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PubMedDate not supplied

Dielectric characterization of thermodynamic first order events in model frozen systems intended for lyophilization.

The degree and ease with which permanent dipoles in a frozen sample orient in an applied electric field is affected during thermal transitions. This motion can be monitored with dielectric analysis (DEA) at low AC frequencies (< approximately 300,000 Hz). The systems characterized with respect to their behavior in the frozen state consisted of common lyophile excipients in aqueous solutions known to exhibit typical thermodynamic first order transitions. Prior to freezing, solution samples were placed on an interdigitated electrodes and served as the dielectric component of the resulting capacitor. Plots of derivative of dielectric permittivity with respect to time (or temperature) showed the presence of frequency independent peaks (signifying a first order event) at temperatures that coincided with eutectic temperatures (ca. -22 degrees C for sodium chloride-water and ca. -5 degrees C for mannitol-water), amorphous to crystalline transition temperatures (ca. -25 degrees C for mannitol-water), and/or freezing point depression values in water. The values obtained by DEA correlated well with differential scanning calorimetry (DSC) and literature values. DEA appears to offer added insight over established techniques by not only determining the temperature at which these events occur, but also by defining the thermodynamic order of the event.

Electrochemistry↗
PubMed1994

Studies on a chitooligosaccharide-specific lectin from Coccinia indica. Thermodynamics and kinetics of umbelliferyl glycoside binding.

Coccinia indica agglutinin (CIA) is a chitooligosaccharide-specific lectin with two binding sites/homodimer of M(r) 32,000. Quenching studies implied tryptophan involvement in binding activity, which was confirmed by chemical modification experiments (A. R. Sanadi and A. Surolia, submitted for publication). Binding of 4-methylumbelliferyl chitooligosaccharides has been carried out to study their binding by CIA. Reversal experiments confirm the validity of the data previously obtained (A. R. Sanadi and A. Surolia, submitted for publication) from intrinsic fluorescence studies. Surprisingly, unlike wheat germ agglutinin, there is no consistent thermodynamic effect of the chromophoric label on binding activities as compared with the native sugars. From the changes in the optical properties of the chromophoric group upon binding to CIA, it has been possible to confirm that the tryptophan located in the binding site is closest to the fourth subsite. Thermodynamic analysis shows that the binding of the labeled tetrasaccharide is very strongly entropically driven, with the terminal, nonreducing sugar residue protruding from the binding pocket. The results of stopped-flow kinetic studies on the binding of the chromophoric trisaccharide by CIA show that the mechanism of binding is a one-step process.

Binding, Competitive↗
PubMedDate not supplied

[Thermodynamic properties of biopolymers in spiral and coiled states in the 4--400 degree K temperature interval].

Possibilities of the adiabatic calorimetry methods in the studies of the biopolymer conformational properties in the wide temperature range including helium temperatures are considered. The low temperature peculiarities of the heat capacity difference for the biopolymers being in helical and coiled states are found. It was shown, that in the presence of biomacromolecules the water in the ice-water phase transition region suffers gradual over the temperature phase transition "order-disorder". It was found, that thermodynamic properties of the linear fibrillar structures over the wide temperature range (including helium temperatures) are essentially defined by the state of molecule solvent built-in the biopolymer helical structure. New data on the interaction mechanisms of dissolved salt ions with the biomacromolecules in the native and denaturated states have been obtained. It is shown that the existence of different fractions of bound water with biopolymer is a fact. A conclusion was made that it is necessary to take into account the data on the thermodynamic properties of biomacromolecules and the water bound to them at low temperatures in order to described completely the conformational properties of biomacromolecules.

Biopolymers↗
PubMed1995

[A comparative computer analysis of thermodynamic parameters of transport RNA secondary structure].

Thermodynamic parameters of the cloverleaf secondary structure of tRNAs of several major taxons (archaebacteria, eubacteria, eukaryotes, chloroplasts, and mitochondria) were subjected to computer analysis. The distribution of free-energy values was close to normal in all groups (except for the mitochondrial tRNA). In the organisms existing under extreme environmental conditions, the stability of the tRNA secondary structure was higher. Comparative analysis of teh frequency of ¿quasi-complementary¿ GU pairs in stems of randomly generated and real sequences demonstrated preferential fixation of such pairs in the contexts with the most favorable thermodynamics parameters. Noncanonic pairs in tRNA stems set limits on the presence of highly mutable CG dinucleotides. Moreover, the effect of noncanonic pairs other than GU on the frequency of such dinucleotides is far more pronounced than that of GU pairs.

Base Sequence↗
PubMed1996

Influence of Ca2+ on kinetics and thermodynamics of the NADPH-dependent microsomal lipid peroxidation.

The effect of Ca2+ on kinetics and thermodynamics of lipid peroxidation in microsomes prepared from liver of male Swiss albino mice (7-8 weeks old) was studied. Ca2+ was found to increase the Vmax in temperature dependent manner. Michaelis-Menten constant (Km) also increased with temperature. However, the linearity and extent of change in Km remained unaffected in presence of Ca2+, and was suggestive of non-competitive and mixed type of activation. The activation constant (Ka) obtained by the replotting of slopes of the Lineweaver-Burk plots against the reciprocal of Ca2+ concentration showed linear variation with temperature. The linear pattern of Arrhenius plots indicated non-involvement of parallel reactions of other intermediate species in the lipid peroxidation. Thermodynamic parameters delta H degree, delta S degree and delta G degree, associated with lipid peroxidation process were studied. The positive value of delta H degree is suggestive of the endothermic nature of the process. It appears that the NADPH induced lipid peroxidation is an entropy driven process.

Animals↗
PubMed1997

Thermodynamics of lectin-carbohydrate interactions. Binding of the core trimannoside of asparagine-linked carbohydrates and deoxy analogs to concanavalin A.

The trisaccharide 3,6-di-O-(alpha-D-mannopyranosyl)-D-mannose, which is present in all asparagine-linked carbohydrates, was previously shown by titration microcalorimetry to bind to the lectin concanavalin A (ConA) with nearly -6 kcal mol-1 greater enthalpy change and 60-fold higher affinity than methyl-alpha-D-mannopyranoside (Mandal, D. K., Kishore, N., and Brewer, C. F. (1994) Biochemistry 33, 1149-1156). Similar studies of the binding of a series of monodeoxy derivatives of the alpha(1-3) residue of the trimannoside showed that this arm was required for high affinity binding (Mandal, D. K., Bhattacharyya, L., Koenig, S. H., Brown, R. D., III, Oscarson, S., and Brewer, C. F. (1994) Biochemistry 33, 1157-1162). In the present paper, a series of monodeoxy derivatives of the alpha(1-6) arm and "core" Man residue of the trimannoside as well as dideoxy and trideoxy analogs were synthesized. Isothermal titration microcalorimetry experiments establish that the 3-, 4-, and 6-hydroxyl groups of the alpha(1-6)Man residue of the trimannoside binds to the lectin, along with the 2- and 4-hydroxyl groups of the core Man residue and the 3- and 4-hydroxyl groups of the alpha(1-3)Man residue. Dideoxy analogs and trideoxy analogs showed losses of affinities and enthalpy values consistent with losses in binding of specific hydroxyl groups of the trimannoside. The free energy and enthalpy contributions to binding of individual hydroxyl groups of the trimannoside determined from the corresponding monodeoxy analogs are observed to be nonlinear, indicating differential contributions of the solvent and protein to the thermodynamics of binding of the analogs. The thermodynamic solution data agree well with the recent x-ray crystal structure of ConA complexed with the trimannoside (Naismith, J. H., and Field, R. A. (1996) J. Biol. Chem. 271, 972-976).

Calorimetry↗
PubMed1997

Thermodynamic regulation of cytochrome oxidase.

It was concluded that cytochrome oxidase was a strange enzyme for three reasons. (1) The thermodynamic flux-force relationship of this enzyme was inverse in some conditions: flux decreased when force increased. (2) The flux-force relationship was not unique and depended on the way in which the thermodynamic span of cytochrome oxidase was changed. (3) The regulation of cytochrome oxidase was different in the same conditions when different external parameters (energy demand, oxygen concentration) were changed. It was also shown that the flux control coefficient of cytochrome oxidase, small at saturating oxygen concentration, increases when oxygen pressure diminishes, approaching unity at very low oxygen concentrations.

Animals↗
PubMed1996

Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.

Empirical free energy calculations of HIV-1 protease crystallographic complexes based on the developed knowledge-based ligand-protein interaction potentials have enabled a detailed thermodynamic analysis. Binding free energies are estimated within an empirical model that postulates that hydrophobic effect, mean field ligand-protein interaction potentials and conformational entropy changes are the dominant forces that determine complex formation. To provide a quantitative framework of the binding thermodynamics contributions the derived knowledge-based potentials have been linked with the hydrophobicity and conformational entropy scales originally developed to explain protein stability. The comparative analysis of studied inhibitors provides reasonable estimates of distinctions in their binding affinity with HIV-1 protease and gives insight into the nature of the binding determinants. The binding free energy changes upon a simple hydrophobic mutation Ile -> Val in the JG-365, MVT-101 and U75875 inhibitors of HIV-1 protease have been evaluated within a model that includes the effects of solvation, cavity formation, conformational entropy and mean field ligand-protein interactions. In general, free energy changes associated with a particular perturbation of a system can not be rigorously decomposed into separate terms from first principles. We explored the relationships between the changes in hydrophobic contributions and mean field ligand-protein interaction energies in the context of a totally buried and dense area of the binding site. We assume, therefore, that these simple hydrophobic deletions would not induce noticeable conformational changes in the enzyme and can be interpreted with some confidence in the framework of the model. The analysis has revealed the decisive effect of the energetics of ligand-protein interactions on the estimated free energy changes.

Amino Acid Substitution↗
PubMed1976

Thermodynamics of native protein/foreign surface interactions. IV. Calorimetric and microelectrophoretic study of human fibrinogen sorption onto glass and LTI-carbon.

1. According to a working hypothesis put forward in the previous papers of this series2-4, the initial phases of native blood/foreign surface interactions have been considered within the framework of a physicochemical model of contact activation at the molecular level. The salient features of this hypothesis are: a) the arrival and adsorption of native plasma proteins on a contact surface overwhelmingly precedes that of the cellular blood components; b) the interaction energy that arises between a particular foreign surface and native plasma proteins settling on it, is a characteristic quantity depending upon the effective surface molecular structure as well as the nature of the proteins; c) the "intensity" of native protein/foreign surface interactions can be treated in terms of thermodynamic quantities since these energy terms are independent of the type of forces acting between protein and surface; and d) depending upon the degree to which the adsorption of a native protein is thermodynamically favored by enthalpy and/or entropy factors, the interaction energy can be utilized to induce conformational changes of varying degree in the sorbed protein. 2. Using glass and low temperature isotropic (LTI) carbon adsorbents, i.e., a known procoagulant and a relevant biomaterial, respectively, the adsorption properties and the potential surface-induced conformational changes of high-purity native human fibrinogen (clottability greater than or equal to 92%) were studied, at 25 degrees C, by 3 independent methods. In all of the experiments performed, a) both adsorbents were employed in the form of particles less than or equal to 1.0 mu representing specific surface areas of 9.85 M2/Gm and 27.7 (nominal) M2/Gm for the glass and LTI-carbon powders, respectively, and b) the fibrinogen was absorbed from a standaridized buffer (pH = 7.2, ionic strength 0.05) using the same fixed surface area/protein solution volume ratio with a given adsorbent. 3. The 25 degrees C adsorption isotherms of fibrinogen obtained for both the glass and LTI-carbon powder adsorbents are not amenable to Langmuir type analysis but indicate multilayer sorption with a possible change in binding mechanism after the completion of the first sorbed monolayer. The adsorptivities attained at first monolayer coverage were slightly greater on glass (approximately 0.76 mug/cm2) than on LTI-carbon (approximately 0.52 mug/cm2). 4. Using a custom-built, thermistorized, isothermal-jacketed microcalorimeter routinely capable of resolving temperature changes of 0.00001 degrees C in 100 ml of aqueous sample volume, the "intensity" of interaction between fibrinogen and each of the microparticulate adsorbents was studied by the direct measurement of the net overall enthalpy changes, hI(SLP)25 arising as a result of protein adsorption. From these values, the net heat of protein sorption has been determined...

Adsorption↗
PubMed1997

Effect of chemical modification of oligohomopyrimidine on triplex formation: thermodynamic and kinetic studies.

To investigate the effect of chemical modification of the third strand on the stability of triplex DNA, we have examined the thermodynamic properties of the triplex formation between a 23-mer double-stranded homopurine-homopyrimidine and each of five kinds of 15-mer chemically modified single-stranded homopyrimidines by isothermal titration calorimetry, and the kinetic properties by interaction analysis system. The modifications of the third strand included two base modifications, two sugar moiety modifications, and one phosphate backbone modification. The thermodynamic and kinetic parameters for the triplex formation were similar in magnitude among the two base-modified and two sugar-modified single strands. By contrast, the binding constant for the triplex formation with the single strand with phosphorothioate backbone was more than ten times as small as that for the other triplex formation. On the basis of the kinetic analyses, the single strand with phosphorothioate backbone was more difficult to associate with and easier to dissociate from the target double strand than the other single strands, which resulted in the much smaller binding constant.

Base Sequence↗
PubMed1998

[Structural bases of changes in the thermodynamic stability of cerebral cortex synapses in albino rats in the postasphyxial period].

Thermodynamic stability of subsynaptic unit system in cortex molecular layer synapses was determined experimentally in albino rats using morphometric methods as a value reciprocal to molecular layer cortex relative surface area. Increase of number of thermodynamically stable large synapses and their complication was found following asphyxia. Synapse reorganization in the course of complication results from intensification of counter forces to hypertrophy of subsynaptic unit system in large interneuronal contacts.

Animals↗
PubMed2006

Overcoming the thermodynamic limitation in asymmetric hydrogen transfer reactions catalyzed by whole cells.

Whole lyophilized cells of an Escherichia coli overexpressing the alcohol dehydrogenase (ADH-'A') from Rhodococcus ruber DSM 44541 were used for the asymmetric reduction of ketones to secondary alcohols. The recycling of the required nicotinamide cofactor (NADH) was achieved in a coupled-substrate process. In the course of the reaction the ketone is reduced to the alcohol and the hydrogen donor 2-propanol is oxidized to acetone by one enzyme. This leads to a thermodynamic equilibrium between all four components determining the maximum achievable conversion. To overcome this limitation an in situ product removal technique (ISPR) for the application with whole cells was developed. In this method the most volatile compound is separated from the reaction vessel by an air flow resulting in a shift of the equilibrium towards the desired secondary alcohol. The so-called stripping process represents a simple and efficient method to overcome the thermodynamic limitation in biocatalytic reactions. Employing this method, the conversion of selected biotransformations was increased up to completeness.

Alcohol Dehydrogenase↗
PubMed2004

Thermodynamic and kinetic data for adduct formation, cis-trans isomerization and redox reactions of ML4 complexes: a case study with rhodium- and iridium-tropp complexes in d8, d9 and d10 valence electron configurations (tropp=dibenzotropylidene phosphanes).

The formation of adducts of the square-planar 16-electron complexes trans-[M(tropp(ph))(2)](+) and cis-[M(tropp(ph))(2)](+) (M=Rh, Ir; tropp(Ph)=5-diphenylphosphanyldibenzo[a,d]cycloheptene) with acetonitrile (acn) and Cl(-), and the redox chemistry of these complexes was investigated by various physical methods (NMR and UV-visible spectroscopy, square-wave voltammetry), in order to obtain some fundamental thermodynamic and kinetic data for these systems. A trans/cis isomerization cannot be detected for [M(tropp(ph))(2)](+) in non-coordinating solvents. However, both isomers are connected through equilibria of the type trans-[M(tropp(ph))(2)](+)+L<==>[ML(tropp(ph))(2)](n)<==>cis-[M(tropp(ph))(2)](+)+L, involving five-coordinate intermediates [ML(tropp(ph))(2)](n) (L=acn, n=+1; L=Cl(-), n=0). Values for K(d) (K(f)), that is, the dissociation (formation) equilibrium constant, and k(d) (k(f)), that is, the dissociation (formation) rate constant, were obtained. The formation reactions are fast, especially with the trans isomers (k(f)>1x10(5) m(-1) s(-1)). The reaction with the sterically more hindered cis isomers is at least one order of magnitude slower. The stability of the five-coordinate complexes [ML(tropp(ph))(2)](n) increases with Ir>Rh and Cl(-)>acn. The dissociation reaction has a pronounced influence on the square-wave (SW) voltammograms of trans/cis-[Ir(tropp(ph))(2)](+). With the help of the thermodynamic and kinetic data independently determined by other physical means, these reactions could be simulated and allowed the setting up of a reaction sequence. Examination of the data obtained showed that the trans/cis isomerization is a process with a low activation barrier for the four-coordinate 17-electron complexes [M(tropp(ph))(2)](0) and especially that a disproportionation reaction 2 trans/cis-[M(tropp(ph))(2)](0)-->[M(tropp(ph))(2)](+)+[M(tropp(ph))(2)](-) may be sufficiently fast to mask the true reactivity of the paramagnetic species, which are probably less reactive than their diamagnetic equilibrium partners.

Journal Article↗
PubMed2004

Molecular evolution using intramolecular acyl migration on myo-inositol benzoates with thermodynamic and kinetic selectors.

A molecular evolution model was successfully demonstrated by combining the intramolecular acyl migration on inositol tribenzoates and boron selectors. The addition of boric acid to 12 members of DCL (dynamic combinatorial library) induced the dramatic amplification of myo-I(2,4,6)Bz(3) (1) with up to 94 % under thermodynamic (see Figure 1 c) control while a portion of phenyl boronic acid caused two significant different distributions: under kinetic control, the pre-equilibrium of DCL shifted to induce the exclusive amplification of 1,4,6-tribenzoyl myo-inositol (7) with decrease of other members up to 82 % from the mixture (see Figure 2 b), and changed gradually to form 2,4,6-tribenzoyl myo-inositol (1) with up to 96 % under thermodynamic control (Figure 2 c).

Journal Article↗
PubMed2005

Template-directed synthesis of multiply mechanically interlocked molecules under thermodynamic control.

The template-directed construction of crown-ether-like macrocycles around secondary dialkylammonium ions (R2NH2+) has been utilized for the expedient (one-pot) and high-yielding synthesis of a diverse range of mechanically interlocked molecules. The clipping together of appropriately designed dialdehyde and diamine compounds around R2NH2+-containing dumbbell-shaped components proceeds through the formation, under thermodynamic control, of imine bonds. The reversible nature of this particular reaction confers the benefits of "error-checking" and "proof-reading", which one usually associates with supramolecular chemistry and strict self-assembly processes, upon these wholly molecular systems. Furthermore, these dynamic covalent syntheses exploit the efficient templating effects that the R2NH2+ ions exert on the macrocyclization of the matched dialdehyde and diamine fragments, resulting not only in rapid rates of reaction, but also affording near-quantitative conversion of starting materials into the desired interlocked products. Once assembled, these "dynamic" interlocked compounds can be "fixed" upon reduction of the reversible imine bonds (by using BH3.THF) to give kinetically stable species, a procedure that can be performed in the same reaction vessel as the inital thermodynamically controlled assembly. Isolation and purification of the mechanically interlocked products formed by using this protocol is relatively facile, as no column chromatography is required. Herein, we present the synthesis and characterization of 1) a [2]rotaxane, 2) a [3]rotaxane, 3) a branched [4]rotaxane, 4) a bis [2]rotaxane, and 5) a novel cyclic [4]rotaxane, demonstrating, in incrementally more complex systems, the efficacy of this one-pot strategy for the construction of interlocked molecules.

Journal Article↗
PubMed2005

Ground-state equilibrium thermodynamics and switching kinetics of bistable [2]rotaxanes switched in solution, polymer gels, and molecular electronic devices.

We report on the kinetics and ground-state thermodynamics associated with electrochemically driven molecular mechanical switching of three bistable [2]rotaxanes in acetonitrile solution, polymer electrolyte gels, and molecular-switch tunnel junctions (MSTJs). For all rotaxanes a pi-electron-deficient cyclobis(paraquat-p-phenylene) (CBPQT4+) ring component encircles one of two recognition sites within a dumbbell component. Two rotaxanes (RATTF4+ and RTTF4+) contain tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) recognition units, but different hydrophilic stoppers. For these rotaxanes, the CBPQT4+ ring encircles predominantly (>90 %) the TTF unit at equilibrium, and this equilibrium is relatively temperature independent. In the third rotaxane (RBPTTF4+), the TTF unit is replaced by a pi-extended analogue (a bispyrrolotetrathiafulvalene (BPTTF) unit), and the CBPQT4+ ring encircles almost equally both recognition sites at equilibrium. This equilibrium exhibits strong temperature dependence. These thermodynamic differences were rationalized by reference to binding constants obtained by isothermal titration calorimetry for the complexation of model guests by the CBPQT4+ host in acetonitrile. For all bistable rotaxanes, oxidation of the TTF (BPTTF) unit is accompanied by movement of the CBPQT4+ ring to the DNP site. Reduction back to TTF0 (BPTTF0) is followed by relaxation to the equilibrium distribution of translational isomers. The relaxation kinetics are strongly environmentally dependent, yet consistent with a single electromechanical-switching mechanism in acetonitrile, polymer electrolyte gels, and MSTJs. The ground-state equilibrium properties of all three bistable [2]rotaxanes were reflective of molecular structure in all environments. These results provide direct evidence for the control by molecular structure of the electronic properties exhibited by the MSTJs.

Journal Article↗
PubMed2007

Synthesis, solution thermodynamics, and X-ray study of CuII [12]metallacrown-4 with GABA hydroxamic acid: an unprecedented crystal structure of a [12]MC-4 with a gamma-aminohydroxamate.

The solution equilibria of gamma-aminobutanehydroxamic acid (GABAha) with H+ and Cu2+ were investigated by potentiometry, titration calorimetry, spectrophotometry, NMR spectroscopy, and ESI-MS. The thermodynamic parameters of the CuII [12]metallacrown-4 obtained for GABAha were compared with those of the corresponding complexes of (S)-alpha-Alaha and beta-Alaha. The stability (-DeltaG0) sequence was beta-Alaha>>alpha-Alaha>GABAha, whereas the order of formation enthalpies (-DeltaH0) was beta-Alaha>>GABAha>alpha-Alaha. These data were interpreted on the basis of the dimensions of the chelate rings and the planarity of the metallamacrocycles. The CuII [12]metallacrown-4 ([12]MC-4) complex of GABAha was isolated and its crystal structure, which is the first reported for a [12]MC-4 of a gamma-aminohydroxamic acid, fully supports the structural features interpreted from the thermodynamic data.

Journal Article↗
PubMed2001

Molecular chirality and the fundamental symmetries of physics: influence of parity violation on rovibrational frequencies and thermodynamic properties.

We introduce the topic of fundamental symmetries of physics in relation to molecular chirality by a brief review of the development and current status of the theory of parity violation in chiral molecules. We then discuss in some detail CHBrClF (bromochlorofluoromethane) as a test case, to which the work of André Collet has contributed importantly. For this molecule and its isotopomers, we report here the first detailed theoretical calculations of the influence of parity violation on statistical thermodynamic properties. High-quality ab initio calculations (RPA, random phase approximation, and CASSCF, complete-active-space self-consistent-field) were performed to determine the small energy difference between R- and S-enantiomers of H and D isotopomers of bromochlorofluoromethane (CHBrClF, CDBrClF), and fluorooxirane ((1)H(3)C(2)OF) introduced by the parity-violating weak interaction. Together with vibrational and rotational frequency shifts caused by parity violation, these were used to determine the statistical thermodynamic quantities from the corresponding partition functions within the separable harmonic and in part also anharmonic adiabatic approximation. Temperature-dependent equilibrium constants for the stereomutation were calculated and are discussed in relation to biochemical homochirality.

Journal Article↗