Effects of nucleobase metalation on frontier molecular orbitals: potential implications for pi-stacking interactions with tryptophan

Biochemical recognition processes mediated through pi-stacking interactions are a potential target for rational drug synthesis. A combination of electrostatic, hydrophobic, solvation, charge-transfer, induction, and dispersion interactions has been used to account for the three-dimensional arrangements observed in such motifs. A principal example involves the interaction of purine and pyrimidine rings of nucleic acids with aromatic amino-acid residues such as tryptophan, phenylalanine, and tyrosine. Protonation, alkylation, or coordination of a metal ion such as Pd(II) or Pt(II) to a nucleobase strengthens this interaction by lowering the energy of the lowest unoccupied molecular orbital (LUMO) of the modified nucleobase and improving overlap with the highest occupied molecular orbital (HOMO) in N-acetyl tryptophan. The relative energy difference between the frontier orbitals of isolated molecules, obtained using Density Functional Theory (DFT), is explored as a predictive tool for the strength of the pi-stacking interaction of the nucleobase/tryptophan pair. From the optimized structures of these species, evaluation of the donor-acceptor HOMO-LUMO gap (Deltaepsilon d-->a) suggests that this parameter is a promising predictor of pi-stacking strength for the donor-acceptor pairs presented in this study. The analysis correlates well with experimental association constants, measured by fluorescence spectroscopy, of metallated and alkylated nucleobases with tryptophan in comparison to free nucleobases.     

Gas phase attachment of water and methanol to Ag(I) complexes with alpha-amino acids in an ion trap mass spectrometer

Electrospray ionization was used to generate gas phase complexes of Ag+ with selected alpha-amino acids. Following storage (isolation without collisional activation) in an ion trap mass spectrometer, the mass spectra produced from the complexes of Ag+ with alpha-amino acids such as alanine, valine and tert-leucine contained peaks consistent with the formation of water or methanol molecule adduct ions. The same adduct ions were not present, however, in the mass spectra generated from the Ag+ complexes with phenylalanine, tyrosine and tryptophan following isolation and storage under similar conditions. For those complexes that showed reactivity, the uptake of water and methanol increased with longer storage times in the ion trap. A preliminary molecular modeling study using phenylalanine demonstrated that the aromatic ring coordinates the Ag+ ion, and the interaction between the metal ion and pi-system, in part, is assumed to prohibit the binding of water or methanol during isolation in the gas phase. This conclusion is supported by a comparison of the adduct formation by the Ag+ complexes with phenylalanine, 4-fluorophenylalanine and alpha-aminocyclohexanepropionic acid. In addition, collision induced dissociation experiments involving the Ag+ complexes of phenylalanine, tyrosine and tryptophan suggest that limiting the coordination of the Ag ion by the complexing molecule (i.e. by loss of a coordinating functional group and/or change in structure due to dissociation) results in the binding of a water or methanol molecule during storage in the ion trap. Surprisingly, the bare Ag+ ion, when trapped and stored under identical experimental conditions, formed neither adduct species, suggesting that the attachment of water or methanol may be due to interactions with a molecular orbital within the Ag+/molecule complex.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

In silico Complexes of Amino Acids and Diamondoids

We report on the specific interaction of a small diamond-like molecule, known as diamondoid, with single amino-acids forming nano/bio molecular complexes. Using time-dependent density-functional theory calculations we have studied two different relative configurations of three prototypical amino acids, phenylalanine, tyrosine, and tryptophan, with the diamondoid. The optical and charge-transfer properties of these complexes exhibit amino acid and topology specific features which can be directly utilized for in the direction of novel biomolecule detection schemes.     

Pd(Ⅱ)与色氨酸、酪氨酸及苯丙氨酸相互作用的荧光光谱

当Pd(Ⅱ)与色氨酸(Trp)、酪氨酸(Tyr)及苯丙氨酸(Phe)等芳香族氨基酸相互作用时,能观察到3种氨基酸的荧光均发生猝灭. 从吸收光谱的变化,温度对猝灭作用的影响以及猝灭常数Ksv,可以判定荧光猝灭作用是由于Pd(Ⅱ)与上述氨基酸形成基态配合物而导致的静态猝灭过程. 并认为在一定浓度的Cl-存在下,Pd(Ⅱ)与氨基酸分别以N, N配位和N, O配位形成以下混配型三元配合物Pd(HR)Cl2 (Trp和Phe体系)和Pd(H2R)Cl2(Tyr体系),并推测了配合物相应的结构. 该荧光猝灭体系不仅可用于研究钯(Ⅱ)与上述芳香族氨基酸的相互作用,也可成为以氨基酸(特别是Trp)作探针高灵敏荧光猝灭法测定钯的基础.     

Complexation between Methyl Viologen (Paraquat) Bis(Hexafluorophosphate) and Dibenzo[24]Crown‐8 Revisited

Paraquat bis(hexafluorophosphate) undergoes stepwise dissociation in acetone. All three species—the neutral molecule, and the mono‐ and dications—are represented significantly under the experimental conditions typically used in host–guest binding studies. Paraquat forms at least four host–guest complexes with dibenzo[24]crown‐8. They are characterized by both 1:1 and 1:2 stoichiometries, and an overall charge of either zero (neutral molecule) or one (monocation). The monocationic 1:1 host–guest complex is the most abundant species under typical (0.5–20 mM ) experimental conditions. The presence of the dicationic 1:1 host–guest complex cannot be excluded on the basis of our experimental data, but neither is it unambiguously confirmed to be present. The two confirmed forms of paraquat that do undergo complexation—the neutral molecule and the monocation—exhibit approximately identical binding affinities toward dibenzo[24]crown‐8. Thus, the relative abundance of neutral, singly, and doubly charged pseudorotaxanes is identical to the relative abundance of neutral, singly, and doubly charged paraquat unbound with respect to the crown ether in acetone. In the specific case of paraquat/dibenzo[24]crown‐8, ion‐pairing does not contribute to host–guest complex formation, as has been suggested previously in the literature.     

Characterization of transient species in laser photolysis of aromatic amino acids using acetone as photosensitizer

The photochemical processes of aromatic amino acids were investigated in aqueous solution using acetone as photosensitizer by KrF (248 nm) laser flash photolysis. Laser-induced transient species were characterized according to kinetic analysis and quenching experiments. The intermediates recorded were assigned to the excited triplet state of tryptophan, the radicals of tryptophan and tyrosine. The excited triplet state of tryptophan produced via a triplet-triplet excitation transfer and the radicals arising from electron transfer reaction has been identified. Neither electron transfer nor energy transfer between triplet acetone and phenylalanine can occur in photolysis of phenylalanine aqueous solution which contains acetone. Furthermore, triplet acetone-induced radical transformation: Trp/N-Tyr→Trp-Tyr/O was observed directly in photolysis of dipeptide (Trp-Tyr) aqueous solution containing acetone, and the transformation resulting from intramolecular electron transfer was suggested.     

电喷雾质谱法研究谷胱甘肽与L型芳香性氨基酸非共价复合物

为探索谷胱甘肽和L型芳香性氨基酸的非共价相互作用, 将一定化学剂量比的还原型γ-谷胱甘肽分别与L型芳香性氨基酸(包括苯丙氨酸、酪氨酸和色氨酸)在室温和生理pH条件下混合后, 温育1 h, 生成非共价复合物, 并使反应完全. 电喷雾质谱测量结果揭示谷胱甘肽和L型芳香性氨基酸反应可以生成非共价复合物. 在二级串级质谱MS2测得的复合物碎片离子峰中, 除芳香性氨基酸离子峰外, 还包括谷胱甘肽及其它再次碎裂产生的b2和y2碎片离子, 进一步确认了非共价复合物的形成. 紫外光谱也证实了电喷雾质谱的实验结果. 为避免严重的离子化效率差异和质谱信号的相互抑制作用, 定量评估了谷胱甘肽和酪氨酸的相互作用, 结果显示反应物的初始浓度应该选择在5×10-5~3.00×10-4 mol/L范围内. 用质谱滴定法测定了谷胱甘肽与3个芳香性氨基酸非共价复合物的解离常数, 结果表明, 谷胱甘肽复合物的稳定性按Tyr, Trp和Phe次序依次增大.     

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.     

Sorption of Amino Acids from Aqueous Solutions by a Polarized Carbon Adsorbent

The adsorption and electrosorption of tyrosine, tryptophan, and phenylalanine on an A-4 model carbon adsorbent from 0.1 N K₂SO₄solutions were investigated at various acidity values of the medium. It was found that the sorption of tyrosine and tryptophan is significantly affected by both the polarization potential of the adsorbent and pH of the solution. For phenylalanine, electrosorption dependences were not measured because of its electrochemical instability under experimental conditions. The electrosorption effect was demonstrated for the low-molecular-weight protein, pepsin.     

Influence of a ring substituent on the tendency to form H(2)O adducts to Ag(+) complexes with phenylalanine analogues in an ion trap mass spectrometer

In a previous report we showed that certain binary Ag(+)-amino acid complexes formed adduct ions by the attachment of a single water and methanol molecule when stored in an ion trap mass spectrometer: complexes with aliphatic amino acids and with 4-fluorophenylalanine formed the adduct ions whereas complexes with phenylalanine and tryptophan did not. In this study we compared the tendency of the Ag(+) complexes derived from phenylalanine, 4-fluorophenylalanine, 4-hydroxyphenylalanine (tyrosine), 4-bromophenylalanine, 4-nitrophenylalanine and aminocyclohexanepropionic acid to form water adducts when stored, without further activation, in the ion trap for times ranging from 1 to 500 ms. Because the donation of pi electron density to the Ag(+) ion is a likely determining factor in complex reactivity, our aim in the present study was to determine qualitatively the influence of para-position substituents on the aromatic ring on the formation of the water adducts. Our results show that the reactivity of the complexes is influenced significantly by the presence of the various substituents. Decreases in [M + Ag](+) ion abundance, and increases in adduct ion abundance, both measured as a function of storage time, follow the trend -NO(2) > -Br > -F > -OH > -H. The complex of Ag(+) with 4-nitrophenylalanine was nearly as reactive towards water as the Ag(+) complex with aminocyclohexanepropionic acid, the last being an amino acid devoid of pi character in the ring system. Collision induced dissociation of the [M + Ag](+) species derived from the amino acids produces, among other products, Ag(+) complexes with a para-substituted phenylacetaldehyde: complexes that also form adduct species when stored in the ion trap. The trends in adduct ion formation exhibited by the aldehyde-Ag(+) complex ions were similar to those observed for the precursor complexes of Ag(+) and the amino acids, confirming the influence of the ring substituent.     

TRIPLET STATE STUDIES OF FLAVlNS BY ELECTRON PARAMAGNETIC RESONANCE—II

Abstract— The triplet states of proteins, bovine serum albumin, ovalbumin and d-amino acid oxidase, were observed by electron paramagnetic resonance at 77°K.
The triplet state of aromatic amino acids, tryptophan, tyrosine and phenylalanine was also detected.
The protein triplet originates from the tryptophan residues of these proteins.
It is suggested that an energy transfer takes place between tyrosine and tryptophan.     

Polarized Raman spectra and intensities of aromatic amino acids phenylalanine,tyrosine and tryptophan

The prominent marker bands in the Raman spectra of the aromatic proteinogenic amino acids phenylalanine, tryptophan and tyrosine have been reinvestigated. Previous studies have been extended by measuring intensities against NaClO₄ as an external standard. Raman spectra were divided into isotropic (trace scattering of symmetric vibrations) and anisotropic (quadrupole scattering of antisymmetric or symmetric vibrations). These intensity and polarization properties of the marker bands were followed through pH changes from about 11–13 to 1–2.     

Interaction of Diquat and Paraquat with Glutathione Studied by Means of Charge-Transfer Chromatography

Abstract

The interaction of reduced and oxidized glutathiones with the herbicides diquat and paraquat was studied by charge-transfer chromatography carried out on un-impregnated cellulose layers. Diquat and paraquat interact both with reduced and oxidized glutathiones forming charge-transfer complexes. The interaction is of hydrophilic character in both cases. The formation of covalently bonded conjugates was not observed. The strength of interaction decreases in ionic (LiCl, NaCl, KCl, MgCl₂ and CaCl₂) environment in the case of oxidized glutathione. The charge of cation had a higher impact on the strength of interaction than that of the hydrated ion radii.     

Enantioseparation of underivatised amino acids by ligand exchange capillary electrophoresis in a counter-electroosmotic mode

Enantiomer separations of underivatised amino acids were carried out by using ligand exchange capillary electrophoresis (LECE). Chiral discrimination is based on the formation of ternary complexes between copper(II), a chiral selector (L-proline or trans-4-hydroxy-L-proline) and an amino acid. All amino acids containing aromatic moieties or not were detected at 214 nm because of their interactions with copper(II). In order to reduce copper(II) adsorption onto capillary walls, we used hexadimethrine bromide to reverse the electroosmotic flow. Using this original strategy, the studied enantiomers migrated in the opposite direction of the anodic electroosmosis. After optimising the analytical conditions taking into account the chiral resolution and the detection sensitivity, we performed very satisfactory enantioseparations not only of aromatic amino acids (tryptophan, tyrosine, phenylalanine and histidine) but also of aliphatic amino acids (threonine, serine, isoleucine and valine). These enantioseparations were performed in a short analysis time at 35 °C. In order to rationalise the obtained results, we evaluated the complexation constants corresponding to the formed ternary complexes by capillary electrophoresis and we used molecular mechanics modelling.     

Cation-pi interactions: structures and energetics of complexation of Na+ and K+ with the aromatic amino acids, phenylalanine, tyrosine, and tryptophan

Threshold collision-induced dissociation of M(+)(AAA) with Xe is studied using guided ion beam tandem mass spectrometry. M(+) include the alkali metal ions Na(+) and K(+). The three aromatic amino acids are examined, AAA = phenylalanine, tyrosine, or tryptophan. In all cases, endothermic loss of the intact aromatic amino acid is the dominant reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies for the M(+)-AAA complexes after accounting for the effects of multiple ion-neutral collisions, internal energy of the reactant ions, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures of the neutral aromatic amino acids and their complexes to Na(+) and K(+) and to provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single-point energy calculations at the B3LYP/6-311++G(3df,3pd) level using the B3LYP/6-31G geometries. Good agreement between theory and experiment is found for all systems. The present results are compared to earlier studies of these systems performed via kinetic and equilibrium methods. The present results are also compared to the analogous Na(+) and K(+) complexes to glycine, benzene, phenol, and indole to elucidate the relative contributions that each of the functional components of these aromatic amino acids make to the overall binding in these complexes.     

Simultaneous determination of aromatic amino acids in human blood plasma by capillary electrophoresis with UV‐absorption detection

Phenylalanine, tyrosine, and tryptophan, also known as aromatic amino acids, are involved in many physiological and pathophysiological conditions and are indicative of the liver and kidney function. In this work, we describe a simple and accurate method for their simultaneous quantification, in a single capillary electrophoresis run. This method requires minimal sample manipulation, no derivatization procedures, and methyl tryptophan as internal standard. The human blood plasma sample was precipitated using sulfosalicylic acid and the supernatant was used for the analysis. All the analytes were baseline resolved within 16 min and detected at 200 nm using Tris phosphate 80 mmol/L at pH 1.4 as the background electrolyte. The proposed method showed good linearity (r = 0.998) and repeatability (intra‐assay RSD < 2.78%, interassay RSD < 5.4%) for all the analytes. The limit of quantification was 13 μmol/L for phenylalanine and 5 μmol/L for tyrosine and tryptophan. The method suitability was tested measuring aromatic amino acids level in 20 chronic kidney disease patients at basal level and after simvastatin/ezetimibe treatment.     

Charge-transfer derivatization in fast-atom-bombardment mass spectrometry

The formation of charge-transfer complexes as derivatization reactions for fast-atom- bombardment (f.a.b.) mass spectrometry has been investigated. The donor N,N,N′,N′- tetramethyl-1,4-phenylenediamine (TMPD) and the acceptor 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) were studied. The f.a.b, spectrum of this complex in glycerol first yielded the cation radical, TMPD⁺ at m/z 164. However, with time the dominant ion becomes (TMPD+H)⁺. Results suggest that although a strong charge-transfer complex is formed, protonation of the donor molecule occurs whenever possible. In dimethylsulfoxide, initial f.a.b, spectra contain (TMPD+H)⁺, but as solvent evaporates, this ion is supplanted by the cation radical. Increased abundances of the cation radicals for charge- transfer complexes are observed in the absence of solvent or with the use of aprotic solvents. Characteristic ultraviolet/visible spectra of charge-transfer complexes clarify the competing processes of electron and proton transfer, and their time dependence. Charge- transfer derivatization is used to increase signals for the donor cation radicals of anthracene/picric acid, pyrene/picric acid, and indole/trinitrofluorenone.     

A computational study on the interaction of the nitric oxide ions NO+ and NO- with the side groups of the aromatic amino acids

The interaction of the nitric oxide ions NO+ and NO- with benzene (C6H6) and the aromatic R-groups of the amino acids phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp) have been examined using the DFT method B3LYP and the conventional electron correlation method MP2. In particular, the structures and complexation energies of the resulting half-sandwich Ar...NO+/- and sandwich [Ar...NO...Ar]+/- complexes have been considered. For the Ar...NO+ complexes, the presence of an electron rich heteroatom within or attached to the ring is found to not preclude the cation...pi bound complex from being the most stable. Furthermore, unlike the anionic complexes, the pi...cation...pi ([Ar...NO...Ar]+) complexes do not correspond to a "doubling" of the parent half-sandwich.     

Platinum(II) polypyridines: A tale of two axes

There are many possible applications for luminescent platinum terpyridine (trpy) complexes, but the emission quantum yield and lifetime vary greatly depending upon the design. One reason is that potentially emissive metal-to-ligand charge-transfer (MLCT) states occur at relatively high energies because a planar coordination geometry is not the best supporting environment for a Pt(III) center. At the same time, strain in the Pt–N sigma bond framework often results in low-lying d–d excited states that effectively quench the emission. One way of differentially lowering the energy of the emitting state, and thereby reducing the effect of d–d states, involves delocalizing the π*(trpy) acceptor orbital onto a 4′-aryl substituent. Delocalizing the ‘hole’ orbital is an alternative approach capable of producing dramatic results. Thus, with the addition of an electron-rich group like –NMe2 or 1-naphthyl to the 4′-position of trpy ligand, the emitting state takes on intraligand charge-transfer (ILCT) character and the excited-state lifetime extends to tens of microseconds in dichloromethane solution. In some systems introduction of a π-donating co-ligand enhances the emission yield, and when the co-ligand is a very electron-rich group like an ethynylarene, the emitting state takes on an admixture of ligand-to-ligand charge-transfer (LLCT) character. Finally, it is possible to destabilize deactivating states by incorporating an ethynylalkane as a strong-field co-ligand, or by utilizing a carbometalating derivative of the trpy ligand. Complexes of the latter support another type of ILCT excitation because of the presence of the formally anionic phenyl moiety, and the emission energy vary greatly depending upon which ligand axis contains the Pt–C bond.