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PubMed1993

Aging, genomic entropy and carcinogenesis: implications derived from longitudinal age-specific colon cancer mortality rate dynamics.

Many types of cancer are intrinsically linked to the process of aging. Aging, from the perspective of the second law of thermodynamics, can be viewed as associated with the inevitable and natural increase in informational entropy of the genome. The molecular biologic basis of increasing genetic informational entropy is the inherent and variable instability of different regions of genome. Colon cancer cells have been shown to have characteristic acquired genetic abnormalities, most commonly, deletions in presumed tumor suppressor genes. Age-specific colon cancer mortality rates in the US from 1958 to 1988 were subjected to longitudinal Gompertzian analysis, a method that may identify and distinguish among genetic, environmental and competitive influences upon mortality. The Strehler-Mildvan modification of the Gompertz relationship between aging and mortality can be used to determine a relative measure of the rate of increase in informational entropy (a reflection of genetic instability) for those genetic factors that are involved in the pathogenesis of colon cancer.

Adult↗

PubMed1995

The importance of polysaccharide configurational entropy in determining the osmotic swelling pressure of concentrated proteoglycan solution and the bulk compressive modulus of articular cartilage.

One important contribution to the osmotic swelling pressure of concentrated proteoglycan and hence the elasticity of articular cartilage arises from the configurational entropy of the polysaccharide chains in the extracellular matrix. The work presented here provides a theoretical determination of this entropy and an analysis of its effect on the equilibrium osmotic swelling pressure of concentrated proteoglycan solutions. This effect is calculated in a manner similar to the Flory-Huggins technique where the solution is treated as a lattice (P. Flory, Principles of polymer chemistry (Cornell Univ. Press, Ithaca, 1953); J. Chem. Phys. 12 (1944) 425). In addition, the charge-related contribution to the elasticity of these materials is reviewed in the form of a Donnan equilibrium model (T. Hill, Faraday Soc. Discussions 21 (1956) 31; A.G. Ogston and J.D. Wells, Biochem. J. 119 (1970) 67; C. Tanford, Physical Chemistry of Macromolecules (Wiley, New York, 1961)). It is found that the configurational entropy of the glycosaminoglycan (GAG) chain polysaccharides together with the charge effects reproduce the equilibrium swelling pressure of concentrated proteoglycan solutions as experimentally determined by J.P.G. Urban et al., Biorheol. 16 (1979) 447. In addition this theoretical model is manifestly independent of the proteoglycan molecular weight, consistent with prior experimental findings (J.P.G. Urban et al., Biorheol. 16 (1979) 447). The model is also extended to include polydispersity of proteoglycan size and to predict the equilibrium bulk compressive modulus of articular cartilage. This work represents the first comprehensive theoretical description of the equilibrium elastic properties of proteoglycan solutions.(ABSTRACT TRUNCATED AT 250 WORDS)

Carbohydrate Conformation↗

PubMed1996

Magnesium-aided folding of group I ribozymes with a minimal loss of entropy.

The aim of this work is to quantify, rationalize and incorporate the effect of Mg(II) ions on the kinetic barriers of entropic origin associated to RNA folding events in vitro. This study encompasses the scaffolding effect of Mg(II) upon the formation of the pseudoknot structural motif which is believed to be crucial for shaping the catalytic core of group I ribozymes. Our results are contrasted with recent experimental probes on folding kinetics. The first set of objectives is accomplished by determining the participation of Mg(II) in the reduction of the conformational entropy cost during folding. First, the dominant contribution to conformational entropy loss associated to loop closure is obtained. The derivation hinges upon the notion that loop closure entails the formation of an inner and outer solvent domain and backbone phosphate groups orient themselves concurrently towards the best dielectric environment. At this point, the role of Mg(II) ions can be assessed by taking into account that Mg(II) coordinates with two adjacent backbone phosphates in unpaired regions. Thus, for a small loop of even length, the energy decrease due to coordination reduces the conformational entropy loss due to phosphate orientation by one half. In the case of pseudoknot formation, the orientational effect prevents the coplanarity of the loops comprising the pseudoknot and allows us to determine the kinetic barrier associated to its formation in the presence of magnesium. Incorporating these facts to kinetically controlled Monte Carlo simulations, we find that the predicted folding pathway for group I introns leads to the phylogenetically inferred secondary structures and allows us to elucidate the magnesium-dependent rate-limiting step in the formation of the P3-P7 pseudoknotted region of the catalytic core.

Base Sequence↗

PubMed1975

Dipole moment, enthalpy, and entropy changes of Hodgkin-Huxley type kinetic units.

Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transformation as a whole. The calculations are based on the experimentally determined Q10 values and the empirical formulae for the rate constants (alpha's and beta's) as functions of membrane potentials in Hodgkin-Huxley type models. From the calculated thermodynamic functions we suggest that the specific structural units of the axon membranes are probably of macromolecular (possible protein-like) dimensions with large dipole moments (hundreds of debyes). The calculated dipole moment changes of a single structural unit indicate that in many cases these dipole moments saturate at strong depolarizations or hyperpolarizations. The transitions in structural units show substantial activation enthalpies and entropies but the net enthalpy and entropy changes are practically negligible for the transition as a whole, i.e. the structural units presumably undergo displacements. While the calculated dipole moment changes associated with structural transformations in Loligo and Myxicola show similar potential dependencies, those for Rana usually show a different behavior. The relevance of the dipole moment changes to gating currents is discussed.

Animals↗

PubMed1984

Information and entropy in a simple evolution model.

A model of evolution which combines mutations and speciation mechanisms is presented and analyzed. Information and entropy of the populations generated by the model are calculated and followed through history. It is found that the model allows simultaneous increase of information and entropy with time, consistent with notions of physical entropy increase as well as biological evolution.

Biological Evolution↗

PubMed2002

Microcanonical analysis of the kinetic method. the meaning of the "apparent entropy".

A rigorous analysis of the kinetic method is carried out using Rice-Ramsperger-Kassel-Marcus (RRKM) theory of microcanonical statistical unimolecular dissociation rates. The model employs a kinetics treatment appropriate for metastable ion dissociation. Proton-bound alkoxide dimer anions are used as model systems, with realistic vibrational and rotational parameters calculated by ab initio methods for the cluster ion and transition states leading to the competitive dissociation channels. The numerical simulations show that the kinetic method plots of ln(I2/I1) versus AAH are nearly linear but can exhibit significant curvature. The apparent entropy obtained in the extended kinetic method is not approximately equal to the thermodynamic entropy difference for dissociation, AAS(T), or for activation, deltadeltaS++(T), either at the effective temperature or at any fixed equilibrium temperature. Instead, the apparent entropy term can be related to the ratio of the microcanonical sum of states of the dissociation transition states for the kinetically selected internal energy of the dissociating ions.

Journal Article↗

PubMed2003

Band-target entropy minimization. A robust algorithm for pure component spectral recovery. Application to complex randomized mixtures of six components.

A newly developed self-modeling curve resolution method, band-target entropy minimization (BTEM), is described. This method starts with the data decomposition of a set of spectroscopic mixture data using singular value decomposition. It is followed by the transformation of the orthonormal basis vectors/loading vectors into individual pure component spectra one at a time. The transformation is based in part on some seminal ideas borrowed from information entropy theory with the desire to maximize the simplicity of the recovered pure component spectrum. Thus, the proper estimate is obtained via minimization of the proposed information entropy function or via minimization of derivative and area of the spectral estimate. Nonnegativity constraints are also imposed on the recovered pure component spectral estimate and its corresponding concentrations. As its name suggests, in this method, one targets a spectral feature readily observed in loading vectors to retain, and then combinations of the loading vectors are searched to achieve the global minimum value of an appropriate objective function. The major advantage of this method is its one spectrum at a time approach and its capability of recovering minor components having low spectroscopic signals. To illustrate the application of BTEM, spectral resolution was performed on FT-IR measurements of very highly overlapping mixture spectra containing six organic species with a two-component background interference (air). BTEM estimates were also compared with the estimates obtained using other self-modeling curve resolution techniques, i.e., SIMPLISMA, IPCA, OPA-ALS, and SIMPLISMA-ALS.

Journal Article↗

PubMed2007

Thermal modulation voltammetry with laser heating at an aqueous|nitrobenzene solution microinterface: determination of the standard entropy changes of transfer for tetraalkylammonium ions.

Thermal modulation voltammetry (TMV) with laser heating was successfully performed at an aqueous|nitrobenzene (NB) solution microinterface, by taking advantage of the fact that laser light with a wavelength of 325.0 nm is optically transparent to the aqueous solution but opaque to the NB solution. When the laser beam impinges upon the interface from the aqueous solution side, a temperature is raised around the interface through the thermal diffusion subsequent to the light-to-heat conversion following the optical absorption by the NB solution near the interface. Based on such a principle, we achieved a fluctuating temperature perturbation around the interface for TMV by periodically irradiating the interface with the laser beam. On the other hand, the fluctuating temperature perturbation has influence on currents for transfer of an ion across the interface to produce fluctuating currents synchronized with the perturbation through temperature coefficients of several variables concerning the transfer, such as the standard transfer potential and the diffusion coefficient of the ion. Consequently, TMV has the possibility of providing information about the standard entropy change of transfer corresponding to a temperature coefficient of the standard transfer potential and a temperature coefficient of the diffusion coefficient. In this work, the aqueous|NB solution interface of 30 microm in diameter was irradiated with the laser beam at 10 Hz, and the currents synchronized with the periodical irradiation were recorded as a function of the potential difference across the interface in order to construct a TM voltammogram. TM voltammograms were measured for transfer of tetramethylammonium, tetraethylammonium, tetrapropylammonium, and tetra-n-butylammonium ions from the aqueous solution to the NB solution, and the standard entropy change of transfer was determined for each ion, according to an analytical procedure based on a mathematical expression of the TM voltammogram. Comparison of the values obtained in this work with the literature values has proved that TMV with laser heating is available for the determination of the standard entropy change of transfer for an ion.

Journal Article↗

PubMed1995

Cold denaturation of an icosahedral virus. The role of entropy in virus assembly.

Assembly of icosahedral viruses is not completely understood at the molecular level. The main puzzle is to answer how chemically identical protein subunits take up unique positionally dependent conformations during the process of assembly. The stability of the ribonucleoprotein particles of cowpea mosaic virus (CPMV) to pressures and subzero temperatures has been studied. At room temperature, reversible pressure denaturation of CPMV is obtained only in the presence of 5.0 M urea. On the other hand, when the temperature is decreased to -15 degrees C, the ribonucleoprotein components denature, at 2.5 kbar, in the presence of 1.0 M urea. At temperatures close to -20 degrees C, denaturation is obtained even in the absence of urea. Whereas the denaturation promoted by pressure and urea at room temperature is reversible, virus particles denatured when the temperature is decreased under pressure cannot reassemble. Bis-ANS binding data suggest that this irreversibility may be related to protein release from RNA, which probably does not occur under denaturating conditions at room temperature. The contributions of enthalpy (delta H*) and entropy (delta S*) for the free energy of association of CPMV are calculated from the cold denaturation curves under pressure. The entropy change is positive and large, making the assembly of ribonucleoprotein components an entropy-driven process, suggesting that the burial of nonpolar side chains during the process of assembly is the structural foundation for CPMV assembly.

Cold Temperature↗

PubMed2000

Variability of molecular descriptors in compound databases revealed by Shannon entropy calculations

A method is introduced to calculate and compare the variability of molecular descriptors in compound databases. Descriptor variability analysis is based on histograms recording the distribution of molecular descriptors and calculation of Shannon entropy (SE), a metric originally applied in digital communication. SE values reflect the variability of descriptor settings. We have calculated a total of 92 molecular descriptors in the ACD and NCI databases and ranked them according to their variability. Significant differences in entropy are observed for a number of descriptors. However, the most variable descriptors are similar in the ACD and NCI databases. Such high-entropy descriptors are preferred tools to discriminate between compounds or account for the diversity of chemical libraries.

Journal Article↗

PubMed1997

Side Chain Entropy and the Activation of Organocobalamins for Carbon-Cobalt Bond Homolysis: Synthesis, Characterization, and Thermolysis of the Neopentyl Derivative of a Unique Cobalamin Analog Lacking a c Side Chain.

Hydrodeamination of the c-amino derivative, 5, of cyanocobalamin (CNCbl) with hydroxylamine-O-sulfonic acid in aqueous base leads to an extensively rearranged product instead of the c side chain truncated derivative, 1, expected from simple deamination. The rearranged product (CNCbl-8-butanamide) crystallizes in the orthorhombic system, space group P2(1)2(1)2(1) with unit cell dimensions a = 16.041(11), b = 21.94(2), and c = 25.43(2) Å. It is devoid of substituents at corrin ring C(7) but quarternized at C(8) with an "upwardly" pseudoaxial methyl group and a d side chain expanded by one methylene group to a butanamide. The corrin ring of this rearranged derivative is significantly flatter (corrin ring fold angle 9.9 degrees ) than CNCbl itself (fold angle 18.0 degrees ). Conversion of CNCbl-8-butanamide to its neopentyl derivative (NpCbl-8-butanamide), a NpCbl analog which lacks a c acetamide side chain, permits a quantitative assessment of the influence of thermal motions of the c side chain on the entropy of activation for carbon-cobalt bond thermal homolysis in NpCbl. NpCbl-8-butanamide is shown to thermolyze homolytically to give products derived from the Np(*) radical quantitatively. The kinetics of the thermolysis of NpCbl-8-butanamide were studied in aerobic aqueous solution at temperatures between 15 and 45 degrees C. After correction of the observed first-order rate constants for the presence of the essentially unreactive base-off species using an established NMR method, an Eyring plot yields the activation parameters DeltaH()(on) = 26.7 +/- 0.1 kcal mol(-)(1) and DeltaS()(on) = 13.2 +/- 0.2 cal mol(-)(1) K(-)(1). While the enthalpy of activation is slightly reduced (6%) from that of NpCbl, the entropy of activation is reduced by 6.1 +/- 0.6 cal mol(-)(1) K(-)(1), or 32 +/- 3%. The c side chain thus contributes about one-third of the total entropic activation of NpCbl for carbon-cobalt bond homolysis, and the entropy of activation for this reaction is probably dominated by changes in the thermal motions of the "upwardly" pseudoaxial a and c acetamide side chains as the reaction progresses.

Journal Article↗

PubMed2003

Continuous symmetry numbers and entropy.

Traditionally, entropy changes are corrected for rotational permutability only if the molecule is perfectly rotationally symmetric. By this approach, only a small fraction of all known molecules must be evaluated in terms of symmetry numbers, while all other molecules are totally exempt of these considerations. A general approach which encompasses all molecules, symmetric or not, is proposed here. It is based on introducing the notion of continuity to symmetry numbers and on allowing noninteger values. In the first part of the account, we provide arguments as to why continuity is needed and what difficulties one may encounter by adopting the "black-or-white" approach to symmetry. In the second part, we provide a working methodology of how to evaluate the symmetry number content of any molecule, symmetric or not. Finally, in the third part, we demonstrate the implications of this approach on entropy issues involving melting points, Jahn-Teller distortions (of fullerene) upon ionization, molecular distortion due to overcrowdedness, permutability of isotopes, and the structure of proton sponges. It is shown that continuous symmetry numbers provide entropy values, which better agree with experimental observations, and that they are capable of identifying correlations between symmetry and physical/chemical measurables.

Journal Article↗

PubMed2006

Enthalpy versus entropy-driven binding of bisphosphonates to farnesyl diphosphate synthase.

We report the results of an ITC (isothermal titration calorimetry) investigation of the binding of six bisphosphonates to the enzyme farnesyl diphosphate synthase (FPPS; EC 2.5.1.10) from Trypanosoma brucei. The bisphosphonates investigated were zoledronate, risedronate, ibandronate, pamidronate, 2-phenyl-1-hydroxyethane-1,1-bisphosphonate, and 1-(2,2-bisphosphonoethyl)-3-iodo pyridinium. At pH = 7.4, both risedronate and the phenylethane bisphosphonate bind in an enthalpy-driven manner (DeltaH approximately -9 to 10 kcal mol-1), but the other four bisphosphonates bind in an entropy-driven manner (DeltaS varying from 31.2 to 55.1 cal K-1 mol-1). However, at pH = 8.5, zoledronate binding switches from entropy to enthalpy-driven. The DeltaG results are highly correlated with FPPS inhibition results obtained using a radiochemical assay (R2 = 0.85, N = 11, P < 0.001). The DeltaH and DeltaS results are interpreted in terms of a model in which bisphosphonates with charged side chains have positive DeltaH values, due to the enthalpic cost of desolvation (due to strong ion-dipole interactions) and, likewise, a positive DeltaS, due to an increase in water entropy (both ligand and protein associated) on ligand binding to FPPS: the hydrophobic effect. For the neutral side chains (risedronate at pH 7.4, 8.5 and zoledronate at pH 8.5, as well as the phenylethane bisphosphonate), binding is overwhelmingly enthalpy-driven, with the enhanced activity of the basic side chain containing species being attributable to their becoming protonated in the active site. Given the large size of the bisphosphonate market and the potential importance of the development of these compounds for cancer immunotherapy and anti-parasitic chemotherapy, these results are of broad general interest in the context of the development of new, potent, and selective FPPS inhibitors.

Animals↗

PubMed2001

Thermolysis of tert-butyl phenylperacetates: delicate control of the rates through contributions from translational and rotational entropy.

The first-order rate constants (k(Y)) at several temperatures in CDCl(3) were measured for thermal decompositions of YC(6)H(4)CH(2)CO(3)C(CH(3))(3) with Y being p-OCH(3), p-OPh, p-CH(3), p-Ph, p-H, p-Cl, m-Cl, and p-NO(2). The relative rates (k(Y)/k(H)) exhibit excellent rho(+)/sigma(+) Hammett correlations with rho(+) < 0, indicating a polar TS. Activation parameters (DeltaH()(Y) and DeltaS()(Y)) and their differential terms (DeltaDeltaH()(Y)(-)(H) and DeltaDeltaS()(Y)(-)(H)) were obtained from the Eyring plot. Differential activation terms (DeltaDeltaH()(Y)(-)(H) and DeltaDeltaS()(Y)(-)(H)) disclose an isokinetic relation with p-CH(3), p-Ph, p-H, p-Cl, and m-Cl (isokinetic temp, 230 K). However, p-OCH(3), and p-OPh show negative deviations, and a positive deviation occurs with p-NO(2). Plot of DeltaDeltaH()(Y)(-)(H) vs sigma(+) exhibits a good linear relation (r = 0.95) with a slope (alpha(1) = -3.34). A better linear correlation (r = 0.97) and steeper slope (alpha(2) = -5.22) were observed for TDeltaDeltaS()(Y)(-)(H) vs sigma(+). Negatively larger slope (alpha(2) = -5.22) may point to entropy control of rates. Differential activation parameters (DeltaDeltaH()(Y)(-)(H) and DeltaDeltaS()(Y)(-)(H)) reflect variations of activation process. Differential activation entropies (DeltaDeltaS()(Y)(-)(H)) are discussed in terms of contributions of translational and rotational entropies. Similar deviation behaviors of p-OCH(3), p-OPh, and p-NO(2) were again observed for the both plots. p-NO(2) can strongly destabilize the cationic site of the polar TS but serves an eminent spin delocalizer for the homolytic TS.

Journal Article↗

PubMed2005

Local and total entropy production and heat and water fluxes in a one-dimensional polymer electrolyte fuel cell.

We show how to determine the local entropy production rate in the various parts of a polymer electrolyte fuel cell producing liquid water from air and hydrogen. We present and solve five sets of transport equations for the heterogeneous, one-dimensional cell at stationary state, equations that are compatible with the second law of thermodynamics. The simultaneous solution of concentration, temperature, and potential profiles gave information about the local entropy production and the heat and water fluxes out of the system. Results for the entropy production can be used to explain the polarization curve, and we find that diffusion in the backing is less important for the potential than charge transport in the membrane. We demonstrate that all coupling effects as defined in nonequilibrium thermodynamics theory are essential for a correct description of the dissipation of energy and also for the small temperature gradients that were calculated here. The heat flux out of the anode was smaller than the heat flux out of the cathode. The cathode surface temperature increased as the current density increased but was smaller than the anode surface temperature for small current densities. This type of modeling may be important for design of cooling systems for fuel cells. The method is general, however, and can be used to analyze batteries and other fuel cells in a similar manner.

Journal Article↗

PubMed2005

Entropy convergence in the hydration thermodynamics of n-alcohols.

Using experimental data from the literature, entropy convergence in the hydration thermodynamics of n-alcohols is shown to occur at about 125 degrees C. The phenomenon is reproduced in a more-than-qualitative manner by means of a theoretical approach that accounts for the entropy contributions associated with (a) creation of a cavity in water, (b) turning on solute-water van der Waals interactions, and (c) turning on the solute-water H-bonding potential. The density of water and the effective size of water molecules with their temperature dependence play the pivotal role for the occurrence of entropy convergence, together with the property of the alcohol hydroxyl group to form the same number of H-bonds with water molecules regardless of the length of the alkyl chain.

Alcohols↗

PubMed2006

Solvent reorganization entropy of electron transfer in polar solvents.

We report the results of molecular dynamics simulations of the solvent reorganization energy of intramolecular electron transfer in a charge-transfer molecule dissolved in water and acetonitrile at varying temperatures. The simulations confirm the prediction of microscopic solvation theories of a positive reorganization entropy in polar solvents. The results of simulations are analyzed in terms of the splitting of the reorganization entropy into the contributions from the solute-solvent interaction and from the alteration of the solvent structure induced by the solute. These two contributions mutually cancel each other, resulting in the reorganization entropy amounting to only a fraction of each component.

Journal Article↗

PubMed2006

Effect of deposited bismuth on the potential of maximum entropy of Pt(111) single-crystal electrodes.

The effect of bismuth adsorption on the entropy of formation of the double layer on Pt(111) electrodes has been studied with the laser-induced temperature jump method. The coulostatic response to the temperature change induced by pulsed laser illumination allows the estimation of the sign and magnitude of the thermal coefficient of the potential drop at the interphase. This is related to the entropy of formation of the double layer, and the particular potential where this thermal coefficient becomes zero can be identified with the potential of maximum entropy of double-layer formation (pme). The effect of bismuth adsorption on the pme depends on the adatom coverage. At high coverages, a marked decrease of the pme is observed. This trend follows the change of the potential of zero charge expected from work function measurements, and it is likely due to the change in the orientation of solvent molecules induced by surface dipoles originated between the adatom and the substrate. At low coverage, the pme increases with the bismuth coverage. The disruption of the water structure due to the presence of the bismuth adatoms is tentatively proposed as the most likely explanation for this behavior.

Journal Article↗