Interaction of dipropyltin(IV) with amino acids,peptides, dicarboxylic acids and DNA constituents

Interaction of dipropyltin(IV) with selected amino acids, peptides, dicarboxylic acids or DNA constituents was investigated using potentiometric techniques. Amino acids form 1?:?1 and 1?:?2 complexes and, in some cases, protonated complexes. The amino acid is bound to dipropyltin(IV) by the amino and carboxylate groups. Serine is complexed to dipropyltin(IV) with ionization of the alcoholic group. A relationship exists between the acid dissociation constant of the amino acids and the formation constants of the corresponding complexes. Dicarboxylic acids form both 1?:?1 and 1?:?2 complexes. Diacids forming five- and six-membered chelate rings are the most stable. Peptides form complexes with stoichiometric coefficients 111(MLH), 110(ML) and 11-1(MLH_?1)(tin: peptide: H⁺). The mode of coordination is discussed based on existing data and previous investigations. DNA constituents inosine, adenosine, uracil, uridine, and thymine form 1?:?1 and 1?:?2 complexes and the binding sites are assigned. Inosine 5′-monophosphate, guanosine 5′-monophosphate, adenosine 5′-monophosphate and adenine form protonated species in addition to 1?:?1 and 1?:?2 complexes. The protonation sites and tin-binding sites were elucidated. Cytosine and cytidine do not form complexes with dipropyltin(IV) due to low basicity of the donor sites. The stepwise formation constants of the complexes formed in solution were calculated using the non-linear least-square program MINIQUAD-75. The concentration distribution of the various complex species was evaluated as a function of pH.     

Synthesis and characterization of water-soluble zinc(II) Schiff-base complexes derived from amino acids and 3-formyl-4-hydroxybenzyl-triphenylphosphonium chloride

Tridentate Schiff-base ligands derived from condensation of 3-formyl-4-hydroxybenzyl-triphenylphosphonium chloride with glycine, L-alanine, L-valine, L-leucine and L-phenylalanine in the presence of Zn(OAc)₂ · 2H₂O form five new water-soluble Zn(II) complexes, which were characterized by elemental analyses, IR, electronic absorption and ¹H, ¹³C NMR spectroscopies. In the IR spectra of the complexes, the difference between the asymmetric and the symmetric carboxylate stretching frequencies is larger than ～210 cm^?1, which implies that the carboxylate groups are monodentate. UV-Vis electronic absorption studies show that Zn(II) functions as a trap for the Schiff-base intermediate. Schiff-base complexes formation were confirmed by the appearance of new signals in the ¹H NMR for the azomethine hydrogen at ～8 ppm and condensed L-amino acids at 3.4–3.8 ppm (C(3)–H). These complexes are formed through coordination of the ONO from the carboxyl, imino and phenoxy groups of the ligands to Zn(II).     

Simple and rapid quantitative determination of lysinoalanine and protein hydrolysate amino acids by high-performance liquid chromatography after derivatization with dansyl chloride

Summary A rapid and simple method for the determination of both lysinoalanine (LAL) and protein hydrolysate amino acids after derivatization with dansyl chloride (5-dimethylaminoaphtalene-1sulfonyl chloride) and separation with RP-HPLC (UV detection) is presented. LAL is analysed in less than 15 minutes and complete separation of 22 amino acids is achieved in less than 30 minutes using single linear gradients of solvents (phosphate buffer and acetonitrile). Quantitative results obtained by HPLC compare well with results of the ion-exchange chromatography (amino acid analyser). The importance of the duration of the derivatization reaction and of the excess of reagent is discussed. As examples, the results of the determination of LAL in two samples of base treated α-casein and 22 samples of soy protein and the results of the analysis of amino acids in two balanced diet mixtures are presented. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Ferrocenyl hetaryl thioketones: A computational study of their conformational stability

In this work, the conformational behavior of ferrocenyl- and hetaryl-functionalized thioketones was studied by means of computational quantum chemical methods. Four hetaryl substituents (furan-2-yl, thiophen-2-yl, selenophen-2-yl, and N-methylpyrrol-2-yl) were taken into account. The conformational space of the four ferrocenyl hetaryl thioketones was explored, and all found conformers were characterized using density functional (B3LYP) and wave function (SCS-MP2) theories. Their stability was explained in terms of intramolecular interactions. Such interactions were described using the methods of natural bond orbitals, “atoms in molecules,” noncovalent interaction index, and localized molecular orbital energy decomposition analysis. The identified conformations essentially differ in the arrangement of hetaryl heteroatom relative to the thiocarbonyl sulfur atom. The furan-2-yl substituent favors an s-trans-like arrangement of its heteroatom, while the remaining hetaryl substituents tend to adopt an s-cis-like arrangement. Such a conformational preference mainly results from the π → π* stabilization between the CS group and the hetaryl ring. Weak intramolecular hydrogen bonding of C H⋯O type was detected in the preferred conformer of ferrocenyl furan-2-yl thioketone. Low-polarity solvents, such as toluene, chloroform, and tetrahydrofuran, have a small effect on the preferred conformers of the four thioketones.     

Interaction between ions and substituted buckybowls: A comprehensive computational study

Complexes formed by substituted buckybowls derived from corannulene and sumanene with sodium cation or chloride anion have been computationally studied by using a variety of methods. Best results have been obtained with the SCS‐MP2 method extrapolated to basis set limit, which reproduces the highest‐level values obtained with the MP2.X method. All bowls form stable complexes with chloride anion, with stabilities ranging from ?6 kcal/mol in the methylated corannulene derivative to ?45 kcal/mol in the CN‐substituted sumanene. The opposite trend is observed in sodium complexes, going from deeply attractive complexes with the methylated derivatives (?36 kcal/mol with sumanene derivative) to slightly repulsive ones in the CN‐substituted bowls (2 kcal/mol in the corannulene derivative). Anion complexes are stabilized by large electrostatic interactions combined with smaller though significant dispersion and induction contributions. Conversely, cation complexes are stabilized by large induction contributions capable of holding together the bowl and the cation even in cases where the electrostatic interaction is repulsive. The effect of substitution is mainly reflected on changes in the molecular electrostatic potential of the bowl and, thus, in the electrostatic contribution to the interaction. Therefore, the variations in the stability of the complexes on substitution could be roughly predicted just considering the changes in the electrostatic interaction. However, other contributions also register changes mainly as a consequence of displacements on the position of the ion at the minimum, so the accurate prediction of the stability of this kind of complexes requires going further than the electrostatic approach. © 2014 Wiley Periodicals, Inc.     

Enthalpies of transfer of amino acids and sodium chloride from water to aqueous fructose at 25°C

Enthalpies of transfer H ₂ of three amino acids glycine, L-alanine, and L-phenylalanine, and of NaCl, from water to aqueous fructose at low fructose mole fraction were determined at 25°C. Comparison with H ₂ for glycine in the presence and absence of KCl shows that the effect of additional ion-dipole interactions is apparent only in more concentrated fructose solutions. Limiting slopes indicate that glycine resembles NaCl more than it does the other two amino acids. The effect on H ₂ of the polarity of the zwitterion is offset and dominated by the growing non-polar side chain. Values of H ₂ for glycine, L-phenylalanine, and NaCl from water to aqueous urea are compared with the results of the present study. A rough colligative effect similiar to that observed for NaCl in a variety of polar mixed aqueous solvents may also be possible for glycine, since the change of the enthalpies of transfer with mole fraction for glycine are the same for transfer to both aqueous urea and fructose.     

Synthesis and characterization of uranium (IV) complexes with various amino acids

Complexes of uranium in its IV oxidation state, using cysteine, glycine, serine and aspartic acid as ligands, have been synthesized. Semi-microanalysis of the complexes indicate 1:1 metal to ligand ratio for all the synthesized complexes. Infrared spectra of solid complexes have been employed to establish the groups, coordinated to the metal ion. Effective magnetic moment of the complexes were also estimated.     

Perfluorophenyl phosphonate analogues of aromatic amino acids: Synthesis,X-ray and DFT studies

Novel perfluorophenyl phosphonate analogues of phenylglycine and homophenylalanine were prepared in good to excellent yields, and subjected to solid state characterization by single-crystal X-ray diffraction analysis, and to investigations with the use of DFT methods.The α-aminophosphonates have a big potential for biological activity, and through S_NAr reactions may give an entrance to further structurally variable analogues of both amino acids.     

Sugar amino acids and related molecules: Some recent developments

To meet the growing demands for the development of new molecular entities for discovering new drugs and materials, organic chemists have started working on many new concepts that can help to assimilate knowledge-based structural diversities more efficiently than ever before. Emulating the basic principles followed by Nature to build its vast repertoire of biomolecules, organic chemists are developing many novel multifunctional building blocks and using them to create ‘nature-like’ and yet unnatural organic molecules. Sugar amino acids constitute an important class of such polyfunctional scaffolds where the carboxyl, amino and hydroxyl termini provide an excellent opportunity to organic chemists to create structural diversities akin to Nature’s molecular arsenal. In recent years, sugar amino acids have been used extensively in the area of peptidomimetic studies. Advances made in the area of combinatorial chemistry can provide the necessary technological support for rapid compilations of sugar amino acidbased libraries exploiting the diversities of their carbohydrate frameworks and well-developed solid-phase peptide synthesis methods. This perspective article chronicles some of the recent applications of various sugar amino acids, furan amino acids, pyrrole amino acids etc. and many other related building blocks in wide-ranging peptidomimetic studies     

A computational study of regioselectivity in a cyclodextrin-mediated Diels-Alder reaction: revelation of site selectivity and the importance of shallow binding and multiple binding modes

The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.     

Effects of thermal history on solid state and melting behavior of amino acids

Dielectric Thermal Analysis (DETA) of drugs, proteins and amino acids reveals a strongly linear conductivity increase prior to and peaking at the melt, associated with dielectric viscoelastic properties of the material. Premelt onset and peak are shown to depend on thermal history. Comparisons of neat amino acid samples to samples heated to 150 °C; dried in a desiccator; or heated above their melting point and cooled show significant premelt and melt shifts. Melts are also correlated with phase transitions observed by Differential Scanning Calorimetry (DSC). Activation energies attributed to charging in the premelt for amino acids were typically 250 J/mole.     

High resolution capillary gas chromatography and gas chromatography–mass spectrometry of protein and non-protein amino acids,amino alcohols,and hydroxycarboxylic acids as their tert-butyldimethylsilyl derivatives

A simple, single-step derivatization technique is presented for capillary GC-FID and GC-MS separation and identification of common protein and non-protein constituents of natural peptides as their tert-butyldimethylsilyl (TBDMS) derivatives. The tert-butyldimethyl-silylation of more than sixty compounds was accomplished with high yields and a single peak observed for each component. The TBDMS derivatives of both the protein and non-protein substances, moreover, exhibit excellent separation on apolar capillary columns and can be resolved completely using a polydimethylsiloxane or 5 % phenyl polydimethylsiloxane column and, complementarily, a 50 % phenyl polydimethylsiloxane column. Retention data and molar responses of the TBDMS derivatives on the polydimethylsiloxane column are compiled. Direct coupling of the 5 % phenyl polydimethylsiloxane column to an ion trap mass spectrometer enabled fast separation and identification of the investigated components, at nanomole to picomole levels, on the basis of retention and mass spectral data. The general usefulness of the method is demonstrated by research into new biologically active peptides isolated from entomopathogenic fungi.     

Selective preconcentration of amino acids and peptides using single drop microextraction in-line coupled with capillary electrophoresis

Single drop microextraction (SDME) can be in-line coupled with capillary electrophoresis by attaching a drop to the tip of a capillary. With a 2-layer drop comprised of an aqueous basic acceptor phase covered with a thin organic layer, acidic analytes in an aqueous acidic donor phase can be extracted into the organic layer and then back-extracted into the acceptor phase. However, preconcentration of amino acids and peptides by SDME is difficult since their zwitterionic properties prevent them from being partitioned in the middle organic phase. When amino acids were derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), amino acids without a charged side chain were converted to carboxylic acids. In the acidic donor phase, those NBD-amino acids were predominantly neutral and they were successfully concentrated into the basic acceptor phase. In the meantime, amino acids with a charged side chain after NBD-F derivatization were not concentrated via SDME. With this selective SDME, we were able to extract acidic and neutral amino acids obtaining several hundred-fold enrichments within 5 min at 25 °C, while leaving basic amino acids—Arg, Lys, and His—in the acidic donor phase. Furthermore, detection sensitivity was enhanced by employing laser-induced fluorescence detection. We then applied this technique to the selective concentration of peptides.     

Complexes of vanadium(III) with aromatic amino acids and l-proline in aqueous solution

The equilibria of the complexation processes of V³⁺ ion with l-phenylalanine, l-tyrosine, l-tryptophan and l-proline in aqueous solution were studied by potentiometric and spectroscopic (UV, Vis, CD) methods. The results indicate that all ligands (except l-tyrosine) form only 1:1 species with vanadium(III) ion in the pH range about 2–5. More complex equilibria were observed in the vanadium(III)–l-tyrosine system. Only in this system relatively stable ML₂ species predominantly exists in the pH range 3–5. The results of spectroscopic measurements indicate that in ML and ML₂ species chelated bounds through O and N atoms appear in all investigated systems. Above pH 5 strong hydrolysis processes of vanadium(III) occurred.     

Conductivity and fluorescence studies on the micellization properties of sodium cholate and sodium deoxycholate in aqueous medium at different temperatures: Effect of selected amino acids

In order to add to the existing knowledge of aqueous solution behavior of bile salts in presence of amino acids, the micellization properties of sodium cholate (NaC) (1 to 20) mmol · kg⁻¹, and sodium deoxycholate (NaDC) (0.5 to 10) mmol · kg⁻¹ in 0.1 mol · kg⁻¹ aqueous solution of glycine, leucine, methionine, and histidine have been investigated at different temperatures (293.15 to 318.15) K at intervals of T = 5 K by using conductivity and fluorescence probe studies. The critical micelle concentration (CMC) values have been determined and elucidated in terms of hydrophobicity as well as hydrophilicity of NaC and NaDC in aqueous solution of these additives. Thermodynamic parameters of micellization viz. standard Gibbs free energy (Δ_micG^o), standard enthalpy (Δ_micH^o), and standard entropy (Δ_micS^o) have also been calculated to extract information regarding the nature of micellization of bile salts in aqueous solutions. The (enthalpy + entropy) compensation plots have been interpreted to the contribution of chemical part towards micellization or stability of the micelle formed.     

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen,oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.     

Probing the bent bonds in cyclopropane systems for gas storage and separation process: A computational study

The hydrogen, carbon dioxide, and carbon monoxide gas adsorption and storage capacity of lithium-decorated cyclopropane ring systems were examined with quantum chemical calculations at density functional theory, DFT M06-2X functional using 6-31G(d) and cc-pVDZ basis sets. To examine the reliability of M06-2X DFT functional, a few representative systems are also examined with complete basis set CBS-QB3 method and CCSD-aug-cc-pVTZ level of theory. The cyclopropane systems can bind to one Li⁺ ion; however, the corresponding the methylated systems can bind with two Li⁺ ions. The cyclopropane systems can adsorb six hydrogen molecules with an average binding energy of 3.8 kcal/mol. The binding free energy (ΔG) values suggest that the hydrogen adsorption process is feasible at 273.15 K. The calculation of desorption energies indicates the recyclable property of gas adsorbed complexes. The same number of CO₂ and CO gas molecules can also be adsorbed with an average binding energy of −14.4 kcal/mol and −10.7 kcal/mol, respectively. The carbon dioxide showed ~3–4 kcal/mol better binding energy as compared to carbon monoxide and hence such designed systems can function as a potential candidate for the separation of these flue gas molecules. The nature of interactions in complexes was examined with atoms in molecules analysis revealed the electrostatic nature for the interaction of Li⁺ ion with cyclopropane rings. The chemical hardness and electrophilicity calculations showed that the gas adsorbed complexes are rigid and therefore robust as gas storage materials.     

Uptake of hydrophobic amino acids and sodium chloride by a strong cation exchanger: Application to desalting and separation by preparative liquid chromatography

Summary The uptake of sodium chloride, leucine and phenylalanine by a strong cation-exchange resin in the sodium form have been compared. Sodium chloride was excluded from the resin, as indicated by its parabolic upwards curved isotherm, and the corresponding desorption edge was sharpened (constant pattern). Isotherms for both amino acids constructed from a single elution experiment displayed slightly downwards curvature; the corresponding desorption edges spread in contrast to the breakthrough ones. The affinities of both amino acids for the resin were higher (from 15 to 40 %) in the presence of 1 M sodium chloride, indicating that hydrophobic interactions played a significant role in the mechanism of sorption. As expected from the isotherms, a mixture of 1 M sodium chloride, leucine and phenylalanine was separated with satisfactory recovery of both amino acids for a column loading of 10 % of the bed volume. Real mother liquors have also been separated under the same conditions.