Hensen, Ulf; Grubmüller, Helmut; Lange, Oliver F
2009-07-01
The quasiharmonic approximation is the most widely used estimate for the configurational entropy of macromolecules from configurational ensembles generated from atomistic simulations. This method, however, rests on two assumptions that severely limit its applicability, (i) that a principal component analysis yields sufficiently uncorrelated modes and (ii) that configurational densities can be well approximated by Gaussian functions. In this paper we introduce a nonparametric density estimation method which rests on adaptive anisotropic kernels. It is shown that this method provides accurate configurational entropies for up to 45 dimensions thus improving on the quasiharmonic approximation. When embedded in the minimally coupled subspace framework, large macromolecules of biological interest become accessible, as demonstrated for the 67-residue coldshock protein. PMID:19658735
Configurational Entropy Revisited
Lambert, Frank L.
2007-09-01
Entropy change is categorized in some prominent general chemistry textbooks as being either positional (configurational) or thermal. In those texts, the accompanying emphasis on the dispersal of matter—independent of energy considerations and thus in discord with kinetic molecular theory—is most troubling. This article shows that the variants of entropy can be treated from a unified viewpoint and argues that to decrease students' confusion about the nature of entropy change these variants of entropy should be merged. Molecular energy dispersal in space is implicit but unfortunately tacit in the cell models of statistical mechanics that develop the configurational entropy change in gas expansion, fluids mixing, or the addition of a non-volatile solute to a solvent. Two factors are necessary for entropy change in chemistry. An increase in thermodynamic entropy is enabled in a process by the motional energy of molecules (that, in chemical reactions, can arise from the energy released from a bond energy change). However, entropy increase is only actualized if the process results in a larger number of arrangements for the system's energy, that is, a final state that involves the most probable distribution for that energy under the new constraints. Positional entropy should be eliminated from general chemistry instruction and, especially benefiting "concrete minded" students, it should be replaced by emphasis on the motional energy of molecules as enabling entropy change.
Configurational entropy of native proteins.
Karplus, M.; Ichiye, T; Pettitt, B. M.
1987-01-01
Simulations of the residual configurational entropy of a protein in the native state suggest that it is nearly an order of magnitude larger than the entropy of denaturation. The implications of this result are discussed.
Maximum entropy tokamak configurations
The new entropy concept for the collective magnetic equilibria is applied to the description of the states of a tokamak subject to ohmic and auxiliary heating. The condition for the existence of steady state plasma states with vanishing entropy production implies, on one hand, the resilience of specific current density profiles and, on the other, severe restrictions on the scaling of the confinement time with power and current. These restrictions are consistent with Goldston scaling and with the existence of a heat pinch. (author)
Configurational entropy of Wigner crystals
Radzvilavičius, Arūnas; 10.1088/0953-8984/23/7/075302
2012-01-01
We present a theoretical study of classical Wigner crystals in two- and three-dimensional isotropic parabolic traps aiming at understanding and quantifying the configurational uncertainty due to the presence of multiple stable configurations. Strongly interacting systems of classical charged particles confined in traps are known to form regular structures. The number of distinct arrangements grows very rapidly with the number of particles, many of these arrangements have quite low occurrence probabilities and often the lowest-energy structure is not the most probable one. We perform numerical simulations on systems containing up to 100 particles interacting through Coulomb and Yukawa forces, and show that the total number of metastable configurations is not a well defined and representative quantity. Instead, we propose to rely on the configurational entropy as a robust and objective measure of uncertainty. The configurational entropy can be understood as the logarithm of the effective number of states; it is...
Configurational entropy in brane-world models
Correa, R. A. C., E-mail: fis04132@gmail.com [CCNH, Universidade Federal do ABC, 09210-580, Santo André, SP (Brazil); Rocha, Roldão da, E-mail: roldao.rocha@ufabc.edu.br [CMCC, Universidade Federal do ABC, 09210-580, Santo André, SP (Brazil); International School for Advanced Studies (SISSA), Via Bonomea 265, 34136, Trieste (Italy)
2015-11-02
In this work we investigate the entropic information on thick brane-world scenarios and its consequences. The brane-world entropic information is studied for the sine-Gordon model and hence the brane-world entropic information measure is shown to be an accurate way for providing the most suitable range for the bulk AdS curvature, in particular from the informational content of physical solutions. Besides, the brane-world configurational entropy is employed to demonstrate a high organisational degree in the structure of the configuration of the system, for large values of a parameter of the sine-Gordon model but the one related to the AdS curvature. The Gleiser and Stamatopoulos procedure is finally applied in order to achieve a precise correlation between the energy of the system and the brane-world configurational entropy.
Configurational entropy in brane-world models
In this work we investigate the entropic information on thick brane-world scenarios and its consequences. The brane-world entropic information is studied for the sine-Gordon model and hence the brane-world entropic information measure is shown to be an accurate way for providing the most suitable range for the bulk AdS curvature, in particular from the informational content of physical solutions. Besides, the brane-world configurational entropy is employed to demonstrate a high organisational degree in the structure of the configuration of the system, for large values of a parameter of the sine-Gordon model but the one related to the AdS curvature. The Gleiser and Stamatopoulos procedure is finally applied in order to achieve a precise correlation between the energy of the system and the brane-world configurational entropy
Configurational entropy in brane-world models
In this work we investigate the entropic information on thick brane-world scenarios and its consequences. The brane-world entropic information is studied for the sine-Gordon model and hence the brane-world entropic information measure is shown to be an accurate way for providing the most suitable range for the bulk AdS curvature, in particular from the informational content of physical solutions. Besides, the brane-world configurational entropy is employed to demonstrate a high organisational degree in the structure of the configuration of the system, for large values of a parameter of the sine-Gordon model but the one related to the AdS curvature. The Gleiser and Stamatopoulos procedure is finally applied in order to achieve a precise correlation between the energy of the system and the brane-world configurational entropy. (orig.)
Total Synthesis and Absolute Configuration of the Marine Norditerpenoid Xestenone
Hiroaki Miyaoka
2009-11-01
Full Text Available Xestenone is a marine norditerpenoid found in the northeastern Pacific sponge Xestospongia vanilla. The relative configuration of C-3 and C-7 in xestenone was determined by NOESY spectral analysis. However the relative configuration of C-12 and the absolute configuration of this compound were not determined. The authors have now achieved the total synthesis of xestenone using their developed one-pot synthesis of cyclopentane derivatives employing allyl phenyl sulfone and an epoxy iodide as a key step. The relative and absolute configurations of xestenone were thus successfully determined by this synthesis.
Absolute Configuration of the Levocloperastine Fendizoate
ZHOU Min; YU Kai-Bei; HU Hong-Gang; LI Feng; LONG Yuan-De
2011-01-01
Crystal structure of the levocloperastine fendizoate （C80H76Cl2N2O10, C20H25ClNO＋· C20H13O4-） has been determined by single-crystal X-ray diffraction. The crystal is of triclinic system, space group P1 with a = 10.1059（18）, b = 11.957（2）, c = 15.383（3） , α = 104.666（2）, β = 90.9700（10）, γ = 110.744（2）°, Z = 1, V = 1670.0（5） 3, Dc = 1.289 g/cm3, F（000） = 684, μ（MoKα） = 0.161 mm-1, Mr = 1296.33, the final R = 0.0343 and wR = 0.0676. The cations and anions are linked by the COO…NH hydrogen bonds of 2.709（3） and 2.690（3） and COO…OH hydrogen bonds of 2.632（3） and 2.631（3） . The configuration of the only one chiral carbon atom in this compound is R（rectus）.
The Role of Configurational Entropy in Amorphous Systems
Kirsten A. Graeser; Patterson, James E.; J. Axel Zeitler; Thomas Rades
2010-01-01
Configurational entropy is an important parameter in amorphous systems. It is involved in the thermodynamic considerations, plays an important role in the molecular mobility calculations through its appearance in the Adam-Gibbs equation and provides information on the solubility increase of an amorphous form compared to its crystalline counterpart. This paper presents a calorimetric method which enables the scientist to quickly determine the values for the configurational entropy at any tempe...
On determining absolute entropy without quantum theory or the third law of thermodynamics
Steane, Andrew M.
2016-04-01
We employ classical thermodynamics to gain information about absolute entropy, without recourse to statistical methods, quantum mechanics or the third law of thermodynamics. The Gibbs–Duhem equation yields various simple methods to determine the absolute entropy of a fluid. We also study the entropy of an ideal gas and the ionization of a plasma in thermal equilibrium. A single measurement of the degree of ionization can be used to determine an unknown constant in the entropy equation, and thus determine the absolute entropy of a gas. It follows from all these examples that the value of entropy at absolute zero temperature does not need to be assigned by postulate, but can be deduced empirically.
Absolute configuration of some dinorlabdanes from the copaiba oil
A novel ent-dinorlabdane (Ι)-13(R)-14,15-dinorlabd-8(17)-ene-3,13-diol was isolated from commercial copaiba oil along with two known dinorlabdanes. The absolute configuration of these dinorditerpenes was established for the first time through synthesis starting from known (Ι)-3-hydroxycopalic acid, which was also isolated from the same oleoresin. (author)
Absolute configuration of some dinorlabdanes from the copaiba oil
Romero, Adriano L.; Baptistela, Lucia H.B.; Imamura, Paulo M. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica], e-mail: imam@iqm.unicamp.br
2009-07-01
A novel ent-dinorlabdane ({iota})-13(R)-14,15-dinorlabd-8(17)-ene-3,13-diol was isolated from commercial copaiba oil along with two known dinorlabdanes. The absolute configuration of these dinorditerpenes was established for the first time through synthesis starting from known ({iota})-3-hydroxycopalic acid, which was also isolated from the same oleoresin. (author)
Absolute configurations of zingiberenols isolated from ginger (Zingiber officinale) rhizomes
The sesquiterpene alcohol zingiberenol, or 1,10-bisaboladien-3-ol, was isolated some time ago from ginger, Zingiber officinale, rhizomes, but its absolute configuration had not been determined. With three chiral centers present in the molecule, zingiberenol can exist in eight stereoisomeric forms. ...
Confirmation of the absolute configuration of (−)-aurantioclavine
Behenna, Douglas C.
2011-04-01
We confirm our previous assignment of the absolute configuration of (-)-aurantioclavine as 7R by crystallographically characterizing an advanced 3-bromoindole intermediate reported in our previous synthesis. This analysis also provides additional support for our model of enantioinduction in the palladium(II)-catalyzed oxidative kinetic resolution of secondary alcohols. © 2010 Elsevier Ltd. All rights reserved.
Configurational entropy of hydrogen-disordered ice polymorphs
Herrero, Carlos P., E-mail: ch@icmm.csic.es; Ramírez, Rafael [Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid (Spain)
2014-06-21
The configurational entropy of several H-disordered ice polymorphs is calculated by means of a thermodynamic integration along a path between a totally H-disordered state and one fulfilling the Bernal-Fowler ice rules. A Monte Carlo procedure based on a simple energy model is used, so that the employed thermodynamic path drives the system from high temperatures to the low-temperature limit. This method turns out to be precise enough to give reliable values for the configurational entropy s{sub th} of different ice phases in the thermodynamic limit (number of molecules N → ∞). The precision of the method is checked for the ice model on a two-dimensional square lattice. Results for the configurational entropy are given for H-disordered arrangements on several polymorphs, including ices Ih, Ic, II, III, IV, V, VI, and XII. The highest and lowest entropy values correspond to ices VI and XII, respectively, with a difference of 3.3% between them. The dependence of the entropy on the ice structures has been rationalized by comparing it with structural parameters of the various polymorphs, such as the mean ring size. A particularly good correlation has been found between the configurational entropy and the connective constant derived from self-avoiding walks on the ice networks.
Configurational entropy of hydrogen-disordered ice polymorphs
Herrero, Carlos P.; Ramírez, Rafael
2014-06-01
The configurational entropy of several H-disordered ice polymorphs is calculated by means of a thermodynamic integration along a path between a totally H-disordered state and one fulfilling the Bernal-Fowler ice rules. A Monte Carlo procedure based on a simple energy model is used, so that the employed thermodynamic path drives the system from high temperatures to the low-temperature limit. This method turns out to be precise enough to give reliable values for the configurational entropy sth of different ice phases in the thermodynamic limit (number of molecules N → ∞). The precision of the method is checked for the ice model on a two-dimensional square lattice. Results for the configurational entropy are given for H-disordered arrangements on several polymorphs, including ices Ih, Ic, II, III, IV, V, VI, and XII. The highest and lowest entropy values correspond to ices VI and XII, respectively, with a difference of 3.3% between them. The dependence of the entropy on the ice structures has been rationalized by comparing it with structural parameters of the various polymorphs, such as the mean ring size. A particularly good correlation has been found between the configurational entropy and the connective constant derived from self-avoiding walks on the ice networks.
Configuration Entropy Calculations for Complex Compounds Technetium
Recently, the study of technetium complexes is rapidly increasing, due to the benefit of 99mTc complexes (one of Tc nuclear isomers), which are widely used for diagnostics. Study of the structure-stability relationship of Tc complexes based on solid angle has been done by Kung using a Solid Angle Factor Sum (SAS). The SAS is hypothesized to be related to stability. SAS has been used by several researchers either for synthesis or designing the reaction route of the Tc complex formation and predicting the geometry of complex structures. Although the advantages of the SAS were very gratifying, but the model does not have the theoretical basis which is able to explain the correlation of steric parameters to physicochemical properties of complexes especially to those connected to a complex's stability. To improve the SAS model, in this research the model was modified by providing a theoretical basis for SAS. The results obtained from the correlation of the SAS value to the thermodynamic stability parameters of simple complexes show the values to have a similar trend as the standard entropy (S0). The entropy approximation model was created by involving some factors which are not used in Kung's model. Entropy optimization to the bond length (ML) has also been done to several complexes. The calculations of SAS value using the calculated R for more than 100 Tc complexes provide a normalized mean value of 0.8545 ± 0.0851 and have similar curve profiles as those of Kung's model. The entropy value can be obtained by multiplying the natural logarithm of the a priori degeneracy of a certain distribution (Ω) and the Boltzmann constant. The results of Ω and In Ω of the Tc complexes have a narrow range. The results of this research are able to provide a basic concept for the SAS to explain the structure-stability relationship and to improve Kung's model. (author)
The Role of Configurational Entropy in Amorphous Systems
Kirsten A. Graeser
2010-05-01
Full Text Available Configurational entropy is an important parameter in amorphous systems. It is involved in the thermodynamic considerations, plays an important role in the molecular mobility calculations through its appearance in the Adam-Gibbs equation and provides information on the solubility increase of an amorphous form compared to its crystalline counterpart. This paper presents a calorimetric method which enables the scientist to quickly determine the values for the configurational entropy at any temperature and obtain the maximum of information from these measurements.
Absolute Configurations of Zingiberenols Isolated from Ginger (Zingiber officinale) Rhizomes.
Khrimian, Ashot; Shirali, Shyam; Guzman, Filadelfo
2015-12-24
Two stereoisomeric zingiberenols in ginger were identified as (3R,6R,7S)-1,10-bisaboladien-3-ol (2) and (3S,6R,7S)-1,10-bisaboladien-3-ol (5). Absolute configurations were assigned by utilizing 1,10-bisaboladien-3-ol stereoisomers and two gas-chromatography columns: a 25 m Hydrodex-β-6TBDM and 60 m DB-5MS. The C-6 and C-7 absolute configurations in both zingiberenols match those of zingiberene present abundantly in ginger rhizomes. Interestingly, zingiberenol 2 has recently been identified as a male-produced sex pheromone of the rice stink bug, Oebalus poecilus, thus indicating that ginger plants may be a potential source of the sex pheromone of this bug. PMID:26606508
Synthesis and Absolute Configuration of the Diynediol from Psathyrella scobinacea
WU Jianzhong; WU Yikang; JIAN Yajun; ZHANG Yihua
2009-01-01
All the four isomers of Scobidiynediol (hepta-4,6-diyne-2,3-diol), a natural product isolated from white-rot fungus Psathyrella scobinacea, were synthesized using either (R)-or(S)-lactate as the source of chirality. The rela-tive configurations of the diols were established by NOE experiments performed on the cyclic acetonides. The rela-tive as well as absolute configurations of the natural Scobidiynediol was assigned as (2S,3S) through comparison of the optical rotation and 1H NMR data.
Assignment of Absolute Configuration to SCH 351448 via Total Synthesis∫
Lael L. Cheung; Marumoto, Shinji; Anderson, Christopher D.; Rychnovsky, Scott D.
2008-01-01
The synthesis and absolute configuration of SCH 351448, an interesting ionophoric natural product, are reported herein. Mukaiyama aldol-Prins and segment-coupling Prins reactions were employed to construct the constituent tetrahydropyrans of SCH 351448. Efforts to assemble the C2-symmetric core of the natural product by a templated olefin metathesis strategy are described, however, a stepwise fragment assembly was ultimately utilized to complete the target molecule.
Configurational entropy of hydrogen-disordered ice polymorphs
Herrero, Carlos P
2014-01-01
The configurational entropy of several H-disordered ice polymorphs is calculated by means of a thermodynamic integration along a path between a totally H-disordered state and one fulfilling the Bernal-Fowler ice rules. A Monte Carlo procedure based on a simple energy model is used, so that the employed thermodynamic path drives the system from high temperatures to the low-temperature limit. This method turns out to be precise enough to give reliable values for the configurational entropy of different ice phases in the thermodynamic limit (number of molecules N --> infinity). The precision of the method is checked for the ice model on a two-dimensional square lattice. Results for the configurational entropy are given for H-disordered arrangements on several polymorphs, including ices Ih, Ic, II, III, IV, V, VI, and XII. The highest and lowest entropy values correspond to ices VI and XII, respectively, with a difference of 3.3\\% between them. The dependence of the entropy on the ice structures has been rational...
Sequence-Dependent Configurational Entropy Change of DNA upon Intercalation
Kolář, Michal; Kubař, T.; Hobza, Pavel
2010-01-01
Roč. 114, č. 42 (2010), s. 13446-13454. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GA203/06/1727 Institutional research plan: CEZ:AV0Z40550506 Keywords : configurational entropy * dna...ligand binding * molecular dynamic Subject RIV: CC - Organic Chemistry Impact factor: 3.603, year: 2010
Absolute configuration and antimicrobial activity of acylhomoserine lactones.
Pomini, Armando M; Marsaioli, Anita J
2008-06-01
(S)-N-Heptanoylhomoserine lactone is an uncommon acyl odd-chain natural product employed by many Gram-negative bacteria as a signaling substance in chemical communication mechanisms known as quorum sensing. The absolute configuration determination of the metabolite produced by the phytopathogen Pantoea ananatis Serrano is reported herein. As with all other substances of this class, the lactone moiety possesses S configuration, corroborating the hypothesis that it shares the same biosynthetic pathway as the (S)-N-hexanoylhomoserine lactone and also that some LuxI homologues can accept both hexanoyl- and heptanoyl-ACP as precursors. Evaluation of the antimicrobial activity of enantiomeric acylhomoserine lactones against three Gram-positive bacteria (Bacillus cereus, B. subtilis, and Staphylococcus aureus) revealed important features between absolute configuration and antimicrobial activity. The N-heptanoylhomoserine lactone was considerably less active than the 3-oxo derivatives. Surprisingly, non-natural (R)-N-(3-oxo-octanoyl)homoserine lactone was as active as the S enantiomer against B. cereus, while the synthetic racemic product was less active than either enantiomer. PMID:18465897
Configurational entropy in $f(R,T)$ brane models
Correa, R A C
2015-01-01
In this work we investigate generalized theories of gravity in the so-called configurational entropy (CE) context. We show, by means of this information-theoretical measure, that a stricter bound on the parameter of $f(R,T)$ brane models arises from the CE. We find that these bounds are characterized by a valley region in the CE profile, where the entropy is minimal. We argue that the CE measure can open a new role and an important additional approach to select parameters in modified theories of gravitation.
Configurational entropy in f(R,T) brane models
Correa, R.A.C. [Universidade Federal do ABC, CCNH, Santo Andre, Sao Paulo (Brazil); Moraes, P.H.R.S. [ITA, Instituto Tecnologico de Aeronautica, Sao Jose dos Campos, Sao Paulo (Brazil)
2016-02-15
In this work we investigate generalized theories of gravity in the so-called configurational entropy (CE) context. We show, by means of this information-theoretical measure, that a stricter bound on the parameter of f(R, T) brane models arises from the CE. We find that these bounds are characterized by a valley region in the CE profile, where the entropy is minimal. We argue that the CE measure can play a new role and might be an important additional approach to selecting parameters in modified theories of gravitation. (orig.)
Configurational Information as Potentially Negative Entropy: The Triple Helix Model
Loet Leydesdorff
2008-10-01
Full Text Available Configurational information is generated when three or more sources of variance interact. The variations not only disturb each other relationally, but by selecting upon each other, they are also positioned in a configuration. A configuration can be stabilized and/or globalized. Different stabilizations can be considered as second-order variation, and globalization as a second-order selection. The positive manifestations and the negative selections operate upon one another by adding and reducing uncertainty, respectively. Reduction of uncertainty in a configuration can be measured in bits of information. The variables can also be considered as dimensions of the probabilistic entropy in the system(s under study. The configurational information then provides us with a measure of synergy within a complex system. For example, the knowledge base of an economy can be considered as such a synergy in the otherwise virtual (that is, fourth dimension of a regime
Enhanced Configurational Entropy in High-Density Nanoconfined Bilayer Ice
Corsetti, Fabiano; Zubeltzu, Jon; Artacho, Emilio
2016-02-01
A novel kind of crystal order in high-density nanoconfined bilayer ice is proposed from molecular dynamics and density-functional theory simulations. A first-order transition is observed between a low-temperature proton-ordered solid and a high-temperature proton-disordered solid. The latter is shown to possess crystalline order for the oxygen positions, arranged on a close-packed triangular lattice with A A stacking. Uniquely among the ice phases, the triangular bilayer is characterized by two levels of disorder (for the bonding network and for the protons) which results in a configurational entropy twice that of bulk ice.
Martiniani, Stefano; Schrenk, K Julian; Stevenson, Jacob D; Wales, David J; Frenkel, Daan
2016-01-01
We present a numerical calculation of the total number of disordered jammed configurations Ω of N repulsive, three-dimensional spheres in a fixed volume V. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011)10.1103/PhysRevLett.106.245502] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014)10.1103/PhysRevLett.112.098002] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom. PMID:26871142
Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin
2013-01-24
A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557
Redetermined structure, intermolecular interactions and absolute configuration of royleanone
Hoong-Kun Fun
2011-05-01
Full Text Available The structure of the title diterpenoid, C20H28O3, {systematic name: (4bS,8aS-3-hydroxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthrene-1,4-dione} is confirmed [Eugster et al. (1993. Private communication (refcode HACGUN. CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclohexane ring adopts a chair conformation whereas the other cyclohexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intramolecular O—H...O hydrogen bond generates an S(5 ring motif. In the crystal, molecules are linked into chains along [010] by O—H...O hydrogen bonds and weak C—H...O interactions. The packing also features C...O [3.131 (3 Å] short contacts.
Shastry, Abhay; Stafford, Charles A.
2015-12-01
We consider a question motivated by the third law of thermodynamics: Can there be a local temperature arbitrarily close to absolute zero in a nonequilibrium quantum system? We consider nanoscale quantum conductors with the source reservoir held at finite temperature and the drain held at or near absolute zero, a problem outside the scope of linear response theory. We obtain local temperatures close to absolute zero when electrons originating from the finite temperature reservoir undergo destructive quantum interference. The local temperature is computed by numerically solving a nonlinear system of equations describing equilibration of a scanning thermoelectric probe with the system, and we obtain excellent agreement with analytic results derived using the Sommerfeld expansion. A local entropy for a nonequilibrium quantum system is introduced and used as a metric quantifying the departure from local equilibrium. It is shown that the local entropy of the system tends to zero when the probe temperature tends to zero, consistent with the third law of thermodynamics.
Topological Research on Standard Absolute Entropies,S(○)298, for Binary Inorganic Compounds
2008-01-01
For predicting the standard entropy of a binary inorganic compound, two novel connectivity indexes mQ,mG and their converse indexes mQ',mG' based on adjacency matrix of molecular graphs and ionic parameters gi, qi were pro-posed. The qi and gi are defined as qi=(1.1+Zi1.1)/(1.7+ni), gi:(1.4d-Zi)/(0.9+ri+ri-1), where Zi, ni, ri are the charge numbers, the outer electronic shell primary quantum numbers, and the radii of ionic I respectively. The good Quantitative Structure-Property Relationship (QSPR) models for the standard entropies of binary inorganic com-pound can be constructed from 0Q,0Q',1G, and 1G', by using a multivariate linear regression (MLR) method and an artificial neural network (NN) method. The correlation coefficient r, the standard error s, and the average absolute deviation of the MLR model and the NN model are 0.9905, 8.29 J·K-1,mol-1 and 6.48 J·K-1·mol-1, and 0.9960,5.37 J·K-1·mol-1 and 3.90 J·K-1·mol-1, respectively, for 371 binary inorganic compounds (training set). The cross-validation by using the leave-one-out method demonstrates that the MLR model is highly reliable from the point of view of statistics. The correlation coefficients, standard deviations and average absolute deviations of pre-dicted values of the standard entropies of other 185 binary inorganic compounds (test set) are 0.9897, 8.64 J·K-1·mol-1 and 6.84 J·K-1·mol-1, and 0.9957, 5.63 J·K-1·mol-1 and 4.18 J·K-1·mol-1 for the MLR model and the Nnmodel, respectively. The results show that the current method is more effective than literature methods for estimat-ing the standard entropy of a binary inorganic compound. Both MLR and NN methods can provide acceptable mod-els for the prediction of the standard entropies of binary inorganic compounds. The NN model for the standard en-tropies appears to be more reliable than the MLR model.
Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua
2014-01-01
The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein–ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337
Deng, Nan-jie; Zhang, Peng; Cieplak, Piotr; Lai, Luhua
2011-10-20
The binding of proteins and ligands is generally associated with the loss of translational, rotational, and conformational entropy. In many cases, however, the net entropy change due to binding is positive. To develop a deeper understanding of the energetics of entropically driven protein-ligand binding, we calculated the absolute binding free energies and binding entropies for two HIV-1 protease inhibitors Nelfinavir and Amprenavir using the double-decoupling method with molecular dynamics simulations in explicit solvent. For both ligands, the calculated absolute binding free energies are in general agreement with experiments. The statistical error in the computed ΔG(bind) due to convergence problem is estimated to be ≥2 kcal/mol. The decomposition of free energies indicates that, although the binding of Nelfinavir is driven by nonpolar interaction, Amprenavir binding benefits from both nonpolar and electrostatic interactions. The calculated absolute binding entropies show that (1) Nelfinavir binding is driven by large entropy change and (2) the entropy of Amprenavir binding is much less favorable compared with that of Nelfinavir. Both results are consistent with experiments. To obtain qualitative insights into the entropic effects, we decomposed the absolute binding entropy into different contributions based on the temperature dependence of free energies along different legs of the thermodynamic pathway. The results suggest that the favorable entropic contribution to binding is dominated by the ligand desolvation entropy. The entropy gain due to solvent release from binding site appears to be more than offset by the reduction of rotational and vibrational entropies upon binding. PMID:21899337
Configurational Entropy,Diffusivity and Potential Energy Landscape in Liquid Argon
DUAN Yong-Ping; MA Cong-Xiao; LI Jia-Yun; LI Cong; WANG Dan; LI Mei-Li; SUN Min-Hua
2009-01-01
The configurational entropy, diffusion coefficient, dynamics and thermodynamics fragility indices of liquid argon are calculated using molecular dynamics simulations at two densities. The relationship between dynamics and thermodynamics properties is studied. The diffusion coefficient depends linearly on configurational entropy, which is consistent with the hypothesis of Adam-Gibbs. The consistence of dynamics and thermodynamics fragility indices demonstrates that dynamical behaviour is governed by thermodynamics behaviour in glass transition of liquid argon.
Antiausterity activity of arctigenin enantiomers: importance of (2R,3R)-absolute configuration.
Awale, Suresh; Kato, Mamoru; Dibwe, Dya Fita; Li, Feng; Miyoshi, Chika; Esumi, Hiroyasu; Kadota, Shigetoshi; Tezuka, Yasuhiro
2014-01-01
From a MeOH extract of powdered roots of Wikstroemia indica, six dibenzyl-gamma-butyrolactone-type lignans with (2S,3S)-absolute configuration [(+)-arctigenin (1), (+)-matairesinol (2), (+)-trachelogenin (3), (+)-nortrachelogenin (4), (+)-hinokinin (5), and (+)-kusunokinin (6)] were isolated, whereas three dibenzyl-gamma-butyrolactone-type lignans with (2R,3R)-absolute configuration [(-)-arctigenin (1*), (-)-matairesinol (2*), (-)-trachelogenin (3*)] were isolated from Trachelospermum asiaticum. The in vitro preferential cytotoxic activity of the nine compounds was evaluated against human pancreatic PANC-1 cancer cells in nutrient-deprived medium (NDM), but none of the six lignans (1-6) with (2S,3S)-absolute configuration showed preferential cytotoxicity. On the other hand, three lignans (1*-3*) with (2R,3R)-absolute configuration exhibited preferential cytotoxicity in a concentration-dependent manner with PC50 values of 0.54, 6.82, and 5.85 microM, respectively. Furthermore, the effect of (-)- and (+)-arctigenin was evaluated against the activation of Akt, which is a key process in the tolerance to nutrition starvation. Interestingly, only (-)-arctigenin (1*) strongly suppressed the activation of Akt. These results indicate that the (2R,3R)-absolute configuration of (-)-enantiomers should be required for the preferential cytotoxicity through the inhibition of Akt activation. PMID:24660468
A "configurational-entropy-loss" law for the non-Arrhenius relaxation in disordered systems
Wang, Yi-zhen; Zhang, Jin-xiu
2012-01-01
Based on Nowick's self-induced ordering theory, we develop a new configurational-entropy relation to describe the non-Arrhenius temperature(T)-dependent relaxation in disordered systems. Both the configurational-entropy loss and the coupling interaction among relaxing units (RUs) are explicitly introduced in this relation; thus, it offers a novel connection between kinetics and thermodynamics that is different from the Adam-Gibbs (A-G) entropy relation, and it generalizes several well-known currently used relations. The present relation can provide direct and more accurate estimates of (i) the intrinsic activation enthalpy, (ii) the T-evolvement of the systematic configurational entropy loss and (iii) the self-induced ordering temperature Tc, which characterizes the coupling interaction among RUs. Application of the theory to experimental relaxation-time data for typical organic liquids demonstrates its validity.
Roussel, Christian; Del Rio, Alberto; Pierrot-Sanders, Johanna; Piras, Patrick; Vanthuyne, Nicolas
2004-05-28
The review covers examples in which chiral HPLC, as a source of pure enantiomers, has been combined with classical methods (X-ray, vibrational circular dichroism (VCD), enzymatic resolutions, nuclear magnetic resonance (NMR) techniques, optical rotation, circular dichroism (CD)) for the on- or off-line determination of absolute configuration of enantiomers. Furthermore, it is outlined that chiral HPLC, which associates enantioseparation process and classical purification process, opens new perspectives in the classical determination of absolute configuration by chemical correlation or chemical interconversion methods. The review also contains a discussion about the various approaches to predict the absolute configuration from the retention behavior of the enantiomers on chiral stationary phases (CSPs). Some examples illustrate the advantages and limitations of molecular modeling methods and the use of chiral recognition models. The assumptions underlying some of these methods are critically analyzed and some possible emerging new strategies are outlined. PMID:15214673
Kisa, Fumiaki; Yamada, Koji; Miyamoto, Tomofumi; Inagaki, Masanori; Higuchi, Ryuichi
2007-07-01
Enantiomeric pairs of sialic acid, D- and L-NeuAc (N-acetylneuraminic acid), were converted to D- and L-arabinose, respectively, by chemical degradation. Using this method, the absolute configuration of the sialic acid residues, NeuAc and NeuGc (N-glycolylneuraminic acid), in the gangliosides from the sea cucumber Cucumaria echinata was determined to be the D-form. Although naturally occurring sialic acids have been believed to be the D-form on the basis of biosynthetic evidence, this is the first report of the determination of the absolute configuration of the sialic acid residues in gangliosides using chemical methods. PMID:17603199
Configurational entropy of polar glass formers and the effect of electric field on glass transition
Matyushov, Dmitry V.
2016-07-01
A model of low-temperature polar liquids is constructed that accounts for the configurational heat capacity, entropy, and the effect of a strong electric field on the glass transition. The model is based on the Padé-truncated perturbation expansions of the liquid state theory. Depending on parameters, it accommodates an ideal glass transition of vanishing configurational entropy and its avoidance, with a square-root divergent enumeration function at the point of its termination. A composite density-temperature parameter ργ/T, often used to represent combined pressure and temperature data, follows from the model. The theory is in good agreement with the experimental data for excess (over the crystal state) thermodynamics of molecular glass formers. We suggest that the Kauzmann entropy crisis might be a signature of vanishing configurational entropy of a subset of degrees of freedom, multipolar rotations in our model. This scenario has observable consequences: (i) a dynamical crossover of the relaxation time and (ii) the fragility index defined by the ratio of the excess heat capacity and excess entropy at the glass transition. The Kauzmann temperature of vanishing configurational entropy and the corresponding glass transition temperature shift upward when the electric field is applied. The temperature shift scales quadratically with the field strength.
Meirovitch, Hagai
2010-01-01
The commonly used simulation techniques, Metropolis Monte Carlo (MC) and molecular dynamics (MD) are of a dynamical type which enables one to sample system configurations i correctly with the Boltzmann probability, P(i)(B), while the value of P(i)(B) is not provided directly; therefore, it is difficult to obtain the absolute entropy, S approximately -ln P(i)(B), and the Helmholtz free energy, F. With a different simulation approach developed in polymer physics, a chain is grown step-by-step with transition probabilities (TPs), and thus their product is the value of the construction probability; therefore, the entropy is known. Because all exact simulation methods are equivalent, i.e. they lead to the same averages and fluctuations of physical properties, one can treat an MC or MD sample as if its members have rather been generated step-by-step. Thus, each configuration i of the sample can be reconstructed (from nothing) by calculating the TPs with which it could have been constructed. This idea applies also to bulk systems such as fluids or magnets. This approach has led earlier to the "local states" (LS) and the "hypothetical scanning" (HS) methods, which are approximate in nature. A recent development is the hypothetical scanning Monte Carlo (HSMC) (or molecular dynamics, HSMD) method which is based on stochastic TPs where all interactions are taken into account. In this respect, HSMC(D) can be viewed as exact and the only approximation involved is due to insufficient MC(MD) sampling for calculating the TPs. The validity of HSMC has been established by applying it first to liquid argon, TIP3P water, self-avoiding walks (SAW), and polyglycine models, where the results for F were found to agree with those obtained by other methods. Subsequently, HSMD was applied to mobile loops of the enzymes porcine pancreatic alpha-amylase and acetylcholinesterase in explicit water, where the difference in F between the bound and free states of the loop was calculated. Currently
Synthesis and Determination of Absolute Configuration of a Divergent Polyhydroxy Enyne Compound
Zhi Jie XUE; Yuan Chao LI
2005-01-01
Polyhydroxy enyne compound (+)-(1'S, 2R, 3S, 5S, 6S)-5,6-dimethoxy-5, 6-dimethyl-2-(1'-hydroxylpropyl-2-ne)-3-vinyl-1,4-dioxane has been synthesized from D-(-)-tartaric acid. A new chiral center was established by nucleophilic addition with 87% de. The modified Mosher's method was employed to confirm the absolute configuration of 17, which assigned the S-configuration at the new chiral center.
Lassen, Peter Rygaard
2005-01-01
enables establishment of the absolute configuration of (-)-hinokiresinol, which is concluded to be S. A total synthesis and resolution of hinokiresinol has been performed to resolve the conflicting reports of the coupling constant of the vinylic protons of the disubstituted double bond in this molecule...
Ahmed, Safwat A.; Ross, Samir A.; Slade, Desmond; Radwan, Mohamed M.; Khan, Ikhlas A.; Mahmoud A. ElSohly
2008-01-01
Three new cannabichromanone derivatives were isolated from high potency cannabis, along with the known cannabichromanone. Full spectroscopic data, including the use of electronic circular dichroism and Mosher ester analysis to determine the absolute configuration of these compounds, are reported. All isolates were tested for antimicrobial, antimalarial, antileishmanial and anti-oxidant activity.
Highlights: ► Variable atomic valence connectivity index δ′i, Ring parameter H, and variable molecular connectivity index mχ′k were proposed. ► A good four-parameter model can be constructed from H and mχ′k by using the best subsets regression analysis method. ► The MLR method can provide an accurate model for the prediction of the standard absolute entropies of gaseous organic compounds. - Abstract: For predicting the standard absolute entropies of gaseous organic compounds, variable molecular connectivity index mχ′k and Ring parameter H, based on adjacency matrix of molecular graphs, variable atomic valence connectivity index δ′i, and the numbers of chains (cycles) atomic of molecule niR, were proposed. The optimal values of parameters c, a, mi, and y included in the definition of δ′i, and mχ′k can be found by optimization method. When c = 0.91, a = 1.3, and y = 0.22, a good four-parameter model can be constructed from H and mχ′k by using the best subsets regression analysis method for the standard absolute entropies of gaseous organic compounds. The results show that the MLR method can provide an accurate model for the prediction of the standard absolute entropies of gaseous organic compounds.
Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces
We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces
Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces
Lotze, Stephan, E-mail: lotze@amolf.nl; Versluis, Jan [FOM Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam (Netherlands); Olijve, Luuk L. C.; Schijndel, Luuk van; Milroy, Lech G.; Voets, Ilja K. [Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands); Bakker, Huib J., E-mail: bakker@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-11-28
We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.
Shi, Xin-Wei; Lu, Qiang-Qiang; Pescitelli, Gennaro; Ivšić, Trpimir; Zhou, Jun-Hui; Gao, Jin-Ming
2016-02-01
A novel sesquiterpenoid dimer, named multistalide C (1), together with two known congeners, shizukaols C (2) and D (3), was isolated from the whole plant of Chloranthus japonicus Sieb. The structures of compounds 1-3 were elucidated by extensive HR-ESI-MS, 1D, and 2D NMR spectroscopic analysis. Compounds 1-3 exhibited significant toxic effects on brine shrimp larvae (Artemia salina). The absolute configuration of 1 was established by CD/TDDFT calculations. The related compound chlorahololide A was also reinvestigated. The previous assignment of the absolute configuration of chlorahololide A and several related sesquiterpenoid dimers, based on an incorrect application of the exciton chirality method, is criticized. PMID:26708509
Pan, Saiyong; Gao, Beiling; Hu, Jialei; Xuan, Jun; Xie, Hujun; Ding, Hanfeng
2016-01-18
The first enantioselective total synthesis of (+)-steenkrotin A has been achieved in 18 steps and 4.2 % overall yield. The key features of the strategy entail a Rh-catalyzed O-H bond insertion followed by an intramolecular carbonyl-ene reaction, two sequential SmI2 -mediated Ueno-Stork and ketyl-olefin cyclizations, and a cascade intramolecular aldol condensation/vinylogous retro-aldol/aldol process with inversion of the relative configuration at the C7 position. The absolute configuration of (+)-steenkrotin A was determined based on the stepwise construction of the stereocenters during the total synthesis. PMID:26660855
Asymmetric Synthesis and Absolute Configuration Assignment of a New Type of Bedaquiline Analogue
Chang-Jiang Qiao; Xiao-Kui Wang; Fei Xie; Wu Zhong; Song Li
2015-01-01
Bedaquiline is the first FDA-approved new chemical entity to fight multidrug-resistant tuberculosis in the last forty years. Our group replaced the quinoline ring with a naphthalene ring, leading to a new type of triarylbutanol skeleton. An asymmetric synthetic route was established for our bedaquiline analogues, and the goal of assigning their absolute configurations was achieved by comparison of experimental and calculated electronic circular dichroism spectra, and was confirmed by the comb...
Debie, Elke
2009-01-01
Vibrational Circular Dichroism (VCD) is no longuer a curious novelty in the field of molecular spectroscopy as VCD spectrometers are commercially available as well as the algorithms to calculate the spectra, which are implemented in various software packages. This makes VCD routinely applicable for the determination of absolute configurations. The VCD technique is gaining interest in mainly pharmaceutical industry and the technique also has been accepted by regulatory agencies (e.g. FDA) as a...
Wu, Zhaodi; Lai, Yongji; Zhou, Lei; Wu, Ye; Zhu, Hucheng; Hu, Zhengxi; Yang, Jing; Zhang, Jinwen; Wang, Jianping; Luo, Zengwei; Xue, Yongbo; Zhang, Yonghui
2016-01-01
Eight pairs of enantiomeric neolignans, norlignans, and sesquineolignans (1a/1b-8a/8b), together with five known neolignans (9a/9b and 10-12), have been isolated from 70% acetone extract of the whole plants of Phyllanthus glaucus Wall. (Euphorbiaceae). The racemic or partial racemic mixtures were successfully separated by chiral HPLC using different types of chiral columns with various mobile phases. Their structures were elucidated on the basis of extensive spectroscopic data. The absolute configurations of 2a/2b were determined by computational analysis of their electronic circular dichroism (ECD) spectrum, and the absolute configurations of other isolates were ascertained by comparing their experimental ECD spectra and optical rotation values with those of structure-relevant compounds reported in literatures. Compounds 4a/4b featured unique sesquineolignan skeletons with a novel 7-4'-epoxy-8'-8''/7'-2'' scaffold, consisting of an aryltetrahydronaphthalene and a dihydrobenzofuran moiety. The planar structures of compounds 2, 3, 7, and 8 were documented previously; however, their absolute configurations were established for the first time in this study. The antioxidant activities of 1a/1b-8a/8b were evaluated using DPPH free radical scavenging assay, and the results demonstrated that compounds 1b and 3b showed potent DPPH radical scavenging activities with IC50 values of 5.987 ± 1.212 and 9.641 ± 0.865 μg/mL, respectively. PMID:27126373
Fleck, Markus; Polyansky, Anton A; Zagrovic, Bojan
2016-04-12
Accurate estimation of configurational entropy from the in silico-generated biomolecular ensembles, e.g., from molecular dynamics (MD) trajectories, is dependent strongly on exhaustive sampling for physical reasons. This, however, creates a major computational problem for the subsequent estimation of configurational entropy using the Maximum Information Spanning Tree (MIST) or Mutual Information Expansion (MIE) approaches for internal molecular coordinates. In particular, the available software for such estimation exhibits serious limitations when it comes to molecules with hundreds or thousands of atoms, because of its reliance on a serial program architecture. To overcome this problem, we have developed a parallel, hybrid MPI/openMP C++ implementation of MIST and MIE, called PARENT, which is particularly optimized for high-performance computing and provides efficient estimation of configurational entropy in different biological processes (e.g., protein-protein interactions). In addition, PARENT also allows for a detailed mapping of intramolecular allosteric networks. Here, we benchmark the program on a set of 1-μs-long MD trajectories of 10 different protein complexes and their components, demonstrating robustness and good scalability. A direct comparison between MIST and MIE on the same dataset demonstrates a superior convergence behavior for the former approach, when it comes to total simulation length and configurational-space binning. PMID:26989950
Wu, Zhaodi; Lai, Yongji; Zhou, Lei; Wu, Ye; Zhu, Hucheng; Hu, Zhengxi; Yang, Jing; Zhang, Jinwen; Wang, Jianping; Luo, Zengwei; Xue, Yongbo; Zhang, Yonghui
2016-01-01
Eight pairs of enantiomeric neolignans, norlignans, and sesquineolignans (1a/1b–8a/8b), together with five known neolignans (9a/9b and 10–12), have been isolated from 70% acetone extract of the whole plants of Phyllanthus glaucus Wall. (Euphorbiaceae). The racemic or partial racemic mixtures were successfully separated by chiral HPLC using different types of chiral columns with various mobile phases. Their structures were elucidated on the basis of extensive spectroscopic data. The absolute configurations of 2a/2b were determined by computational analysis of their electronic circular dichroism (ECD) spectrum, and the absolute configurations of other isolates were ascertained by comparing their experimental ECD spectra and optical rotation values with those of structure-relevant compounds reported in literatures. Compounds 4a/4b featured unique sesquineolignan skeletons with a novel 7-4′-epoxy-8′-8′′/7′-2′′ scaffold, consisting of an aryltetrahydronaphthalene and a dihydrobenzofuran moiety. The planar structures of compounds 2, 3, 7, and 8 were documented previously; however, their absolute configurations were established for the first time in this study. The antioxidant activities of 1a/1b–8a/8b were evaluated using DPPH free radical scavenging assay, and the results demonstrated that compounds 1b and 3b showed potent DPPH radical scavenging activities with IC50 values of 5.987 ± 1.212 and 9.641 ± 0.865 μg/mL, respectively. PMID:27126373
Configurational entropy as a bounding of Gauss-Bonnet braneworld models
Correa, R A C; Dutra, A de Souza; de Paula, W; Frederico, T
2016-01-01
Configurational entropy has been revealed as a reliable method for constraining some parameters of a given model [Phys. Rev. D \\textbf{92} (2015) 126005, Eur. Phys. J. C \\textbf{76} (2016) 100]. In this letter we calculate the configurational entropy in Gauss-Bonnet braneworld models. Our results restrict the range of acceptability of the Gauss-Bonnet scalar values. In this way, the information theoretical measure in Gauss-Bonnet scenarios opens a new window to probe situations where the additional parameters, responsible for the Gauss-Bonnet sector, are arbitrary. We also show that such an approach is very important in applications that include p and Dp-branes and various superstring-motivated theories.
Asymmetric Synthesis and Absolute Configuration Assignment of a New Type of Bedaquiline Analogue
Chang-Jiang Qiao
2015-12-01
Full Text Available Bedaquiline is the first FDA-approved new chemical entity to fight multidrug-resistant tuberculosis in the last forty years. Our group replaced the quinoline ring with a naphthalene ring, leading to a new type of triarylbutanol skeleton. An asymmetric synthetic route was established for our bedaquiline analogues, and the goal of assigning their absolute configurations was achieved by comparison of experimental and calculated electronic circular dichroism spectra, and was confirmed by the combined use of circular dichroism and NMR spectroscopy.
Asymmetric Synthesis and Absolute Configuration Assignment of a New Type of Bedaquiline Analogue.
Qiao, Chang-Jiang; Wang, Xiao-Kui; Xie, Fei; Zhong, Wu; Li, Song
2015-01-01
Bedaquiline is the first FDA-approved new chemical entity to fight multidrug-resistant tuberculosis in the last forty years. Our group replaced the quinoline ring with a naphthalene ring, leading to a new type of triarylbutanol skeleton. An asymmetric synthetic route was established for our bedaquiline analogues, and the goal of assigning their absolute configurations was achieved by comparison of experimental and calculated electronic circular dichroism spectra, and was confirmed by the combined use of circular dichroism and NMR spectroscopy. PMID:26690407
Burgueño-Tapia, Eleuterio; Joseph-Nathan, Pedro
2015-10-01
Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented. PMID:26669125
Junior, Fernando M S; Covington, Cody L; de Albuquerque, Ana Carolina F; Lobo, Jonathas F R; Borges, Ricardo M; de Amorim, Mauro B; Polavarapu, Prasad L
2015-11-25
(-)-Centratherin is a bioactive sesquiterpenoid lactone, whose absolute configuration (AC) was not established, but has been proposed based on those of germacrane precursors. To verify this proposal, the experimental electronic circular dichroism (ECD), electronic dissymmetry factor (EDF), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and vibrational dissymmetry factor (VDF) spectra of (-)-centratherin have been analyzed with the corresponding density functional theoretical predictions. These analyses suggest the AC of naturally occurring (-)-centratherin to be (6R,7R,8S,10R,2'Z). PMID:26565920
Mehta, Goverdhan; Sreenivas, K.
2002-01-01
An enantioselective total synthesis of (−)-sulcatine G 4 from the readily available (+)-diquinane diol 6 has been accomplished. This leads to the establishment of the absolute configuration of the natural product (+)-sulcatine G as 1.
Absolute configuration of 2-sec-butyl-4,5-dihydrothiazole in male mouse urine.
Cavaggioni, Andrea; Mucignat-Caretta, Carla; Zagotto, Giuseppe
2003-11-01
The absolute configuration of 2-sec-butyl-4,5-dihydrothiazole (DHT) in urine of adult male mice was determined through chiral trifluoroacetyl derivative capillary chromatography by comparing the retention time with synthetic standards. (S)-DHT was extracted from fresh urine, while neither (R)-DHT nor the racemization of (S)-DHT were detected. We can conclude that DHT in urine possesses the S configuration, although we cannot exclude a minor component in the R configuration. (S)-DHT was then characterized for binding to the complex of major urinary proteins of male mouse urine (MUP) and for a behavioral response, the competitive scent marking behavior (countermarking). The binding constant of (S)-DHT to MUP (determined by competitive displacement) was 8.2 +/- 0.6 microM (mean +/- SD) and was 10.5 +/- 0.6 microM for R-DHT, thus excluding a relevant difference in binding. (S)-DHT modified countermarking in a peculiar way. Male mice were slow in countermarking urinary spots streaked 2 days earlier and on top of which (S)-DHT was added shortly before the test. This response was not seen when adding (S)-DHT to freshly streaked urinary spots or to clean paper. Unlike (S)-DHT, (R)-DHT prompted countermarking rather than delaying it. We can further conclude that (S)-DHT in male mouse urine is an aversive chemosignal for countermarking. PMID:14654447
Merten, Christian; Smyrniotopoulos, Vangelis; Tasdemir, Deniz
2015-11-21
Correct assignment of the stereogenic centers of highly flexible linear diterpenes (LDs) is challenging. Herein we report the first application of VCD spectroscopy for the absolute configuration determination of LDs of algal origin and provide experimental and computational procedures, such as a fragmentation approach, which will facilitate the use of VCD spectroscopy for configuration assignments of LDs. PMID:26399505
Determination of absolute configuration using ab initio calculation of optical rotation.
Stephens, P J; Devlin, F J; Cheeseman, J R; Frisch, M J; Bortolini, O; Besse, P
2003-01-01
Ab initio Density Functional Theory (DFT) calculations of transparent spectral region, discrete frequency specific rotations were used to assign the absolute configurations (ACs) of: 1, 2H-naphtho[1,8-bc]thiophene 1-oxide; 2, m-F-phenyl glycidic acid methyl ester; 3, o-Br-phenyl glycidic acid methyl ester; 4, p-CH(3)-phenyl glycidic acid methyl ester; 5, 2-(1-hydroxyethyl)-chromen-4-one; and 6, 6-Br-2-(1-hydroxyethyl)-chromen-4-one. The ACs of 5 and 6 were previously determined via X-ray crystallography to be: 5, R(-)/S(+); 6, R(+)/S(-). The ACs obtained using [alpha](D) are the same for both 5 and 6: R(+)/S(-). We conclude that the previously reported AC of 5 is incorrect. PMID:12884375
Bentley, Keith W; Zhang, Peng; Wolf, Christian
2016-02-01
High-throughput experimentation (HTE) has emerged as a widely used technology that accelerates discovery and optimization processes with parallel small-scale reaction setups. A high-throughput screening (HTS) method capable of comprehensive analysis of crude asymmetric reaction mixtures (eliminating product derivatization or isolation) would provide transformative impact by matching the pace of HTE. We report how spontaneous in situ construction of stereodynamic metal probes from readily available, inexpensive starting materials can be applied to chiroptical chemosensing of the total amount, enantiomeric excess (ee), and absolute configuration of a wide variety of amines, diamines, amino alcohols, amino acids, carboxylic acids, α-hydroxy acids, and diols. This advance and HTS potential are highlighted with the analysis of 1 mg of crude reaction mixtures of a catalytic asymmetric reaction. This operationally simple assay uses a robust mix-and-measure protocol, is amenable to microscale platforms and automation, and provides critical time efficiency and sustainability advantages over traditional serial methods. PMID:26933684
Pomini, Armando M; Cruz, Pedro L R; Gai, Cláudia; Araújo, Welington L; Marsaioli, Anita J
2009-12-01
The acyl-homoserine lactones (acyl-HSLs) produced by Methylobacterium mesophilicum isolated from orange trees infected with the citrus variegated chlorosis (CVC) disease have been studied, revealing the occurrence of six long-chain acyl-HSLs, i.e., the saturated homologues (S)-N-dodecanoyl (1) and (S)-N-tetradecanoyl-HSL (5), the uncommon odd-chain N-tridecanoyl-HSL (3), the new natural product (S)-N-(2E)-dodecenoyl-HSL (2), and the rare unsaturated homologues (S)-N-(7Z)-tetradecenoyl (4) and (S)-N-(2E,7Z)-tetradecadienyl-HSL (6). The absolute configurations of all HSLs were determined as 3S. Compounds 2 and 6 were synthesized for the first time. Antimicrobial assays with synthetic acyl-HSLs against Gram-positive bacterial endophytes co-isolated with M. mesophilicum from CVC-infected trees revealed low or no antibacterial activity. PMID:19919062
Total synthesis and absolute configuration assignment of MRSA active garcinol and isogarcinol.
Socolsky, Cecilia; Plietker, Bernd
2015-02-01
A short total synthesis of (±)-garcinol and (±)-isogarcinol, two endo-type B PPAPs with reported activity against methiciline resistant Staphylococcus aureus (MRSA), is presented. The separation of framework-constructing from framework-decorating steps and the application of two highly regio- and stereoselective Pd-catalysed allylations, that is, the Pd-catalysed decarboxylative Tsuji-Trost allylation and the diastereoselective Pd-catalysed allyl-allyl cross-coupling, are key elements that allowed the total synthesis to be accomplished within 13 steps starting from acetylacetone. After separation of the enantiomers the absolute configurations of the four natural products (i.e., (-)-garcinol, (+)-guttiferone E (i.e., ent-garcinol), (-)-isogarcinol, and (+)-isoxanthochymol (i.e., ent-isogarcinol)) were assigned based on ECD spectroscopy. PMID:25537962
Synthesis, Crystal Structure and Absolute Configuration of(+)-O-Phenyl Cyclophosphorodiamidate
何可; 周正洪; 李康应; 赵国锋; 唐除痴; 王宏根
2003-01-01
The title compound, (+)-O-phenyl cyclophosphorodiamidate (C28H33N2O2P, Mr = 460.53), has been synthesized and characterized by 31P NMR, 1H NMR and elemental analysis. X-ray diffraction analysis at 273(2) K indicates that it belongs to orthorhombic system, space group P212121 with a = 11.518(4), b = 13.449(4), c = 16.539(5)(A°), V = 2562(1)(A°)3, Z = 4, Dc = 1.194 g/cm3, F(000) = 984 and μ(MoKα) = 0.134 mm-1. The structure parameters were refined by full-matrix least-squares on F2 to R = 0.0459 and wR = 0.0640. The flack x parameter is 0.03(10), and the absolute configuration of the phosphorus atom in the title compound is S.
Structure and Absolute Configuration of Ginkgolide B Characterized by IR- and VCD Spectroscopy
Andersen, Niels Højmark; Christensen, N.J.; Lassen, Peter Rygaard; Freedman, T.B.N.; Nafie, L.A.; Stromgaard, K.; Hemmingsen, L.
2010-01-01
Experimental and calculated (B3LYP/6-31G(d)) vibrational Circular dichroism (VCD) and IR spectra are compared, illustrating that the structure and absolute configuration of ginkgolide B (GB) may be characterized directly in solution. A conformational search for GB using MacroModel and subsequent......, displaying different intramolecular hydrogen bonding. Differences between measured and calculated IR and VCD spectra for GB at certain wavenumbers are rationalized in terms of interactions with solvent, intermolecular GB-GB interactions, and the potential presence of more than one conformer. This is the...... first detailed investigation of the spectroscopic fingerprint region (850-1300 cm(-1)) of the natural product GB employing infrared absorption and VCD spectroscopy. Chirality 22:217-223, 2010....
Absolute Configuration Determination of Azulenyl Diols Isolated From Asymmetric Pinacol Coupling.
Dragu, Eugenia Andreea; Naubron, Jean-Valere; Hanganu, Anamaria; Razus, Alexandru C; Nica, Simona
2015-11-01
A convenient enantioselective approach for the pinacol coupling of 1-acetylazulene involving easily accessible (R)- or (S)-BINOLs as chiral additive is reported. This supposes the preformation of the chiral titanium-BINOL complex in 1:2 ratio and subsequent reduction with zinc when, 2,3-di(azulen-1-yl)butane-2,3-diol can be isolated in around 60% enantiomeric excess. The absolute configuration of the isolated enantiomers was assigned by comparison of the experimental and Boltzmann-weighted calculated VCD and ECD spectra and assigned as (+)-(2S;3S)-di(azulen-1-yl)butane-2,3-diol. Chirality 27:826-834, 2015. © 2015 Wiley Periodicals, Inc. PMID:26364568
Lefevre, Sara; Héloin, Alexandre; Pitrat, Delphine; Mulatier, Jean-Christophe; Vanthuyne, Nicolas; Jean, Marion; Dutasta, Jean-Pierre; Guy, Laure; Martinez, Alexandre
2016-04-15
New host compounds combining a cyclotriveratrylene (CTV) unit and three binaphthol moieties have been synthesized enantiomerically and diastereomerically pure. The use of a chemical correlation allows for the assignment of their absolute configuration. The energy barrier of epimerization was measured, suggesting that no intramolecular hydrogen bonding occurs between the hydroxyl groups of the binaphthols. These open-shell host compounds were then tested in the recognition of carbohydrates; a preferential binding of mannose toward glucose was observed, and good diastereoselectivities were reached (up to 1:10). This recognition of sugar derivatives by open-shell CTV-based host compounds is unprecedented and opens up the way for a wider use of this easily accessible class of molecules as chiral sensors. PMID:27010215
Wolkenstein, Klaus; Sun, Han; Falk, Heinz; Griesinger, Christian
2015-10-28
Complete structural elucidation of natural products is often challenging due to structural complexity and limited availability. This is true for present-day secondary metabolites, but even more for exceptionally preserved secondary metabolites of ancient organisms that potentially provide insights into the evolutionary history of natural products. Here, we report the full structure and absolute configuration of the borolithochromes, enigmatic boron-containing pigments from a Jurassic putative red alga, from samples of less than 50 μg using microcryoprobe NMR, circular dichroism spectroscopy, and density functional theory calculations and reveal their polyketide origin. The pigments are identified as spiroborates with two pentacyclic sec-butyl-trihydroxy-methyl-benzo[gh]tetraphen-one ligands and less-substituted derivatives. The configuration of the sec-butyl group is found to be (S). Because the exceptional benzo[gh]tetraphene scaffold is otherwise only observed in the recently discovered polyketide clostrubin from a present-day Clostridium bacterium, the Jurassic borolithochromes now can be unambiguously linked to the modern polyketide, providing evidence that the fossil pigments are almost originally preserved secondary metabolites and suggesting that the pigments in fact may have been produced by an ancient bacterium. The borolithochromes differ fundamentally from previously described boronated polyketides and represent the first boronated aromatic polyketides found so far. Our results demonstrate the potential of microcryoprobe NMR in the analysis of previously little-explored secondary metabolites from ancient organisms and reveal the evolutionary significance of clostrubin-type polyketides. PMID:26443920
Jusuf, Sutjano; Loll, Patrick J; Axelsen, Paul H
2003-04-01
Oligomerization and ligand binding are thermodynamically cooperative processes in many biochemical systems, and the mechanisms giving rise to cooperative behavior are generally attributed to changes in structure. In glycopeptide antibiotics, however, these cooperative processes are not accompanied by significant structural changes. To investigate the mechanism by which cooperativity arises in these compounds, fully solvated molecular dynamics simulations and quasiharmonic normal-mode analysis were performed on chloroeremomycin, vancomycin, and dechlorovancomycin. Configurational entropies were derived from the vibrational modes recovered from ligand-free and ligand-bound forms of the monomeric and dimeric species. Results indicate that both ligand binding and dimerization incur an entropic cost as vibrational activity in the central core of the antibiotic is shifted to higher frequencies with lower amplitudes. Nevertheless, ligand binding and dimerization are cooperative because the entropic cost of both processes occurring together is less than the cost of these processes occurring separately. These reductions in configurational entropy are more than sufficient in magnitude to account for the experimentally observed cooperativity between dimerization and ligand binding. We conclude that biochemical cooperativity can be mediated through changes in vibrational activity, irrespective of the presence or absence of concomitant structural change. This may represent a general mechanism of allostery underlying cooperative phenomena in diverse macromolecular systems. PMID:12656635
The sesquiterpenoid nootkatone and the absolute configuration of a dibromo derivative.
Sauer, Anne M; Fronczek, Frank R; Zhu, Betty C R; Crowe, William E; Henderson, Gregg; Laine, Roger A
2003-05-01
Nootkatone, or (4R,4aS,6R)-4,4a,5,6,7,8-hexahydro-4,4a-dimethyl-6-(1-methylethenyl)naphthalen-2(3H)-one, C(15)H(22)O, a sesquiterpene with strong repellent properties against Formosan subterranean termites and other insects, has the valencene skeleton. The dibromo derivative (1S,3R,4S,4aS,6R,8aR)-1,3-dibromo-6-isopropyl-4,4a-dimethyl-1,2,3,4,5,6,7,8-octahydronaphthalen-2-one, C(15)H(24)Br(2)O, has two independent molecules in the asymmetric unit, which differ in the rotation of the isopropyl group with respect to the main skeleton. The C-Br distances are in the range 1.950 (4)-1.960 (4) A. Both independent molecules form zigzag chains, with very short intermolecular carbonyl-carbonyl interactions, having the perpendicular motif and O...C distances of 2.886 (6) and 2.898 (6) A. These chains are flanked by intermolecular Br...Br interactions of distances in the range 4.067 (1)-4.218 (1) A. The absolute configuration of the dibromo derivative was determined, from which that of nootkatone was inferred. PMID:12743407
蔡觉晓; 周正洪; 唐除痴; 王宏根
2002-01-01
The title compound (+)-((-hydroxybenzyl)phenylphosphinic acid (C13H13O3P, Mr = 248.20) has been synthesized and characterized by 31P NMR, 1H NMR and elemental analysis. X-ray diffraction analysis at 293(2) K indicates that the compound belongs to monoclinic system, space group C2 with cell parameters: a = 23.560(8), b = 6.947(2), c = 7.854(3) (A。）, β = 91.273(6)°, V = 1285.2(7) (A。）3, Z = 4, Dc = 1.283 g/cm3, F(000) = 520 and ((MoK() = 0.207 mm-1. The number of independent reflections amounts to 1991, of which 1507 are observed reflections. The crystal structure has been determined by direct methods (SHELXL-97). The structure parameters are refined by full-matrix least-squares on F2 to R = 0.0437 and wR = 0.0893. The flack x parameter is - 0.0001. The absolute configuration of the (-carbon in the title compound is S.
Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.
Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok
2011-05-01
The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts. PMID:21754362
Fristrup, Peter; Lassen, Peter Rygaard; Tanner, David Ackland;
2008-01-01
obtained using DFT/B3LYP calculations, and the differences between experiment and theory are discussed. The absolute configuration at the benzylic position was established as being (R), (S) and (R) for the cis, trans and geminal dimethylsubstituted phenyloxiranes, respectively. In all three cases the...
The iso-structural viscosity, configurational entropy and fragility of oxide liquids
Yue, Yuanzheng
2009-01-01
This paper describes how the fragility of a liquid is linked to the ratio between the energy barrier (Eeq) for the equilibrium viscous behavior and that (Eiso) for the non-equilibrium iso-structural viscous behavior. Using the concept of iso-structural viscosity, two functions describing the...... variation of the configurational entropy (Sc) with temperature (T) are obtained from the Avramov-Milchev (AM) and the Vogel-Fulcher- Tammann (VFT) viscosity equations, respectively. The two Sc(T) functions exhibit different relations to the liquid fragility. The AM Sc(T) function is a power function with...... VFT equation is not only a dynamical, but also a thermodynamic model. It is proved that for oxide liquids, the VFT equation describes viscosity data better than the AM equation, provided the pre-exponential factor η0 is fixed to a generally accepted value, e.g., 10-3.5 Pa s....
Santoro, Ernesto; Mazzeo, Giuseppe; Petrovic, Ana G; Cimmino, Alessio; Koshoubu, Jun; Evidente, Antonio; Berova, Nina; Superchi, Stefano
2015-08-01
The absolute configuration (AC) of the plant phytotoxin inuloxin A, produced by Inula viscosa, and of the fungal phytotoxin seiricardine A, obtained from Seiridium fungi, pathogen for cypress, has been determined by experimental measurements and theoretical simulations of chiroptical properties of three related methods, namely, Optical Rotatory Dispersion (ORD), Electronic Circular Dichroism (ECD), and Vibrational Circular Dichroism (VCD). Computational prediction by Density Functional Theory (DFT) of VCD spectra and by Time-dependent DFT (TDDFT) of ORD and ECD spectra allowed to assign (7R,8R,10S) AC to naturally occurring (+)-inuloxin A. In the case of compound (-)-seiricardine A, which lacks useful for the analysis UV-Vis absorption, and thus provides a hardly detectable ECD spectrum and quite low ORD values, an introduction of a suitable chromophore by chemical derivatization was performed. The corresponding derivative, 2-O-p-bromobenzoate ester, gave rise to an intense ECD spectrum and higher ORD and VCD values. The comparison of computed spectra with the experimental ones allowed to assign (1S,2R,3aS,4S,5R,7aS) AC to (-)-2-O-p-bromobenzoate ester of seiricardine A and then to (-)-seiricardine A. This study further supports a recent trend of concerted application of more than a single chiroptical technique toward an unambiguous assignment of AC of flexible and complex natural products. Moreover, the use of chemical derivatization, with insertion of suitable chromophoric moieties has allowed to treat also UV-Vis transparent molecules by ECD and ORD spectroscopies. PMID:25817835
Evidente, Marco; Santoro, Ernesto; Petrovic, Ana G; Cimmino, Alessio; Koshoubu, Jun; Evidente, Antonio; Berova, Nina; Superchi, Stefano
2016-10-01
The absolute configuration of phytotoxins inuloxins B and C, produced by Inula viscosa, and with potential herbicidal activity for the management of parasitic plants, has been determined by Time-dependent density functional theory computational prediction of electronic circular dichroism and optical rotatory dispersion spectra. The inuloxin B has been converted to its 5-O-acetyl derivative, which due to its more constrained conformational features facilitated the computational analysis of its chiroptical properties. The analysis based on experimental and computed data led to assignment of absolute configuration to naturally occurring (+)-inuloxin B and (-)-inuloxin C as (7R,8R,10S,11S) and (5S,7S,8S,10S), respectively. PMID:27498046
Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker
2013-05-16
Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here
Lauridsen, A.; Cornett, Claus; Christensen, S. B.
1991-01-01
alpha-beta-Unsaturated esters of allylic alcohols have been shown to exhibit exciton coupling by circular dichroic spectroscopy. This coupling permits the establishment of the absolute configuration. The method was used to prove the absolute configuration at C-2 of archangelolide. Detailed NMR sp...... spectral studies of the prepared model structures may be used as a reference for stereoisomeric guaianolides....
Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.
2009-02-01
Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.
Network Entropy Based on Topology Configuration and Its Computation to Random Networks
LI Ji; WANG Bing-Hong; WANG Wen-Xu; ZHOU Tao
2008-01-01
A definition of network entropy is presented, and as an example, the relationship between the value of network entropy of ER network model and the connect probability p as well as the total nodes N is discussed. The theoretical result and the simulation result based on the network entropy of the ER network are in agreement well with each other. The result indicated that different from the other network entropy reported before, the network entropy defined here has an obvious difference from different type of random networks or networks having different total nodes. Thus, this network entropy may portray the characters of complex networks better. It is also pointed out that, with the aid of network entropy defined, the concept of equilibrium networks and the concept of non-equilibrium networks may be introduced, and a quantitative measurement to describe the deviation to equilibrium state of a complex network is carried out.
Bergmann, Jan; Lassen, Stephan; Prange, Andreas [GKSS Research Center Geesthacht, Institute for Coastal Research, Max-Planck Strasse, 21502, Geesthacht (Germany)
2004-03-01
A fast and sensitive method was developed for the determination of the absolute configuration of selenomethionine. The enantiomers of selenomethionine were converted into diastereomeric isoindole derivatives by reaction with o-phthaldialdehyde and N-isobutyryl-l-cysteine. This easy-to-handle reaction proceeds quantitatively in a few minutes at room temperature. Separation and detection of the diastereomers was achieved by reversed-phase high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (RP-HPLC/ICP-MS) using a conventional C18 reversed-phase column. Detection limits of about 4 {mu}g L{sup -1} were obtained. The method was applied to the determination of the configuration of selenomethionine extracted from antarctic krill, which turned out to possess the l-configuration. (orig.)
Youichi Takata
2010-04-01
Full Text Available In order to clarify the adsorption behavior of cationic surfactants on the air/aqueous electrolyte solution surface, we derived the theoretical equation for the surface tension. The equation includes the electrical work required for charging the air/water surface and the work attributable to the configurational entropy in the adsorbed film. By fitting the equation to the experimental data, we determined the binding constant between adsorbed surfactant ion and counterion, and found that the bromide ions, rather than the chloride ions, are preferentially adsorbed by the air/water surface. Furthermore, it was suggested that the contribution of configurational entropy to the surface tension is predominant in the presence of electrolytes because of the increase in the surface density of surfactant molecules associated with decreasing the repulsive interaction between their hydrophilic groups.
Development of methodology to assign absolute configurations using vibrational circular dichroism
Kuppens, T
2006-01-01
De kennis van de 3D structuur van actieve bestanddelen van chirale medicijnen is zeer belangrijk, aangezien stereo-isomeren dikwijls een verschillende activiteit vertonen. Er zijn meerdere technieken beschikbaar om deze Absolute Configuratie te bepalen (eenkristal x-straal diffractie bijv.). Een nieuwe methode die sterk in opmars is en heel wat voordelen biedt is gebaseerd op het vibrationeel circulair dichroïsme (VCD). Het VCD fenomeen is een gevolg van de optische activiteit van een medium ...
Banerjee, Atreyee; Nandi, Manoj Kumar; Sastry, Srikanth; Bhattacharyya, Sarika Maitra
2016-01-01
In this paper, we present a study of supercooled liquids interacting with the Lennard Jones (LJ) potential and the corresponding purely repulsive (Weeks-Chandler-Andersen or WCA) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs (AG) relation, we show that the difference in the dynamics of these two syst...
Youichi Takata; Hiroaki Tagashira; Atsushi Hyono; Hiroyuki Ohshima
2010-01-01
In order to clarify the adsorption behavior of cationic surfactants on the air/aqueous electrolyte solution surface, we derived the theoretical equation for the surface tension. The equation includes the electrical work required for charging the air/water surface and the work attributable to the configurational entropy in the adsorbed film. By fitting the equation to the experimental data, we determined the binding constant between adsorbed surfactant ion and counterion, and found that the br...
Jiang, Ren-Wang; Lane, Amy L.; Mylacraine, Lauren; Hardcastle, Kenneth I.; Fairchild, Craig R.; Aalbersberg, William; Hay, Mark E.; Kubanek, Julia
2012-01-01
Cytotoxicity-guided fractionation of the green macroalga Tydemania expeditionis led to isolation of four sulfate-conjugated triterpenoids including one new lanostane-type triterpenoid disulfate, lanosta-8-en-3,29-diol-23-oxo-3,29-disodium sulfate (1), and three known cycloartane-type triterpenoid disulfates, cycloartan-3,29-diol-23-one 3,29-disodium sulfate (2), cycloart-24-en-3,29-diol-23-one 3,29-disodium sulfate (3), and cycloartan-3,23,29-triol 3,29-disodium sulfate (4). Extensive 1D and 2D NMR analyses in combination with X-ray crystallography established the structure and absolute configuration of 1 and allowed determination of the absolute configurations of 2–4 with a revision of previously assigned configuration at C-5. Each natural product was moderately cytotoxic in tumor cell and invertebrate toxicity assays. Of the natural products, only 4 exhibited significant antifungal activity at whole-tissue natural concentrations against the marine pathogen Lindra thalassiae. Comparison of the biological activities of natural products with their desulfated derivatives indicated that sulfation does not appear to confer cytotoxicity or antifungal activity. PMID:18763828
Kuwada, Takeshi; Fukui, Miyako; Hata, Toshiyuki; Choshi, Tominari; Nobuhiro, Junko; Ono, Yukio; Hibino, Satoshi
2003-01-01
The specific optical rotations of (R)-oxopropaline D calculated by two ab initio MO methods were +52+/-31 degrees and +61+/-29 degrees, respectively, and (+)-oxopropaline D (3) was presumed to have an R-configuration. On the basis of this theoretical result, the reaction of 1-litio-beta-carboline with (R)-glyceraldehyde acetonide followed by oxidation with MnO(2) gave (R)-oxopropaline D acetonide (4a), which was consistent with the previously synthesized (+)-oxopropaline D acetonide (4) in all respects. From the results of theoretical calculations and the experimental synthesis, we determined that natural (+)-oxopropaline D (3) has an R-configuration. PMID:12520122
The quaternary carbon-containing alcohols (1-6) were resolved enantioselectively by various lipases such as PFL (Pseudomonas fluorescens lipase), LAK (Pseudomonas fluorescens lipase), CRL (Candida rugosa lipase) and PCL (Pseudomonas cepacia lipase). The enzymatic resolution of racemic alcohol (±)-2 gave the excellent enantioselectivity in favor of (S)-2d in 99% ee, while those of the racemic alcohols (1, 3, 4, 5 and 6) gave the resolved alcohols with moderate to good enantioselectivity. Also, their absolute configurations were determined by chemical transformation to the known compounds
Ohtsuki, Takashi; Koyano, Takashi; Kowithayakorn, Thaworn; Yamaguchi, Naoto; Ishibashi, Masami
2004-12-01
A labdane-diterpene, austroinulin (1), together with several known flavonoids and sesquiterpenes were isolated from leaves of Blumea glomerata (Compositae). Austroinulin (1) and most of the flavonoids showed cytotoxicity against HeLa cells, while austroinulin (1) exhibited a cell cycle inhibition effect at the G1 stage at the concentration of 15.2 microg/mL (47.2 microM). The absolute configuration of 1 was revised as 5S,6R,7S,8S,9R,10R on the basis of the modified Mosher's method. PMID:15643553
Herwig, P.; Zawatzky, K.; Schwalm, D.; Grieser, M.; Heber, O.; Jordon-Thaden, B.; Krantz, C.; Novotný, O.; Repnow, R.; Schurig, V.; Vager, Z.; Wolf, A.; Trapp, O.; Kreckel, H.
2015-09-01
We have applied the method of foil-induced Coulomb Explosion Imaging (FCEI) to determine the handedness of a homochiral sample of the compound trans-2,3-dideuterooxirane C2OH2D2. We determined the compound to be of the (R, R)-econfiguration with a statistical significance of 5σ. As the molecular sample was chemically linked to the stereochemical reference standard glyceraldehyde, our assignment constitutes an independent verification of the absolute handedness of all compounds linked to this reference substance.
Zhang, Lei-lei; Xue, Hai; Li, Li; Lu, Xiao-fan; Chen, Zhi-wei; Lu, Gang
2015-06-01
Racemic (±)-F18 (10-chloromethyl-11-demethyl-12-oxo-calanolide A), an analog of nature product (+)-calanolide A, is a new anti-HIV-1 nonnucleoside reverse transcript inhibitor (NNRTI). A successful enantioseparation of (±)-F18 offering (R)-F18 and (S)-F18 was achieved by a chiral stationary phase prepared HPLC. Their absolute configurations were determined by measurement of their electronic circular dichroisms combined with modem quantum-chemical calculations. Further investigation revealed that (R)-F18 and (S)-F18 shared a similar anti-HIV activities, however, (R)-F18 was more potent than (S)-F18 against wild-type virus, K101E mutation and P225H mutation pseudoviruses. PMID:26521445
Zhao, Dan; Li, Zheng-Qiu; Cao, Fei; Liang, Miao-Miao; Pittman, Charles U; Zhu, Hua-Jie; Li, Li; Yu, Shi-Shan
2016-08-01
This study discusses the choice of different simplified models used in computations of electronic circular dichroism (ECD) spectra and other chiroptical characteristics used to determine the absolute configuration (AC) of the complex natural product sibiricumin A. Sections of molecules containing one chiral center with one near an aromatic group have large effects on the ECD spectra. Conversely, when the phenyl group is present on a substituent without a nonstereogenic center, removal of this section will have little effect on ECD spectra. However, these nonstereogenic-center-containing sections have large effects on calculated optical rotations (OR) values since the OR value is more sensitive to the geometries of sections in a molecule. In this study, the wrong AC of sibiricumin A was reassigned as (7R,8S,1'R,7'R,8'S)-. Chirality 28:612-617, 2016. © 2016 Wiley Periodicals, Inc. PMID:27428019
Evidente, Marco; Boari, Angela; Vergura, Stefania; Cimmino, Alessio; Vurro, Maurizio; Ash, Gavin; Superchi, Stefano; Evidente, Antonio
2015-09-01
A new 3-substituted-5-diazenylcyclopentendione named kongiidiazadione was isolated from culture filtrates of Diaporthe kongii, associated with stem cankers on sunflower in Australia. Kongiidiazadione was characterized by spectroscopic (essentially nuclear magnetic resonance [NMR] and high-resolution, electrospray ionization, mass spectrometry [HRESIMS]) methods as (-)-5-diazenyl-3-hydroxymethyl-cyclopent-3-en-1,2-dione. The stereochemistry of the diazenyl group was determined by IR spectroscopy, while the (R) absolute configuration at C(5) was assigned by computational analysis of its electronic circular dichroism (ECD) spectrum. When assayed on leaf disks of different plant species at 5 mM, the kongiidiazadione had a differential impact, causing clear necrosis, in particular to Helianthus annuus. Moreover, kongiidiazadione proved to have a weak antibacterial activity against gram-positive Bacillus amyloliquefaciens. PMID:26011252
Banerjee, Atreyee; Nandi, Manoj Kumar; Sastry, Srikanth; Bhattacharyya, Sarika Maitra
2016-07-01
In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in this paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density.
Absolute configuration of micromelin
Hoong-Kun Fun
2011-07-01
Full Text Available The title compound {systematic name: 7-methoxy-6-[(1R,2R,5R-5-methyl-4-oxo-3,6-dioxabicyclo[3.1.0]hexan-2-yl]-2H-chromen-2-one}, C15H12O6, is a coumarin, which was isolated from the roots of Micromelum glanduliferum. There are two molecules in the asymmetric unit with slight differences in bond angles. In both molecules, the furan ring adopts a flattened envelope conformation. In the crystal, molecules are linked by weak C—H...O interactions into chains along the a axis. Aromatic π–π stacking interactions with centroid–centroid distances in the range 3.6995 (11–3.8069 (11 Å and C...O short contacts [3.030 (2–3.171 (3 Å] also occur.
邓永坤
2012-01-01
主要研究绝对值方程Ax＋B｜z｜=b的求解问题．首先通过利用极大熵理论将该绝对值方程转化为光滑方程组，建立求解该形式绝对值问题的Newton-SOR方法，并对算法的收敛性进行分析和证明；最后通过数值试验对算法的有效性进行测试．%This paper is concerned with the absolute value equation Ax ＋ B ｜ x ｜ = b. First, using the maximum entropy function, and absolute value equations problem could be transformed into the approximation unconstrained differentiable problem, then using the Newton -SOR method to solve this problem. Theoretic analysis shows that the proposed method is effective. Numerical results indicate that the method is feasible and effective to absolute value equations problem.
Covington, Cody L; Nicu, Valentin P; Polavarapu, Prasad L
2015-10-22
Quantum chemical (QC) predictions of vibrational circular dichroism (VCD) spectra for the keto form of 3-benzoylcamphor and conformationally flexible diacetates of spiroindicumide A and B are presented. The exciton chirality (EC) model has been briefly reviewed, and a procedure to evaluate the relevance of the EC model has been presented. The QC results are compared with literature experimental VCD spectra as well as with those obtained using the EC model for VCD. These comparisons reveal that the EC contributions to bisignate VCD couplets associated with the C═O stretching vibrations of benzoylcamphor, spiroindicumide A diacetate, and spiroindicumide B diacetate are only ∼30%, ∼3%, and ∼15%, respectively. With such meager EC contributions, the correct absolute configurations (ACs) suggested in the literature for spiroindicumide A diacetate and spiroindicumide B diacetate molecules using the EC concepts can be considered fortuitous. The possibilities for obtaining wrong AC predictions using the EC concepts for VCD are identified, and guidelines for the future use of this model are presented. PMID:26401833
Entropic measure for localized energy configurations: Kinks, bounces, and bubbles
Gleiser, Marcelo, E-mail: mgleiser@dartmouth.edu [Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755 (United States); Stamatopoulos, Nikitas, E-mail: nstamato@dartmouth.edu [Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755 (United States)
2012-07-09
We construct a configurational entropy measure in functional space. We apply it to several nonlinear scalar field models featuring solutions with spatially-localized energy, including solitons and bounces in one spatial dimension, and critical bubbles in three spatial dimensions, typical of first-order phase transitions. Such field models are of widespread interest in many areas of physics, from high energy and cosmology to condensed matter. Using a variational approach, we show that the higher the energy of a trial function that approximates the actual solution, the higher its relative configurational entropy, defined as the absolute difference between the configurational entropy of the actual solution and of the trial function. Furthermore, we show that when different trial functions have degenerate energies, the configurational entropy can be used to select the best fit to the actual solution. The configurational entropy relates the dynamical and informational content of physical models with localized energy configurations.
Scafato, P.; Caprioli, F.; Pisani, L.; Padula, Daniele; Santoro, F.; Mazzeo, G.; Abbate, S.; Lebon, F.; Longhi, G.
2013-01-01
Roč. 69, č. 50 (2013), s. 10752-10762. ISSN 0040-4020 Institutional support: RVO:61388963 Keywords : ORD * ECD * VCD * vibronic features * absolute configuration * conformations * phenyl hindered rotation Subject RIV: CC - Organic Chemistry Impact factor: 2.817, year: 2013
Cheluvaraja, Srinath; Meirovitch, Hagai
2008-01-01
The hypothetical scanning molecular dynamics (HSMD) method is a relatively new technique for calculating the absolute entropy, S, and free energy, F, from a given sample generated by any simulation procedure. Thus, each sample conformation, i, is reconstructed by calculating transition probabilities that their product leads to the probability of i, hence to the entropy. HSMD is an exact method where all interactions are considered, and the only approximation is due to insufficient sampling. In previous studies HSMD (and HS Monte Carlo - HSMC) has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks, and peptides in a α-helix, extended, and hairpin microstates. In this paper HSMD is developed further as applied to the flexible 7-residue surface loop, 304-310 (Gly-His-Gly-Ala-Gly-Gly-Ser) of the enzyme porcine pancreatic α-amylase. We are mainly interested in entropy and free energy differences ΔS = Sfree - Sbound (and ΔF=Ffree-Fbound) between the free and bound microstates of the loop, which are obtained from two separate MD samples of these microstates without the need to carry out thermodynamic integration. As for peptides, we find that relatively large systematic errors in Sfree and Sbound (and Ffree and Fbound) are cancelled in ΔS (ΔF) which is thus obtained efficiently with high accuracy, i.e., with a statistical error of 0.1-0.2 kcal/mol (T=300 K) using the AMBER force field and AMBER with the implicit solvation GB/SA. We provide theoretical arguments in support of this cancellation, discuss in detail the problems involved in the computational definition of a microstate in conformational space, suggest potential ways for enhancing efficiency further, and describe the next development where explicit water will replace implicit solvation. PMID:26619992
Determination of the absolute configuration of natural products%天然产物绝对构型的确定
孔令义; 王鹏
2013-01-01
天然产物结构研究一直是天然药物化学相关领域最重要的工作之一,尤其对天然产物绝对构型(AC)的确定更是具有挑战性的研究内容,目前得到国内外学者越来越多的关注.在过去的几十年里已发展了许多技术和方法用来确定天然产物的绝对构型,包括直接法(或绝对方法),例如X射线单晶衍射(XRD)、电子圆二色谱(ECD)、振动圆二色谱(VCD)及拉曼光学活性(ROA)；使用已知绝对构型的参照物或衍生化试剂的间接法(或相对方法),例如利用经验规则的圆二色谱,以及利用手性衍生化试剂各向异性效应的核磁共振法(NMR).但由于这些方法适用的化合物类型和结构不尽相同,目前尚没有一种通用技术涵盖所有类型天然产物绝对构型的测定,我们只能灵活应用各种技术和方法才能确定大部分天然产物的绝对构型.本综述总结了大多数当前天然产物绝对构型测定中常用的以及具有潜在前景的技术和方法,并简要介绍了它们的原理及特点.%Structural elucidation of natural products is always one of the most important tasks for natural product researchers in related fields.Particularly,the absolute configuration (AC),being a great challenge for natural product chemists,has attracted much attention.During the past few decades,many techniques and approaches have been developed to determine the AC of natural products,including direct (or absolute) methods,e.g.X-ray diffraction (XRD),electronic and vibrational circular dichroism (ECD and VCD),and Raman optical activity (ROA),as well as indirect (or relative) methods using a reference or a derivatizing agent with known AC,e.g.CD with empirical rules and nuclear magnetic resonance (NMR) utilizing anisotropic effects of chiral derivatizing agents.However,none of the currently applied techniques is capable of dominating AC determination,since they each have their respective limitations corresponding to the
Rúnarsson, Ögmundur Vidar; Benkhäuser, Christian; Christensen, Niels Johan;
2015-01-01
/6-31G(d,p) level of theory. The absolute configuration of (+)-2 was also determined to (R,R)-2 by anomalous X-ray diffraction (AXRD) in a chiral space group P2(1)2(1)2(1) using Cu-irradiation resulting in a very low Flack parameter of -0.06(3), despite the heaviest element being an oxygen atom, thus......The first reported twisted bis-lactam, a racemic Troger's base (TB) analogue (2), was resolved into its enantiomers on a chiral stationary phase HPLC column. The absolute configuration of (+)-2 was determined to be (R,R)-2 by comparing experimental and calculated vibrational circular dichroism (VCD......) and electronic circular dichroism (ECD) spectra. The absolute configuration of (-)-2 was determined by comparing experimental and calculated electronic circular dichroism (ECD) spectra. The corresponding theoretical spectra were calculated using the lowest energy conformation of (R,R)-2 and (S,S)-2 at the B3LYP...
Rúnarsson, Ögmundur Vidar; Benkhäuser, Christian; Christensen, Niels Johan; Ruiz, Josep Artacho; Ascic, Erhad; Harmata, Michael; Snieckus, Victor; Rissanen, Kari; Fristrup, Peter; Lützen, Arne; Wärnmark, Kenneth
2015-08-21
The first reported twisted bis-lactam, a racemic Tröger's base (TB) analogue (2), was resolved into its enantiomers on a chiral stationary phase HPLC column. The absolute configuration of (+)-2 was determined to be (R,R)-2 by comparing experimental and calculated vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectra. The absolute configuration of (-)-2 was determined by comparing experimental and calculated electronic circular dichroism (ECD) spectra. The corresponding theoretical spectra were calculated using the lowest energy conformation of (R,R)-2 and (S,S)-2 at the B3LYP/6-31G(d,p) level of theory. The absolute configuration of (+)-2 was also determined to (R,R)-2 by anomalous X-ray diffraction (AXRD) in a chiral space group P212121 using Cu-irradiation resulting in a very low Flack parameter of -0.06(3), despite the heaviest element being an oxygen atom, thus unambiguously confirming the results from the spectroscopic studies. We conclude that, for the Tröger's base (TB) analogue (2), we may rank the reliability of the individual methods for AC determination as AXRD ≫ VCD > ECD, while the synergy of all three methods provides very strong confidence in the assigned ACs of (+)-(R,R)-2 and (-)-(S,S)-2. PMID:26244379
Tsallis, Constantino
2011-01-01
Clausius introduced, in the 1860s, a thermodynamical quantity which he named {\\it entropy} $S$. This thermodynamically crucial quantity was proposed to be {\\it extensive}, i.e., in contemporary terms, $S(N) \\propto N$ in the thermodynamic limit $N \\to\\infty$. A decade later, Boltzmann proposed a functional form for this quantity which connects $S$ with the occurrence probabilities of the microscopic configurations (referred to as {\\it complexions} at that time) of the system. This functional ...
Andrade, Francisco A. da C.; Mendes, Maricleide P. de L.; Fonseca, Neuracy C. da, E-mail: fandrade@ufba.br [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Instituto de Quimica. Departamento de Quimica Organica
2013-06-15
The mandelic, atrolactic and lactic acid esters of the (S)-2-methyl-1-butanol were examined as diastereomeric derivatives for the stereochemical analysis of the mentioned acids by {sup 1}H nuclear magnetic resonance (NMR) at 300 MHz. The diastereomeric esters showed distinctive signals in the methylenic absorption range (O-CH{sub 2}-CH) of the alcoholic moieties. By spectral analysis at this region, absolute configurations were attributed, chemical shifts of the correspondent pro-(R) and pro-(S) hydrogens from the methylene group of the alcohol moiety were assigned and enantiomeric compositions were determined for the original partially resolved acids. (author)
Yang, Sheng-Xiang; Gao, Jin-Ming; Laatsch, Hartmut; Tian, Jun-Mian; Pescitelli, Gennaro
2012-08-01
A new azaphilone derivative, named fusarone (1), has been isolated from the ethyl acetate soluble extract of the fermentation broth of an endophytic fungus, Fusarium sp. LN-12, isolated from the leaves of Melia azedarach Linn. The structure of the new compound was established on the basis of extensive spectroscopic analysis, including 1D-NMR and 2D-NMR ((1) H-(1)H COSY, TOCSY, HSQC, HMBC, and NOESY) experiments. The absolute configurations of fusarone (1) and of a second related azaphilone were determined by means of electronic circular dichroism spectroscopy and optical rotation calculations. PMID:22678988
The mandelic, atrolactic and lactic acid esters of the (S)-2-methyl-1-butanol were examined as diastereomeric derivatives for the stereochemical analysis of the mentioned acids by 1H nuclear magnetic resonance (NMR) at 300 MHz. The diastereomeric esters showed distinctive signals in the methylenic absorption range (O-CH2-CH) of the alcoholic moieties. By spectral analysis at this region, absolute configurations were attributed, chemical shifts of the correspondent pro-(R) and pro-(S) hydrogens from the methylene group of the alcohol moiety were assigned and enantiomeric compositions were determined for the original partially resolved acids. (author)
CHEN; Fanrong(陈繁荣); Rodney; C.Ewing
2003-01-01
Spent UO2 fuel will rapidly be altered to U6+ phases in nuclear waste repositories. Because most uranyl phases are based on sheet or chain structures and usually contain several molecular water groups, site-mixing, vacancies, as well as disorder in the orientation of hydrogen bonds may occur. A systematic survey of the published crystallographic data for uranates, uranyl oxide hydrates, phosphates, silicates, carbonates, and sulfates demonstrates that site-mixing apparently occurs in the structures of at least 31 uranyl phases. Calculations of the ideal site-mixing entropy indicate that the residual contribution that arises from substitution and vacancies to the third-law entropies of some uranyl phases is large. A brief examination of the crystal chemistry of water molecules in uranyl phases suggests that considerable residual entropy may be caused by the disorder of hydrogen bonds associated with interstitial H2O groups. In the geochemical environment that expected to occur in the near-field of nuclear waste repositories, the existence of structure-configurational entropy may reduce the uranium concentration of several log units in solutions equilibrated with some uranyl phases. Therefore, compositional analysis and structural determinations must be made on the samples used in calorimetric measurements, and the calorimetric data must be combined with solubility data to evaluate the thermodynamic stability of the interested phases.
Lagoutte, Roman; Šebesta, Petr; Jiroš, Pavel; Kalinová, Blanka; Jirošová, Anna; Straka, J.; Černá, K.; Šobotník, Jan; Cvačka, Josef; Jahn, Ullrich
2013-01-01
Roč. 19, č. 26 (2013), s. 8515-8524. ISSN 0947-6539 R&D Projects: GA ČR GAP506/10/1466 Institutional support: RVO:61388963 Keywords : asymmetric synthesis * configuration determination * pheromones * total synthesis * Wittig reactions Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013
Alwera, Shiv; Bhushan, Ravi
2016-08-01
Diastereomers of (RS)-propranolol were synthesized using (S)-levofloxacin-based new chiral derivatizing reagents (CDRs). Levofloxacin was chosen as the pure (S)-enantiomer for its high molar absorptivity (εo ∼ 24000) and availability at a low price. Its -COOH group had N-hydroxysuccinimide and N-hydroxybenzotriazole, which acted as good leaving groups during nucleophilic substitution by the amino group of the racemic (RS)-propranolol; the CDRs were characterized by UV, IR, (1) H-NMR, high resolution mass spectrometry (HRMS) and carbon, hydrogen, nitrogen, and sulphur fundamental elemental components analyser (CHNS). Diastereomers were separated quantitatively using open column chromatography; absolute configuration of the diastereomers was established and the reagent moiety was detagged under microwave-assisted acidic conditions. (S)- and (R)-propranolol as pure enantiomers and (S)-levofloxacin were separated, isolated and characterized. Optimized lowest-energy structures of the diastereomers were developed using Gaussian 09 Rev. A.02 program and hybrid density functional B3LYP with 6-31G* basis set (based on density functional theory) for explanation of elution order and configuration. In addition, RP HPLC conditions for separation of diastereomers were optimized with respect to pH, concentration of buffer, flow rate of mobile phase and nature of organic modifier. HPLC separation method was validated as per International Conference on Harmonization guidelines. With the systematic application of various analytical techniques, absolute configuration of the diastereomers (and the native enantiomers) of (RS)-propranolol was established. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26682898
Sadia Sultan
2014-09-01
Full Text Available The anti-inflammatory drug predinisolone (1 was reduced to 20β-hydroxyprednisolone (2 by the marine endophytic fungus Penicilium lapidosum isolated from an alga. The structural elucidation of 2 was achieved by 1D- and 2D-NMR, MS, IR data. Although, 2 is a known compound previously obtained through microbial transformation, the data provided failed to prove the C20 stereochemistry. To solve this issue, DFT and TD-DFT calculations have been carried out at the B3LYP/6–31+G (d,p level of theory in gas and solvent phase. The absolute configuration of C20 was eventually assigned by combining experimental and calculated electronic circular dichroism spectra and 3JHH chemical coupling constants.
Rossi, Daniela; Nasti, Rita; Marra, Annamaria; Meneghini, Silvia; Mazzeo, Giuseppe; Longhi, Giovanna; Memo, Maurizio; Cosimelli, Barbara; Greco, Giovanni; Novellino, Ettore; Da Settimo, Federico; Martini, Claudia; Taliani, Sabrina; Abbate, Sergio; Collina, Simona
2016-05-01
The chiral separation of enantiomeric couples of three potential A3 adenosine receptor antagonists: (R/S)-N-(6-(1-phenylethoxy)-2-(propylthio)pyrimidin-4-yl)acetamide (), (R/S)-N-(2-(1-phenylethylthio)-6-propoxypyrimidin-4-yl)acetamide (), and (R/S)-N-(2-(benzylthio)-6-sec-butoxypyrimidin-4-yl)acetamide () was achieved by high-performance liquid chromatography (HPLC). Three types of chiroptical spectroscopies, namely, optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD), were applied to enantiomeric compounds. Through comparison with Density Functional Theory (DFT) calculations, encompassing extensive conformational analysis, full assignment of the absolute configuration (AC) for the three sets of compounds was obtained. Chirality 28:434-440, 2016. © 2016 Wiley Periodicals, Inc. PMID:27095007
Mendoza-Espinoza, José Alberto; López-Vallejo, Fabian; Fragoso-Serrano, Mabel; Pereda-Miranda, Rogelio; Cerda-García-Rojas, Carlos M
2009-04-01
The structural reassignment, absolute configuration, and conformational behavior of the highly flexible natural product hypurticin (pectinolide E), 6S-[3'S,5'R,6'S-triacetoxy-1Z-heptenyl]-5S-acetoxy-5,6-dihydro-2H-pyran-2-one (1), were ascertained by a molecular modeling protocol, which includes extensive conformational searching, geometry optimization by DFT B3LYP/DGDZVP calculations, and comparison between the theoretical (DFT) and experimental (1)H-(1)H NMR coupling constants. Hyptolide (2), a related cytotoxic 5,6-dihydro-2H-pyran-2-one that increased the S phase of the HeLa cell cycle, was employed as a reference substance to validate the theoretical protocol designed to characterize the 3D properties of compound 1. The related synthetic derivative, tri-O-acetyl-3,6-dideoxy-d-glucose diphenyldithioacetal (14), was prepared by a six-step reaction sequence starting from d-glucose and served as an enantiopure building block to reinforce the structural and configurational assignment of 1. This protocol proved to be an important tool for the structural characterization of highly flexible bioactive polyoxygenated natural products. PMID:19265396
Aguilar-Pineda, G. E.; Olivares-Quiroz, L.
2014-01-01
Temperature and chemically induced denaturation comprise two of the most characteristic mechanisms to achieve the passage from the native state N to any of the unstructured states Dj in the denatured ensemble in proteins and peptides. In this work we present a full analytical solution for the configurational partition function qs of a homopolymer chain poly-X in the extended Zwanzig model (EZM) for a quasisigmoidal denaturation profile. This solution is built up from an EZM exact solution in...
Easy Absolute Values? Absolutely
Taylor, Sharon E.; Mittag, Kathleen Cage
2015-01-01
The authors teach a problem-solving course for preservice middle-grades education majors that includes concepts dealing with absolute-value computations, equations, and inequalities. Many of these students like mathematics and plan to teach it, so they are adept at symbolic manipulations. Getting them to think differently about a concept that they…
Silva, Alexandre Fonseca Povoa da, E-mail: alexandre.povoa@mar.mil.br [Centro Tecnologico da Marinha em Sao Paulo (CTMSP), Sao Paulo, SP (Brazil); Bitelli, Ulysses d' Utra; Mura, Luiz Ernesto Credidio; Lima, Ana Cecilia de Souza; Betti, Flavio; Santos, Diogo Feliciano dos, E-mail: ubitelli@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)
2015-07-01
The use of neutron activation foils is a widely spread technique applied to obtain nuclear parameters then comparing the results with those calculated using specific methodologies and available nuclear data. By irradiation of activation foils and subsequent measurement of its induced activity, it is possible to determine the neutron flux at the position of irradiation. The power level during operation of the reactor is a parameter which is directly proportional to the average neutron flux throughout the core. The objective of this work is to gather data from irradiation of gold foils symmetrically placed along a cylindrically configured core which presents only a small excess reactivity in order to derive the power generated throughout the spatial thermal and epithermal neutron flux distribution over the core of the IPEN/MB-01 Nuclear Reactor, eventually lending to a proper calibration of its nuclear channels. The foils are fixed in a Lucite plate then irradiated with and without cadmium sheaths so as to obtain the absolute thermal and epithermal neutron flux. The correlation between the average power neutron flux resulting from the gold foils irradiation, and the average power digitally indicated by the nuclear channel number 6, allows for the calibration of the nuclear channels of the reactor. The reactor power level obtained by thermal neutron flux mapping was (74.65 ± 2.45) watts to a mean counting per seconds of 37881 cps to nuclear channel number 10 a pulse detector, and 0.719.10{sup -5} ampere to nuclear linear channel number 6 (a non-compensated ionization chamber). (author)
The use of neutron activation foils is a widely spread technique applied to obtain nuclear parameters then comparing the results with those calculated using specific methodologies and available nuclear data. By irradiation of activation foils and subsequent measurement of its induced activity, it is possible to determine the neutron flux at the position of irradiation. The power level during operation of the reactor is a parameter which is directly proportional to the average neutron flux throughout the core. The objective of this work is to gather data from irradiation of gold foils symmetrically placed along a cylindrically configured core which presents only a small excess reactivity in order to derive the power generated throughout the spatial thermal and epithermal neutron flux distribution over the core of the IPEN/MB-01 Nuclear Reactor, eventually lending to a proper calibration of its nuclear channels. The foils are fixed in a Lucite plate then irradiated with and without cadmium sheaths so as to obtain the absolute thermal and epithermal neutron flux. The correlation between the average power neutron flux resulting from the gold foils irradiation, and the average power digitally indicated by the nuclear channel number 6, allows for the calibration of the nuclear channels of the reactor. The reactor power level obtained by thermal neutron flux mapping was (74.65 ± 2.45) watts to a mean counting per seconds of 37881 cps to nuclear channel number 10 a pulse detector, and 0.719.10-5 ampere to nuclear linear channel number 6 (a non-compensated ionization chamber). (author)
Richet, P.; Robie, R.A.; Hemingway, B.S.
1986-01-01
Heat-capacity measurements have been made between 8 and 370 K on an annealed and a rapidly quenched diopside glass. Between 15 and 200 K, Cp does not depend significantly on the thermal history of the glass. Below 15 K Cp is larger for the quenched than for the annealed specimen. The opposite is true above 200 K as a result of what is interpreted as a secondary relaxation around room temperature. The magnitude of these effects, however, is small enough that the relative entropies S(298)-S(0) of the glasses differ by only 0.5 J/mol K, i.e., a figure within the combined experimental uncertainties. The insensitivity of relative entropies to thermal history supports the assumption that the configurational heat capacity of the liquid may be taken as the heat capacity difference between the liquid and the glass (??Cp). Furthermore, this insensitivity allows calculation of the residual entropies at 0 K of diopside glasses as a function of the fictive temperature from the entropy of fusion of diopside and the heat capacities of the crystalline, glassy and liquid phases. For a glass with a fictive temperature of 1005 K, for example, this calorimetric residual entropy is 24.3 ?? 3 J/mol K, in agreement with the prediction made by RICHET (1984) from an analysis of the viscosity data with the configurational-entropy theory of relaxation processes of Adam and Gibbs (1965). In turn, all the viscosity measurements for liquid diopside, which span the range 0.5-4?? 1013 poise, can be quantitatively reproduced through this theory with the calorimetrically determined entropies and ??Cp data. Finally, the unclear significance of "activation energies" for structural interpretations of viscosity data is emphasized, and the importance of ??Cp and glass-transition temperature systematics for determining the composition and temperature dependences of the viscosity is pointed out. ?? 1986.
Mang, Chao-Yong; Liu, Cai-Ping; Liu, Guang-Ming; Jiang, Bei; Lan, Hai; Wu, Ke-Chen; Yan, Ya; Li, Hai-Fei; Yang, Ming-Hui; Zhao, Yu
2015-02-01
A cyclic dipeptide often has the multiple configurations and the abundant conformations. The density functional theory (DFT) method is used to search the preferred conformation of the most probable configuration for cordycedipeptide A isolated from the culture liquid of Cordyceps sinensis. The time-dependent DFT approach is exploited to describe the profile of electronic circular dichroism (CD). The calculated results show that the most probable configuration is 3S6R7S, whose preferred conformation has a negative optical rotation and a positive lowest energy electronic CD band.
Shunsaku Ohta
2005-01-01
@@ 1Introduction Linderol A (1), a monoterpene-polyketide, was isolated in 1995 from the fresh bark of Lindera umbellata (Lauraceae), and its absolute structure was not determined[1]. It was also reported potent inhibitory activity of 1 on the melanin biosynthesis of the cultured B-16 melanoma cells[1]. See Fig. 1. On the other hand,we reported in 1995 an interesting multi-tandem reaction of coumarin derivatives (2; W = electron withdrawing group) by treatment with CH2 = S(O)Me2 to yield stereoselectively a tricyclic 2-substituted cyclopenta [ b ] benzofuran-3-ol derivative (4) via a cyclopropane intermediate (3) (Scheme 1)[2].
张鹏; 张卫国; 曾玉婷
2016-01-01
文章运用可能性绝对偏差和比例熵分别度量风险和分散化程度，提出了具有风险控制和线性交易成本的终期财富最大化的多阶段模糊投资组合模型。运用可能理论，将该模型转化为显示的非线性动态优化问题。由于投资过程存在交易成本，上述模型为具有路径依赖性的动态优化问题。文章提出了前向动态规划方法求解。最后，通过实证研究比较了不同熵的取值投资组合最优投资比例和最终财富的变化。%This paper considers a multi-period fuzzy portfolio selection problem maximizing the terminal wealth imposed by risk control, in which risk of assets and the divergence measure of portfolio are, respectively, meas-ured by fuzzy absolute deviation and proportion entropy.Based on the theories of possibility theory, the proposed model is transformed into a crisp nonlinear programming problem.Because of the transaction costs, the multi-period portfolio selection is a dynamic optimization problem with path dependence.Furthermore, a forward dynamic programming method is designed to obtain the optimal portfolio strategy.Finally, an example is given to illustrate the behavior of the proposed model and the designed algorithm.
Bekenstein Entropy is String Entropy
Halyo, Edi
2009-01-01
We argue that Bekenstein entropy can be interpreted as the entropy of an effective string with a rescaled tension. Using the AdS/CFT correspondence we show that the Bekenstein entropy on the boundary CFT is given by the entropy of a string at the stretched horizon of the AdS black hole in the bulk. The gravitationally redshifted tension and energy of the string match those required to reproduce Bekenstein entropy.
Mughal, Muhammad Aurang Zeb
2009-01-01
The concept of absolute time is a hypothetical model from the laws of classical physics postulated by Isaac Newton in the Principia in 1687. Although the Newtonian model of absolute time has since been opposed and rejected in light of more recent scholarship, it still provides a way to study science with reference to time and understand the phenomena of time within the scientific tradition. According to this model, it is assumed that time runs at the same rate for all the observers in the uni...
Costa, Carlos Casimiro da; Costa, Jacinta Casimiro da
2012-01-01
Tomorrow, I m recovering my Thursday child as an absolute beginner , Transporting you to the essential touch of surface skin and space, Only for you, i do not regret, looking for education in a materia set. My love is your love , my materiality is you making things, The legacy of our ethnography, craftsmen s old and disappear, make me strong hard feelings, Recovering experiences and knowledge sprinkled in powder of stone, wood and metal ( ) reflecting in your dirty face the ...
Chen, Xing
2016-01-01
Projective measurement can increase the entropy of a state $\\rho$, the increased entropy is not only up to the basis of projective measurement, but also has something to do with the properties of the state itself. In this paper we define this increased entropy as basis entropy. And then we discuss the usefulness of this new concept by showing its application in explaining the success probability of Grover's algorithm and the existence of quantum discord. And as shown in the paper, this new co...
Phillips, Alfred, Jr.
Summ means the entirety of the multiverse. It seems clear, from the inflation theories of A. Guth and others, that the creation of many universes is plausible. We argue that Absolute cosmological ideas, not unlike those of I. Newton, may be consistent with dynamic multiverse creations. As suggested in W. Heisenberg's uncertainty principle, and with the Anthropic Principle defended by S. Hawking, et al., human consciousness, buttressed by findings of neuroscience, may have to be considered in our models. Predictability, as A. Einstein realized with Invariants and General Relativity, may be required for new ideas to be part of physics. We present here a two postulate model geared to an Absolute Summ. The seedbed of this work is part of Akhnaton's philosophy (see S. Freud, Moses and Monotheism). Most important, however, is that the structure of human consciousness, manifest in Kenya's Rift Valley 200,000 years ago as Homo sapiens, who were the culmination of the six million year co-creation process of Hominins and Nature in Africa, allows us to do the physics that we do. .
He, Jiangtao; Polavarapu, Prasad L.
2005-05-01
The enantiomers of 2-(2-chlorophenoxy) propanoic acid and 2-(3-chlorophenoxy) propanoic acid were resolved on a chiral HPLC column and investigated using mid-infrared vibrational circular dichroism (VCD). Experimental infrared vibrational absorption and VCD spectra were measured in CDCl 3 solution in the 2000-900 cm -1 region and compared with the ab initio predictions of absorption and VCD spectra. The predicted spectra were obtained with density functional theory using B3LYP/6-31G* basis set for the stable and dominant conformers. But the predicted spectra did not provide unambiguous structural information due to intermolecular hydrogen bonding in solution. To eliminate the hydrogen bonding effects, the acids were converted to the corresponding methyl esters and the experimental absorbance and VCD spectra of methyl esters were measured. B3LYP predicted spectra were also obtained for the stable and dominant conformers of the esters. From a comparison of the experimental VCD spectra of methyl esters with corresponding ab initio predictions, the absolute configurations of esters, and therefore of their parent acids, are unambiguously determined to be (+)-( R).
Astuti, Valerio; Christodoulou, Marios; Rovelli, Carlo
2016-01-01
Building on a technical result by Brunnemann and Rideout on the spectrum of the Volume operator in Loop Quantum Gravity, we show that the dimension of the space of the quadrivalent states --with finite-volume individual nodes-- describing a region with total volume smaller than $V$, has \\emph{finite} dimension, bounded by $V \\log V$. This allows us to introduce the notion of "volume entropy": the von Neumann entropy associated to the measurement of volume.
Universal entropy relations: entropy formulae and entropy bound
Liu, Hang; Meng, Xin-he; Xu, Wei; Zhu, Bin
2016-01-01
We survey the applications of universal entropy relations in black holes with multi-horizons. In sharp distinction to conventional entropy product, the entropy relationship here not only improve our understanding of black hole entropy but was introduced as an elegant technique trick for handling various entropy bounds and sum. Despite the primarily technique role, entropy relations have provided considerable insight into several different types of gravity, including massive gravity, Einstein-...
Arithmetic of quantum entropy function
Quantum entropy function is a proposal for computing the entropy associated with the horizon of a black hole in the extremal limit, and is related via AdS/CFT correspondence to the dimension of the Hilbert space in a dual quantum mechanics. We show that in N = 4 supersymmetric string theories, quantum entropy function formalism naturally explains the origin of the subtle differences between the microscopic degeneracies of quarter BPS dyons carrying different torsion, i.e. different arithmetical properties. These arise from additional saddle points in the path integral - whose existence depends on the arithmetical properties of the black hole charges - constructed as freely acting orbifolds of the original AdS2 x S2 near horizon geometry. During this analysis we demonstrate that the quantum entropy function is insensitive to the details of the infrared cutoff used in the computation, and the details of the boundary terms added to the action. We also discuss the role of the asymptotic symmetries of AdS2 in carrying out the path integral in the definition of quantum entropy function. Finally we show that even though quantum entropy function is expected to compute the absolute degeneracy in a given charge and angular momentum sector, it can also be used to compute the index. This can then be compared with the microscopic computation of the index.
K B Athreya
2009-09-01
It is shown that (i) every probability density is the unique maximizer of relative entropy in an appropriate class and (ii) in the class of all pdf that satisfy $\\int fh_id_=_i$ for $i=1,2,\\ldots,\\ldots k$ the maximizer of entropy is an $f_0$ that is proportional to $\\exp(\\sum c_i h_i)$ for some choice of $c_i$. An extension of this to a continuum of constraints and many examples are presented.
Das, Diptarka
2010-01-01
The laws of mechanics of stationary black holes bear a close resemblance with the laws of thermodynamics. This is not only a mathematical analogy but also a physical one that helps us answer deep questions related to the thermodynamic properties of the black holes. It turns out that we can define an entropy which is purely geometrical for black holes. In this thesis we explain Wald's formulation which identifies black hole entropy for an arbitrary covariant theory of gravity. We would like to know precisely what inputs go into arriving at Wald's formalism. This expression for the entropy clearly depends on the precise form of the action. The secondary theme of this thesis is to distinguish thermodynamic laws which are kinematic from those which are dynamical. We would like to see explicitly in the derivation of these laws, where exactly the form of action plays a role. In the beginning we motivate the definition of entropy using the Einstein-Hilbert Lagrangian. We encounter the Zeroth law, the Hawking radiati...
Carnot to Clausius: caloric to entropy
This paper discusses how the Carnot engine led to the formulation of the second law of thermodynamics and entropy. The operation of the engine is analysed both in terms of heat as the caloric fluid and heat as a form of energy. A keystone of Carnot's thinking was the absolute conservation of caloric. Although the Carnot analysis was partly incorrect, Clausius showed that by reinterpreting Carnot's caloric as entropy he was able to formulate the second law
Pesin's Entropy Formula for Systems Between and
Tian, Xueting
2014-09-01
In this article we give a new observation of Pesin's entropy formula, motivated from Mañé's proof of (Ergod Theory Dyn Sys 1:95-102, 1981). Let be a compact Riemann manifold and be a diffeomorphism on . If is an -invariant probability measure which is absolutely continuous relative to Lebesgue measure and nonuniformly-Hlder-continuous(see Definition 1.1), then we have Pesin's entropy formula, i.e., the metric entropy satisfies where are the Lyapunov exponents at with respect to Nonuniformly-H lder-continuous is a new notion from probabilistic perspective weaker than
Thien Nguyen; Lukas Schmid; Mariano Croce
2014-01-01
The recent fiscal crisis in the EU and the slow-down of the BRICS countries have raised world-wide concerns about future global growth prospects. We examine the role of doubts about both local and foreign economic shocks by constructing an international endogenous growth model with technology diffusion across countries. In this setting, endogenous technology spillovers generate global growth shocks. When agents have concerns for robustness, country-specific shocks (1) alter global entropy, an...
Universal entropy relations: entropy formulae and entropy bound
Liu, Hang; Xu, Wei; Zhu, Bin
2016-01-01
We survey the applications of universal entropy relations in black holes with multi-horizons. In sharp distinction to conventional entropy product, the entropy relationship here not only improve our understanding of black hole entropy but was introduced as an elegant technique trick for handling various entropy bounds and sum. Despite the primarily technique role, entropy relations have provided considerable insight into several different types of gravity, including massive gravity, Einstein-Dilaton gravity and Horava-Lifshitz gravity. We present and discuss the results for each one.
Teaching Absolute Value Meaningfully
Wade, Angela
2012-01-01
What is the meaning of absolute value? And why do teachers teach students how to solve absolute value equations? Absolute value is a concept introduced in first-year algebra and then reinforced in later courses. Various authors have suggested instructional methods for teaching absolute value to high school students (Wei 2005; Stallings-Roberts…
Entropy Bounds for Constrained Two-Dimensional Fields
Forchhammer, Søren Otto; Justesen, Jørn
1999-01-01
The maximum entropy and thereby the capacity of 2-D fields given by certain constraints on configurations are considered. Upper and lower bounds are derived.......The maximum entropy and thereby the capacity of 2-D fields given by certain constraints on configurations are considered. Upper and lower bounds are derived....
On the Absolute Continuity of the Blackwell Measure
Bárány, Balázs; Kolossváry, István
2015-04-01
In 1957, Blackwell expressed the entropy of hidden Markov chains using a measure which can be characterised as an invariant measure for an iterated function system with place-dependent weights. This measure, called the Blackwell measure, plays a central role in understanding the entropy rate and other important characteristics of fundamental models in information theory. We show that for a suitable set of parameter values the Blackwell measure is absolutely continuous for almost every parameter in the case of binary symmetric channels.
Carnot to Clausius: Caloric to Entropy
Newburgh, Ronald
2009-01-01
This paper discusses how the Carnot engine led to the formulation of the second law of thermodynamics and entropy. The operation of the engine is analysed both in terms of heat as the caloric fluid and heat as a form of energy. A keystone of Carnot's thinking was the absolute conservation of caloric. Although the Carnot analysis was partly…
Eosinophils; Absolute eosinophil count ... the white blood cell count to give the absolute eosinophil count. ... than 500 cells per microliter (cells/mcL). Normal value ranges may vary slightly among different laboratories. Talk ...
Entropy and Energy, – a Universal Competition
Ingo MÃƒÂ¼ller
2008-01-01
When a body approaches equilibrium, energy tends to a minimum and entropy tends to a maximum. Often, or usually, the two tendencies favour different configurations of the body. Thus energy is deterministic in the sense that it favours fixed positions for the atoms, while entropy randomizes the positions. Both may exert considerable forces in the attempt to reach their objectives. Therefore they have to compromise; indeed, under most circumstances it is the available free energy which achieves...
Garattini, R
2002-01-01
A simple model of spacetime foam, made by two different types of wormholes in a semiclassical approximation, is taken under examination: one type is a collection of $N_{w}$ Schwarzschild wormholes, while the other one is made by Schwarzschild-Anti-de Sitter wormholes. The area quantization related to the entropy via the Bekenstein-Hawking formula hints a possible selection between the two configurations. Application to the charged black hole are discussed.
Garattini, Remo
A simple model of space-time foam, made by two different types of wormholes in a semiclassical approximation, is taken under examination: one type is a collection of Nw Schwarzschild wormholes, while the other one is made by Schwarzschild-Anti-de Sitter wormholes. The area quantization related to the entropy via the Bekenstein-Hawking formula hints a possible selection between the two configurations. Application to the charged black hole are discussed.
Topological entropy of autonomous flows
Badii, R. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
When studying fluid dynamics, especially in a turbulent regime, it is crucial to estimate the number of active degrees of freedom or of localized structures in the system. The topological entropy quantifies the exponential growth of the number of `distinct` orbits in a dynamical system as a function of their length, in the infinite spatial resolution limit. Here, I illustrate a novel method for its evaluation, which extends beyond maps and is applicable to any system, including autonomous flows: these are characterized by lack of a definite absolute time scale for the orbit lengths. (author) 8 refs.
Absolute nuclear material assay
Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.
2010-07-13
A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.
Absolute nuclear material assay
Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.
2012-05-15
A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.
Bekenstein-Hawking Entropy as Entanglement Entropy
Feng, Yu-Lei
2015-01-01
We show that the Bekenstein-Hawking entropy $S_{BH}$ should be treated as an entanglement entropy, provided that the formation and evaporation of a black hole can be described by quantum unitary evolutions. To confirm this statement, we derive statistical mechanics from quantum mechanics effectively by means of open quantum systems. Then a new definition of Boltzmann entropy for a quantum closed system is given to count microstates in a way consistent with the superposition principle. In particular, this new Boltzmann entropy is a constant that depends only on the dimension of the system's relevant Hilbert subspace. Based on this new definition, some kind of "detailed balance" condition is obtained to stabilize the thermal equilibrium between two macroscopic subsystems within a larger closed system. However, the required "detailed balance" condition between black hole and matter would be broken, if the Bekenstein-Hawking entropy was treated as Boltzmann entropy together with the Hawking temperature as thermal...
Schechter, J.; Shahid, M. N.
2012-01-01
We discuss the possibility of using experiments timing the propagation of neutrino beams over large distances to help determine the absolute masses of the three neutrinos.......We discuss the possibility of using experiments timing the propagation of neutrino beams over large distances to help determine the absolute masses of the three neutrinos....
The Nernst theorem and the statistical entropy of the NUT-Kerr-Newman black hole
Using quantum statistical method, we obtain the partition function of Bose field and Fermi field on the background of the axisymmetrical NUT-Kerr-Newman black hole. The difficult to solve wave equation is avoided. Then via the membrane model we calculate the entropy of Bose field and Fermi field of the black hole. Though discussing, we derive that the black hole's entropy consists of two parts. According to the property that the entropy is an extensive quantity, we know that the entropy is the contribution of two thermodynamic systems. On this basis, a new Bekenstein-Smarr formula is given. It is shown that the entropy expressed by two thermodynamic systems will approach zero, when the radiation temperature approaches absolute zero.It satisfies Nernst theorem. The entropy can be taken as the Planck absolute entropy. (authors)
Quantum dynamical entropy revisited
We define a new quantum dynamical entropy, which is a 'hybrid' of the closely related, physically oriented entropy introduced by Alicki and Fannes in 1994, and of the mathematically well-developed, single-argument entropy introduced by Connes, Narnhofer and Thirring in 1987. We show that this new quantum dynamical entropy has many properties similar to the ones of the Alicki-Fannes entropy, and also inherits some additional properties from the CNT entropy. In particular, the 'hybrid' entropy interpolates between the two different ways in which both the AF and the CNT entropy of the shift automorphism on the quantum spin chain agree with the usual quantum entropy density, resulting in even better agreement. Also, the new quantum dynamical entropy generalizes the classical dynamical entropy of Kolmogorov and Sinai in the same way as does the AF entropy. Finally, we estimate the 'hybrid' entropy both for the Powers-Price shift systems and for the noncommutative Arnold map on the irrational rotation C*-algebra, leaving some interesting open problems. (author)
Cheluvaraja, Srinath; Meirovitch, Hagai
2006-07-14
Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed. PMID:16848609
Physical entropy, information entropy and their evolution equations
无
2001-01-01
Inspired by the evolution equation of nonequilibrium statistical physics entropy and the concise statistical formula of the entropy production rate, we develop a theory of the dynamic information entropy and build a nonlinear evolution equation of the information entropy density changing in time and state variable space. Its mathematical form and physical meaning are similar to the evolution equation of the physical entropy: The time rate of change of information entropy density originates together from drift, diffusion and production. The concise statistical formula of information entropy production rate is similar to that of physical entropy also. Furthermore, we study the similarity and difference between physical entropy and information entropy and the possible unification of the two statistical entropies, and discuss the relationship among the principle of entropy increase, the principle of equilibrium maximum entropy and the principle of maximum information entropy as well as the connection between them and the entropy evolution equation.
Urban Kordes
2005-10-01
Full Text Available The paper tries to tackle the question of connection between entropy and the living. Definitions of life as the phenomenon that defies entropy are overviewed and the conclusion is reached that life is in a way dependant on entropy - it couldn't exist without it. Entropy is a sort of medium, a fertile soil, that gives life possibility to blossom. Paper ends with presenting some consequences for the field of artificial intelligence.
Urban Kordes
2015-01-01
The paper tries to tackle the question of connection between entropy and the living. Definitions of life as the phenomenon that defies entropy are overviewed and the conclusion is reached that life is in a way dependant on entropy - it couldn't exist without it. Entropy is a sort of medium, a fertile soil, that gives life possibility to blossom. Paper ends with presenting some consequences for the field of artificial intelligence.
Entropy of Baker's Transformation
栾长福
2003-01-01
Four theorems about four different kinds of entropies for Baker's transformation are presented. The Kolmogorov entropy of Baker's transformation is sensitive to the initial flips by the time. The topological entropy of Baker's transformation is found to be log k. The conditions for the state of Baker's transformation to be forbidden are also derived. The relations among the Shanonn, Kolmogorov, topological and Boltzmann entropies are discussed in details.
Huynh, Tri H.V.; Shim, Irene; Bohr, Henrik;
2012-01-01
diastereomeric pairs 11a/11b and 12a/12b were separated by HPLC and the absolute configuration assigned by VCD technique in combination with ab initio Hartree–Fock calculations. Analogues 11a (RS-isomer) and 12b (RR-isomer) inhibited EAAT1 (IC50 values 5.5 and 3.8 μM, respectively), whereas analogues 11b (SS...... rodents, respectively. In this paper, we present the design, synthesis, and pharmacological evaluation of seven 7-N-substituted analogues of UCPH-101/102. Analogue 9 inhibited EAAT1 in the micromolar range (IC50 value 20 μM), whereas analogues 8 and 10 were inactive (IC50 values >100 μM). The......-isomer) and 12a (SR-isomer) failed to inhibit EAAT1 uptake (IC50 values >300 μM)....
Entropies and fractal dimensions
Sparavigna, Amelia Carolina
2016-01-01
In this paper, we discuss the relation between entropy and the fractal dimension, a statistical index which is measuring the complexity of a given pattern, embedded in given spatial dimensions. We will consider the Shannon entropy and the generalized entropies of Tsallis and Kaniadakis
Emanuel Guariglia
2016-01-01
The entropies of Shannon, Rényi and Kolmogorov are analyzed and compared together with their main properties. The entropy of some particular antennas with a pre-fractal shape, also called fractal antennas, is studied. In particular, their entropy is linked with the fractal geometrical shape and the physical performance.
Entropy estimates for simple random fields
Forchhammer, Søren; Justesen, Jørn
We consider the problem of determining the maximum entropy of a discrete random field on a lattice subject to certain local constraints on symbol configurations. The results are expected to be of interest in the analysis of digitized images and two dimensional codes. We shall present some examples...
National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Absolute Gravity data (78 stations) was received in July 1993. Principal gravity parameters include Gravity Value, Uncertainty, and Vertical Gradient. The...
Çuhadar, C.Hakan
2008-01-01
Musicians are debated people in the academic circles with the claim of they have both various characteristics and different cognitive personalities on the analogy those other people. One of these different characteristics is absolute pitch ability. Absolute pitch (AP) is a cognitive ability which can be characterized as to identify any tones (labeling) at a given pitch without using any external references. According to the different studies which were held in different times, the prevalence ...
Okada, H.; Alekseev, I.; Bravar, A; Bunce, G.; Dhawan, S.; Eyser, K. O.; Gill, R; Haeberli, W.; Huang, H.; Jinnouchi, O.; Makdisi, Y.; Nakagawa, I.; Nass, A.; Saito, N; Stephenson, E.
2007-01-01
Precise and absolute beam polarization measurements are critical for the RHIC spin physics program. Because all experimental spin-dependent results are normalized by beam polarization, the normalization uncertainty contributes directly to final physics uncertainties. We aimed to perform the beam polarization measurement to an accuracy of $\\Delta P_{beam}/P_{beam} < 5%$. The absolute polarimeter consists of Polarized Atomic Hydrogen Gas Jet Target and left-right pairs of silicon strip detector...
Absolute surface energy determination
Metois, J. J.; Muller, P.
2007-01-01
Experimental determination of absolute surface energies remains a challenge. We propose a simple method based on two independent measurements on 3D and 2D equilibrium shapes completed by the analysis of the thermal fluctuation of an isolated step. Using then basic equations (Wulff' theorem, Gibbs-Thomson equation, thermodynamics fluctuation of an isolated step) allows us to extract the absolute surface free energy of a singular face. The so-proposed method can be applied when (i) all orientat...
Finiteness of entropy for granular media equations
Tugaut, Julian
2015-01-01
The current work deals with the granular media equation, which prob-abilistic interpretation is the McKean-Vlasov diffusion. It is well-known that the Laplacian provides a regularization of the solution. Indeed, for any t > 0, the solution is absolutely continuous with respect to the Lebesgue measure. It has also been proven that all the moments are bounded for positive t. However, the finiteness of the entropy of the solution is a new result, that we present here.
Volkenstein, Mikhail V
2009-01-01
The book "Entropy and Information" deals with the thermodynamical concept of entropy and its relationship to information theory. It is successful in explaining the universality of the term "Entropy" not only as a physical phenomenon, but reveals its existence also in other domains. E.g., Volkenstein discusses the "meaning" of entropy in a biological context and shows how entropy is related to artistic activities. Written by the renowned Russian bio-physicist Mikhail V. Volkenstein, this book on "Entropy and Information" surely serves as a timely introduction to understand entropy from a thermodynamic perspective and is definitely an inspiring and thought-provoking book that should be read by every physicist, information-theorist, biologist, and even artist.
The Nernst theorem and statistical entropy in a (1+1)-dimensional charged black hole
It was derived that the bosonic and fermionic entropies in (1+1)-dimensional charged black hole directly by using the quantum statistical method. The result is the same as the integral expression obtained by solving the wave equation approximately. Then it is obtained the statistical entropy of the black hole by integration via the improved brick-wall method, membrane model. The derived entropy satisfies the thermodynamic relation. When the radiation temperature of the black hole tends to zero, so does the entropy. It obeys Nernst theorem. So it can be taken as Planck absolute entropy
RNA Thermodynamic Structural Entropy.
Juan Antonio Garcia-Martin
Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http
Thermodynamic efficiency and entropy production in the climate system.
Lucarini, Valerio
2009-08-01
We present an outlook on the climate system thermodynamics. First, we construct an equivalent Carnot engine with efficiency eta and frame the Lorenz energy cycle in a macroscale thermodynamic context. Then, by exploiting the second law, we prove that the lower bound to the entropy production is eta times the integrated absolute value of the internal entropy fluctuations. An exergetic interpretation is also proposed. Finally, the controversial maximum entropy production principle is reinterpreted as requiring the joint optimization of heat transport and mechanical work production. These results provide tools for climate change analysis and for climate models' validation. PMID:19792088
Maximum-entropy probability distributions under Lp-norm constraints
Dolinar, S.
1991-01-01
Continuous probability density functions and discrete probability mass functions are tabulated which maximize the differential entropy or absolute entropy, respectively, among all probability distributions with a given L sub p norm (i.e., a given pth absolute moment when p is a finite integer) and unconstrained or constrained value set. Expressions for the maximum entropy are evaluated as functions of the L sub p norm. The most interesting results are obtained and plotted for unconstrained (real valued) continuous random variables and for integer valued discrete random variables. The maximum entropy expressions are obtained in closed form for unconstrained continuous random variables, and in this case there is a simple straight line relationship between the maximum differential entropy and the logarithm of the L sub p norm. Corresponding expressions for arbitrary discrete and constrained continuous random variables are given parametrically; closed form expressions are available only for special cases. However, simpler alternative bounds on the maximum entropy of integer valued discrete random variables are obtained by applying the differential entropy results to continuous random variables which approximate the integer valued random variables in a natural manner. All the results are presented in an integrated framework that includes continuous and discrete random variables, constraints on the permissible value set, and all possible values of p. Understanding such as this is useful in evaluating the performance of data compression schemes.
Relative entropy equals bulk relative entropy
Jafferis, Daniel L; Maldacena, Juan; Suh, S Josephine
2015-01-01
We consider the gravity dual of the modular Hamiltonian associated to a general subregion of a boundary theory. We use it to argue that the relative entropy of nearby states is given by the relative entropy in the bulk, to leading order in the bulk gravitational coupling. We also argue that the boundary modular flow is dual to the bulk modular flow in the entanglement wedge, with implications for entanglement wedge reconstruction.
Statistical entropy of de Sitter space
Quantum gravity in 2+1 dimensions with a positive cosmological constant can be represented as an SL(2,C) Chern-Simons gauge theory. The symmetric vacuum of this theory is a degenerate configuration for which the gauge fields and spacetime metric vanish, while de Sitter space corresponds to a highly excited thermal state. Carlip's approach to black hole entropy can be adapted in this context to determine the statistical entropy of de Sitter space. We find that it equals one-quarter the area of the de Sitter horizon, in agreement with the semiclassical formula. (author)
A deduction of generalized quantum entropies within the Tsallis and Kaniadakis frameworks is derived using a generalization of the ordinary multinomial coefficient. This generalization is based on the respective deformed multiplication and division. We show that the two above entropies are consistent with ones arbitrarily assumed at other contexts. -- Highlights: → Derivation of generalized quantum entropies. → Generalized combinatorial method. → Non-Gaussian quantum statistics.
RNA thermodynamic structural entropy
Garcia-Martin, Juan Antonio; Clote, Peter
2015-01-01
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute th...
Calibration with Absolute Shrinkage
Øjelund, Henrik; Madsen, Henrik; Thyregod, Poul
2001-01-01
In this paper, penalized regression using the L-1 norm on the estimated parameters is proposed for chemometric je calibration. The algorithm is of the lasso type, introduced by Tibshirani in 1996 as a linear regression method with bound on the absolute length of the parameters, but a modification...
Black Hole Entropy from Entropy of Hawking Radiation
Aghapour, Sajad
2016-01-01
We provide a simple way for calculating the entropy of a Schwarzschild black hole from the entropy of its Hawking radiation. To this end, we show that if a thermodynamic system loses its energy only through the black body radiation, its loss of entropy is always 3/4 of the entropy of the emitted radiation. This proposition enables us to relate the entropy of an evaporating black hole to the entropy of its Hawking radiation. Explicitly, by calculating the entropy of the Hawking radiation emitted in the full period of evaporation of the black hole, we find the Bekenstein-Hawking entropy of the initial black hole.
Renyi extrapolation of Shannon entropy
Zyczkowski, K
2003-01-01
Relations between Shannon entropy and Renyi entropies of integer order are discussed. For any N-point discrete probability distribution for which the Renyi entropies of order two and three are known, we provide an lower and an upper bound for the Shannon entropy. The average of both bounds provide an explicit extrapolation for this quantity. These results imply relations between the von Neumann entropy of a mixed quantum state, its linear entropy and traces.
WANG, DONG-SHENG
2012-01-01
Regarding the strange properties of quantum entropy and entanglement, e.g., the negative quantum conditional entropy, we revisited the foundations of quantum entropy, namely, von Neumann entropy, and raised the new method of quantum fine-grained entropy. With the applications in entanglement theory, quantum information processing, and quantum thermodynamics, we demonstrated the capability of quantum fine-grained entropy to resolve some notable confusions and problems, including the measure of...
Santos, A. P.; Silva, R.; Alcaniz, J. S.; Anselmo, D. H. A. L.
2011-08-01
A deduction of generalized quantum entropies within the Tsallis and Kaniadakis frameworks is derived using a generalization of the ordinary multinomial coefficient. This generalization is based on the respective deformed multiplication and division. We show that the two above entropies are consistent with ones arbitrarily assumed at other contexts.
Berman, Marcelo Samuel
2009-01-01
After a discussion on several limiting cases where General Relativity turns into less sophisticated theories, we find that in the correct thermodynamical and cosmological weak field limit of Einstein's field equations the entropy of the Universe is R^(3/2) -- dependent, where R stands for the radius of the causally related Universe. Thus, entropy grows in the Universe, contrary to Standard Cosmology prediction.
Entropy and Ionic Conductivity
Zhang, Yong-Jun
2012-01-01
It is known that the ionic conductivity can be obtained by using the diffusion constant and the Einstein relation. We derive it here by extracting it from the steady electric current which we calculate in three ways, using statistics analysis, an entropy method, and an entropy production approach.
Tanase, Viorel Iulian; Balan, Mihai; Paraschiv, Ruxandra Victoria
2011-01-01
The article shows that the repartition of the maximum entropy is the uniform repartition and contains the highest disorder degree which means the highest quantity of information in potential status. Entropy which measures the disorder is not opposite to the Quantity of Information (the dimension for order) but the potential of the Quantity of Information.
da Cruz, Wellington
2002-01-01
We consider the {\\it fractal von Neumann entropy} associated with the {\\it fractal distribution function} and we obtain for some {\\it universal classes h of fractons} their entropies. We obtain also for each of these classes a {\\it fractal-deformed Heisenberg algebra}. This one takes into account the braid group structure of these objects which live in two-dimensional multiply connected space.
Klauber, Robert D.
2010-01-01
Entropy decreases on the Earth due to day/night temperature differences. This decrease exceeds the decrease in entropy on the Earth related to evolution by many orders of magnitude. Claims by creationists that science is somehow inconsistent with regard to evolution are thus show to be baseless.
Marder, Daniel
The Second Law of Thermodynamics demonstrates the idea of entropy, the tendency of ordered energy to free itself and thus break apart the system that contains it and dissipate that system into chaos. When applied to communications theory, entropy increases not only with noise but with the density of information--particles of possible meaning…
Pedro Cabral
2013-11-01
Full Text Available Entropy is a useful concept that has been used to describe the structure and behavior of different systems. We summarize its multifaceted character with regard to its implications for urban sprawl, and propose a framework to apply the concept of entropy to urban sprawl for monitoring and management.
Since the recent convincing evidence for massive neutrinos in oscillation experiments, the next task is to determine the absolute masses of neutrinos. A unique pattern of neutrino masses will be hopefully fixed in the future superbeam experiments and neutrino factories. However, the determination of the exact scale is more complicated and depends on the mass of the lightest neutrino ( mμ )min . If ( mμ)min ≥ 0.35 eV, the future tritium β decay experiments ( e.g. KATRIN) will have a chance to establish absolute neutrino masses. For smaller masses, 0.004 eV ≤ (mμ)min ≤ 0.35 eV, if neutrinos are Majorana particles, an additional information can be derived from the neutrinoless double β decay (ββ)0μ of nuclei and again the absolute neutrino masses can be fixed. If, however, (mμ)min ≤ 0.004 eV, none of the present and foreseeable future experiments is known to be able to fix the mass scale. (author)
The reformulation of Lieb's entropy conjecture, in the frame of the harmonic analysis on the SO(3) group, makes it evident that the exact value of the classical entropy of a pure quantum state, which belongs to the Hilbert space Hsub(J) of a (2J+1) - dimensional, unitary, irreducible representation Usub(J) of the SO(3) group, depends only on the parameters which characterize the orbits of Usub(J) in Hsub(J). In the case J = 1 we give the exact analytic dependence of the classical entropy of a quantum state on the parameter which characterizes the orbits and as a consequence we obtain a verification of Lieb's entropy conjecture. We verify this conjecture also for any value of J for the states of the canonical basis of Hsub(J). A natural generalization of Lieb's entropy conjecture, which is a new ''phenomenon'' in the harmonic analysis on SO(3), is discussed in the case J = 1. (author)
Entropy, Perception, and Relativity
Jaeger, Stefan
2008-01-01
In this paper, I expand Shannon's definition of entropy into a new form of entropy that allows integration of information from different random events. Shannon's notion of entropy is a special case of my more general definition of entropy. I define probability using a so-called performance function, which is de facto an exponential distribution. Assuming that my general notion of entropy reflects the true uncertainty about a probabilistic event, I understand that our perceived uncertainty differs. I claim that our perception is the result of two opposing forces similar to the two famous antagonists in Chinese philosophy: Yin and Yang. Based on this idea, I show that our perceived uncertainty matches the true uncertainty in points determined by the golden ratio. I demonstrate that the well-known sigmoid function, which we typically employ in artificial neural networks as a non-linear threshold function, describes the actual performance. Furthermore, I provide a motivation for the time dilation in Einstein's Sp...
Entropic Measure for Localized Energy Configurations: Kinks, Bounces, and Bubbles
Gleiser, Marcelo
2011-01-01
We construct a configurational entropy measure in functional space. We apply it to several nonlinear scalar field models featuring solutions with spatially-localized energy, including solitons and bounces in one spatial dimension, and critical bubbles in three spatial dimensions, typical of first-order phase transitions. Such field models are of widespread interest in many areas of physics, from high energy and cosmology to condensed matter. Using a variational approach, we show that the higher the energy of a trial function that approximates the actual solution, the higher its relative configurational entropy. Furthermore, we show that when different trial functions have degenerate energies, the configurational entropy can be used to select the best fit to the actual solution. The configurational entropy relates the dynamical and informational content of physical models and can be applied to any nonlinear field model.
Entanglement Entropy of AdS Black Holes
Maurizio Melis
2010-11-01
Full Text Available We review recent progress in understanding the entanglement entropy of gravitational configurations for anti-de Sitter gravity in two and three spacetime dimensions using the AdS/CFT correspondence. We derive simple expressions for the entanglement entropy of two- and three-dimensional black holes. In both cases, the leading term of the entanglement entropy in the large black hole mass expansion reproduces exactly the Bekenstein-Hawking entropy, whereas the subleading term behaves logarithmically. In particular, for the BTZ black hole the leading term of the entanglement entropy can be obtained from the large temperature expansion of the partition function of a broad class of 2D CFTs on the torus.
Numerical viscosity of entropy stable schemes for systems of conservation laws. Final Report
Discrete approximations to hyperbolic systems of conservation laws are studied. The amount of numerical viscosity present in such schemes is quantified and related to their entropy stability by means of comparison. To this end conservative schemes which are also entropy conservative are constructed. These entropy conservative schemes enjoy second-order accuracy; moreover, they admit a particular interpretation within the finite-element frameworks, and hence can be formulated on various mesh configurations. It is then shown that conservative schemes are entropy stable if and only if they contain more viscosity than the mentioned above entropy conservative ones
The numerical viscosity of entropy stable schemes for systems of conservation laws. I
Tadmor, Eitan
1987-01-01
Discrete approximations to hyperbolic systems of conservation laws are studied. The amount of numerical viscosity present in such schemes is quantified and related to their entropy stability by means of comparison.To this end, conservative schemes which are also entropy-conservative are constructed. These entropy-conservative schemes enjoy second-order accuracy; moreover, they can be interpreted as piecewise-linear finite-element methods, and hence can be formulated on various mesh configurations. It is then shown that conservative schemes are entropy stable, if and (for three-point schemes) only they contain more viscosity than that present in the above-mentioned entropy-conservative ones.
The numerical viscosity of entropy stable schemes for systems of conservation laws
Tadmor, E.
1985-01-01
Discrete approximations to hyperbolic systems of conservation laws are studied. The amount of numerical viscosity present in such schemes, is quantified and related to their entropy stability by means of comparison. To this end, conservative schemes which are also entropy conservative are constructed. These entropy conservative schemes enjoy second-order accuracy; moreover, they admit a particular interpretation within the finite-element frameworks, and hence can be formulated on various mesh configurations. It is then shown that conservative schemes are entropy stable if and only if they contain more viscosity than the mentioned above entropy conservative ones.
Black hole thermodynamical entropy
Tsallis, Constantino [Centro Brasileiro de Pesquisas Fisicas and National Institute of Science and Technology for Complex Systems, Rio de Janeiro, RJ (Brazil); Santa Fe Institute, Santa Fe, NM (United States); Cirto, Leonardo J.L. [Centro Brasileiro de Pesquisas Fisicas and National Institute of Science and Technology for Complex Systems, Rio de Janeiro, RJ (Brazil)
2013-07-15
As early as 1902, Gibbs pointed out that systems whose partition function diverges, e.g. gravitation, lie outside the validity of the Boltzmann-Gibbs (BG) theory. Consistently, since the pioneering Bekenstein-Hawking results, physically meaningful evidence (e.g., the holographic principle) has accumulated that the BG entropy S{sub BG} of a (3+1) black hole is proportional to its area L{sup 2} (L being a characteristic linear length), and not to its volume L{sup 3}. Similarly it exists the area law, so named because, for a wide class of strongly quantum-entangled d-dimensional systems, S{sub BG} is proportional to lnL if d=1, and to L{sup d-1} if d>1, instead of being proportional to L{sup d} (d {>=} 1). These results violate the extensivity of the thermodynamical entropy of a d-dimensional system. This thermodynamical inconsistency disappears if we realize that the thermodynamical entropy of such nonstandard systems is not to be identified with the BG additive entropy but with appropriately generalized nonadditive entropies. Indeed, the celebrated usefulness of the BG entropy is founded on hypothesis such as relatively weak probabilistic correlations (and their connections to ergodicity, which by no means can be assumed as a general rule of nature). Here we introduce a generalized entropy which, for the Schwarzschild black hole and the area law, can solve the thermodynamic puzzle. (orig.)
Leonid M. Martyushev
2015-06-01
Full Text Available The entropy production (inside the volume bounded by a photosphere of main-sequence stars, subgiants, giants, and supergiants is calculated based on B–V photometry data. A non-linear inverse relationship of thermodynamic fluxes and forces as well as an almost constant specific (per volume entropy production of main-sequence stars (for 95% of stars, this quantity lies within 0.5 to 2.2 of the corresponding solar magnitude is found. The obtained results are discussed from the perspective of known extreme principles related to entropy production.
OKADA; BRAVAR, A.; BUNCE, G.; GILL, R.; HUANG, H.; MAKDISI, Y.; NASS, A.; WOOD, J.; ZELENSKI, Z.; ET AL.
2007-09-10
Precise and absolute beam polarization measurements are critical for the RHIC spin physics program. Because all experimental spin-dependent results are normalized by beam polarization, the normalization uncertainty contributes directly to final physics uncertainties. We aimed to perform the beam polarization measurement to an accuracy Of {Delta}P{sub beam}/P{sub beam} < 5%. The absolute polarimeter consists of Polarized Atomic Hydrogen Gas Jet Target and left-right pairs of silicon strip detectors and was installed in the RHIC-ring in 2004. This system features proton-proton elastic scattering in the Coulomb nuclear interference (CNI) region. Precise measurements of the analyzing power A{sub N} of this process has allowed us to achieve {Delta}P{sub beam}/P{sub beam} = 4.2% in 2005 for the first long spin-physics run. In this report, we describe the entire set up and performance of the system. The procedure of beam polarization measurement and analysis results from 2004-2005 are described. Physics topics of AN in the CNI region (four-momentum transfer squared 0.001 < -t < 0.032 (GeV/c){sup 2}) are also discussed. We point out the current issues and expected optimum accuracy in 2006 and the future.
Okada, H; Bravar, A; Bunce, G; Dhawan, S; Eyser, K O; Gill, R; Haeberli, W; Huang, H; Jinnouchi, O; Makdisi, Y; Nakagawa, I; Nass, A; Saitô, N; Stephenson, E; Sviridia, D; Wise, T; Wood, J; Zelenski, A
2007-01-01
Precise and absolute beam polarization measurements are critical for the RHIC spin physics program. Because all experimental spin-dependent results are normalized by beam polarization, the normalization uncertainty contributes directly to final physics uncertainties. We aimed to perform the beam polarization measurement to an accuracy of $\\Delta P_{beam}/P_{beam} < 5%$. The absolute polarimeter consists of Polarized Atomic Hydrogen Gas Jet Target and left-right pairs of silicon strip detectors and was installed in the RHIC-ring in 2004. This system features \\textit{proton-proton} elastic scattering in the Coulomb nuclear interference (CNI) region. Precise measurements of the analyzing power $A_N$ of this process has allowed us to achieve $\\Delta P_{beam}/P_{beam} =4.2%$ in 2005 for the first long spin-physics run. In this report, we describe the entire set up and performance of the system. The procedure of beam polarization measurement and analysis results from 2004-2005 are described. Physics topics of $A...
Entropy in Corporate Information Systems
Victor Y. Tsvetkov
2014-03-01
Full Text Available This paper describes the stages of entropy formation. It depicts the basic definitions of the corporate information systems. This paper describes the quality of entropy, the duration of the entropy in the corporate information system. The article also gives a paradigmatic description of the action of information entropy in time.
Renormalized entanglement entropy
Taylor, Marika
2016-01-01
We develop a renormalization method for holographic entanglement entropy based on area renormalization of entangling surfaces. The renormalized entanglement entropy is derived for entangling surfaces in asymptotically locally anti-de Sitter spacetimes in general dimensions and for entangling surfaces in four dimensional holographic renormalization group flows. The renormalized entanglement entropy for disk regions in $AdS_4$ spacetimes agrees precisely with the holographically renormalized action for $AdS_4$ with spherical slicing and hence with the F quantity, in accordance with the Casini-Huerta-Myers map. We present a generic class of holographic RG flows associated with deformations by operators of dimension $3/2 < \\Delta < 5/2$ for which the F quantity increases along the RG flow, hence violating the strong version of the F theorem. We conclude by explaining how the renormalized entanglement entropy can be derived directly from the renormalized partition function using the replica trick i.e. our re...
Anomalies and entanglement entropy
Nishioka, Tatsuma; Yarom, Amos(Department of Physics, Technion, Haifa, 32000, Israel)
2016-01-01
We initiate a systematic study of entanglement and Renyi entropies in the presence of gauge and gravitational anomalies in even-dimensional quantum field theories. We argue that the mixed and gravitational anomalies are sensitive to boosts and obtain a closed form expression for their behavior under such transformations. Explicit constructions exhibiting the dependence of entanglement entropy on boosts is provided for theories on spacetimes with non-trivial magnetic fluxes and (or) non-vanish...
Psychotherapy as entropy management
McKenzie, Karen; Murray, George
2013-01-01
We present the hypothesis that the laws of thermodynamics can be usefully applied to psychotherapy. In this model psychotherapy is presented as a means of entropy management, whereby the patient trades entropy (in this case the expressed symptoms of mental disorder) with the therapist. The therapist serves to increase the capacity of the patient, both through developing a shared understanding of the challenges the patient faces and through generating shared solutions. This process can be unde...
Feasible Histories, Maximum Entropy
We consider the broadest possible consistency condition for a family of histories, which extends all previous proposals. A family that satisfies this condition is called feasible. On each feasible family of histories we choose a probability measure by maximizing entropy, while keeping the probabilities of commuting histories to their quantum mechanical values. This procedure is justified by the assumption that decoherence increases entropy. Finally, a criterion for identifying the nearly classical families is proposed
Bousso, Raphael
2016-01-01
We show that known entropy bounds constrain the information carried off by radiation to null infinity. We consider distant, planar null hypersurfaces in asymptotically flat spacetime. Their focussing and area loss can be computed perturbatively on a Minkowski background, yielding entropy bounds in terms of the energy flux of the outgoing radiation. In the asymptotic limit, we obtain boundary versions of the Quantum Null Energy Condition, of the Generalized Second Law, and of the Quantum Bousso Bound.
Gross, D. H. E.
2006-01-01
The physical meaning of entropy is analyzed in the context of statistical, nuclear, atomic physics and cosmology. Only the microcanonical Boltzmann entropy leads to no contradictions in several simple, elementary and for thermodynamics important situations. The conventional canonical statistics implies several serious errors and misinterpretations. This has far reaching consequences for phase-separations as well for the usual formulations of the second law. Applications in cosmology suffer un...
Pal, Subrata; Pratt, Scott
2003-01-01
For central heavy ion collisions at the RHIC energy, the entropy per unit rapidity dS/dy at freeze-out is extracted with minimal model dependence from available experimental measurements of particle yields, spectra, and source sizes estimated from two-particle interferometry. The extracted entropy rapidity density is consistent with lattice gauge theory results for a thermalized quark-gluon plasma with an energy density estimated from transverse energy production at RHIC.
John Scales Avery
2012-01-01
In this essay, human society is regarded as a “superorganism”, analogous to colonies of social insects. The digestive system of the human superorganism is the global economy, which ingests both free energy and resources, and later excretes them in a degraded form. This process involves an increase in entropy. Early in the 20th century, both Frederick Soddy and Nicholas Georgescu-Roegen discussed the relationship between entropy and economics. Soddy called for an index system to regulate the m...
Entropy and economic modelling
D F Batten; Roy, J R
1982-01-01
Entropy-maximizing models have been focused predominantly at the microscopic level of social and economic activities, their use being advocated by urban geographers, mathematicians, and microeconomists. By maintaining a sharp distinction between the behavioural and statistical aspects of entropy, various submodels may be formulated to generate the most probable pattern of individual choice behaviour. It may nevertheless be possible to regard each submodel of activity as an essential component...
Anomalies and Entanglement Entropy
Nishioka, Tatsuma
2015-01-01
We initiate a systematic study of entanglement and Renyi entropies in the presence of gauge and gravitational anomalies in even-dimensional quantum field theories. We argue that the mixed and gravitational anomalies are sensitive to boosts and obtain a closed form expression for their behavior under such transformations. Explicit constructions exhibiting the dependence of entanglement entropy on boosts is provided for theories on spacetimes with non-trivial magnetic fluxes and (or) non-vanishing Pontryagin classes.
Guevara, E
2006-01-01
We propose the study of quantum games from the point of view of quantum information theory and statistical mechanics. Every game can be described by a density operator, with its entropy equal to von Neumann's and its evolution given by the quantum replicator dynamics. There exists a strong relationship between game theory, quantum information theory and statistical physics. The density operator and entropy are the bonds between these theories. The analysis we propose for the study of these games is based on the properties of entropy, the amount of information that a player can obtain about his opponent and a maximum or minimum entropy criterion. The natural trend of a physical system is to its maximum entropy state. The minimum entropy state is a characteristic of a "manipulated" system i.e. externally controlled or imposed. There exists tacit rules inside a system that do not need to be specified nor clarified and search the system equilibrium under the collective welfare principle. The other rules are impos...
Optical tweezers absolute calibration
Dutra, R S; Neto, P A Maia; Nussenzveig, H M
2014-01-01
Optical tweezers are highly versatile laser traps for neutral microparticles, with fundamental applications in physics and in single molecule cell biology. Force measurements are performed by converting the stiffness response to displacement of trapped transparent microspheres, employed as force transducers. Usually, calibration is indirect, by comparison with fluid drag forces. This can lead to discrepancies by sizable factors. Progress achieved in a program aiming at absolute calibration, conducted over the past fifteen years, is briefly reviewed. Here we overcome its last major obstacle, a theoretical overestimation of the peak stiffness, within the most employed range for applications, and we perform experimental validation. The discrepancy is traced to the effect of primary aberrations of the optical system, which are now included in the theory. All required experimental parameters are readily accessible. Astigmatism, the dominant effect, is measured by analyzing reflected images of the focused laser spo...
Aunion, Jose Luis Alcaraz; /Barcelona, IFAE
2010-07-01
This thesis presents the measurement of the charged current quasi-elastic (CCQE) neutrino-nucleon cross section at neutrino energies around 1 GeV. This measurement has two main physical motivations. On one hand, the neutrino-nucleon interactions at few GeV is a region where existing old data are sparse and with low statistics. The current measurement populates low energy regions with higher statistics and precision than previous experiments. On the other hand, the CCQE interaction is the most useful interaction in neutrino oscillation experiments. The CCQE channel is used to measure the initial and final neutrino fluxes in order to determine the neutrino fraction that disappeared. The neutrino oscillation experiments work at low neutrino energies, so precise measurement of CCQE interactions are essential for flux measurements. The main goal of this thesis is to measure the CCQE absolute neutrino cross section from the SciBooNE data. The SciBar Booster Neutrino Experiment (SciBooNE) is a neutrino and anti-neutrino scattering off experiment. The neutrino energy spectrum works at energies around 1 GeV. SciBooNE was running from June 8th 2007 to August 18th 2008. In that period, the experiment collected a total of 2.65 x 10{sup 20} protons on target (POT). This thesis has used full data collection in neutrino mode 0.99 x 10{sup 20} POT. A CCQE selection cut has been performed, achieving around 70% pure CCQE sample. A fit method has been exclusively developed to determine the absolute CCQE cross section, presenting results in a neutrino energy range from 0.2 to 2 GeV. The results are compatible with the NEUT predictions. The SciBooNE measurement has been compared with both Carbon (MiniBoonE) and deuterium (ANL and BNL) target experiments, showing a good agreement in both cases.
Dupuis, Frédéric; Wilde, Mark M.
2016-03-01
This paper introduces "swiveled Rényi entropies" as an alternative to the Rényi entropic quantities put forward in Berta et al. (Phys Rev A 91(2):022333, 2015). What distinguishes the swiveled Rényi entropies from the prior proposal of Berta et al. is that there is an extra degree of freedom: an optimization over unitary rotations with respect to particular fixed bases (swivels). A consequence of this extra degree of freedom is that the swiveled Rényi entropies are ordered, which is an important property of the Rényi family of entropies. The swiveled Rényi entropies are, however, generally discontinuous at α =1 and do not converge to the von Neumann entropy-based measures in the limit as α rightarrow 1, instead bounding them from above and below. Particular variants reduce to known Rényi entropies, such as the Rényi relative entropy or the sandwiched Rényi relative entropy, but also lead to ordered Rényi conditional mutual information and ordered Rényi generalizations of a relative entropy difference. Refinements of entropy inequalities such as monotonicity of quantum relative entropy and strong subadditivity follow as a consequence of the aforementioned properties of the swiveled Rényi entropies. Due to the lack of convergence at α =1, it is unclear whether the swiveled Rényi entropies would be useful in one-shot information theory, so that the present contribution represents partial progress toward this goal.
Absolute neutrino mass measurements
Wolf, Joachim
2011-10-01
The neutrino mass plays an important role in particle physics, astrophysics and cosmology. In recent years the detection of neutrino flavour oscillations proved that neutrinos carry mass. However, oscillation experiments are only sensitive to the mass-squared difference of the mass eigenvalues. In contrast to cosmological observations and neutrino-less double beta decay (0v2β) searches, single β-decay experiments provide a direct, model-independent way to determine the absolute neutrino mass by measuring the energy spectrum of decay electrons at the endpoint region with high accuracy. Currently the best kinematic upper limits on the neutrino mass of 2.2eV have been set by two experiments in Mainz and Troitsk, using tritium as beta emitter. The next generation tritium β-experiment KATRIN is currently under construction in Karlsruhe/Germany by an international collaboration. KATRIN intends to improve the sensitivity by one order of magnitude to 0.2eV. The investigation of a second isotope (137Rh) is being pursued by the international MARE collaboration using micro-calorimeters to measure the beta spectrum. The technology needed to reach 0.2eV sensitivity is still in the R&D phase. This paper reviews the present status of neutrino-mass measurements with cosmological data, 0v2β decay and single β-decay.
Comparisons of Black Hole Entropy
Kupferman, Judy
2016-01-01
In this thesis I examine several different concepts of black hole entropy in order to understand whether they describe the same quantity. I look at statistical and entanglement entropies, Wald entropy and Carlip's entropy from conformal field theory, and compare their behavior in a few specific aspects: divergence at the BH horizon, dependence on space time curvature and behavior under a geometric variation. I find that statistical and entanglement entropy may be similar but they seem to differ from the entropy of Wald and Carlip. Chapters 2 and 3 overlap with 1010.4157 and 1310.3938. Chapter 4 does not appear elsewhere.
The Elusive Nature of Entropy and Its Physical Meaning
Milivoje M. Kostic
2014-02-01
Full Text Available Entropy is the most used and often abused concept in science, but also in philosophy and society. Further confusions are produced by some attempts to generalize entropy with similar but not the same concepts in other disciplines. The physical meaning of phenomenological, thermodynamic entropy is reasoned and elaborated by generalizing Clausius definition with inclusion of generated heat, since it is irrelevant if entropy is changed due to reversible heat transfer or irreversible heat generation. Irreversible, caloric heat transfer is introduced as complementing reversible heat transfer. It is also reasoned and thus proven why entropy cannot be destroyed but is always generated (and thus over-all increased locally and globally, at every space and time scales, without any exception. It is concluded that entropy is a thermal displacement (dynamic thermal-volume of thermal energy due to absolute temperature as a thermal potential (dQ = TdS, and thus associated with thermal heat and absolute temperature, i.e., distribution of thermal energy within thermal micro-particles in space. Entropy is an integral measure of (random thermal energy redistribution (due to heat transfer and/or irreversible heat generation within a material system structure in space, per absolute temperature level: dS = dQSys/T = mCSysdT/T, thus logarithmic integral function, with J/K unit. It may be also expressed as a measure of “thermal disorder”, being related to logarithm of number of all thermal, dynamic microstates W (their position and momenta, S = kBlnW, or to the sum of their logarithmic probabilities S = −kB∑pilnpi, that correspond to, or are consistent with the given thermodynamic macro-state. The number of thermal microstates W, is correlated with macro-properties temperature T and volume V for ideal gases. A system form and/or functional order or disorder are not (thermal energy order/disorder and the former is not related to Thermodynamic entropy. Expanding
Kay, Bernard S
2015-01-01
We give an account of the matter-gravity entanglement hypothesis which, unlike the standard approach to entropy based on coarse-graining, offers a definition for the entropy of a closed system as a real and objective quantity. We explain how this new approach offers an explanation for the Second Law of Thermodynamics in general and a non-paradoxical understanding of information loss during black hole formation and evaporation in particular. We also very briefly review some recent related work on the nature of equilibrium states involving quantum black holes and point out how it promises to resolve some puzzling issues in the current version of the string theory approach to black hole entropy.
Angel Garrido
2011-07-01
Full Text Available Our paper analyzes some aspects of Uncertainty Measures. We need to obtain new ways to model adequate conditions or restrictions, constructed from vague pieces of information. The classical entropy measure originates from scientific fields; more specifically, from Statistical Physics and Thermodynamics. With time it was adapted by Claude Shannon, creating the current expanding Information Theory. However, the Hungarian mathematician, Alfred Rényi, proves that different and valid entropy measures exist in accordance with the purpose and/or need of application. Accordingly, it is essential to clarify the different types of measures and their mutual relationships. For these reasons, we attempt here to obtain an adequate revision of such fuzzy entropy measures from a mathematical point of view.
Information Entropy Dynamics and Maximum Entropy Production Principle
Fradkov, Alexander L.; Shalymov, Dmitry S.
2014-01-01
The asymptotic convergence of probability density function (pdf) and convergence of differential entropy are examined for the non-stationary processes that follow the maximum entropy principle (MaxEnt) and maximum entropy production principle (MEPP). Asymptotic convergence of pdf provides new justification of MEPP while convergence of differential entropy is important in asymptotic analysis of communication systems. A set of equations describing the dynamics of pdf under mass conservation and...
Estimating Absolute Site Effects
Malagnini, L; Mayeda, K M; Akinci, A; Bragato, P L
2004-07-15
The authors use previously determined direct-wave attenuation functions as well as stable, coda-derived source excitation spectra to isolate the absolute S-wave site effect for the horizontal and vertical components of weak ground motion. They used selected stations in the seismic network of the eastern Alps, and find the following: (1) all ''hard rock'' sites exhibited deamplification phenomena due to absorption at frequencies ranging between 0.5 and 12 Hz (the available bandwidth), on both the horizontal and vertical components; (2) ''hard rock'' site transfer functions showed large variability at high-frequency; (3) vertical-motion site transfer functions show strong frequency-dependence, and (4) H/V spectral ratios do not reproduce the characteristics of the true horizontal site transfer functions; (5) traditional, relative site terms obtained by using reference ''rock sites'' can be misleading in inferring the behaviors of true site transfer functions, since most rock sites have non-flat responses due to shallow heterogeneities resulting from varying degrees of weathering. They also use their stable source spectra to estimate total radiated seismic energy and compare against previous results. they find that the earthquakes in this region exhibit non-constant dynamic stress drop scaling which gives further support for a fundamental difference in rupture dynamics between small and large earthquakes. To correct the vertical and horizontal S-wave spectra for attenuation, they used detailed regional attenuation functions derived by Malagnini et al. (2002) who determined frequency-dependent geometrical spreading and Q for the region. These corrections account for the gross path effects (i.e., all distance-dependent effects), although the source and site effects are still present in the distance-corrected spectra. The main goal of this study is to isolate the absolute site effect (as a function of frequency
Dimensional Equations of Entropy
Sparavigna, Amelia Carolina
2015-01-01
Entropy is a quantity which is of great importance in physics and chemistry. The concept comes out of thermodynamics, proposed by Rudolf Clausius in his analysis of Carnot cycle and linked by Ludwig Boltzmann to the number of specific ways in which a physical system may be arranged. Any physics classroom, in its task of learning physics, has therefore to face this crucial concept. As we will show in this paper, the lectures can be enriched by discussing dimensional equations linked to the entropy of some physical systems.
Rezaei, Seyed Saeed Changiz
2013-01-01
The entropy of a graph is a functional depending both on the graph itself and on a probability distribution on its vertex set. This graph functional originated from the problem of source coding in information theory and was introduced by J. K\\"{o}rner in 1973. Although the notion of graph entropy has its roots in information theory, it was proved to be closely related to some classical and frequently studied graph theoretic concepts. For example, it provides an equivalent definition for a gra...
Entanglement Entropy and Duality
Radicevic, Djordje
2016-01-01
Using the algebraic approach to entanglement entropy, we study several dual pairs of lattice theories and show how the entropy is completely preserved across each duality. Our main result is that a maximal algebra of observables in a region typically dualizes to a non-maximal algebra in a dual region. In particular, we show how the usual notion of tracing out external degrees of freedom dualizes to a tracing out coupled to an additional summation over superselection sectors. We briefly comment on possible extensions of our results to more intricate dualities, including holographic ones.
For some years now two different expressions have been in use for maximum entropy image restoration and there has been some controversy over which one is appropriate for a given problem. Here two further entropies are presented and it is argued that there is no single correct algorithm. The properties of the four different methods are compared using simple 1D simulations with a view to showing how they can be used together to gain as much information as possible about the original object. (orig.)
Gross, D H E
2006-01-01
The physical meaning of entropy is analyzed in the context of statistical, nuclear, atomic physics and cosmology. Only the microcanonical Boltzmann entropy leads to no contradictions in several simple, elementary and for thermodynamics important situations. The conventional canonical statistics implies several serious errors and misinterpretations. This has far reaching consequences for phase-separations as well for the usual formulations of the second law. Applications in cosmology suffer under the ubiquitous use of canonical statistics. New reformulations in terms of microcanonical statistics are highly demanded but certainly difficult.
F. TopsÃƒÂ¸e
2001-09-01
Full Text Available Abstract: In its modern formulation, the Maximum Entropy Principle was promoted by E.T. Jaynes, starting in the mid-fifties. The principle dictates that one should look for a distribution, consistent with available information, which maximizes the entropy. However, this principle focuses only on distributions and it appears advantageous to bring information theoretical thinking more prominently into play by also focusing on the "observer" and on coding. This view was brought forward by the second named author in the late seventies and is the view we will follow-up on here. It leads to the consideration of a certain game, the Code Length Game and, via standard game theoretical thinking, to a principle of Game Theoretical Equilibrium. This principle is more basic than the Maximum Entropy Principle in the sense that the search for one type of optimal strategies in the Code Length Game translates directly into the search for distributions with maximum entropy. In the present paper we offer a self-contained and comprehensive treatment of fundamentals of both principles mentioned, based on a study of the Code Length Game. Though new concepts and results are presented, the reading should be instructional and accessible to a rather wide audience, at least if certain mathematical details are left aside at a rst reading. The most frequently studied instance of entropy maximization pertains to the Mean Energy Model which involves a moment constraint related to a given function, here taken to represent "energy". This type of application is very well known from the literature with hundreds of applications pertaining to several different elds and will also here serve as important illustration of the theory. But our approach reaches further, especially regarding the study of continuity properties of the entropy function, and this leads to new results which allow a discussion of models with so-called entropy loss. These results have tempted us to speculate over
Y. BAR-YAM
2004-01-01
We discuss the role of scale dependence of entropy/complexity and its relationship to component interdependence. The complexity as a function of scale of observation is expressed in terms of subsystem entropies for a system having a description in terms of variables that have the same a priori scale. The sum of the complexity over all scales is the same for any system with the same number of underlying degrees of freedom (variables), even though the complexity at specific scales differs due t...
Brustein, Ram
2000-01-01
The identification of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic space-like region. This "causal entropy bound", scaling as the square root of EV, and thus lying around the geometric mean of Bekenstein's S/ER and holographic S/A bounds, is checked in various "critical" situations. In the case of limited gravity, Bekenstein's bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso's holographic bound are stronger than Bekenstein's, while naive holography is too tight, and hence typically wrong.
Brustein, R; Veneziano, G
1999-01-01
The identification of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic space-like region. This "causal entropy bound", scaling as the square root of EV, and thus lying around the geometric mean of Bekenstein's S/ER and holographic S/A bounds, is checked in various "critical" situations. In the case of limited gravity, Bekenstein's bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso...
Third law of thermodynamics as a key test of generalized entropies.
Bento, E P; Viswanathan, G M; da Luz, M G E; Silva, R
2015-02-01
The laws of thermodynamics constrain the formulation of statistical mechanics at the microscopic level. The third law of thermodynamics states that the entropy must vanish at absolute zero temperature for systems with nondegenerate ground states in equilibrium. Conversely, the entropy can vanish only at absolute zero temperature. Here we ask whether or not generalized entropies satisfy this fundamental property. We propose a direct analytical procedure to test if a generalized entropy satisfies the third law, assuming only very general assumptions for the entropy S and energy U of an arbitrary N-level classical system. Mathematically, the method relies on exact calculation of β=dS/dU in terms of the microstate probabilities p(i). To illustrate this approach, we present exact results for the two best known generalizations of statistical mechanics. Specifically, we study the Kaniadakis entropy S(κ), which is additive, and the Tsallis entropy S(q), which is nonadditive. We show that the Kaniadakis entropy correctly satisfies the third law only for -1law for q<1. Finally, we give a concrete example of the power of our proposed method by applying it to a paradigmatic system: the one-dimensional ferromagnetic Ising model with nearest-neighbor interactions. PMID:25768456
Nernst Theorem and Statistical Entropy of 5-Dimensional Rotating Black Hole
ZHAO Ren; WU Yue-Qin; ZHANG Li-Chun
2003-01-01
In this paper, by using quantum statistical method, we obtain the partition function of Bose field and Fermi field on the background of the 5-dimensional rotating black hole. Then via the improved brick-wall method and membrane model, we calculate the entropy of Bose field and Fermi field of the black hole. And it is obtained that the entropy of the black hole is not only related to the area of the outer horizon but also is the function of inner horizon's area. In our results, there are not the left out term and the divergent logarithmic term in the original brick-wall method.The doubt that why the entropy of the scalar or Dirac field outside the event horizon is the entropy of the black hole in the original brick-wall method does not exist. The influence of spinning degeneracy of particles on entropy of the black hole is also given. It is shown that the entropy determined by the areas of the inner and outer horizons will approach zero,when the radiation temperature of the black hole approaches absolute zero. It satisfies Nernst theorem. The entropy can be taken as the Planck absolute entropy. We provide a way to study higher dimensional black hole.
Third law of thermodynamics as a key test of generalized entropies
Bento, E. P.; Viswanathan, G. M.; da Luz, M. G. E.; Silva, R.
2015-02-01
The laws of thermodynamics constrain the formulation of statistical mechanics at the microscopic level. The third law of thermodynamics states that the entropy must vanish at absolute zero temperature for systems with nondegenerate ground states in equilibrium. Conversely, the entropy can vanish only at absolute zero temperature. Here we ask whether or not generalized entropies satisfy this fundamental property. We propose a direct analytical procedure to test if a generalized entropy satisfies the third law, assuming only very general assumptions for the entropy S and energy U of an arbitrary N -level classical system. Mathematically, the method relies on exact calculation of β =d S /d U in terms of the microstate probabilities pi. To illustrate this approach, we present exact results for the two best known generalizations of statistical mechanics. Specifically, we study the Kaniadakis entropy Sκ, which is additive, and the Tsallis entropy Sq, which is nonadditive. We show that the Kaniadakis entropy correctly satisfies the third law only for -1 law for q <1 . Finally, we give a concrete example of the power of our proposed method by applying it to a paradigmatic system: the one-dimensional ferromagnetic Ising model with nearest-neighbor interactions.
Dynamical entropy of quasifree automorphisms
The dynamical entropy of quasifree automorphisms and quasifree states is calculated and shown to be the entropy of the shift created by the group velocity. Some continuity properties are proved. (Author)
The role of configurational entropy in biochemical cooperativity.
Jusuf, Sutjano; Loll, Patrick J; Axelsen, Paul H
2002-04-10
Cooperativity is a common biochemical phenomenon in which two or more otherwise independent processes are thermodynamically coupled. Because cooperative processes are usually attended by changes in molecular conformation, thermodynamic coupling is usually attributed to an enthalpy-driven mechanism. In the family of glycopeptide antibiotics that includes vancomycin, however, cooperative phenomena occur that cannot be explained by conformational change. In this communication, we demonstrate that cooperativity in these systems can arise solely from changes in vibrational activity. PMID:11929222
Algebraic entropy for algebraic maps
We propose an extension of the concept of algebraic entropy, as introduced by Bellon and Viallet for rational maps, to algebraic maps (or correspondences) of a certain kind. The corresponding entropy is an index of the complexity of the map. The definition inherits the basic properties from the definition of entropy for rational maps. We give an example with positive entropy, as well as two examples taken from the theory of Bäcklund transformations. (letter)
Ansari, Mohammad H.
2016-01-01
A common approach to evaluate entropy in quantum systems is to solve a master-Bloch equation to determine density matrix and substitute it in entropy definition. However, this method has been recently understood to lack many energy correlators. The new correlators make entropy evaluation to be different from the substitution method described above. The reason for such complexity lies in the nonlinearity of entropy. In this paper we present a pedagogical approach to evaluate the new correlator...
Be Resolute about Absolute Value
Kidd, Margaret L.
2007-01-01
This article explores how conceptualization of absolute value can start long before it is introduced. The manner in which absolute value is introduced to students in middle school has far-reaching consequences for their future mathematical understanding. It begins to lay the foundation for students' understanding of algebra, which can change…
Entropy Effects in Chelation Reactions.
Chung, Chung-Sun
1984-01-01
The entropy change for a reaction in aqueous solution can be evaluated as a combination of entropy factors. Valuable insight or understanding can be obtained from a detailed examination of these factors. Several entropy effects of inorganic chemical reactions are discussed as examples. (Author/JN)
Hansen, Frank
2016-06-01
Incremental information, as measured by the quantum entropy, is increasing when two ensembles are united. This result was proved by Lieb and Ruskai, and it is the foundation for the proof of strong subadditivity of quantum entropy. We present a truly elementary proof of this fact in the context of the broader family of matrix entropies introduced by Chen and Tropp.
Entropy is a Mathematical Formula
Garai, Jozsef
2003-01-01
The microscopic explanation of entropy has been challenged from both experimental and theoretical point of view. The expression of entropy is derived from the first law of thermodynamics indicating that entropy or the second law of thermodynamics is not an independent law.
Relations Among Some Fuzzy Entropy Formulae
卿铭
2004-01-01
Fuzzy entropy has been widely used to analyze and design fuzzy systems, and many fuzzy entropy formulae have been proposed. For further in-deepth analysis of fuzzy entropy, the axioms and some important formulae of fuzzy entropy are introduced. Some equivalence results among these fuzzy entropy formulae are proved, and it is shown that fuzzy entropy is a special distance measurement.
Rescaling Temperature and Entropy
Olmsted, John, III
2010-01-01
Temperature and entropy traditionally are expressed in units of kelvin and joule/kelvin. These units obscure some important aspects of the natures of these thermodynamic quantities. Defining a rescaled temperature using the Boltzmann constant, T' = k[subscript B]T, expresses temperature in energy units, thereby emphasizing the close relationship…
Stationarity of extremum entropy fluid bodies in general relativity
Schiffrin, Joshua S.
2015-09-01
We consider perfect fluid bodies (‘stars’) in general relativity that are axisymmetric, asymptotically flat, and that admit a maximal hypersurface. We show that configurations that extremize the total entropy at fixed ADM mass, ADM angular momentum, and total particle number are stationary with circular flow. For such stars, this establishes that thermodynamic equilibrium implies dynamic equilibrium.
Zucker, M. H.
This paper is a critical analysis and reassessment of entropic functioning as it applies to the question of whether the ultimate fate of the universe will be determined in the future to be "open" (expanding forever to expire in a big chill), "closed" (collapsing to a big crunch), or "flat" (balanced forever between the two). The second law of thermodynamics declares that entropy can only increase and that this principle extends, inevitably, to the universe as a whole. This paper takes the position that this extension is an unwarranted projection based neither on experience nonfact - an extrapolation that ignores the powerful effect of a gravitational force acting within a closed system. Since it was originally presented by Clausius, the thermodynamic concept of entropy has been redefined in terms of "order" and "disorder" - order being equated with a low degree of entropy and disorder with a high degree. This revised terminology more subjective than precise, has generated considerable confusion in cosmology in several critical instances. For example - the chaotic fireball of the big bang, interpreted by Stephen Hawking as a state of disorder (high entropy), is infinitely hot and, thermally, represents zero entropy (order). Hawking, apparently focusing on the disorderly "chaotic" aspect, equated it with a high degree of entropy - overlooking the fact that the universe is a thermodynamic system and that the key factor in evaluating the big-bang phenomenon is the infinitely high temperature at the early universe, which can only be equated with zero entropy. This analysis resolves this confusion and reestablishes entropy as a cosmological function integrally linked to temperature. The paper goes on to show that, while all subsystems contained within the universe require external sources of energization to have their temperatures raised, this requirement does not apply to the universe as a whole. The universe is the only system that, by itself can raise its own