Thermodynamic Studies on Amino Acid Solvation in Aqueous Urea

The present paper discusses the behaviour of transfer free energy of some amino acids from water to 4M, 6M and 8M aqueous urea. Dissection of transfer free energy into cavity term, interaction term and electrical term reveals that cavity forming free energy of transfer ΔG⁰_t (cav) plays an important role in dictating actual interaction of amino acids in aqueous urea. Cavity forming free energy of transfer has been estimated by using Scaled Particle Theory (SPT).     

The chemical stability of L-isoleucine,L-threonine,and L-serine in aqueous solutions of KCl at 298.15 K

The experimental saturated solubilities of L-isoleucine, L-threonine, and L-serine in aqueous mixtures of a KCl solution at 298.15 K are presented in this article. The solubilities are measured by gravimetric method. In the present study the theoretical calculation of the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy, dipole-dipole interaction effect have been computed. The chemical effects of the transfer Gibbs energies for the present amino acids have been obtained by subtracting the cavity effects and dipole-dipole interaction effects from the ΔG_t⁰(i). The stability of the experimental amino acids in aqueous KCl in terms of thermodynamic parameters is explained.     

Transfer Thermodynamics of Protein in Denaturing and Stabilizing Media

Free energies of transfer (ΔG_t) of RibonucleaseA (RNaseA) from water to aqueous solutions of urea (4 M, 6 M and 8 M), a protein denaturing solvent as well as ΔG_t of RibonucleaseA, β‐Lactoglobulin, α‐Chymotripsin and ChymotrypsinogenA from water to aqueous glycerol (10%, 20%, 30% and 40%), a protein stabilizing solvent has been dissected into cavity term [ΔG_t(cav)] and interaction term [ΔG_t(int)]. The interaction free energy includes all types of interactions like hard‐soft, hydrogen bonding, electrostatic, etc. The cavity forming free energies have been calculated using the standard version of scaled particle theory (SPT) with well‐reported SPT parameters. It has been found that transfer free energies of cavity terms ΔG_t(cav) for native protein from water to urea‐water and water to aqueous glycerol follow almost opposite trends. This primarily indicates there may be some correlation between cavity creation energies and protein denaturing and stabilizing ability of a solvent. The results are in agreement with those obtained from preferential binding coefficient studies in these media.     

Solvation thermodynamics of L-cystine,L-tyrosine,and L-leucine in aqueous-electrolyte media

Solubilities of L-cystine, L-tyrosine, and L-leucine in aqueous NaCl media at 298.15 K have been studied. Indispensable and related solvent parameters such as molar mass, molar volume, etc., were also determined. The results are used to evaluate the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy and dipole-dipole interaction effects during the course of solvation. Various weak interactions involving solute–solvent or solvent–solvent molecules were characterized in order to find their role on the solvation of these amino acids.     

Multicanonical Monte Carlo calculation of the free‐energy map of the base–amino acid interaction

The specific interactions between base pairs and amino acids were studied by the multicanonical Monte Carlo method. We sampled numerous interaction configurations and side‐chain conformations of the amino acid by the multicanonical algorithm, and calculated the free energies of the interactions between an amino acid at given C_α positions and a fixed base pair. The contour maps of free energy derived from this calculation represent the preferred C_α position of the amino acid around the base, and these maps of various combinations of bases and amino acids can be used to quantify the specificity of intrinsic base–amino acid interactions. Similarly, enthalpy and entropy maps will provide further details of the specific interactions. We have also calculated the free‐energy map of the orientations of the C_α C_β bond vector, which indicates the preferential orientation of the amino acid against the base. We compared the results obtained by the multicanonical method with those of the exhaustive sampling and canonical Monte Carlo methods. The free‐energy map of the base–amino acid interaction obtained by the multicanonical simulation method was nearly identical to the accurate result derived from the exhaustive sampling method. This indicates that a single multicanonical Monte Carlo simulation can produce an accurate free‐energy map. Multicanonical Monte Carlo sampling produced free‐energy maps that were more accurate than those produced by canonical Monte Carlo sampling. Thus, the multicanonical Monte Carlo method can serve as a powerful tool for estimating the free‐energy landscape of base–amino acid interactions and for elucidating the mechanism by which amino acids of proteins recognize particular DNA base pairs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 954–962, 2000     

Elucidation of the Key Role of [Ru(bpy)3]2+ in Photocatalyzed RAFT Polymerization

Photocatalysis reactions using [Ru^II(bpy)₃]²⁺ were studied on the example of visible‐light‐sensitized reversible addition–fragmentation chain transfer (RAFT) polymerization. Although both photoinduced electron‐ and energy‐transfer mechanisms are able to describe this interaction, no definitive experimental proof has been presented so far. This paper investigates the actual mechanism governing this reaction. A set of RAFT agents was selected, their redox potentials measured by cyclic voltammetry, and relaxed triplet energies calculated by quantum mechanics. Gibbs free‐energy values were calculated for both electron‐ and energy‐transfer mechanisms. Quenching rate constants were determined by laser flash photolysis. The results undoubtedly evidence the involvement of a photoinduced energy‐transfer reaction. Controlled photopolymerization experiments are discussed in the light of the primary photochemical process and photodissociation ability of RAFT agent triplet states.     

Calculation of thermodynamics of gas-liquid solutions for 15 homologous series of solutes in n-hexadecane via a cavity-interaction-based method

A thermodynamic model is presented for the calculation of ΔG _s ^o (298.15 K) (gas → liquid) and the sum of free energy of cavity formation and interaction. The process of solution is divided into (a) the free energy of immersion solvent molecular volume for pure compounds, (b) the free energy of vaporization, (c) a correction term, and (d) the excess free energy. Likewise, it is shown that the free energy of vaporization and correction term play the main role in a gas-liquid solution. This model calculates the total excess free energy of solution, which is divided into two major parts: a combinatorial portion, which accounts for differences in the sizes of molecules, and a residual portion, which takes into account the different solvent-solvent and solvent-solute interactions. The model was applied to a solution of 15 homologous series of polar and nonpolar solutes in n-hexadecane. The text was submitted by the authors in English.     

A New Approach for the Photosynthetic Antenna–Reaction Center Complex with a Model Organized Around an s‐Triazine Linker

Two new artificial mimics of the photosynthetic antenna‐reaction center complex have been designed and synthesized (BDP‐H₂P‐C₆₀ and BDP‐ZnP‐C₆₀). The resulting electron‐donor/acceptor conjugates contain a porphyrin (either in its free‐base form (H₂P) or as Zn‐metalated complex (ZnP)), a boron dipyrrin (BDP), and a fulleropyrrolidine possessing, as substituent of the pyrrolidine nitrogen, an ethylene glycol chain terminating in an amino group C₆₀‐X‐NH₂ (X=spacer). In both cases, the three different components were connected by s‐triazine through stepwise substitution reactions of cyanuric chloride. In addition to the facile synthesis, the star‐type arrangement of the three photo‐ and redox‐active components around the central s‐triazine unit permits direct interaction between one another, in contrast to reported examples in which the three components are arranged in a linear fashion. The energy‐ and electron‐transfer properties of the resulting electron‐donor/acceptor conjugates were investigated by using UV/Vis absorption and emission spectroscopy, cyclic voltammetry, and femtosecond transient absorption spectroscopy. Comparison of the absorption spectra and cyclic voltammograms of BDP‐H₂P‐C₆₀ and BDP‐ZnP‐C₆₀ with those of BDP‐H₂P, BDP‐ZnP and BDP‐C₆₀, which were used as references, showed that the spectroscopic and electrochemical properties of the individual constituents are basically retained, although some appreciable shifts in terms of absorption indicate some interactions in the ground state. Fluorescence lifetime measurements and transient absorption experiments helped to elucidate the antenna function of BDP, which upon selective excitation undergoes a rapid and efficient energy transfer from BDP to H₂P or ZnP. This is then followed by an electron transfer to C₆₀, yielding the formation of the singlet charge‐separated states, namely BDP‐H₂P ^.+‐ C₆₀ ^.? and BDP‐ZnP ^.+‐ C₆₀ ^{. ?}. As such, the sequence of energy transfer and electron transfer in the present models mimics the events of natural photosynthesis.     

Ion‐Induced Fragmentation of Amino Acids: Effect of the Environment

In general, radiation‐induced fragmentation of small amino acids is governed by the cleavage of the C? C_α bond. We present results obtained with 300 keV Xe²⁰⁺ ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C? C_α bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C? C_α bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a “buffer” for the excess energy, capable of rapidly redistributing excess energy and charge.     

Ruthenium (II) 1,10-Phenanthroline Salts as Mobile Phase Additives for the Separation and Indirect Detection of Free Amino Acids

Abstract

Ruthenium (II) 1,10-phenanthroline, Ru(phen)²⁺ ₃, salts are used as ion interaction reagents in a basic mobile phase for the retention, resolution, and indirect photometric detection (IPD) of free amino acids on a polystyrene divinylbenzene (Hamilton PRP-1) column. Mobile phase Ru(phen)²⁺ ₃ concentration and pH and type and concentration of organic modifier and counteranion affect retention and IPD. Underivatized amino acid elution order is influenced by side chain structure typical of ion exchange processes. Detection limits for the separation and detection of free amino acids using an isocratic elution condition are about 0.1 nmole for lower retained amino acids and 0.25 nmole for higher retained amino acids for a 3:1 signal:noise ratio. Gradient elution is possible but at higher detection limits.     

Simple Synthesis of Ruthenium π Complexes of Aromatic Amino Acids and Small Peptides

The interaction of [Ru(η⁶‐C₁₀H₈)(Cp)]⁺ (Cp=C₅H₅) with aromatic amino acids (L ‐phenylalanine, L ‐tyrosine, L ‐tryptophane, D ‐phenylglycine, and L ‐threo‐3‐phenylserine) under visible‐light irradiation gives the corresponding [Ru(η⁶‐amino acid)(Cp)]⁺ complexes in near‐quantitative yield. The reaction proceeds in air at room temperature in water and tolerates the presence of non‐aromatic amino acids (except those which are sulfur containing), monosaccharides, and nucleotides. The complex [Ru(η⁶‐C₁₀H₈)(Cp)]⁺ was also used for selective labeling of Tyr and Phe residues of small peptides, namely, angiotensin I and II derivatives.     

Triel–hydride triel bond between ZX3 (Z = B and Al; X = H and Me) and THMe3 (T = Si,Ge and Sn)

Complexes between THMe₃ (T = Si, Ge and Sn) and ZX₃ (Z = B and Al; X = H and Me) have been characterized using MP2/aug‐cc‐pVTZ calculations. These complexes are chiefly stabilized by a triel–hydride triel bond with the T–H bond pointing to the π‐hole on the triel atom. The triel–hydride interaction is mainly attributed to the charge transfer from the T–H bond orbital to the empty p orbital of the triel atom. These complexes are very stable with a large interaction energy (>10 kcal mol^?1) excluding THMe₃···BMe₃ (T = Si and Ge), indicating that the sp²‐hydridized triel atom has a strong affinity for the T–H bond. The formation of THMe₃···BH₃ results in proton transfer, characterized by conversion of orbital interaction and large charge transfer (ca 0.5e). The large deformation is primarily responsible for the abnormally greater interaction energy in THMe₃···BH₃ (>30 kcal mol^?1) than in the AlH₃ analogue. Methyl substitution on the triel atom weakens the triel–hydride interaction and causes a larger interaction energy in THMe₃···AlMe₃ with respect to its BMe₃ counterpart. Most of these interactions possess characteristics of covalent bonds. Polarization makes a contribution to the stability of most complexes nearly equivalent to the electrostatic term.     

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5‐ethyl‐6‐phenylphenanthridinium and uncharged 3,8‐diamino‐6‐phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge‐transfer terms are also important. The ΔG of ethidium intercalation to DNA was estimated at ?4.5 kcal mol^?1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non‐covalent stacking (including charge‐transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

Rose Bengal‐Sensitized Photooxidation of the Dipeptides l‐Tryptophyl‐l‐Phenylalanine,l‐Tryptophyl‐l‐Tyrosine and l‐Tryptophyl‐l‐Tryptophan: Kinetics,Mechanism and Photoproducts¶

The Rose Bengal‐sensitized photooxidations of the dipeptides l ‐tryptophyl‐l ‐phenylalanine (Trp‐Phe), l ‐tryptophyl‐l ‐tyrosine (Trp‐Tyr) and l ‐tryptophyl‐l ‐tryptophan (Trp‐Trp) have been studied in pH 7 water solution using static photolysis and time‐resolved methods. Kinetic results indicate that the tryptophan (Trp) moiety interacts with singlet molecular oxygen (O₂(¹Δ_g)) both through chemical reaction and through physical quenching, and that the photooxidations can be compared with those of equimolecular mixtures of the corresponding free amino acids, with minimum, if any, influence of the peptide bond on the chemical reaction. This is not a common behavior in other di‐ and polypeptides of photooxidizable amino acids. The ratio between chemical (k_r) and overall (k_t) rate constants for the interaction O₂(¹Δ_g)‐dipeptide indicates that Trp‐Phe and Trp‐Trp are good candidates to suffer photodynamic action, with k_rlk_t values of 0.72 and 0.60, respectively (0.65 for free Trp). In the case of Trp‐Tyr, a lower k_rlk_t value (0.18) has been found, likely as a result of the high component of physical deactivation of O₂(¹Δ_g) by the tyrosine moiety. The analysis of the photooxidation products shows that the main target for O₂(¹Δ_g) attack is the Trp group and suggests a much lower accumulation of kynurenine‐type products, as compared with free Trp. This is possibly because of the occurrence of another accepted alternative pathway of oxidation that gives rise to 3a‐oxidized hydrogenated pyrrolo[2,3‐b]indoles.     

Ab initio reaction path for cisplatin interaction with L‐cysteine and L‐methionine

Ab initio calculations are used to track the reaction pathway of interaction between cisplatin and the sulfur‐containing amino acids cysteine (Cys) and methionine (Met). Structures of all reactive species as well as thermodynamic and kinetic properties were calculated and discussed based on the role played by the level of theory. Twenty‐three different levels of theory were examined including HF, DFT, and perturbation theory at MP2 and MP4(SDQ) orders. The rate constant for a second‐order associative ligand exchange mechanism (k₂) was calculated by means of transition state theory. This quantity is quite sensitive to small fluctuation of activation free energy, therefore is a good benchmark to assess the performance of different methods of calculations. The k₂ values predicted by DFT methods were in best agreement with experiment, found equal to (10²k₂ in M^?1 s^?1) 3.42 for Met (PBE1PBE) and 1.90 for Cys (B3P86). The experimental values are 3.6 and 2.2 for Met and Cys, respectively. The solvent effect plays a primary role to the kinetic properties, accounting for ～30% of the activation Gibbs free energy. The outcomes from the present study promptly show the adequacy of distinct theoretical approaches to describe the reactivity of cisplatin, thus might be useful for further studies involving other Pt(II) complexes. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical Study of the Reaction Formalhydrazone with Singlet Oxygen. Fragmentation of the C=N Bond,Ene Reaction and Other Processes

Photobiologic and synthetic versatility of hydrazones has not yet been established with ¹O₂ as a route to commonly encountered nitrosamines. Thus, to determine whether the “parent” reaction of formalhydrazone and ¹O₂ leads to facile C=N bond cleavage and resulting nitrosamine formation, we have carried out CCSD(T)//DFT calculations and analyzed the energetics of the oxidation pathways. A [2 + 2] pathway occurs via diradicals and formation of 3‐amino‐1,2,3‐dioxazetidine in a 16 kcal/mol^?1 process. Reversible addition or physical quenching of ¹O₂ occurs either on the formalhydrazone carbon for triplet diradicals at 2–3 kcal mol^?1, or on the nitrogen (N(3)) atom forming zwitterions at ~15 kcal/mol^?1, although the quenching channel by charge‐transfer interaction was not computed. The computations also predict a facile conversion of formalhydrazone and ¹O₂ to hydroperoxymethyl diazene in a low‐barrier ‘ene’ process, but no 2‐amino‐oxaziridine‐O‐oxide (perepoxide‐like) intermediate was found. A Benson‐like analysis (group increment calculations) on the closed‐shell species are in accord with the quantum chemical results.     

A quantum chemical study of the interaction of monomethyl mercury cation with G,H, S,and Y amino acids

Within DFT(B3LYP) methods, the potential interaction surface of a monomethyl mercury cation with G, H, S, and Y amino acids entering into the composition of the active cavity of acetylcholinesterase is studied. The preference for different centeres of amino acids for the interaction with the metal atom is investigated. The principal possibility of C_α-deprotonation of amino acid as a result of the interaction with the electronegative carbon center of methylmercury is analyzed. The effect of deprotonation is shown to cause demethylation of methylmercury. Iterative action is assumed to occur in Hg(II) and MeHg⁺ biochemical objects, which explains the high toxicity of microconcentrations of these compounds.     

Thermodynamic Properties of Transfer for Tetraphenylarsonium Tetraphylborate from Water to n—Alkanols

Solubilities of tetraphenylarsonium tetraphenylborate(Ph4AsB-Ph4) in water,methanol,ethanol, 1-propanol,1-butanol,1-pentanol,1-hexanol and 1-octanol at T=293.2,298.2,303.2 and 308.2 K have been determined by spectrophotometry,The standard transfer Gibbs energy (△trG^0w→s) and entropy (△trS^0w→s) of Ph4AsBPh4 from water to the n-alkanols at temerature from 293.2 K to 308.2 K have been obtained.Fur-thermore,the contribution of microscopic interaction to the standard Gibbs energy of transfer for Ph4AsBPh4 was calculated and discussed,The results show that the effect of hydrophobic inderaction of Ph4AsBPh4 on its transfer process is the most im-portant factor .According to the thermodynamical principle,the transfer process of Ph4AsBPh4 from water to the n-alkanols is the entropy dominanted.     

Photoreaction of Ketoprofen with Tryptophan and Tyrosine in Phosphate Buffer Solution

Reaction of excited ketoprofen (KP) with tryptophan (Trp) and tyrosine (Tyr) in a phosphate buffer solution was studied by the transient absorption spectroscopy. Both amino acids, which would interact with KP in bovine serum albumin [Monti, S. [2009] Phys. Chem. Chem. Phys., 11, 9104–9113], accelerated the proton transfer reaction to yield 3‐ethylbenzophenone ketyl biradical (EBPH) from KP carbanion, which was produced by photoexcitation of KP^? through decarboxylation. By means of the actinometry method with benzophenone, the reaction quantum yield was successfully estimated to be fairly large, and Trp, Tyr, DOPA and 4‐methylphenol were found to be a good proton donor for the carbanion. The formation rate constants of EBPH by the amino acids (k_r) were also determined to be (2.7 ± 0.1) × 10⁹ M^?1s^?1 for Trp and (7.8 ± 0.4) × 10⁸ M^?1s^?1 for Tyr, which were larger than those by basic amino acids and dipeptides reported. The reason for the highly efficient proton transfer reaction with Trp and Tyr would be explained by difference of the activation energy for the reaction. These results suggest that the proton transfer should be a key process for an initial photoreaction of KP with a protein, causing photosensitization in vivo.     

Proton transfer at the carboxylic sites of amino acids: A single water molecule catalyzed process

Ab initio calculations at MP2 level of theory were used to study the proton transfer at the carboxylic sites of amino acids, in the isolated, mono‐ and di‐hydrated forms. In the case of water dimer, two interaction modes with glycine neutral structures (see Fig. 3 ) were explored, corresponding to the concerted and stepwise reaction pathways. Their transition states can be described as (H₂O? H? OH₂)⁺ [Fig. 4 (a)] and (H₂O‐‐‐H? OH₂)⁺ [Fig. 4 (b)], respectively. The energy analysis indicated that the concerted pathway is preferred. In the isolated, mono‐ and di‐hydrated glycine complexes, the activation barriers of the proton transfer at the carboxylic sites were calculated to be 34.49, 16.59, and 13.36 kcal mol^?1, respectively. It was thus shown that the proton transfer is significantly assisted and catalyzed by water monomer so that it can take place at room temperature. Instead, the further addition of water molecules plays solvent effects rather than catalytic effects to this proton transfer process. The above results obtained with discrete water molecules were supported by the solvent continuum calculated data. It was also observed that the heavy dependence of the solvent continuum models on dipole moments may produce misleading results. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009