CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field

High-level ab initio calculations have been carried out to study weak CH/pi interactions and as a check of the CHARMM force field for aromatic amino acids. Comparisons with published data indicate that the MP2/cc-pVTZ level of theory is suitable for calculations of CH/pi interaction, including the T-shape benzene dimer. This level of theory was, therefore, applied to investigate CH/pi interactions between ethene or cis-2-butene and benzene in a variety of orientations. In addition, complexes between ethene and a series of model compounds (toluene, methylindole and p-cresol) representing the aromatic amino acids were studied motivated by the presence of CH/pi interactions in biological systems. Ab initio binding energies were compared to the binding energies obtained with the CHARMM22 force field. In the majority of orientations, CHARMM22 reproduces the preferred binding modes, with excellent agreement for the benzene dimer. Small discrepancies found in the calculations involving methylindole along with a survey of published thermodynamic data for the aromatic amino acids prompted additional optimization of the tryptophan force field. Partial atomic charges, Lennard-Jones parameters, and force constants were improved to obtain better intra- and intermolecular properties, with significant improvements obtained in the reproduction of experimental heats of sublimation for indole and free energies of aqueous solvation for methylindole.     

A force field for molecular simulation of tetrabutylphosphonium amino acid ionic liquids

An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs.     

Enantiomeric separation of unusual secondary aromatic amino acids

Summary High-performance liquid chromatographic and gas chromatographic methods were developed for the separation of unusual secondary aromatic amino acids. Amino acids containing 1,2,3,4-tetrahydroisoquinoline, 1,2,3,4-tetrahydronorharmane-1-carboxylic acid and 1,2,3,4-tetrahydro-3-carboxy-2-carboline moieties were synthetized in racemic or chiral forms. The high-performance liquid chromatography was carried out either on a teicoplanin-containing chiral stationary phase or on an achiral C₁₈ column. In the latter case the diastereomers of the amino acids formed by precolumn derivatization with the chiral reagents 2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl isothiocyanate or 1-fluoro-2,4-dinitrophenyl-5-L-alanine amide were separated. The gas chromatographic analyses were based on separation on a Chirasil-L-Val column. Presented at: Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 3–5, 1997     

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all‐atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side‐chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met‐enkephalin (CHO‐Tyr‐Gly‐Gly‐Phe‐Met‐NH₂) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard‐Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H‐Gly‐Tyr‐Asp‐Pro‐Glu‐Thr‐Gly‐Thr‐Trp‐Gly‐OH) reasonably reproduced a native‐like β‐hairpin structure in water although the C‐terminal and side‐chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene. Parameters were optimized for benzene and then transferred directly to toluene, with parameters for the methyl moiety of toluene taken from the previously published work on the alkanes. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the electrostatic parameters, for the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters. The absolute values of the Lennard-Jones parameters were determined by comparing computed and experimental heats of vaporization, molecular volumes, free energies of hydration, and dielectric constants. The newly developed parameter set was extensively tested against additional experimental data such as diffusion constants, heat capacities at constant pressure, and isothermal compressibilities including data as a function of temperature. Moreover, the structures of liquid benzene, liquid toluene, and solutions of each in water were studied. In the case of benzene, the computed and experimental total distribution function were compared, with the developed model shown to be in excellent agreement with experiment.     

Electron transfer from aromatic amino acids to triplet quinones

The photoreduction of 1,4-benzoquinone, 1,4-naphthoquinone, 9,10-anthraquinone (AQ) and several methylated or halogenated derivatives in argon-saturated acetonitrile-water mixtures by indole, N-acetyltryptophan and N-acetyltyrosine was studied by time-resolved UV-vis spectroscopy using 20 ns UV laser pulses. The quinone triplet state is quenched by the aromatic amino acids and the rate constants are (1-5)x10(9)M(-1)s(-1). The semiquinone radical anion Q.(-) is the major observable transient after electron transfer from amino acids to the quinone triplet state. Termination of Q.(-) and amino acid derived radicals takes place in the mus-ms range. The effects of structure and other specific properties of quinones and amino acids are discussed. The radicals are subjects of intercept with oxygen, whereby hydrogen peroxide is eventually formed. The quantum yield of oxygen uptake Phi(-O2) as a measure of formation of hydrogen peroxide increases with increasing amino acid concentration, approaching Phi(-O2) for AQ in air-saturated solution.     

Conformationally rigid aromatic amino acids as potential building blocks for abiotic foldamers

This communication describes the development of conformationally constrained unnatural aromatic amino acids, constructed on rigid backbone wherein the carboxyl and amino groups project in two dimensions (planes) on the aromatic framework. Such a feature offers the possibility of design and development of conformationally ordered synthetic oligomers with intriguing structural architectures distinct from those classically observed. Furthermore, such amino acids will have the potential to extend the conformational space available for foldamer design with diverse backbone conformation and structural architectures.     

Study on the interaction mechanism between aromatic amino acids and quercetin

In this paper, we selected quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) as the research objects to investigate the change rules in the reaction process. The thermodynamic functions (Ka, ΔG, and ΔS) of the interactions between quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) were measured by isothermal titration calorimetry. The values of binding constant (Ka) reached maximum at 25°C; the entropies and Gibbs free energies were both negative at different temperatures. The kinetic parameters of quercetin and amino acids in the interaction process was determined by microcalorimetry. The results inferred that the driving force of the reaction was hydrogen bond or van der Waals force.     

Rational design of MOFs constructed from modified aromatic amino acids

Three Phe and Tyr derivatives, 2-amino-3-(4-aminophenyl)-propionic acid (AAP), 3E-[5-(2-amino-2-carboxyethyl)-2-methoxyphenyl]-acrylic acid (AMPA) and 3-(4-aminophenyl)-2-(carboxymethyl-amino)-propionic acid (ACP) have been chosen as the ligands to construct four kinds of novel metal-organic frameworks (MOFs) (five structures). These structures are, [Cd(II){(R)-AAP}(Py)(H(2)O)](ClO(4)), (R)-1; [Cd(II){(S)-AAP}(H(2)O)(2)](ClO(4)), (S)-2; [Zn(2) (II){(R,S)-AMPA}(H(2)O)], (R,S)-3; [Zn(2) (II){(R)-ACP}(Py)(3)](ClO(4))(2), (R)-4; and the inversion twin of (R)-1. Rational design to adjust the "depth" and the "width" of ligands can mediate the size and the shape of the grids of these 2D layers. Additionally, among these compounds, three pure chiral coordination polymers are obtained, owing to the inducement of chirality by the modified amino acids. This property makes them potential NLO materials.     

Tetramethylcyclobutadiene)cobalt complexes of protected aromatic amino acids*

Reactions of [(C4Me4)Co(MeCN)3]PF6 with aromatic amino acid derivatives give the arene complexes [(C4Me4)Co(amino acid)]PF6 (amino acid = ethyl ester of N-acetylphenylalanine, N-acetyltyrosine or N-acetyltryptophan) in 75–85% yields; the structure of the tyrosine complex was determined by X-ray diffraction.     

Synthesis of phosphinic and phosphonic analogs of aromatic amino acids

The reaction of aryl and aralkyl aldoximes with hypophosphorous acid resulted in aminophosphinic acids, which were oxidized into the corresponding aminophosphonic acids. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 137–140, January, 1997.     

Ab initio force field for simulations of proteins and nucleic acids

We present a new self-consistent set of ab initio analytical pair potential to predict specific nonbonded interactions of protein with nucleic acid, of protein with protein, and of nucleic acid with nucleic acid. The purpose of this study is to represent the interaction between biological molecules with an accuracy equivalent to the ab initio molecular orbital calculations, which are used as reference data to obtain the pair potentials. Atoms in nucleic acids and proteins are classified according to their chemical environments. An “effective charge,” a modification of a charge obtained from the Mulliken population analysis, is introduced and used to represent the electrostatic energy. More than 30,000 SCF interaction energies have been calculated to provide the reference data for the fitting procedure that we have adopted in the parameterization of the potentials. The standard deviation is 1.61 kcal/mol for interaction energies spanning the range from about ?220 kcal/mol to +20 kcal/mol. Molecular dynamics simulations, using the above new set of force field, have been performed successfully for the systems where adequate treatments of specific interactions are required: The stability of α-helix of C-peptide and the interaction of spermine with oligonucleotide are examined as preliminary examples.     

Spectrophotometric determination of aromatic and heterocyclic amino acids in mixtures

A procedure for the determination of individual aromatic and heterocyclic amino acids in mixtures was developed with the use of the Vierordt method. Amino acids can be simultaneously determined by this procedure in the concentration range (0.4-3.0) x 10^-3 M. The determination errors for binary and ternary mixtures were no greater than 5 and 10%, respectively. The determination error increases with a decrease in the concentration of a particular component and with an increase in the number of components in the test mixture.