Logistic distributed activation energy model--part 2: application to cellulose pyrolysis

The pyrolysis behavior of cellulose has been investigated by using thermogravimetric analysis (TGA). The non-isothermal TGA data obtained at different heating rates have been analyzed simultaneously. Pattern Search Method has been proposed for the estimation of the model parameter values. Predicted values from the logistic distributed activation energy model have been compared with the experimental data and the results have indicated that the model describes the kinetic behavior of cellulose pyrolysis very well. The mean value and standard deviation of the logistic activation energy distribution for cellulose pyrolysis are found to be 258.5718 kJ mol(-1) and 2.6601 kJ mol(-1), the reaction order is 1.1101 and the k(0) is 1.6218×10(17) s(-1).     

Conformation of histidine model peptides. II. Spectroscopic properties of the imidazole chromophore.

Semi-empirical molecular orbital calculations have been carried out for the free base and cationic forms of imidazole so as to obtain data which are required for the calculation of the chiroptical properties of molecules that contain this chromophoric group. The polarization, energy, and monopolar charge distribution are reported for the lowest energy electronic transitions. The absorption spectra for imidazole have been determined to 180 nm and circular dichroism spectra for L -histidinol and L -2-amino-1-butanol have been measured.     

Determination of solution conformation of DNA backbone: application of homonuclear (J, delta) spectroscopy

Homonuclear two-dimensional (J, delta) proton spectroscopy has been suggested as a method for the measurement of 1H-31P coupling constants in oligonucleotides. The technique has been applied to a dinucleoside monophosphate G2'p5'C and a deoxydecanucleotide d(ACATCGATGT). PCILO energy calculations have been carried out to find minimum energy conformations with respect to the DNA backbone torsion angle epsilon, and these have been considered for the interpretation of the observed H3'-31P coupling constants in oligonucleotides.     

Electrokinetic energy conversion studies of urine-oxalic acid systems across urinary bladder membrane.

Electrokinetic studies of urine-oxalic acid systems with increasing concentration of oxalic acid in urine have been carried out across urinary bladder membranes. It has been found that electro-osmotic flux and streaming current decrease with increase in concentration of oxalic acid in urine while hydrodynamic flux and streaming potential increase with increase in concentration. Kinetic energy term (alpha 1) and polarizability term (alpha 2) have been computed for these systems and it has been found that polarizability decreases much faster with increase in concentration of oxalic acid in urine. Electrokinetic energy conversion of these systems have been computed and it has been found that electrokinetic energy conversion is maximum for urine and it decreases with increase in concentration of oxalic acid in urine. Poor energy conversion may lead to sluggish flushing action which may ultimately lead to formation of urinary calculi in the bladder and so present study may be of some use in predicting electrophysiology of the bladder.     

On energy conservation and transfer in mitochondria

Structural and functional features of energy conservation and transfer in mitochondria have been examined in the light of recent developments, and hypothetical schemes for energy coupling and transfer have been presented.Supported by USPHS grant AM-08126 to Y.H. and San Diego County Heart Association Grant-in-Aid 97-71 to W.G.H.Recipient of USPHS career Development Award 1-K4-GM38291.     

Studies on hydrogen bonds. Part V--Hydrogen bonding in energy minimization studies of peptides

An energy term, representing the N-H...O type of hydrogen bond, which is a function of the hydrogen bond length (R) and angle (theta) has been introduced in an energy minimization program, taking into consideration its interpolation with the non-bonded energy for borderline values of R and theta. The details of the mathematical formulation of the derivatives of the hydrogen bond function as applicable to the energy minimization have been given. The minimization technique has been applied to hydrogen bonded two and three linked peptide units (gamma-turns and beta-turns), and having Gly, Ala and Pro side chains. Some of the conformational highlights of the resulting minimum energy conformations are a) the occurrence of the expected 4----1 hydrogen bond in all of the burn-turn tripeptide sequences and b) the presence of an additional 3----1 hydrogen bond in some of the type I and II tripeptides with the hydrogen bonding scheme in such type I beta-turns occurring in a bifurcated form. These and other conformational features have been discussed in the light of experimental evidence and theoretical predictions of other workers.     

Kink dynamics in inhomogeneous DNA

A mathematical model for studies of peculiar features of the dynamics of local conformational distortions (kinks) has been constructed. General formulas determining the dependence of the main dynamic characteristics of kinks: size, energy, density of energy, and velocity on the composition of inhomogeneous DNA have been obtained. Quantitative estimations of the characteristics have been made for kinks activated in inhomogeneous polynucleotide chains with sequences analogous to promoter sequences A1, A2, and A3 of bacteriophage T7 genome.     

Conformational analysis of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-α-D-galactopyranoside by MM and Langevin dynamics simulations

The conformational space of methyl 6-O-[(R)- and (S)- 1-carboxyethyl]-α-D-galactopyranoside has been investigated. A grid search employing energy minimization at each grid point over the three major degrees of freedom, namely φ, ψ and ω, identified low energy regions. The R-isomer shows five low energy conformers within ca. 1 kcal mol−1 of the global energy minimum. The S-isomer has two conformers within a few tenths of a kcal mol−1 of the global energy minimum. Langevin dynamics simulations have been have been performed at 300 K for 30 ns of each isomer. The φ dihedral angle has as its major conformer (g−1) for the R-isomer whereas it is the (g+) conformer for the S-isomer. For the ψ dihedral angle the (t) conformer has the highest population for both isomers. The dihedral angle ω has the (g+) conformer most highly populated, both for the R- and S-isomer. The above five and two conformational states for the R- and S-isomers, respectively, make up 90% in each case of the populated states during the Langevin dynamics (LD) simulations. Rate constants for the ω dihedral angle have been calculated based on a number correlation function. Three bond homo- and heteronuclear, i.e. proton and carbon-13, coupling constants have been calculated from the dynamics trajectories for comparison to experimental values. The heteronuclear coupling constant H2′,C6 has been measured for the S-isomer and found to be 3.3 Hz. The J value calculated from the LD simulations, namely 2.6 Hz, is in fair agreement with experiment. A comparison to the X-ray structure of the R-isomer shows that the conformation of the crystalline compound occupies the low energy region most highly populated as a single R-conformer (30%) during the LD simulations. This revised version was published online in August 2006 with corrections to the Cover Date.     

16 Mechanical energy,protein motion,and the possible origin of life between mica sheets

The origins of life require reliable energy sources. One feasible energy source has not been considered until recently. This is mechanical energy-work (Hansma, 2010, 2012). The spaces between moving muscovite mica sheets are the environment in which mechanical energy is hypothesized to have been involved in the origins of life. Mechanical energy from moving mica sheets has two main sources: (1) The open-and-shut motions of mica sheets in response to water movements in and out between the sheets, and (2) Thermal cycles of day and night acting on bubble ‘defects’ between mica sheets. This mechanical energy is hypothesized to have been involved in the formation (and breaking) of covalent bonds, the rearrangement of polymers and molecular aggregates, and the budding-off of protocells, in the earliest form of cell division. Furthermore, it is hypothesized that the mechanical energy from mica sheets moving open-and-shut is the source of the common open-and-shut motions of enzymes, originating from a protobiotic era when mechanical energy was plentiful and chemical energy was not yet available.     

Ergoline Derivatives as a Probe for Featuring the 5-HT1A Receptor Pharmacophore

A 5-HT_1A pharmacophore has been obtained employing a set of rigid templates encompassing the 5-HT1A structure. The use of rigid templates allowed us to overcome the discrepancy found when flexible structures where the energy of the active conformers are sometimes higher than the global minimum energy are used. On the basis of the results herein reported the three-dimensional requirements necessary for the binding interaction have been defined within this set of molecules. In this study forbidden zones of the receptor have been characterised. The pharmacophore model derived places some agonist/antagonist pharmacophore models appeared in the literature.     

The use of the AMBER force field in conformational analysis of carbohydrate molecules: Determination of the solution conformation of methyl α-lactoside by NMR spectroscopy,assisted by molecular mechanics and dynamics calculations

The solution conformation of methyl α-lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements hot It in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady-state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [ε = 1 * r and 80 Debyes (D)] in an exhaustive way, and have been complemented with specific calculations at intermediate ε values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. The experimental results indicate that the β(1 → 4)-glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its lime in the region close to the global minimum. It is shown that the over estimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when Used at low dielectric constant (ε < 20 D). The matching between the expected and observed facts increases for ε > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides. © 1995 John Wiley & Sons, Inc.     

Studies on Hydrogen Bonds Part V-Hydrogen Bonding in Energy Minimization Studies of Peptides

Abstract

An energy term, representing the N—H…O type of hydrogen bond, which is a function of the hydrogen bond length (R) and angle (θ) has been introduced in an energy minimization program, taking into consideration its interpolation with the non-bonded energy for borderline values of R and θ. The details of the mathematical formulation of the derivatives of the hydrogen bond function as applicable to the energy minimization have been given. The minimization technique has been applied to hydrogen bonded two and three linked peptide units (γ-turns and β-turns), and having Gly, Ala and Pro side chains. Some of the conformational highlights of the resulting minimum energy conformations are a) the occurrence of the expected 4?1 hydrogen bond in all of the β-turn tripeptide sequences and b) the presence of an additional 3?1 hydrogen bond in some of the type I and II tripeptides with the hydrogen bonding scheme in such type I β-turns occurring in a bifurcated form. These and other conformational features have been discussed in the light of experimental evidence and theoretical predictions of other workers.     

The influence of secondary interactions on complex stability and double proton transfer reaction in 2-[1H]-pyridone/2-hydroxypyridine dimers

The 2-[1H]-pyridone/2-hydroxypyridine tautomeric pair and its 6-substituted complexes have been studied with the use of DFT(M05) method. The intermolecular interaction energy has been calculated and discussed in the light of secondary interaction concept. The attractive secondary interactions of O/NH and O/OH type and OH/NH and OH/OH repulsions have been analyzed in terms of stabilizing or destabilizing influence on intermolecular behavior. The transition states of the double proton transfer reaction have been found and the energy of activation has been determined. The activation energy of the proton transfer reaction, geometry of the complexes and transition states show NH(2) and/or OH groups influence the properties of complexes and transition states. The HOMA index of aromaticity was applied to describe the π-electron delocalization in the heterocyclic rings.     

Absolute reaction rate and kinetics of protein adsorption at solid-liquid interfaces.

Extents of adsorption of bovine serum albumin from aqueous solution to the surface of alumina, silica, carbon and chromium powder have been studied as function of time for various values of bulk protein concentration, pH, ionic strength and temperature. The rates of adsorption in all cases have been observed to fit in the first order rate equation with two different rate constants Ka1 and Ka2. Effects of addition of SDS, CTAB and neutral salts on values of Ka1 and Ka2 have also been studied. Using Arrhenius equation the activation energy values Ea1 and Ea2 have been evaluated from the values of Ka1 and Ka2 at three different temperatures, respectively. The corresponding values of enthalpy of activation (delta H*), entropy of activation (delta S*), and free energy of activation (delta G*) have been evaluated using Eyring's equation of absolute reaction rate. The mechanism of protein adsorption has been discussed in the light of basic principles of absolute reaction rate. It has been found that for Ka1 the delta H*1 greater than T delta S*1 and for Ka2 T delta S*2 greater than H*2, i.e. the anchorage and binding of protein to the surface are enthalpy controlled processes whereas the surface denaturation as well as rearrangement and folding is an entropy controlled process. The role of diffusion on rate of adsorption has also been discussed.     

The dependence on energy and K+ ions of the accumulation of glutamate by rat liver mitochondria

The time courses of the changes of glutamate content in rat liver mitochondria have been followed after either removing the energy supply or applying an energy supply. When the energy supply is inhibited, or when energy is dissipated by uncoupling, the glutamate is lost in a few minutes. The poison avenaciolide also causes glutamate to be lost. Uptake of glutamate requires an energy supply and proceeds as a first-order process with rate constants 0.059 min^?1 at 10 °C, 0.16 min^?1 at 20 °C, and 0.30 min^?1 at 30 °C. The glutamate distribution between mitochondria and medium in presence of an energy supply approaches the distribution holding for pyruvate. The uptake of glutamate appears to have a requirement for K⁺ ions in the medium.     

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

We have theoretically and experimentally studied the binding of two different ligands to wild-type ribonuclease T₁ (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln. The binding of the natural substrate 3′-GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3′-monophosphate (2AP), and relative free energies of binding of these ligands to the mutant and the wild-type (wt) enzyme have been calculated by free energy perturbation methods. The free energy perturbations predict that the mutant RNT1-Gln-46 binds 2AP better than 3′GMP, in agreement with experiments on dinucleotides. Four free energy perturbations, forming a closed loop, have been performed to allow the detection of systematic errors in the simulation procedure. Because of the larger number of atoms involved, it was necessary to use a much longer simulation time for the change in the protein, i.e., the perturbation from Glu to Gln, than in the perturbation from 3′-GMP to 2AP. Finally the structure of the binding site is analyzed for understanding differences in catalytic speed and binding strength. © 1993 Wiley-Liss, Inc.     

Modeling Lanthanide Complexes: Towards the Theoretical Design of Light Conversion Molecular Devices

Theoretical techniques have been developed and/or improved to predict the molecular structure of lanthanide complexes which were used to calculate their electronic properties, in particular, their electronic spectra and energy levels necessary to calculate the rates of energy transfer from the ligands to the metal ion. The molecular structure has been obtained by the SMLC/AM1 (Sparkle Model for the Calculation of Lanthanide Complexes – Austin Model 1) model where the lanthanide ion is simulated by a sparkle implemented into the AM1 Hamiltonian used to perform a HF-SCF (Hartree-Fock Self-Consistent Field) calculation. The previous implementation of the SMLC/AM1 model (sparkle/1) involving only two parameters has been generalized to be consistent with the AM1 Hamiltonian and the new model (sparkle/2) significantly improved the prediction of molecular structures of Eu(III) complexes. For the electronic spectra and energy level calculations of the lanthanide complexes the model replaces the metal ion by a point charge with the ligands held in their positions as determined by the SMLC/AM1 model, and uses a INDO/S-CI (intermediate neglect of differential overlap/spectroscopic-configuration interaction) model. A preliminary study of the solvent effects on the absorption spectra of the free ligand is also presented. For the ligand-lanthanide ion energy transfer Fermi's golden rule is used with the multipolar and exchange mechanisms being implemented and tested for several complexes. These theoretical techniques have been applied to several complexes yielding very good results when compared to experimental data as well as predictions for the molecular and electronic structures and the relative contributions of the mechanisms for the energy transfer rates. This revised version was published online in June 2006 with corrections to the Cover Date.     

Conformational studies on beta-bend containing a cis peptide unit.

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds--either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C gamma-endo and C gamma-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.     

Physiological and metabolic functions of melatonin

Melatonin is a lipophilic hormone, mainly produced and secreted at night by the pineal gland. Melatonin synthesis is under the control of postganglionic sympathetic fibers that innervates the pineal gland. Melatonin acts via high affinity G protein-coupled membrane receptors. To date, three different receptor subtypes have been identified in mammals: MT1 (Mel 1a) and MT2 (Mel 1b) and a putative binding site called MT3. The chronobiotic properties of the hormone for resynchronization of sleep and circadian rhythms disturbances has been demonstrated both in animal models or in clinical trials. Several other physiological effects of melatonin in different peripheral tissues have been described in the past years. In this way, it has been demonstrated that the hormone is involved in the regulation of seasonal reproduction, body weight and energy balance. This contribution has been focused to review some of the physiological functions of melatonin as well as the role of the hormone in the regulation of energy balance and its possible involvement in the development of obesity.     

Sensing nutrient and energy status by SnRK1 and TOR kinases

The perception of nutrient and energy levels inside and outside the cell is crucial to adjust growth and metabolism to available resources. The signaling pathways centered on the conserved TOR and SnRK1/Snf1/AMPK kinases have crucial and numerous roles in nutrient and energy sensing and in translating this information into metabolic and developmental adaptations. In plants evidence is mounting that, like in other eukaryotes, these signaling pathways have pivotal and antagonistic roles in connecting external or intracellular cues to many biological processes, including ribosome biogenesis, regulation of translation, cell division, accumulation of reserves and autophagy. Data on the plant TOR pathway have been hitherto rather scarce but recent findings have shed new light on its roles in plants. Moreover, the distinctive energy metabolism of photosynthetic organisms may reveal new features of these ancestral eukaryotic signaling elements.