Cavitation free energy for organic molecules having various sizes and shapes

Cavitation free energy DeltaG(cav), corresponding to the formation of an excluded volume cavity in water, is calculated for a large set of organic molecules employing the thermodynamic integration procedure, which is realized as the original two-step algorithm for growing the interaction potential between the hard cavity wall and the water molecules. A large variety of solute systems is considered. Their characteristic radii change in the range 3-7 A; spherical cavities with radii 3-6 A are also studied. The interaction between water molecules is described by the four-site nonpolarizable TIP4P model. The diversity of the trial molecular set is provided by using a specially formulated nonspherical criterion classifying the cavity shapes according to their deviation from a sphere. Molecular objects were partly taken from the data base NCI Diversity with the aid of this criterion. The so-computed free energies are approximated by the linear volume dependence DeltaG(cav)V = XiV, where V is the cavity volume. This relation works fairly well until the cavity size becomes very large (the effective radius larger than 7 A). The volume dependence valid for solutes of arbitrary shapes can be included in a calculation of the nonpolar free energy component as required in the implicit water model.     

In silico prediction of drug solubility: 2. Free energy of solvation in pure melts

The solubility of drugs in water is investigated in a series of papers and in the current work. The free energy of solvation, DeltaG*(vl), of a drug molecule in its pure drug melt at 673.15 K (400 degrees C) has been obtained for 46 drug molecules using the free energy perturbation method. The simulations were performed in two steps where first the Coulomb and then the Lennard-Jones interactions were scaled down from full to no interaction. The results have been interpreted using a theory assuming that DeltaG*(vl) = DeltaG(cav) + E(LJ) + E(C)/2 where the free energy of cavity formation, DeltaG(cav), in these pure drug systems was obtained using hard body theories, and E(LJ) and E(C) are the Lennard-Jones and Coulomb interaction energies, respectively, of one molecule with the other ones. Since the main parameter in hard body theories is the volume fraction, an equation of state approach was used to estimate the molecular volume. Promising results were obtained using a theory for hard oblates, in which the oblate axial ratio was calculated from the molecular surface area and volume obtained from simulations. The Coulomb term, E(C)/2, is half of the Coulomb energy in accord with linear response, which showed good agreement with our simulation results. In comparison with our previous results on free energy of hydration, the Coulomb interactions in pure drug systems are weaker, and the van der Waals interactions play a more important role.     

On the cavitation energy of water

Free-energy-perturbation theory from molecular dynamics calculations has been used to obtain the DeltaG of adjoining cavities' formation in water. The DeltaGs for systems with three, five and seven cavities are compared with that of a single cavity of the same volume, and found to be in good agreement. The conditions under which the analytical formulation of the energy of cavity formation proposed by Pierotti holds are discussed. The data for a single cavity have been tabulated and can lend themselves to a simple numerical implementation in standard quantum chemical packages, which can be used when high accuracy for DeltaG(cav) is required.     

Host-guest interaction of L-tyrosine with beta-cyclodextrin

The inclusion complexes of beta-cyclodextrin (beta-CD) with l-tyrosine (l-TYN) were investigated by using spectrophotometers. The absorption and fluorescence enhancement occurs with beta-CD and l-TYN forms 1:1 inclusion complex. The unusual blue shift of hydroxyl ion in the beta-CD medium confirms OH groups present in the interior part of the beta-CD cavity and -COOH group present in the upper part of the beta-CD cavity. A mechanism is proposed to explain inclusion process. The inclusion interaction was examined and the thermodynamic parameters of inclusion process DeltaG, DeltaH and DeltaS were determined. The results indicated that the inclusion process was an exergonic and spontaneous process. Stable solid inclusion complexes were established and characterized by FT-IR, scanning electron microscope (SEM) methods.     

Thermodynamic study of the complexation of trivalent actinide and lanthanide cations by ADPTZ, a tridentate N-donor ligand

To better understand the bonding in complexes of f-elements by polydentate N-donor ligands, the complexation of americium(III) and lanthanide(III) cations by 2-amino-4,6-di-(pyridin-2-yl)-1,3,5-triazine (ADPTZ) was studied using a thermodynamic approach. The stability constants of the 1:1 complexes in a methanol/water mixture (75/25 vol %) were determined by UV-visible spectrophotometry for every lanthanide(III) ion (except promethium), and yttrium(III) and americium(III) cations. The thermodynamic parameters (DeltaH degrees , DeltaS degrees) of complexation were determined from the temperature dependence of the stability constants and by microcalorimetry. The trends of the variations of DeltaG degrees , DeltaH degrees , and DeltaS degrees across the lanthanide series are compared with published results for other tridentate ligands and confirm strongly ionic bonding in the lanthanide-ADPTZ complexes. Comparison of the thermodynamic properties between the Am- and Ln-ADPTZ complexes highlights an increase in stability of the complexes by a factor of 20 in favor of the americium cation. This difference arises from a more exothermic reaction enthalpy in the case of Am, which is correlated with a greater degree of covalency in the americium-nitrogen bonds. Quantum chemistry calculations performed on a series of trivalent actinide and lanthanide-ADPTZ complexes support the experimental results, showing a slightly greater covalence in the actinide-ligand bonds that originates from a charge transfer from the ligand sigma orbitals to the 5f and 6d orbitals of the actinide ion.     

Synthesis and characterization of Mn(II), Au(III) and Zr(IV) hippurates complexes

Mn(II), Au(III) and Zr(III) complexes with N-benzoylglycine (hippuric acid) (abbreviation hipH) were synthesized and characterized by elemental analysis, molar conductivity, magnetic measurements, spectral methods (mid-infrared, (1)H NMR, mass, X-ray powder diffraction and UV/vis spectra) and simultaneous thermal analysis (TG and DTG) techniques. The molar conductance measurements proved that all hippuric acid complexes are non-electrolytes. The electronic spectra and magnetic susceptibility measurements were used to infer the structures. The IR spectra of the ligand and its complexes are used to identify the type of bonding. The kinetic thermodynamic parameters such as: E*, DeltaH*, DeltaS* and DeltaG* are estimated from the DTG curves. The free ligand and its complexes have been studied for their possible biological antifungal activity.     

Study on the inclusion complexes of cryptotanshinone with beta-cyclodextrin and hydroxypropyl-beta-cyclodextrin

The inclusion complexes of beta-cyclodextrin (beta-CD) and HP-beta-cyclodextrin (HP-beta-CD) with a kind of tanshinone, cryptotanshinone (CTan) were investigated by using spectrophotometry. Stable inclusion complexes were established in solution and in solid state and were characterized by UV, IR and 1H NMR spectra, respectively. The optimum pH for inclusion is about 7.5. Stoichiometry of the inclusion complex is 1:1. The stabilities of beta-CD and HP-beta-CD to CTan were in the order: beta-CD相似文献   

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.     

Dynamics in host-guest complexes of molecular tweezers and clips

The dynamics in the host-guest complexes of the molecular tweezers 1 a,b and clips 2 a,b with 1,2,4,5-tetracyanobenzene (TCNB, 3) and tropylium tetrafluoroborate (4) as guest molecules were analyzed by temperature-dependent 1H NMR spectroscopy. The TCNB complexes of tweezers 1 a,b were found to be particularly stable (dissociation barrier: DeltaG(++)=16.8 and 15.7 kcal mol(-1), respectively), more stable than the TCNB complexes of clips 2 a,b and the tropylium complex of tweezer 1 b (dissociation barrier: DeltaG(++)=12.4, 11.2, and 12.3 kcal mol(-1), respectively). A detailed analysis of the kinetic and thermodynamic data (especially the negative entropies of activation found for complex dissociation) suggests that in the transition state of dissociation the guest molecule is still clipped between the aromatic tips of the host molecule. The 1H NMR analysis of the TCNB complexes 3@1 b and 3@2 a at low temperatures (T<-80 degrees C) showed that 3 undergoes fast rotation inside the cavity of tweezer 1 b or clip 2 a (rotational barrier: DeltaG( not equal)=11.7 and 8.3 kcal mol(-1), respectively). This rotation of a guest molecule inside the host cavity can be considered to be the dynamic equilibration of noncovalent conformers. In the case of clip complex 3@2 a the association and rotational barriers are smaller by DeltaDeltaG(++)=3-4 kcal mol(-1) than those in tweezer complexes 3@1 a,b. This can be explained by the more open topology of the trimethylene-bridged clips compared to the tetramethylene-bridged tweezers. Finally, the bromo substituents in the newly prepared clip 2 b have a substantial effect on the kinetics and thermodynamics of complex formation. Clip 2 b forms weaker complexes with (TCNB, 3) and tetracyanoquinodimethane (TCNQ, 12) and a more stable complex with 2,4,7-trinitrofluoren-9-ylidene (TNF, 13) than the parent clip 2 a. These results can be explained by a less negative electrostatic potential surface (EPS) inside the cavity and a larger van der Waals contact surface of 2 b compared to 2 a. In the case of the highly electron-deficient guest molecules TCNB and TCNQ the attractive electrostatic interaction is predominant and hence responsible for the thermodynamic complex stability, whereas in the case of TNF with its extended pi system, dispersion forces are more important for host-guest binding.     

Study on the supramolecular multirecognition mechanism of beta-naphthol/beta-cyclodextrin/anionic surfactant in a tolnaftate hydrolysis system

Based on the fact that tolnaftate degrade to beta-naphthol sodium (RONa) at 5.00 mol/L NaOH solution and RO(-) was protonated to ROH after being acidified and adjusted to the pH 4.50 by acetic acid-sodium acetate buffer solution, we studied and discussed the mechanism of the supramolecular multirecognition interaction among the anionic surfactants sodium lauryl sulfate (SLS), beta-cyclodextrin (beta-CD), and beta-naphthol (ROH) by means of fluorescence spectrum, surface tension of the solution, infrared spectrograms, and (1)HNMR spectroscopy. The apparent formation constant of the ternary inclusion complex was determined to be (5.48 +/- 0.13) x 10(3) L(2)/mol(2). The thermodynamic parameters (DeltaG degrees, DeltaH degrees, DeltaS degrees ) for the formation of the inclusion complexes were obtained from the van't Hoff equation. It was indicated that the multiple and synergistic protection effect of SLS and beta-CD on the excited singlet state ROH played very important roles in the enhancement of the fluorescence of ROH. Results showed that, at room temperature, the naphthalene ring of ROH and the hydrophobic hydrocarbon chain of SLS were included into the cavity of beta-CD to form a ROH/SLS/beta-CD ternary inclusion complex with stoichiometry of 1:1:1, which provided effective protection for the excited state of ROH and increased the fluorescent intensity of ROH obviously.     

Effects of sugars and polyols on the stability of azurin in ice

This study represents the first attempt to gain a quantitative estimate of the protective influence of sugars (sucrose and trehalose) and polyols (sorbitol and glycerol) on the thermodynamic stability (DeltaG degrees ) of a protein in low-temperature part-frozen aqueous solutions. The method, based on guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, distinguishes between the effects of cooling to subfreezing temperatures from those induced specifically by the formation of a solid ice phase. The results point out that in the liquid state the generally stabilizing effect (at molar concentrations) of these polyhydric compounds is markedly attenuated on cooling to subfreezing temperatures such that at -15 degrees C, only sucrose still exerts a significant increase in DeltaG degrees . At this temperature, and in the absence of additives, the formation of ice caused a progressive destabilization of the native fold, DeltaG degrees decreasing up to 3-4 kcal/mol as the fraction of liquid water in equilibrium with ice (V(L) was reduced to less than 1%. Unexpectedly, denaturation profiles in ice at selected V(L) demonstrate that none of the above sugars and polyols counters effectively the decrease in protein stability at small V(L). Only trehalose was able to partly attenuate the ice perturbation, raising DeltaG degrees by a modest 0.6-0.8 kcal/mol relative to the salt reference. In all cases the reduction in DeltaG degrees caused by the solidification of water correlates with the decrease in m-value. The implication is that DeltaASA of unfolding is smaller in ice because protein-ice interactions either increase the solvent-accessible surface area (ASA) of the native fold (partial unfolding) or reduce the ASA of the denatured state (compaction), or both. Information on the protein tertiary structure in ice, in the absence and in the presence of sucrose or glycerol, suggests that these osmolytes play an important role in maintaining a compact native state that in their absence is expanded and partly unfolded. Thus, it appears that the prevailing mechanism by which these osmolytes act as cryoprotectants is through preservation of the native conformation in the liquidus rather than by increasing the thermodynamic stability of the native fold.     

Spectroscopic, and thermal studies of some new binuclear transition metal(II) complexes with hydrazone ligands containing acetoacetanilide and isoxazole

A new chelating ligand, 2-(2-(5-tert-butylisoxazol-3-yl)hydrazono)-N-(2,4-dimethylphenyl)-3-oxobutanamide (HL), and its four binuclear transition metal complexes, M(2)(L)(2) (micro-OCH(3))(2) [M=Ni(II), Co(II), Cu(II), Zn(II)], were synthesized using the procedure of diazotization, coupling and metallization. Their structures were postulated based on elemental analysis, (1)H NMR, MALDI-MS, FT-IR spectra and UV-vis electronic absorption spectra. Smooth films of these complexes on K9 glass substrates were prepared using the spin-coating method and their absorption properties were evaluated. The thermal properties of the metal(II) complexes were investigated by thermogravimetry (TG) and differential scanning calorimetry (DSC). Different thermodynamic and kinetic parameters namely activation energy (E*), enthalpy of activation (DeltaH*), entropy of activation (DeltaS*) and free energy change of activation (DeltaG*) are calculated using Coats-Redfern (CR) equation.     

Specific anions effects of on the stability of azurin in ice

This investigation represents a first attempt to gain a quantitative estimate of the effects of the anions sulfate, citrate, acetate, chloride and thiocyanate on the thermodynamic stability (DeltaG degrees) of a model globular protein in ice at -15 degrees C. The method, based on guanidinium chloride denaturation of the azurin mutant C112S from Pseudomonas aeruginosa, distinguishes between the effects of cooling to subfreezing temperatures from those induced specifically by the formation of a solid ice phase. The results confirm that, both in liquid and frozen states, kosmotropes (sulfate, citrate and acetate) increase significantly protein stability, relative to chloride, whereas the chaotrope thiocyanate decreases it. Throughout, their stabilizing efficacy was found to rank according to the Hofmeister series, sulfate>citrate>acetate>chloride>thiocyanate, although the magnitude of Delta(DeltaG degrees) exhibited a distinct sensitivity among the anions to low temperature and to ice formation. In the liquid state, lowering the temperature from +20 to -15 degreesC weakens considerably the stabilizing efficacy of the organic anions citrate and acetate. Among the anions sulfate stands out as the only strong stabilizer at subfreezing temperatures while SCN- becomes an even stronger denaturant. Freezing of the solution in the presence the "neutral" salt NaCl destabilizes the protein, DeltaG degrees progressively decreasing up to 3-4 kcal/mol as the fraction of liquid water in equilibrium with ice (VL) is reduced to less than 1%. Kosmotropes do attenuate the decrease in protein stability in ice although in the case of citrate and acetate, their efficacy diminishes sharply as the liquid fraction shrinks to below 2.7%. On the contrary, sulfate is remarkable for it maintains constantly high the stability of azurin in liquid and frozen solutions, down to the smallest VL (0.5%) examined. Throughout, the reduction in DeltaG degrees caused by the solidification of water correlates with the decrease in the denaturant m value, an indirect indication that protein-ice interactions generally lead to partial unfolding of the native state. It is proposed that binding of the kosmotropes to the ice interface may inhibit protein adsorption to the solid phase and thereby counter the ice perturbation.     

Spectroscopic, thermal and biological studies of the coordination compounds of sulfasalazine drug: Mn(II), Hg(II), Cr(III), ZrO(II), VO(II) and Y(III) transition metal complexes

The complexations of sulfasalazine (H3Suz) with some of transition metals have been investigated. Three types of complexes, [Mn(HSuz)-2(H2O)4] x 2H2O, [M(HSuz)-2(H2O)2] x xH2O (M=Hg(II), ZrO(II) and VO(II), x=4, 8 and 6, respectively) and [M(HSuz)-2(Cl)(H2O)3] x xH2O (M=Cr(III) and Y(III), x=5 and 6, respectively) were obtained and characterized by physicochemical and spectroscopic methods. The IR spectra of the complexes suggest that the H3Suz behaves as a bidentate ligand. The thermal decomposition of the complexes as well as thermodynamic parameters (DeltaE*, DeltaH*, DeltaS* and DeltaG*) were estimated using Coats-Redfern and Horowitz-Metzger equations. In vitro antimicrobial activities of the H3Suz and the complexes were tested.     

A study of the stability of alkaline-earth metal complexes with fluoride and chloride ions at various temperatures by potentiometry with ion-selective electrodes

The complexes of the alkaline earth metals with fluoride and chloride were studied over the temperature range 15-85 degrees . The stability constants of the MX(+) complexes were determined by potentiometry with fluoride and chloride ion-selective electrodes and the appropriate thermodynamic functions (DeltaH(0)(298), DeltaS(0)(298) and DeltaG(0)(298)) were calculated.     

Thermodynamic parameters for the binding of inorganic and organic anions by biogenic polyammonium cations

Thermodynamic parameters for the interaction of protonated biogenic polyamines with inorganic or organic polyanions were studied potentiometrically (H(+)-glass electrode) and calorimetrically, at 25 degrees C. No background salt was used in the measurements to avoid interferences, and the formation constants and formation enthalpies were extrapolated to zero ionic strength. Species formed are ALH(r) [L=Cl(-), SO(4)(2-), HPO(4)(2-), P(2)O(7)(4-) and P(3)O(10)(5-); tartrate, malate, citrate, glutamate, 1,2,3-propanetricarboxylate, 1,2,3,4-butanetetracarboxylate], with r=1,2...(n+m-2) and r=1,2...(n+m-1) for inorganic and organic ligands, respectively (n, m=maximum degree of protonation of amine and ligand, respectively). The stability of the various species formed is a function of charges involved in the formation reaction. DeltaH(0) values are generally positive, and therefore these complexes are entropically stabilized. Results are discussed in connection with several previously reported data on similar systems. DeltaG(0) and TDeltaS(0) follow a linear trend as a function of polyammonium cation and inorganic or carboxylic anion charges. DeltaG(0) and TDeltaS(0) charge relationships are reported. In particular, mean values of DeltaG(0) and TDeltaS(0) for single interaction were calculated: DeltaG(0)=7.0 kJ mol(-1) n(-1), TDeltaS(0)=9.1 kJ mol(-1) n(-1) and DeltaG(0)=5.7 kJ mol(-1) n(-1) and TDeltaS(0)=8.7 kJ mol(-1) n(-1), for the species of inorganic and organic polyanions, respectively (n=number of possible salt bridges). A linear relationship was also found for TDeltaS(0) versus DeltaG(0), whose equation is TDeltaS(0)=-7-1.39 DeltaG(0) (with r=0.9409; r, correlation coefficient). The body of correlations found for these thermodynamic parameters shows quite good predictive value.     

Heteroditopic ligand accommodating a fused phenanthroline and a schiff base cavity as molecular spacer in the study of electron and energy transfer

The synthesis and characterisation of the heteroditopic ligand N,N'-bis(3,5-di-tert-butylsalicylidene)-5,6-(1,10-phenanthroline)diamine (DPSalH(2)) bearing a phenanthroline and a bis(salicylidene)diimine cavity are reported. This versatile ligand combines two of the most widely used ligands in coordination chemistry. Sequential metallation of the phenanthroline end with Ru(II) and the salophenic cavity with Cu(II) is described. Electrochemical behaviour of the supramolecular complexes [Ru(bpy)(2)(DPSalH(2))](2+) and [Ru(bpy)(2)(DPSalCu)](2+) are analysed in connection with UV/Vis and EPR spectroscopy. The data for the one-electron-reduced species and the singly oxidised species of the binuclear Ru(II)-Cu(II) complex confirmed the formation of metalloradical complexes. Density functional calculations on the free ligand and the copper-only complex indicate in both cases that the HOMOs and LUMOs are developed on the Schiff base cavity with minor contributions on the bipyridine end. These findings support a bichromophoric character for our ruthenium complexes in the ground state, a necessary condition in the design of supramolecular systems for the study of electron transfer. Photophysical studies indicate fast quenching of the triplet excited state in both complexes, which suggests strong intercomponent excited-state interactions. Evidence is presented that this quenching is due to intramolecular electron transfer, at least in the case of [Ru(bpy)(2)(DPSalH(2))](2+), for which a charge-separated state with a remarkable lifetime of about 30 mus was observed.     

Activation of C-H / H-H bonds by rhodium(II) porphyrin bimetalloradicals

Reactivity, kinetic, and thermodynamic studies are reported for reactions of a rhodium(II) bimetalloradical with H(2), and with the methyl C-H bonds for a series of substrates CH(3)R (R = H, CH(3), OH, C(6)H(5)) using a m-xylyl diether tethered diporphyrin ligand. Bimolecular substrate reactions involving the intramolecular use of two metalloradical centers and preorganization of the four-centered transition state (M*...X...Y*...M) result in large rate enhancements as compared to termolecular reactions of monometalloradicals. Activation parameters and deuterium kinetic isotope effects for the substrate reactions are reported. The C-H bond reactions become less thermodynamically favorable as the substrate steric requirements increase, and the activation free energy (DeltaG++) decreases regularly as DeltaG degrees becomes more favorable. An absolute Rh-H bond dissociation enthalpy of 61.1 +/- 0.4 kcal mol(-1) is directly determined, and the derived Rh-CH(2)R BDE values increase regularly with the increase in the C-H BDE.     

Thermodynamic parameters governing the self-assembly of head-head-head lanthanide bimetallic helicates

The heterobitopic ligands L ABX (X=1, 2, 3, 4 or 5), differing only by a Cl or NEt(2) substituent, have been designed to complex with a pair of lanthanide ions to form triple-stranded bimetallic helicates of overall composition [Ln2(L ABX)3]6+. The percentage of HHH (head-head-head) isomer, in which each of the three ligand strands coordinates to the same lanthanide ion with the same coordination unit, is deciding the ability of the ligands to selectively form heterobimetallic complexes containing one luminescent and one magnetic or two different luminescent ions. It deviates significantly from the statistical value of 25 % and ranges from 6-20 % for L AB2 complexes to 93-96 % for L AB4 complexes. The equilibrium between HHT (head-head-tail) and HHH isomers has been investigated in detail for homobimetallic helicates (Ln=Y, La, Ce, Pr, Nd, Sm, Eu, Lu) by means of variable temperature NMR and thermodynamic parameters have been determined. The equilibrium is characterized by small values of DeltaH and DeltaS, which vary in opposite direction along the lanthanide series for complexes with the same ligand in a way that keeps the value of DeltaG almost constant. The results are interpreted in terms of differences in interstrand stacking, ion-dipole interactions and metal-metal repulsion.