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Internal Energy (internal + energy)
Selected AbstractsDFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2010Valeri I. Poltev Abstract We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the "classical" B conformation (BI-form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence-dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII-like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548,2559, 2010 [source] Entropy considerations in kinetic method experimentsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2004Chrys WesdemiotisArticle first published online: 7 SEP 200 Abstract In extended kinetic method experiments, relative binding enthalpies (,affinities') and relative entropies are obtained based on unimolecular dissociation kinetics. A series of ion-bound dimers AXBi is formed, in which the sample (A) and structurally similar reference molecules (Bi) are bridged by a central cation or anion (X). The branching ratios of the AXBi set to AX and BiX are determined at different internal energies, usually by subjecting AXBi to collisionally activated dissociation at various collision energies. The dependence of the natural logarithm of the branching ratios on the corresponding BiX bond enthalpies (X affinities of Bi) is evaluated as a function of internal energy to thereby deduce the AX bond enthalpy (X affinity of A) as well as an apparent relative entropy of the competitive dissociation channels, ,(,Sapp). Experiments with proton- and Na+ -bound dimers show that this approach can yield accurate binding enthalpies. In contrast, the derived ,(,Sapp) values do not correlate with the corresponding thermodynamic entropy differences between the channels leading to AX and BiX, even after scaling. The observed trends are reconciled by the transition state switching model. According to this model, the kinetics of barrierless dissociations, such as those encountered in kinetic method studies, are dominated by a family of tight transition states (,entropy bottlenecks') lying lower in energy than the corresponding dissociation thresholds. In general, the relative energies of these tight transition states approximately match those of the dissociation products, but their relative entropies tend to be much smaller, as observed experimentally. Copyright © 2004 John Wiley & Sons, Ltd. [source] Distribution Function and Thermodynamic Potentials of a Self-Avoiding ChainMACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2006Aleksey D. Drozdov Abstract Summary: An explicit expression is derived for the distribution function of end-to-end vectors for a flexible self-avoiding chain. Based on this relation, analytical formulas are developed for the free and internal energies of a chain with excluded-volume interactions. Force,stretch relations are obtained at uniaxial tension and compression. The effects of strength of segment interactions on the shapes of the distribution function and the force-displacement diagram, as well as on the mean-square end-to-end distance and stiffness of a chain are studied numerically. The dimensionless distribution function P versus the dimensionless end-to-end vector Q* for self-repellent chains with ,,=,0.0, 0.4, 0.8, 1.2, and 1.6, from top to bottom, respectively. [source] Comparison of 17,-estradiol structures from x-ray diffraction and solution NMRMAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2005Fernando Commodari Abstract The NMR-derived structure of estrogen (17,-estradiol, E2), the drug of choice for postmenopausal women, was compared with a recent literature crystal x-ray structure of Fab-bound E2. 1H and 13C NMR spectra of E2 were acquired in DMSO- d6. Assignments were obtained from an analysis of DQF-COSY, TOCSY, HETCOR, HMQC and HMBC 2D NMR spectra. The 1H and 13C NMR assignments are the first reported for E2 in DMSO- d6. Two solution structures, S1 and S2, were obtained with molecular modeling using NOE constraints. S1 overlaps with the crystal structure for all rings. S2 shows prominent differences in the C-ring (C9C11C12C13) segment, which deviates from a chair conformation, and excellent overlap in the A-, B- and D-rings of E2. The C-ring in S2 adopts a boat conformation as opposed to a chair conformation in the x-ray and S1 structures. The S2 structure is about 6° more twisted than the bound x-ray and S1 models. The S1, S2 and x-ray structures had ring bowing values of 10.1 ± 0.3, 11 ± 1 and 10.37°, respectively. Of the 100 solution conformers generated, 83 had S1 conformation and 17 had S2 conformation, with average internal energies of 112 ± 2 and 141 ± 2 kcal mol,1, respectively. The 100 S1 - and S2 - derived conformers showed a r.m.s.d. of 0.72 Ĺ for all atoms. The x-ray, S1 and S2 C18O17 distances were 2.93, 2.92 ± 0.01 and 2.93 ± 0.01 Ĺ, respectively, and the O3O17 distances were 11.06, 11.18 ± 0.12, and 10.89 ± 0.05 Ĺ, respectively. Copyright © 2005 John Wiley & Sons, Ltd. [source] Java applet on computation of thermodynamic properties of steam and R134a refrigerantCOMPUTER APPLICATIONS IN ENGINEERING EDUCATION, Issue 4 2003F. L. Tan Abstract This paper describes the application of Java programming on the computation of thermodynamic properties of steam and the HFC-134a, 1,1,1,2-tetrafluoroethane (R134a) refrigerant through the Java applets. The Java applets can compute thermodynamic properties of steam and R134a refrigerant, such as specific volume, internal energy, enthalpy, and entropy in the phases of saturated mixture, compressed liquid, and superheated vapor. The calculated values are accurate compared to the standard reference properties tables for steam and refrigerant. © 2004 Wiley Periodicals, Inc. Comput Appl Eng Educ 11: 211,225, 2003; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.10049 [source] Thermodynamic Properties and Plasma Phase Transition in dense HydrogenCONTRIBUTIONS TO PLASMA PHYSICS, Issue 5-6 2004V. S. Filinov Abstract The internal energy and equation of state of dense hydrogen are investigated by direct path integral Monte Carlo method simulations which are further improved in comparison to our previous results. Data for four isotherms , T = 10, 000K, 30, 000K, 50, 000K, and 100, 000K , are presented. For T = 10, 000K it is shown that the internal energy is lowered due to droplet formation for densities of the order 1023cm,3 giving direct support for the existence of a plasma phase transition in megabar hydrogen. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Analysis of the solid phase stress tensor in multiphase porous mediaINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 4 2007William G. Gray Abstract Conservation equations for mass, momentum, energy, and entropy are formulated for the phases and interfaces of a three-phase system consisting of a solid and two immiscible fluids. The microscale equations are averaged to the macroscale by integration over a representative elementary volume. Thermodynamic statements for each of the phases and interface entities are also formulated at the microscale and then averaged to the macroscale. This departure from most uses of thermodynamics in macroscale analysis ensures consistency between models and parameters at the two scales. The expressions for the macroscale rates of change of internal energy are obtained by differentiating the derived forms for energy and making use of averaging theorems. These thermodynamic expressions, along with the conservation equations, serve as constraints on the entropy inequality. A linearization of the resulting equations is employed to investigate the theoretical origins of the Biot coefficient that relates the hydrostatic part of the total stress tensor to the normal force applied at the solid surface by the pore fluids. The results here are placed in the context of other formulations and expressions that appear in the literature. Copyright © 2006 John Wiley & Sons, Ltd. [source] Direct computation of thermodynamic properties of chemically reacting air with consideration to CFDINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 4 2003Joe IannelliArticle first published online: 2 SEP 200 Abstract This paper details a two-equation procedure to calculate exactly mass and mole fractions, pressure, temperature, specific heats, speed of sound and the thermodynamic and jacobian partial derivatives of pressure and temperature for a five-species chemically reacting equilibrium air. The procedure generates these thermodynamic properties using as independent variables either pressure and temperature or density and internal energy, for CFD applications. An original element in this procedure consists in the exact physically meaningful solution of the mass-fraction and mass-action equations. Air-equivalent molecular masses for oxygen and nitrogen are then developed to account, within a mixture of only oxygen and nitrogen, for the presence of carbon dioxide, argon and the other noble gases within atmospheric air. The mathematical formulation also introduces a versatile system non-dimensionalization that makes the procedure uniformly applicable to flows ranging from shock-tube flows with zero initial velocity to aerothermodynamic flows with supersonic/hypersonic free-stream Mach numbers. Over a temperature range of more than 10000 K and pressure and density ranges corresponding to an increase in altitude in standard atmosphere of 30000 m above sea level, the predicted distributions of mole fractions, constant-volume specific heat, and speed of sound for the model five species agree with independently published results, and all the calculated thermodynamic properties, including their partial derivatives, remain continuous, smooth, and physically meaningful. Copyright © 2003 John Wiley & Sons, Ltd. [source] A simple reactive gasdynamic model for the computation of gas temperature and species concentrations behind reflected shock waves,INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 4 2008H. Li A simple gasdynamic model, called CHEMSHOCK, has been developed to predict the temporal evolution of combustion gas temperature and species concentrations behind reflected shock waves with significant energy release. CHEMSHOCK provides a convenient simulation method to study various sized combustion mechanisms over a wide range of conditions. The model consists of two successive suboperations that are performed on a control mass during each infinitesimal time step: (1) first the gas mixture is allowed to combust at constant internal energy and volume; (2) then the gas is isentropically expanded (or compressed) at frozen composition to the measured pressure. The CHEMSHOCK model is first validated against results from a one-dimensional reacting computational fluid dynamics (CFD) code for a representative case of heptane/O2/Ar mixture using a reduced mechanism. CHEMSHOCK is found to accurately reproduce the results of the CFD calculation with significantly reduced computational time. The CHEMSHOCK simulation results are then compared to experimental results, for gas temperature and water vapor concentration, obtained using a novel laser sensor based on fixed-wavelength absorption of two H2O rovibrational transitions near 1.4 ,m. Excellent agreement is found between CHEMSHOCK simulations and measurements in a progression of shock wave tests: (1) in H2O/Ar, with no energy release; (2) in H2/O2/Ar, with relatively small energy release; and (3) in heptane/O2/Ar, with large energy release. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 189,198, 2008 [source] Thermal expansion and atomic displacement parameters of cubic KMgF3 perovskite determined by high-resolution neutron powder diffractionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2002I. G. Wood The structure of KMgF3 has been determined by high-resolution neutron powder diffraction at 4.2,K, room temperature and at 10,K intervals from 373,K to 1223,K. The material remains cubic at all temperatures. The average volumetric coefficient of thermal expansion in the range 373,1223,K was found to be 7.11,(3) × 10,5,K,1. For temperatures between 4.2 and 1223,K, a second-order Grüneisen approximation to the zero-pressure equation of state, with the internal energy calculated via a Debye model, was found to fit well, with the following parameters: ,D = 536,(9),K, Vo = 62.876,(6),Ĺ3, = 6.5,(1) and (VoKo/,,) = 3.40,(2) × 10,18,J, where ,D is the Debye temperature, Vo is the volume at T = 0, is the first derivative with respect to pressure of the incompressibility (Ko) and ,, is a Grüneisen parameter. The atomic displacement parameters were found to increase smoothly with T and could be fitted using Debye models with ,D in the range 305,581,K. At 1223,K, the displacement of the F ions was found to be much less anisotropic than that in NaMgF3 at this temperature. [source] Toward accurate relative energy predictions of the bioactive conformation of drugsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2009Keith T. Butler Abstract Quantifying the relative energy of a ligand in its target-bound state (i.e. the bioactive conformation) is essential to understand the process of molecular recognition, to optimize the potency of bioactive molecules and to increase the accuracy of structure-based drug design methods. This is, nevertheless, seriously hampered by two interrelated issues, namely the difficulty in carrying out an exhaustive sampling of the conformational space and the shortcomings of the energy functions, usually based on parametric methods of limited accuracy. Matters are further complicated by the experimental uncertainty on the atomic coordinates, which precludes a univocal definition of the bioactive conformation. In this article we investigate the relative energy of bioactive conformations introducing two major improvements over previous studies: the use sophisticated QM-based methods to take into account both the internal energy of the ligand and the solvation effect, and the application of physically meaningful constraints to refine the bioactive conformation. On a set of 99 drug-like molecules, we find that, contrary to previous observations, two thirds of bioactive conformations lie within 0.5 kcal mol,1 of a local minimum, with penalties above 2.0kcal mol,1 being generally attributable to structural determination inaccuracies. The methodology herein described opens the door to obtain quantitative estimates of the energy of bioactive conformations and can be used both as an aid in refining crystallographic structures and as a tool in drug discovery. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Internal energy distribution of peptides in electrospray ionization : ESI and collision-induced dissociation spectra calculationJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2008Alireza Pak Abstract The internal energy of ions and the timescale play fundamental roles in mass spectrometry. The main objective of this study is to estimate and compare the internal energy distributions of different ions (different nature, degree of freedom ,DOF' and fragmentations) produced in an electrospray source (ESI) of a triple-quadrupole instrument (Quattro I Micromass). These measurements were performed using both the Survival Yield method (as proposed by De Pauw) and the MassKinetics software (kinetic model introduced by Vékey). The internal energy calibration is the preliminary step for ESI and collision-induced dissociation (CID) spectra calculation. meta -Methyl-benzylpyridinium ion and four protonated peptides (YGGFL, LDIFSDF, LDIFSDFR and RLDIFSDF) were produced using an electrospray source. These ions were used as thermometer probe compounds. Cone voltages (Vc) were linearly correlated with the mean internal energy values ( Do collisions inside the collision cell play a relevant role in CID-LIFT experiments?,JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2007Gloriano Moneti Abstract Collision experiments are a valid approach to characterize the ionic species generated by matrix assisted laser desorption ionization (MALDI). When a time-of-flight analyzer is employed, three different approaches are available for these experiments: the postsource decay (PSD), the LIFT and the MALDI-TOF/TOF. The last two are of particular interest because of the overcoming of the PSD problems related to mass calibration of the product ion spectra. Experiments performed by LIFT on linear or cyclic peptides, in presence or in absence of collision gas in the collision cell, gave evidence of an unexpected behavior: the two spectra were practically superimposable, and in the former case only a few new fragmentation channels were activated with low yield. These results mean that the selected ion exhibits a large amount of internal energy, capable of promoting fragmentation processes in the time window corresponding to the flight time between ion source and the acceleration electrode placed after the collision cell. Experiments performed by varying the plume density show that this internal energy uptake occurs in the expanding plume, through multiple collisions. The LIFT data have been compared with those achieved by collisions of ESI-generated [MH]+ ions of angotensin II performed under ,in-source' conditions and by triple-quadrupole experiments. The obtained results show a strong similarity among the spectra, indicating that the internal energy uptake in a MALDI source is comparable with that of 40-eV ions colliding with Ar in a triple-quadrupole instrument. Copyright © 2006 John Wiley & Sons, Ltd. [source] Entropy considerations in kinetic method experimentsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2004Chrys WesdemiotisArticle first published online: 7 SEP 200 Abstract In extended kinetic method experiments, relative binding enthalpies (,affinities') and relative entropies are obtained based on unimolecular dissociation kinetics. A series of ion-bound dimers AXBi is formed, in which the sample (A) and structurally similar reference molecules (Bi) are bridged by a central cation or anion (X). The branching ratios of the AXBi set to AX and BiX are determined at different internal energies, usually by subjecting AXBi to collisionally activated dissociation at various collision energies. The dependence of the natural logarithm of the branching ratios on the corresponding BiX bond enthalpies (X affinities of Bi) is evaluated as a function of internal energy to thereby deduce the AX bond enthalpy (X affinity of A) as well as an apparent relative entropy of the competitive dissociation channels, ,(,Sapp). Experiments with proton- and Na+ -bound dimers show that this approach can yield accurate binding enthalpies. In contrast, the derived ,(,Sapp) values do not correlate with the corresponding thermodynamic entropy differences between the channels leading to AX and BiX, even after scaling. The observed trends are reconciled by the transition state switching model. According to this model, the kinetics of barrierless dissociations, such as those encountered in kinetic method studies, are dominated by a family of tight transition states (,entropy bottlenecks') lying lower in energy than the corresponding dissociation thresholds. In general, the relative energies of these tight transition states approximately match those of the dissociation products, but their relative entropies tend to be much smaller, as observed experimentally. Copyright © 2004 John Wiley & Sons, Ltd. [source] Energy consumption in the Islamic Republic of IranOPEC ENERGY REVIEW, Issue 3 2000A.M. Samsam Bakhtiari During the 20th century, energy consumption in the Islamic Republic of Iran was continually on the increase, from a per capita level of 200 kilogrammes of oil equivalent (koe) for traditional energies at the onset to more than 1,700 koe for commercial energies at the century's close. The main stimulants fuelling Iran's energy consumption were: (i) revenue from oil exports (wealth-creating); (ii) a growing population; (iii) the countrywide rural-urban shift; and (iv) relatively low domestic retail prices charged for energy vectors. For a country well endowed with hydrocarbon resources, it is not surprising that the internal consumption of refined products and natural gas grew to fill 99 per cent of its primary energy needs. During the 1990s, domestic consumption of natural gas exploded. Gas even came to rival refined products, securing up to 45 per cent of total primary energy. Future natural gas expansion will be based upon the country's ample reserves, and gas will undoubtedly become Iran's dominant source of internal energy in the 21st century,thereby liberating liquid fuels for export. Iran's dwindling crude oil production will also put pressure on the internal use of refined products, as consumption and exports come to vie for the same barrel. Exports being vital to the national economy, consumption will have to be reined in. [source] Radio frequency magnetic field effects on molecular dynamics and iron uptake in cage proteinsBIOELECTROMAGNETICS, Issue 4 2010Oscar Céspedes Abstract The protein ferritin has a natural ferrihydrite nanoparticle that is superparamagnetic at room temperature. For native horse spleen ferritin, we measure the low field magnetic susceptibility of the nanoparticle as 2.2,×,10,6,m3,kg,1 and its Néel relaxation time at about 10,10,s. Superparamagnetic nanoparticles increase their internal energy when exposed to radio frequency magnetic fields due to the lag between magnetization and applied field. The energy is dissipated to the surrounding peptidic cage, altering the molecular dynamics and functioning of the protein. This leads to an increased population of low energy vibrational states under a magnetic field of 30,µT at 1,MHz, as measured via Raman spectroscopy. After 2,h of exposure, the proteins have a reduced iron intake rate of about 20%. Our results open a new path for the study of non-thermal bioeffects of radio frequency magnetic fields at the molecular scale. Bioelectromagnetics 31:311,317, 2010. © 2010 Wiley-Liss, Inc. [source] Effects of radio frequency magnetic fields on iron release from cage proteinsBIOELECTROMAGNETICS, Issue 5 2009Oscar Céspedes Abstract Ferritin, the iron cage protein, contains a superparamagnetic ferrihydrite nanoparticle formed from the oxidation and absorption of Fe2+ ions. This nanoparticle increases its internal energy when exposed to alternating magnetic fields due to magnetization lag. The energy is then dissipated to the surrounding proteic cage, affecting its functioning. In this article we show that the rates of iron chelation with ferrozine, an optical marker, are reduced by up to a factor of 3 in proteins previously exposed to radio frequency magnetic fields of 1 MHz and 30 µT for several hours. The effect is non-thermal and depends on the frequency-amplitude product of the magnetic field. Bioelectromagnetics 30:336,342, 2009. © 2009 Wiley-Liss, Inc. [source]
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