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At least 307 records · Page 17Linked to original sources

PubMed2006

Entropy-controlled supramolecular photochirogenesis: enantiodifferentiating Z-E photoisomerization of cyclooctene included and sensitized by permethylated 6-O-modified beta-cyclodextrins.

Permethylated 6-O-modified beta-cyclodextrins 2a-2d were synthesized as novel photosensitizing hosts with a flexible skeleton. Circular dichroism (CD) and 2D NMR spectral examinations of benzoate 2a revealed that the benzoate moiety is deeply included into its own cavity in aqueous solution. Upon addition of (Z)-cyclooctene (1Z) to a 50% aqueous methanol solution of 2a at 25 degrees C, the benzoate moiety of 2a was gradually excluded from the cavity as indicated by the CD spectral changes; the Job's plot revealed the formation of a 1:1 complex of 2a with 1Z. The binding constants for the complexation of 1Z by 2a were determined by CD spectral titration in 50% aqueous methanol at various temperatures. The van't Hoff analysis of the obtained data afforded the thermodynamic parameters (DeltaH degrees = -3.1 kJ mol(-1), DeltaS degrees = 48.5 J mol(-1) K(-1)), demonstrating the entropy-driven complexation by the permethylated cyclodextrin. This is in sharp contrast to the complexation of 1Z by nonmethylated beta-cyclodextrin benzoate that is driven by enthalpy (DeltaH degrees = -31.8 kJ mol(-1) and DeltaS degrees = -51.1 J mol(-1) K(-1)). Upon supramolecular photosensitization with 2a-2d, 1Z isomerized to the (E)-isomer (1E) in moderate enantiomeric excesses (ee's), which however displayed significant temperature dependence with accompanying switching of the product's chirality in an extreme case. Such dynamic behavior of ee is very different from that reported for the photosensitization with nonmethylated cyclodextrin benzoate, where the product's ee is controlled by host occupancy. Eyring treatment of the ee obtained at various temperatures (<0 degrees C) gave the differential activation parameters for the enantiodifferentiation process occurring in the supramolecular exciplex, revealing the crucial role of entropy, as indicated by the DeltaDeltaS(++) value changing dynamically from +4 to -24 J K(-1) mol(-1). The origin of the contrasting behavior of permethylated versus nonmethylated cyclodextrin hosts is inferred to be the conformational flexibility of the former host, which enables the entropy-driven guest complexation in the ground state and the entropy-controlled enantiodifferentiation in the excited state.

Journal Article↗

PubMed2006

Thermodynamic functions of conformational changes. 2. Conformational entropy as a measure of information accumulation.

Various folded molecular structures contain different amount of information. The relative amount of information may be related to relative entropy or entropy change. The conformational entropy change for n-butane has been computed as the function of rotation around the central C-C bond. It appears that the g+ or g- conformers contain about 16% more information than the anti-structure. Furthermore, the syn conformation with the two groups eclipsed contained about 42% more information than the fully staggered anti orientation. The conformational entropy function calculated from 3N - 7 internal degrees of freedom was found to be a continuous function.

Journal Article↗

PubMed2006

Thermodynamic functions of conformational changes: conformational network of glycine diamide folding, entropy lowering, and informational accumulation.

A refined grid of a conformational potential energy surface (PES) and a conformational entropy surface for glycine diamide was generated by ab initio molecular computations. The possible network of reaction paths was recognized in terms of the linear combinations of internal coordinates corresponding to conrotatory and disrotatory modes of motions. Such a Woodward-Hoffmann-like path selection principle was detected for the folding of this peptide from extended to some virtually cyclic structure. It seemed reasonable to assume that this principle (or its generalized form) might be applicable to protein folding. A reaction path network was projected on the potential energy, and a continuous entropy surface was constructed under the condition of reduced dimensionality. The low entropy of the folded conformation indicated an information accumulation between 326% and 1414% with respect to the fully extended or unfolded structure. It is found that the location of existing and 'latent' critical points on the surface is revealed by the extrema and inflection points of the entropy curve.

Journal Article↗

PubMed1999

Predicting the total entropy of melting: application to pharmaceuticals and environmentally relevant compounds.

Experimental entropy of melting values for physical property estimation schemes, such as solubility and vapor pressure, are not readily available. In this study a semiempirical equation, which contains two molecular parameters, is used to estimate the total entropy of melting for a variety of pharmaceutically and environmentally relevant compounds. A database of experimental entropy values consisting of over 370 different compounds was compiled from literature. A molecular rotational symmetry number and a molecular flexibility number for each compound were defined. The simple equation does very well in predicting the total entropy of melting for the complex set of molecules with an average error of 21%.

Thermodynamics↗

PubMed2004

Cationic lanthanide complexes of neutral tripodal N,O ligands: enthalpy versus entropy-driven podate formation in water.

The cationic lanthanide complexes of two neutral tripodal N,O ligands, tpa (tris[(2-pyridyl)methyl]amine) and tpaam (tris[6-((2-N,N-diethylcarbamoyl)pyridyl)methyl]amine) are studied in water. The analysis of the proton lanthanide induced NMR shifts indicate that there is no abrupt structural change in the middle of the rare-earth series. Unexpectedly, the formation constant values of the lanthanide podates of tpaam and tpa in D2O at 298 K are similar, suggesting that the addition of the three amide groups to the ligand tpa does not lead to any increase in stability of the lanthanide complexes of tpaam in respect to tpa, even though the amide groups are coordinated to the metal in aqueous solution. The measurement of the enthalpy and entropy changes of the complexation reactions shows that the two similar ligands tpa and tpaam have different driving forces for lanthanide complexation. Indeed, the formation of tpa podates benefits from an exothermic enthalpy change associated with a small entropy change, whereas the complexation reaction with tpaam is clearly entropy-driven though opposed by a positive enthalpy change. The hydration states of the europium complexes were measured by luminescence and show the coordination of 4-5 water ligands in [Eu(tpa)]3+ whereas there are only 2 in [Eu(tpaam)]3+. Therefore the heptadentate ligand tpaam releases the translational entropy of more water molecules than does the tetradentate ligand tpa.

Journal Article↗

PubMed1999

Crystal structure retrieval by maximum entropy analysis of atomic resolution incoherent images

In this paper, we discuss the application of the maximum entropy method to atomic resolution Z-contrast images acquired in a scanning transmission electron microscope. Z-contrast is an incoherent imaging technique, and can be described as a convolution between an object function (the real-space map of the columnar scattering cross-section to high angles) and a point spread function (the effective electron probe). As such, we show that the technique is ideally suited to maximum entropy analysis which can, given an electron probe distribution, retrieve the 'most likely' Z-contrast object function. Using both simulated and experimentally acquired data, we explore the capabilities of maximum entropy analysis when applied to atomic resolution Z-contrast images, drawing conclusions on both the range of applicability of the technique and the nature of the retrieved crystal structures. Ultimately, we show the way in which the combination of Z-contrast imaging with maximum entropy analysis can be used to yield important information on unexpected atomic structures.

Journal Article↗

PubMed1999

Heart rate variability of preterm neonates quantified by energy entropy.

Identifying variables predictive of neurobehavioural sequelae is a key objective in the study of high-risk neonates. Examination of heart rate variability (HRV) characteristics may be a finer discriminator of the neonate's response to physiologic stressors than the mean heart rate. The energy entropy of the heart beat tachogram, computed in four different domains, was used to quantify the HRV in 13 preterm neonates. The entropies of energies were computed from 1024 interbeat time intervals obtained once per week from 26 to 35 weeks postconceptional age (PCA). The energy entropy computed in three of the domains, like the standard deviation of intervals, distinguished between the 10 neonates that were measured at 35 weeks PCA with 100% specificity and 67% sensitivity, but did not distinguish between healthy and unhealthy neonates at earlier ages. The findings suggest that energy entropy may be a discerning measure of physiologic stress in the preterm infant, although future research is needed to refine the test and determine statistical significance.

Cardiotocography↗

PubMed2005

Comparing landscape calculations with calorimetric data on ortho-terphenyl, and the question of the configurational fraction of the excess entropy.

Mossa et al. [Phys. Rev. E 65, 041205 (2002)] have calculated the total and configurational entropies of supercooled ortho-terphenyl liquid using the potential-energy landscape formalism and a simplified model of the intermolecular potential. I show here that the agreement of their calculated configurational entropy with the experimental data depends on what is assumed about the configurational fraction of the excess entropy and its temperature dependence. In particular, if the configurational fraction is taken as 0.70 and independent of temperature the agreement is excellent; if a marked temperature dependence of that fraction inferred from calorimetric data is assumed the agreement is only fair at best. This marked temperature dependence of the configurational fraction also implies some implausible behavior of contributions to the excess entropy at the Kauzmann temperature, but no obvious reason for disregarding it presents itself.

Journal Article↗

PubMed2005

Entropy production in a two-dimensional reversible Gray-Scott system.

The entropy production sigma is calculated in the time evolution processes toward a Turing-like pattern and a chaotic pattern in a two-dimensional reaction-diffusion system. The contributions of reaction and diffusion to the entropy production are evaluated separately. Though its contribution to total sigma is about 5%, the entropy production in diffusion foretells the moving direction of the dots (reaction spots) and the line-shaped patterns. The entropy production of the entire system sigma depicts well the cooperative dynamics and evolution of chaotic dot patterns. It is suggested that sigma can be a scalar measure for quantitative studies of hierarchic pattern dynamics. The relation is also discussed between the bifurcation parameter and the distance from thermodynamic equilibrium.

Journal Article↗

PubMed2006

Orientation polarization from faster motions in the ultraviscous and glassy diethyl phthalate and its entropy.

Dielectric spectra of the beta relaxation in glassy and ultraviscous liquid diethyl phthalate show that its relaxation strength Delta epsilon(beta), the distribution of times, and the relaxation rate are more sensitive to temperature T in the ultraviscous liquid than in the glassy state. The Delta epsilon(beta) against temperature plot has an elbow-shaped break near T(g) of approximately 181 K, which is remarkably similar to that observed in the entropy, enthalpy, and volume against temperature plots, and in the plot of Delta epsilon(beta) against the liquid's entropy minus its 0 K value. The ratio of Delta epsilon(beta) to diethyl phthalate's entropy, after subtracting the 0 K value, is 1.08 x 10(-3) mol K/J in the glassy state at 120.4 K, which decreases slowly to 0.81 x 10(-3) mol K/J at 176 K near T(g) and thereafter rapidly increases to 1.57 x 10(-3) mol K/J at 190 K. Variation in Delta epsilon(beta) parallels the variation of the entropy. A change in the activation energy of the beta process at T>T(g) indicates that its rate is also determined by the structure of the ultraviscous liquid. Features of beta relaxation are consistent with localized motions of molecules and may not involve small-angle motions of all molecules.

Journal Article↗

PubMed2006

Identification of the minimal protein-folding nucleus through loop-entropy perturbations.

To explore the plasticity and structural constraints of the protein-folding nucleus we have constructed through circular permutation four topological variants of the ribosomal protein S6. In effect, these topological variants represent entropy mutants with maintained spatial contacts. The proteins were characterized at two complementary levels of detail: by phi-value analysis estimating the extent of contact formation in the transition-state ensemble and by Hammond analysis measuring the site-specific growth of the folding nucleus. The results show that, although the loop-entropy alterations markedly influence the appearance and structural location of the folding nucleus, it retains a common motif of one helix docking against two strands. This nucleation motif is built around a shared subset of side chains in the center of the hydrophobic core but extends in different directions of the S6 structure following the permutant-specific differences in local loop entropies. The adjustment of the critical folding nucleus to alterations in loop entropies is reflected by a direct correlation between the phi-value change and the accompanying change in local sequence separation.

Biophysical Phenomena↗

PubMed1979

Lyapounov variable: Entropy and measurement in quantum mechanics.

We discuss the question of the dynamical meaning of the second law of thermodynamics in the framework of quantum mechanics. Previous discussion of the problem in the framework of classical dynamics has shown that the second law can be given a dynamical meaning in terms of the existence of so-called Lyapounov variables-i.e., dynamical variables varying monotonically in time without becoming contradictory. It has been found that such variables can exist in an extended framework of classical dynamics, provided that the dynamical motion is suitably unstable. In this paper we begin to extend these results to quantum mechanics. It is found that no dynamical variable with the characteristic properties of nonequilibrium entropy can be defined in the standard formulation of quantum mechanics. However, if the Hamiltonian has certain well-defined spectral properties, such variables can be defined but only as a nonfactorizable superoperator. Necessary nonfactorizability of such entropy operators M has the consequence that they cannot preserve the class of pure states. Physically, this means that the distinguishability between pure states and corresponding mixtures must be lost in the case of a quantal system for which the algebra of observables can be extended to include a new dynamical variable representing nonequilibrium entropy. We discuss how this result leads to a solution of the quantum measurement problem. It is also found that the question of existence of entropy of superoperators M is closely linked to the problem of defining an operator of time in quantum mechanics.

Journal Article↗

PubMed1990

Does the maximum entropy method improve sensitivity?

Maximum entropy reconstruction has been used in several fields to produce visually striking reconstructions of positive objects (images, densities, spectra) from noisy, indirect measurements. In magnetic resonance spectroscopy, this technique is notable for its apparent noise suppression and its avoidance of the artifacts that affect discrete Fourier transform spectra of short (zero-extended) data records. In the general case where the length of the reconstructed spectrum exceeds that of the data record or where a convolution kernel is incorporated in the reconstruction, no known analytical solution to the reconstruction problem exists. Consequently, knowledge of the properties of maximum entropy reconstruction has been mainly anecdotal, based on a small selection of published reconstructions. However, in the limiting case where the lengths of the reconstructed spectrum and the data record are the same and a convolution kernel is not applied, the problem can be solved analytically. The solution has a simple structure that helps explain several commonly observed features of maximum entropy reconstructions--for example, the biases in the recovered intensities and the fact that noise near the baseline is more successfully suppressed than is noise superimposed on broad features in the spectrum. The solution also shows that the noise suppression offered by maximum entropy reconstruction could (in this special case) be equally well obtained by a "cosmetic" device: simply displaying the conventional Fourier transform reconstruction using a certain nonlinear plotting scale for the vertical (y) coordinate.

Journal Article↗

PubMed1994

On producing more complexity than entropy in replication.

RNA replication in the bacteriophage Q beta system can, in principle, transmit sequence complexity at a higher rate than it increases entropy. Expanding the variety of nucleotides, through novel base-pair interactions, would move the threshold at which synthesis produces more complexity than entropy away from near equilibrium while accelerating the system approach to equilibrium. A decrease in sequence complexity during polymerization, leading to a many-to-one monomer correspondence with template, cannot be reversed, owing to symmetry restrictions. In terms of the kinetic mechanism, uncertainty associated with the the path of depolymerization yields a path entropy which selectively prolongs the reverse reaction. Together with an elevation in thermodynamic entropy, therefore, there are two possible sources of irreversibility in a physical process. Some implications of kinetic irreversibility are considered in relation to the second law of thermodynamics and to the processing and translation of mRNA.

Allolevivirus↗

PubMed1994

Cold denaturation of a repressor-operator complex: the role of entropy in protein-DNA recognition.

The mechanisms by which regulatory proteins recognize specific DNA sequences are not fully understood. Here we examine the basis for the stability of a protein-DNA complex, using hydrostatic pressure and low temperature. Pressure converts the DNA-binding Arc repressor protein from a native state to a denatured, molten-globule state. Our data show that the folding and dimerization of Arc repressor in the temperature range 0-20 degrees C are favored by a large positive entropy value, so that the reaction proceeds in spite of an unfavorable positive enthalpy. On binding operator DNA, Arc repressor becomes extremely stable against denaturation. However, the Arc repressor-operator DNA complex is cold-denatured at subzero temperatures under pressure, demonstrating that the favorable entropy increases greatly when Arc repressor binds tightly to its operator sequence but not a nonspecific sequence. We show how an increase in entropy may operate to provide the protein with a mechanism to distinguish between a specific and a nonspecific DNA sequence. It is postulated that the formation of the Arc-operator DNA complex is followed by an increase in apolar interactions and release of solvent which would explain its entropy-driven character, whereas this solvent would not be displaced in nonspecific complexes.

Bacteriophage P22↗

PubMedDate not supplied

Entropy and cortical activity: information theory and PET findings.

Functional segregation requires convergence and divergence of neuroanatomical connections. Furthermore, the nature of functional segregation suggests that (1) signals in convergent afferents are correlated and (2) signals in divergent efferents are uncorrelated. The aim of this article is to show that this arrangement can be predicted mathematically, using information theory and an idealized model of cortical processing. In theory, the existence of bifurcating axons limits the number of independent output channels from any small cortical region, relative to the number of inputs. An information theoretic analysis of this special (high input:output ratio) constraint indicates that the maximal transfer of information between inputs, to a cortical region, and its outputs will occur when (1) extrinsic connectivity to the area is organized such that the entropy of neural activity in afferents is optimally low and (2) connectivity intrinsic to the region is arranged to maximize the entropy measured at the initial segments of projection neurons. Under the constraints of the model, a low entropy is synonymous with high correlations between axonal firing rates (and vice versa). Consequently this antisymmetric arrangement of functional activity in convergent and divergent connections underlying functional segregation is exactly that predicted by the principle of maximum preservation of information, considered in the context of axonal bifurcation. The hypothesis that firing in convergent afferents is correlated (has low entropy) and spatially coherent was tested using positron emission tomographic measurements of cortical synaptic function in man. This hypothesis was confirmed.

Afferent Pathways↗

PubMed1999

Aging alteration of cardiac vagosympathetic balance assessed through the tone-entropy analysis.

BACKGROUND: Age-associated alterations of cardiac autonomic functions have been investigated intensively through heart rate variability analyses. However, changes with age in cardiac vagosympathetic balance remain to be elucidated. METHODS: We studied 142 male subjects (30-69 yr) at a health care center in Kyoto, Japan. Electrocardiographic data were collected from subjects in a recumbent position for 10 min in the morning. Analysis was done by classifying the subjects into four age groups. In a pharmacological experiment carried out in December 1996, tone was verified to reflect the cardiac vagosympathetic balance, and entropy the total autonomic neural efferent activity. We assessed the heart rate variability through the tone-entropy (T-E) analysis that was described previously. In essence, two indexes, tone and entropy, were defined on a distribution of successive variations of heart period. RESULTS: No significant differences were detected in clinical conditions among the four age groups. Tone increased and entropy decreased significantly with age. The aging process was expressed as a curvilinear path in T-E space. Compared to the pharmacological experiment, it was observed that aging degenerated the heart function from an ordinary to a denervated one. The same aging path was superimposed in the opposite direction on the heart recovery path after dynamic exercise in which cardiac vagosympathetic balance tended toward vagus division, corresponding with restoration of total autonomic activity. CONCLUSIONS: An age-related reduction in cardiac autonomic function was consistent with previous reports. The vagosympathetic balance was altered with this reduction: vagal predominance was impaired significantly in proportion to the withdrawal of total cardiac autonomic activity.

Adrenergic beta-Antagonists↗

PubMed1984

Heat capacity and entropy changes of calmodulin induced by calcium binding.

Microcalorimetric titrations were carried out in order to analyze the structural changes of calmodulin caused by Ca2+-binding. Measurements were made both in the absence and in the presence of Mg2+, at 5, 15, and 25 degrees C. Titrations of calmodulin with Ca2+ in the absence of Mg2+ showed that the Ca2+-binding reaction is endothermic and thus is driven solely by the large entropy change. Following the method of Sturtevant (1977), the magnitudes of the hydrophobic and intramolecular vibrational contributions to the heat capacity and entropy changes of calmodulin on Ca2+-binding were estimated. In both the absence and the presence of Mg2+, Ca2+-binding to every site of calmodulin gives rise to an increase in hydrophobic entropy and thus to an "assembling" of nonpolar groups, which are scattered on the surface of the molecule in Ca2+-free calmodulin. Ca2+-binding to calmodulin also gives rise to an increase in vibrational entropy, indicating a "softening" of the overall structure.

Binding Sites↗