their overall chiral recognition. The effects of various amines as co-modifiers upon retention and overall enantioselectivity of amino acid derivatives in polar organic solvents was systematically investigated. In general, retention times decreased with increasing amine concentrations without a distinct alteration of enantioselectivity. All analytes were rapidly resolved on the CSP with the methanol-based mobile phase containing 87 mM acetic acid and 7 mM triethylamine.     

Effects of starvation for 4-20 days on the amino acid content of Biomphalaria glabrata as determined by cellulose HPTLC-densitometry with confirmation of identity using silica gel and RP-18 W plates with two mobile phases causing inversion of the separation mechanism

The effects of starvation at 4, 7, 10, 14, and 20 days on the amino acid content of Biomphalaria glabrata was determined by high performance thin layer chromatography (HPTLC)-densitometry. Cultures of control and starved snails were prepared for each duration of time. Samples were extracted using ethanol-water (70:30), and supernatant was collected after multiple centrifugations. Samples and standards were applied as bands using a CAMAG Linomat 4 onto cellulose HPTLC plates and developed in a 2-butanol-pyridine-acetic acid-water (39:34:10:26) mobile phase before spraying with ninhydrin detection reagent and scanning with a CAMAG 3 scanner to quantify ornithine (Orn), glycine (Gly), alanine (Ala), valine (Val), and leucine (Leu). Amino acid identification was confirmed by HPTLC on silica gel plates and RP-18?W plates using two different mobile phases causing inversion of the separation mechanism. Starvation led to an overall decrease in amino acid content in comparison to the control snails, however, the amount of amino acids in the starved snails had no correlation with the duration of starvation.     

Reactions of guaiazulene with thiophene-2,5-dicarbaldehyde and furan-2,5-dicarbaldehyde in methanol in the presence of hexafluorophosphoric acid: a facile preparation and properties of delocalized dicarbenium-ion compounds stabilized by two 3-guaiazulenyl groups and a thiophene (or furan) ring

Reaction of guaiazulene (1) with thiophene-2,5-dicarbaldehyde (2) in methanol in the presence of hexafluorophosphoric acid at 25 °C for 3 h gives as high as 90% isolated yield of the delocalized dicarbenium-ion compound, 2,5-thienylenebis(3-guaiazulenylmethylium) bis(hexafluorophosphate) (3). Similarly, reaction of 1 with furan-2,5-dicarbaldehyde (4) under the same conditions as the above reaction affords the corresponding dicarbenium-ion compound, 2,5-furylenebis(3-guaiazulenylmethylium) bis(hexafluorophosphate) (5), in 84% isolated yield. Along with a facile preparation and the spectroscopic and electrochemical properties of 3 and 5, comparative studies on the ¹H and ¹³C NMR spectral and chemical properties of 3 and 5 with those of the delocalized mono- and dicarbenium-ion compounds [i.e., (3-guaiazulenyl)(2-thienyl)methylium hexafluorophosphate (7), (2-furyl)(3-guaiazulenyl)methylium hexafluorophosphate (9), α,α′-bis(3-guaiazulenylmethylium) bis(tetrafluoroborate) (10), 1,2-phenylenebis(3-guaiazulenylmethylium) bis(hexafluorophosphate) (11), and 1,4-phenylenebis(3-guaiazulenylmethylium) bis(tetrafluoroborate) (12)] are reported. Moreover, referring to the results of the X-ray crystallographic analyses of 7, 9, 11, and 12, the optimized 2,5-thienylenebis(3-guaiazulenylmethylium)- and 2,5-furylenebis(3-guaiazulenylmethylium)-ion structures for 3 and 5, calculated by a WinMOPAC (version 3.0) program using PM3 as a semiempirical Hamiltonian, are described.     

Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes

Understanding the factors influencing the stability of protein mutants is an important task in molecular and computational biology. In this work, we have approached this problem by examining the relative importance of secondary structure and solvent accessibility of the mutant residue for understanding/predicting the stability of protein mutants. We have used hydrophobic, electrostatic and hydrogen bond free energy terms and nine unique physicochemical, energetic and conformational properties of amino acids in the present study and these parameters have been related with changes in thermal stability (DeltaTm) of all the single mutants of lysozymes based on single and multiple correlation coefficients. As expected the properties reflecting hydrophobicity and hydrophobic free energy play a major role to distinguish stabilizing and destabilizing mutants. The hydrophobic free energy due to carbon and nitrogen atoms distinguish the stability of coil and strand mutations to the accuracy of 100 and 90%, respectively. In agreement with previous results, the subgroup classification based on secondary structure and the information about its location in the structure yielded good relationship with the experimental DeltaTm. We revealed that the secondary structure information is equally or more important than solvent accessibility for understanding the stability of protein mutants. The comparison of amino acid properties with free-energy terms indicate that the energetic contribution explains the mutant stability better in coil region whereas the amino acid properties do better in strand region. Further, the combination of free energies with amino acid properties increased the correlation significantly. The present study demonstrates the importance of classifying the mutants based on secondary structure to the stability of proteins upon mutations.     

Reactions of guaiazulene with methyl terephthalaldehydate and 2-hydroxy- and 4-hydroxybenzaldehydes in methanol in the presence of hexafluorophosphoric acid: comparative studies on molecular structures and spectroscopic, chemical and electrochemical properties of monocarbocations stabilized by 3-guaiazulenyl and phenyl groups

Reaction of guaiazulene (1) with methyl terephthalaldehydate (2) in methanol in the presence of hexafluorophosphoric acid at 25 °C for 2 h under aerobic conditions gives (3-guaiazulenyl)[4-(methoxycarbonyl)phenyl]methylium hexafluorophosphate (5) in 94% yield. Similarly, reactions of 1 with 2-hydroxybenzaldehyde (3) and 4-hydroxybenzaldehyde (4) under the same reaction conditions as 2 give (3-guaiazulenyl)(2-hydroxyphenyl)methylium hexafluorophosphate (6) and (3-guaiazulenyl)(4-hydroxyphenyl)methylium hexafluorophosphate (7) in 89 and 97% yields, respectively. Comparative studies on the molecular structures as well as the spectroscopic, chemical and electrochemical properties of the monocarbocation compounds 5-7 stabilized by 3-guaiazulenyl and 4-(methoxycarbonyl)phenyl (or 2-hydroxy- or 4-hydroxyphenyl) groups are reported.