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PubMed2006

Expanded thermodynamic model for microbial true yield prediction.

Thermodynamic methods to predict true yield and stoichiometry of bacterial reactions have been widely used in biotechnology and environmental engineering. However, yield predictions are often inaccurate for certain simple organic compounds. This work evaluates an existing method and identifies the cause of prediction errors for compounds with low degree of reductance of carbon. For these compounds, carbon, not energy or reducing equivalents, constrains growth. Existing thermodynamically-based models do not account for the potential of carbon-limited growth. The improved method described here consists of four balances: carbon balance, nitrogen balance, electron balance, and energy balance. Two efficiency terms, K1 and K2 are defined and estimated from a priori analysis. The results show that K1 and K2 are nearly the same in value so that only one coefficient, K = 0.41 is used in the modified model. Comparisons with observed yields show that use of the new model and parameters results in significantly improved yield estimation based on inclusion of the carbon balance. The average estimation error is less than 6% for the data set presented.

Bacteria↗
PubMed2005

Protein flexibility and ligand rigidity: a thermodynamic and kinetic study of ITAM-based ligand binding to Syk tandem SH2.

The Syk tandem Src homology 2 domain (Syk tSH2) constitutes a flexible protein module involved in the regulation of Syk kinase activity. The Syk tSH2 domain is assumed to function by adapting the distance between its two SH2 domains upon bivalent binding to diphosphotyrosine ligands. A thermodynamic and kinetic analysis of ligand binding was performed by using surface plasmon resonance (SPR). Furthermore, the effect of binding on the Syk tSH2 structural dynamics was probed by hydrogen/deuterium exchange and electrospray mass spectrometry (ESI-MS). Two ligands were studied: 1, a flexible peptide derived from the tSH2 recognition ITAM sequence at the gamma chain of the FcepsilonRI-receptor, and 2, a ligand in which the amino acids between the two SH2 binding motifs in ligand 1 have been replaced by a rigid linker of comparable length. Both ligands display comparable affinity for Syk tSH2 at 25 degrees C, yet a major difference in thermodynamics is observed. Upon binding of the rigid ligand, 2, the expected entropy advantage is not realized. On the contrary, 2 binds with a considerably higher entropy price of approximately 9 kcal mol-1, which is attributed to a further decrease in protein flexibility upon binding to this rigid ligand. The significant reduction in deuterium incorporation in the Syk tSH2 protein upon binding of either 1 or 2, as monitored by ESI-MS, indicates a major reduction in protein dynamics upon binding. The results are consistent with a two-step binding model: after an initial binding step, a rapid structural change of the protein occurs, followed by a second binding step. Such a bivalent binding model allows high affinity and fast dissociation kinetics, which are very important in transient signal-transduction processes.

Intracellular Signaling Peptides and Proteins↗
PubMed2003

Thermodynamics and kinetics of the hydride-transfer cycles for 1-aryl-1,4-dihydronicotinamide and its 1,2-dihydroisomer.

Five 1-(p-substituted phenyl)-1,4-dihydronicotinamides (GPNAH-1,4-H(2)) and five 1-(p-substituted phenyl)-1,2-dihydronicotinamides (GPNAH-1,2-H(2)) were synthesized, which were used to mimic NAD(P)H coenzyme and its 1,2-dihydroisomer reductions, respectively. When the 1,4-dihydropyridine (GPNAH-1,4-H(2)) and the 1,2-dihydroisomer (GPNAH-1,2-H(2)) were treated with p-trifluoromethylbenzylidenemalononitrile (S) as a hydride acceptor, both reactions gave the same products: pyridinium derivative (GPNA(+)) and carbanion SH(-) by a hydride one-step transfer. Thermodynamic analysis on the two reactions shows that the hydride transfer from the 1,2-dihydropyridine is much more favorable than the hydride transfer from the corresponding 1,4-dihydroisomer, but the kinetic examination displays that the former reaction is remarkably slower than the latter reaction, which is mainly due to much more negative activation entropy for the former reaction. When the formed pyridinium derivative (GPNA(+)) was treated with SH(-), the major reduced product was the corresponding 1,4-dihydropyridine along with a trace of the 1,2-dihydroisomer. Thermodynamic and kinetic analyses on the hydride transfer from SH(-) to GPNA(+) all suggest that the 4-position on the pyridinium ring in GPNA(+) is much easier to accept the hydride than the 2-position, which indicates that when the 1,4-dihydropyridine is used the hydride donor to react with S, the formed pyridinium derivative GPNA(+) may return to the 1,4-dihydropyridine by a hydride transfer cycle; but when the 1,2-dihydropyridine is used as the hydride donor, the formed pyridinium derivative can not return to the 1,2-dihydropyridine by the hydride reverse transfer from SH(-) to GPNA(+). These results clearly show that the hydride-transfer cycle is favorable for the 1,4-dihydronicotinamides, but unfavorable for the corresponding 1,2-dihydroisomers.

Electron Transport↗
PubMed2005

Receptor-assisted combinatorial chemistry: thermodynamics and kinetics in drug discovery.

Current drug discovery using combinatorial chemistry involves synthesis followed by screening, but emerging methods involve receptor-assistance to combine these steps. Adding stoichiometric amounts of receptor during library synthesis alters the kinetics or thermodynamics of the synthesis in a way that identifies the best-binding library members. Three main methods have emerged thus far in receptor-assisted combinatorial chemistry: dynamic combinatorial libraries, receptor-accelerated synthesis, and a new method, pseudo-dynamic libraries. Pseudo-dynamic libraries apply both thermodynamics and kinetics to amplify library members to easily observable levels, and attain selectivity heretofore unseen in receptor-assisted systems.

Combinatorial Chemistry Techniques↗
PubMed1994

A thermodynamic scale for leucine zipper stability and dimerization specificity: e and g interhelical interactions.

The leucine zipper is a dimeric coiled-coil protein structure composed of two amphipathic alpha-helices with the hydrophobic surfaces interacting to create the dimer interface. This structure has been found to mediate the dimerization of two abundant classes of DNA binding proteins: the bZIP and bHLH-Zip proteins. Several workers have reported that amino acids in the e and g positions of the coiled coil can modulate dimerization stability and specificity. Using the bZIP protein VBP as a host molecule, we report a thermodynamic scale (delta delta G) for 27 interhelical interactions in 35 proteins between amino acids in the g and the following e positions (g<==>e') of a leucine zipper coiled coil. We have examined the four commonly occurring amino acids in the e and g positions of bZIP proteins, lysine (K), arginine (R), glutamine (Q), glutamic acid (E), as well as the only other remaining charged amino acid aspartic acid (D), and finally alanine (A) as a reference amino acid. These results indicate that E<==>R is the most stable interhelical pair, being 0.35 kcal/mol more stable than E<==>K. A thermodynamic cycle analysis shows that the E<==>R pair is 1.33 kcal/mol more stable than A<==>A with -1.14 kcal/mol of coupling energy (delta delta Gint) coming from the interaction of E with R. The E<==>K coupling energy is only -0.14 kcal/mol. E interacts with more specificity than Q. The R<==>R pair is less stable than the K<==>K by 0.24 kcal/mol. R interacts with more specificity than K. Q forms more stable pairs with the basic amino acids K and R rather than with E. Changing amino acids in the e position to A creates bZIP proteins that form tetramers.

Amino Acid Sequence↗
PubMed1975

Thermodynamic considerations of the setting reaction in Ag3Sn amalgams.

The setting reaction of Ag3Sn amalgams may be thought of as a liquid phase sintering problem in which the reactants seek to form products with the lowest thermodynamic potential. We discuss the thermodynamic and kinetic considerations of this reaction. The lowering of free energy has been given as the reason for the formation of the gamma1, gamma2,and beta1 phases and a qualitative reaction coordinate diagram has been hypothesized. The barrier height for the formation of the beta1 phase has been determined to be 137 kJ/mol.

Dental Alloys↗
PubMed1990

Thermodynamic study of phase transfer of precipitates on SiC whisker reinforced glass ceramics.

Physiochemical properties of glass ceramics in weakly buffered, supersaturated, metastable calcium and phosphate solution were studied. Formations of calcium phosphate precipitates were also analyzed thermodynamically. All biomaterials examined here showed primarily dissolution process and subsequent nucleation. Dissolution was enhanced in those which contained Na2O and/or SiC. The dissolution of calcium and phosphate ions from biomaterials and subsequent nucleation of calcium phosphate salts after induction time resulted in a stable equilibrium having solubility characteristics similar to octacalcium phosphate (OCP). The most soluble material, CPSN-SiC, showed an initial transient equilibrium with amorphous calcium phosphate (ACP). From above results, calcium phosphate ceramics had certain driving force of its own which kept the equilibrium of solution to OCP thermodynamically for 7 days. Despite the favorable solubility equilibrium attained, there still remain problems for clinical application.

Biocompatible Materials↗
PubMed2006

Thermodynamic perspectives on the molecular mechanisms providing protein adsorption resistance that include protein-surface interactions.

Current theories regarding the molecular mechanisms that provide protein adsorption resistance primarily focus on the characteristics of various types of surface-tethered chains and their interactions with water but often neglect their interactions with the protein. Such theories thus do not provide a complete explanation for protein adsorption resistance. The real issue that must be addressed is which properties enable surfaces to interact with water more favorably than with proteins. To address this issue, a thermodynamic treatment of protein adsorption to surface-tethered chains is presented and specific molecular-level interactions are addressed that contribute to enthalpy, entropy, and free energy changes that are involved during protein adsorption processes. Based on this analysis, it is proposed that two independently controllable sets of criteria provide conditions that are thermodynamically favorable for protein adsorption resistance: (1) well-hydrated long flexible surface-tethered chains with packing density sufficiently low to allow chain mobility while still providing complete surface coverage, and (2) surface-tethered chains that contain hydrogen-bondable groups that are readily accessible to water molecules but not to the hydrogen bond-forming groups of a protein.

Adsorption↗
PubMedDate not supplied

Kinetic and thermodynamic characterization of HIV-1 protease inhibitors.

Interaction kinetic and thermodynamic analyses provide information beyond that obtained in general inhibition studies, and may contribute to the design of improved inhibitors and increased understanding of molecular interactions. Thus, a biosensor-based method was used to characterize the interactions between HIV-1 protease and seven inhibitors, revealing distinguishing kinetic and thermodynamic characteristics for the inhibitors. Lopinavir had fast association and the highest affinity of the tested compounds, and the interaction kinetics were less temperature-dependent as compared with the other inhibitors. Amprenavir, indinavir and ritonavir showed non-linear temperature dependencies of the kinetics. The free energy, enthalpy and entropy (DeltaG, DeltaH, DeltaS) were determined, and the energetics of complex association (DeltaG(on), DeltaH(on), DeltaS(on)) and dissociation (DeltaG(off), DeltaH(off), DeltaS(off)) were resolved. In general, the energetics for the studied inhibitors was in the same range, with the negative free energy change (DeltaG < 0) due primarily to increased entropy (DeltaS > 0). Thus, the driving force of the interaction was increased degrees of freedom in the system (entropy) rather than the formation of bonds between the enzyme and inhibitor (enthalpy). Although the DeltaG(on) and DeltaG(off) were in the same range for all inhibitors, the enthalpy and entropy terms contributed differently to association and dissociation, distinguishing these phases energetically. Dissociation was accompanied by positive enthalpy (DeltaH(off) > 0) and negative entropy (DeltaS(off) < 0) changes, whereas association for all inhibitors except lopinavir had positive entropy changes (DeltaS(on) > 0), demonstrating unique energetic characteristics for lopinavir. This study indicates that this type of data will be useful for the characterization of target-ligand interactions and the development of new inhibitors of HIV-1 protease.

Carbamates↗
PubMed2003

Using the polymer partitioning method to probe the thermodynamic activity of poorly water-soluble drugs solubilized in model lipid digestion products.

The thermodynamic activity of solubilized drug is an important determinant of the extent of absorption of lipophilic drugs from the gastrointestinal tract. In this study, the polymer partitioning method was evaluated for its use in the determination of the thermodynamic activity of lipophilic drugs when solubilized in colloidal digestion products, using drug in dilute solution as a reference ideal solution. The lipophilic drugs griseofulvin, diazepam, and danazol partitioned into a polymeric receiver phase from non-micellar solution as a function of drug lipophilicity. The concentration of drug that partitioned into the polymer was linearly proportional to the concentration of free drug in solution, and this allowed the measured partition coefficient to be utilized as an indicator of the drug activity coefficient. The addition of a solubilizing species such as bile salt micelles caused a reduction in drug activity of a similar magnitude to that predicted from micelle equilibrium solubility data in the identical micellar solutions. The addition of micelle swelling lipids such as lecithin and fatty acids resulted in further reductions in activity coefficient. The ability to measure drug activity in model digestive systems has potential for application in the rational development of improved lipid-based formulations of poorly water-soluble drugs for oral administration.

Bile Acids and Salts↗
PubMed2004

Thermodynamics of sublimation, crystal lattice energies, and crystal structures of racemates and enantiomers: (+)- and (+/-)-ibuprofen.

Thermodynamic differences between ibuprofen (IBP) racemate and the (+)-enantiomer were studied by X-ray diffraction, thermoanalysis, and crystal energy calculations. The thermodynamic functions of sublimation (as a measure of crystal lattice energy) were obtained by the transpiration method. The sublimation enthalpies (DeltaH(sub)) of (+/-)-IBP and (+)-IBP are 115.8 +/- 0.6 and 107.4 +/- 0.5 kJ. mol(-1), respectively. Using the temperature dependency of the saturated vapor pressure, the relative fractions of enthalpy and entropy of the sublimation process were calculated, and the sublimation process for both the racemate and the enantiomer was found to be enthalpy driven (62%). Two different force fields, Mayo et al. (M) and Gavezzotti (G), were used for comparative analysis of crystal lattice energies. Both force fields revealed that the van der Waals term contributes more to the packing energy in (+)-IBP than in (+/-)-IBP. The hydrogen bonding energy, however, contributes at 29.7 and 32.3% to the total crystal lattice energy in (+)-IBP and (+/-)-IBP (M), respectively. Furthermore, different structure fragments of the IBP molecule were analyzed with respect to their contribution to nonbonded van der Waals interactions. The effect of the C-H distance on the van der Waals term of the crystal lattice energy was also studied.

Crystallization↗
PubMed2006

Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by hydroxybenzoic acids.

Temperature dependencies of saturated vapor pressure and heat capacities for the 2-, 3-, and 4-hydroxybenzoic acids were measured and thermodynamic functions of sublimation calculated (2-hydroxybenzoic acid: DeltaG(sub) (298) = 38.5 kJ/mol; DeltaH(sub) (298) = 96.6 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 191 +/- 3 J/mol . K; 3-hydroxybenzoic acid: DeltaG(sub) (298) = 50.6 kJ/mol; DeltaH(sub) (298) = 105.2 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 180 +/- 2 J/mol . K; 4-hydroxybenzoic acid: DeltaG(sub) (298) = 55.0 kJ/mol; DeltaH(sub) (298) = 113.3 +/- 0.7 kJ/mol; DeltaS(sub) (298) = 193 +/- 2 J/mol . K). Analysis of crystal lattice packing energies based on geometry optimization of the molecules in the crystal using diffraction data and the program Dmol(3) was carried out. The energetic contributions of van der Waals, Coulombic, and hydrogen bond terms to the total packing energy were analyzed. The fraction of hydrogen bond energy in the packing energy increases as: 3-hydroxybenzoic (29.7%) < 2-hydroxybenzoic (34.7%) < 4-hydroxybenzoic acid (42.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven process.

1-Octanol↗
PubMed2006

Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by paracetamol, acetanilide, and phenacetin.

Temperature dependencies of saturated vapor pressure for the monoclinic modification of paracetamol (acetaminophen), acetanilide, and phenacetin (acetophenetidin) were measured and thermodynamic functions of sublimation calculated (paracetamol: DeltaGsub298=60.0 kJ/mol; DeltaHsub298=117.9+/-0.7 kJ/mol; DeltaSsub298=190+/-2 J/mol.K; acetanilide: DeltaGsub298=40.5 kJ/mol; DeltaHsub298=99.8+/-0.8 kJ/mol; DeltaSsub298=197+/-2 J/mol.K; phenacetin: DeltaGsub298=52.3 kJ/mol; DeltaHsub298=121.8+/-0.7 kJ/mol; DeltaSsub298=226+/-2 J/mol.K). Analysis of packing energies based on geometry optimization of molecules in the crystal lattices using diffraction data and the program Dmol3 was carried out. Parameters analyzed were: (a) energetic contribution of van der Waals forces and hydrogen bonding to the total packing energy; (b) contributions of fragments of the molecules to the packing energy. The fraction of hydrogen bond energy in the packing energy increases as: phenacetin (17.5%)<acetanilide (20.4%)<paracetamol (34.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Activity coefficients of the drugs in n-octanol were calculated from cryoscopic data and by estimation of dilution enthalpy obtained from solubility and calorimetric experiments (for infinite dissolution). Solubility temperature dependencies in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven for paracetamol; for acetanilide and phenacetin, entropy driven.

1-Octanol↗
PubMed1978

Thermodynamics of aqueous solutions of parabens.

The solubility of a related series of parabens was determined in water at four temperatures. The parabens chosen were the methyl through n-butyl p-hydroxybenzoates, and the temperature variations were 5 degrees increments from 25 to 40 degrees. These solutes are useful preservatives, especially combinations of the methyl and propyl ester derivatives. The chemical relationship of these compounds varied by successive linear methylene additions on the ester portion of the molecules. The thermodynamic values obtained for these aqueous systems could be related to these molecular variants since the remainder of the molecule was constant. For the overall thermodynamics, the free energy functions such as the ideal, actual, and excess were found to be smooth, nonlinear functions of the number of carbon atoms in the alkyl portion of the paraben esters. A linear relationship with the number of carbon atoms in the ester portion of these esters was found with the partial excess free energy of the solute.

Parabens↗
PubMed1979

Controlled drug release from polymeric delivery devices V: Hydroxy group effects on drug release kinetics and thermodynamics.

The effects of progesterone hydroxylation on silicone matrix drug release kinetics and thermodynamics were investigated. Hydroxylation at positions 11, 17, and/or 21 substantially reduced progesterone release. The magnitude of this reduction depended on the number and position of the hydroxy groups and could be attributed to decreased polymer matrix diffusivity (Dm) and polymer solubility (Cp). Thermodynamically, hydroxy group addition to positions 11 and/or 21 reduced the activation energy for matrix diffusion (Ed,m) but increased the solvation energy for dissolution in silicone polymer (delta HT,m)). Adding an hydroxy group to position 17 increased the Ed,m but decreased the delta HT,m. The overall (Ed,m) + delta H(T,m)) values were relatively constant and independent of hydroxylation.

Delayed-Action Preparations↗
PubMed1982

Interaction of povidone with aromatic compounds III: Thermodynamics of the binding equilibria and interaction forces in buffer solutions at varying pH values and varying dielectric constant.

The complex formation of a series of aromatic compounds with povidone was studied in buffer solutions and organic solvent mixtures by equilibrium dialysis. For all the ligand molecules studied, a linear relationship was found between r, the number of moles of bound ligand per mole of povidone, and the free ligand concentration. The binding constants and the free energies of binding (-delta F), were greater for compounds in the nonionic state and increased with the number of hydroxyl groups which were capable of forming hydrogen bonds. They decreased with temperature elevation. The thermodynamic data showed entropy gains during the binding process accompanied by small negative enthalpy values. The increased ability to form hydrogen bonds and the increase in ionization of the ligand molecule was reflected in more negative delta H and decreasing delta S values. (The thermodynamic values were interpreted on the basis of the "iceberg" concept of water structure.) From these entropy and enthalpy changes, hydrogen and hydrophobic bondings appeared to be the most important types of binding. In organic solvent mixtures, the association constants lowered with increasing ethanol or propylene glycol concentration; a line relationship between the free energy and the dielectric constant of the solvent mixtures was observed.

Buffers↗
PubMed1983

Thermodynamics of distribution of p-substituted phenols between aqueous solution and organic solvents and phospholipid vesicles.

The distribution of p-substituted phenols between 0.15 M NaCl and a range of organic solvents (including 1-octanol) was examined over a range of temperatures. The thermodynamic parameters of transfer, delta G, delta H, and delta S, were determined and the values examined in the light of Hildebrand and Scott's solubility parameter theory, and the collision complexes between solute and organic solvent. Delta H of transfer was positive for nonpolar solvents and negative for 1-octanol; the transfer processes were entropy and enthalpy dominated, respectively. The distribution of the phenols into phospholipid vesicles was examined below the phase-transition temperature. Although delta G of transfer for vesicle-water systems was similar to that for octanol-water systems, the full thermodynamic analysis indicated that the two systems were dissimilar. The use of vesicle distribution data in structure-activity studies is discussed.

Phenols↗
PubMed1986

Physicochemical study of percutaneous absorption enhancement by dimethyl sulfoxide: kinetic and thermodynamic determinants of dimethyl sulfoxide mediated mass transfer of alkanols.

By first determining the thermodynamic activities and activity coefficients of methanol, 1-butanol and 1-octanol in binary dimethyl sulfoxide:water media, it has been possible to separate solubilizing (thermodynamic) effects of dimethyl sulfoxide from its kinetic (diffusive) influence as they relate to the skin permeation of these small, nonelectrolyte alkanols. This was done by normalizing the experimental permeability coefficients found with full-thickness hairless mouse skin membranes to unit activity in the vehicle. When the dimethyl sulfoxide media were placed on both sides of the skin sections in a two compartment diffusion cell, activity-adjusted permeability coefficients of the permeants were invariant to dimethyl sulfoxide concentrations of 50% strength. Thus, up to this concentration and in the absence of net solvent crosscurrents, the permeabilities of methanol, 1-butanol, and 1-octanol appear to be strictly determined by partitioning into the stratum corneum. However, when the dimethyl sulfoxide percentage strength was raised to greater than or equal to 75%, activity-adjusted permeability increased systematically and profoundly, indicating severe barrier impairment with increased diffusion across the horny layer (kinetic effect). When neat dimethyl sulfoxide was placed on both sides of the skin, the experimental permeability coefficients of the three alcohols were maximal and equal in magnitude, suggesting total functional impairment of the stratum corneum. When the dimethyl sulfoxide media were placed in contact with the stratum corneum surface of the skin membranes only, accelerating effects were noted at dimethyl sulfoxide concentrations less than 50%, further supporting the idea that solvent cross flows themselves disrupt the horny structure. The degree of impairment was quantified under all experimental circumstances.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcohols↗