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).     

Thermodynamic analysis of the interaction of factor VIII with von Willebrand factor

Factor VIII (FVIII) is a glycoprotein that plays an important role in the intrinsic pathway of coagulation. In circulation, FVIII is protected upon binding to von Willebrand factor (VWF), a chaperone molecule that regulates its half-life, distribution, and activity. Despite the biological significance of this interaction, its molecular mechanisms are not fully characterized. We determined the equilibrium and activation thermodynamics of the interaction between FVIII and VWF. The equilibrium affinity determined by surface plasmon resonance was temperature-dependent with a value of 0.8 nM at 35 °C. The FVIII-VWF interaction was characterized by very fast association (8.56 × 10(6) M(-1) s(-1)) and fast dissociation (6.89 × 10(-3) s(-1)) rates. Both the equilibrium association and association rate constants, but not the dissociation rate constant, were dependent on temperature. Binding of FVIII to VWF was characterized by favorable changes in the equilibrium and activation entropy (TΔS° = 89.4 kJ/mol, and -TΔS(++) = -8.9 kJ/mol) and unfavorable changes in the equilibrium and activation enthalpy (ΔH° = 39.1 kJ/mol, and ΔH(++) = 44.1 kJ/mol), yielding a negative change in the equilibrium Gibbs energy. Binding of FVIII to VWF in solid-phase assays demonstrated a high sensitivity to acidic pH and a sensitivity to ionic strength. Our data indicate that the interaction between FVIII and VWF is mediated mainly by electrostatic forces, and that it is not accompanied by entropic constraints, suggesting the absence of conformational adaptation but the presence of rigid "pre-optimized" binding surfaces.     

Investigation and optimisation of the drying of reduced glutathione by steered molecular dynamics simulation

The drying of reduced glutathione from a series of aqueous–ethanol binary solutions at 300 K (below human body temperature) and 330 K (above human body temperature) was investigated in detail by steered molecular simulation and an umbrella sampling method with the Gromacs software package and Gromos96(53a6) united atomic force field. The results show that electrostatic interactions between glutathione and solvent represent the main resistance to drying. When the aqueous solution was gradually changed to pure ethanol, the energy of electrostatic interaction between glutathione and solvent molecules increased by 445.088 kJ/mol, and the drying potential of mean force (PMF) free energy also fell by 253.040 kJ/mol. However, an increase in temperature from 300 to 330 K in the aqueous solution only results in an increase of 23.013 kJ/mol in electrostatic interaction energy and a decrease of 34.956 kJ/mol in drying PMF free energy. Furthermore, we show that hydrogen bonding is the major form of electrostatic interaction involved, and directly affects the drying of glutathione. Therefore, choosing water-miscible solvents that minimise hydrogen-bond formation with glutathione will enhance its drying rate, and this is likely to be more efficient than increasing the temperature of the process. Thus, a power-saving technology can be used to produce the high bioactivity medicines.     

Structural insight into the mechanism of epothilone A bound to beta-tubulin and its mutants at Arg282Gln and Thr274Ile

Epothilone A (EpoA) is under investigation as an antitumor agent. To provide better understanding of the activity of EpoA against cancers, by theoretical studies such as using docking method, molecular dynamics simulation and density functional theory calculations, we identify several key residues located on β-tubulin as the active sites to establish an active pocket responsible for interaction with EpoA. Eight residues (Arg276, Asp224, Asp26, His227, Glu27, Glu22, Thr274, and Met363) are identified as the active sites to form the active pocket on β-tubulin. The interaction energy is predicted to be -121.3?kJ/mol between EpoA and β-tubulin. In the mutant of β-tubulin at Thr274Ile, three residues (Arg359, Glu27, and His227) are identified as the active sites for the binding of EpoA. In the mutant of β-tubulin at Arg282Gln, three residues (Arg276, Lys19, and His227) serve as the active sites. The interaction energy is reduced to -77.2?kJ/mol between EpoA and Arg282Gln mutant and to -50.2?kJ/mol between EpoA and Thr274Ile mutant. The strong interaction with β-tubulin is significant to EpoA's activity against cancer cells. When β-tubulin is mutated either at Arg282Gln or at Thr274Ile, the decreased strength of interaction explains the activity reduced for EpoA. Therefore, this work shows that the structural basis of the active pocket plays an important role in regulating the activity for EpoA with a Taxol-like mechanism of action to be promoted as an antitumor agent.     

Stopped-flow kinetic studies of the cellulase-catalyzed conversion of cellulose to glucose

The kinetics of the cellulase-catalyzed conversion of soluble cellulose into glucose have been studied over a range of substrate concentrations and temperatures, and at pH values ranging from 4.75 to 7.0. Lineweaver-Burk plots were linear and led to V = 6.2muM/s and K(m) = 13.1 mM at pH 5.8 and 25.0 degrees C. The pK values corresponding to the free enzyme are 4.8 and 6.8 and are consistent with carboxyl and imidazole groups as the active ionizing species. These pK values were little changed in the enzyme-substrate intermediate that reacts in the ratedetermining step, suggesting that the ionizing groups are still free in this intermediate. The activation energy corresponding to V/K(m) is 80.6 kJ/mol, and that corresponding to V is 38.7 kJ/mol. The corresponding entropies of activation are 21 J K(-1) mol(-1) and -157 J K(-1) mol(-1), respectively.     

Dipole-dipole interaction stabilizes the transition state of apurinic/apyrimidinic endonuclease--abasic site interaction

Human apurinic/apyrimidinic (AP) endonuclease (hAPE) initiates the repair of an abasic site (AP site). To gain insight into the mechanisms of damage recognition of hAPE, we conducted surface plasmon resonance spectroscopy to study the thermodynamics and kinetics of its interaction with substrate DNA containing an abasic site (AP DNA). The affinity of hAPE binding toward DNA increased as much as 6-fold after replacing a single adenine (equilibrium dissociation constant, K(D), 5.3 nm) with an AP site (K(D), 0.87 nm). The enzyme-substrate complex formation appears to be thermodynamically stabilized and favored by a large change in Gibbs free energy, DeltaG degrees (-50 kJ/mol). The latter is supported by a high negative change in enthalpy, DeltaH degrees (-43 kJ/mol) and also positive change in entropy, DeltaS degrees (24 J/(K mol)), and thus the binding process is spontaneous at all temperatures. Analysis of kinetic parameters reveals small enthalpy of activation for association, DeltaH degrees++(ass) (-17 kJ/mol), and activation energy for association (E(a), -14 kJ/mol) when compared with the enthalpy of activation for dissociation, DeltaH degrees++(diss) (26 kJ/mol), and activation energy in the reverse direction (E(d), 28 kJ/mol). Furthermore, varying concentration of KCl showed an increase in binding affinity at low concentration but complete abrogation of the binding at higher concentration, implying the importance of hydrophobic, but predominantly ionic, forces in the Michaelis-Menten complex formation. Thus, low activation energy and the enthalpy of activation, which are perhaps a result of dipole-dipole interactions, play critical roles in AP site binding of APE.     

Behavior of Aromatic Molecules in Silicalite by the Direct Integration of the Configurational Integral

Abstract

Adsorption data of aromatic molecules adsorbed in silicalite show highly unusual characteristics which were attributed to structural effects caused by the comparable size of molecules and pores. In this study, the interaction of aromatic compounds with silicalite are examined on the molecular level. The interactions are calculated by atom-atom approximation using Lennard-Jones potentials. The constants are calculated, without fitting, from Kirkwood-Muller formulas. Benzene and p-xylene are represented as a rigid structure of 12 and 18 atom centers. The model is anisotropic.

The diffusional behavior of molecules is examined by minimizing the potential energy in the channels which requires less computational time than Molecular Dynamics. The activation energy for the diffusion of benzene, 27.6 kJ/mol, is in excellent agreement with data, 28.8 kJ/mol. The results indicate that both molecules can enter the smaller zig-zag channels. The energetically most favorable location in the main channels is the mid-point between intersections. All rotations are restricted in the channels but the molecules can rotate in any direction (with some movement of the center) at intersections.

The Henry's law constant and internal energy of adsorption at zero coverage are calculated by direct integration of the configurational integral. Direct integration is more efficient than Monte Carlo and Molecular Dynamics simulations since the molecules are highly restricted in the pores. The predicted internal energy of adsorption, ? 54.86 and ? 75.30 kJ/mol for benzene and p-xylene is in good agreement with data of ? 50.92 and ? 62.15 kJ/mol respectively. There is appreciable difference between the predicted and experimental Henry's law constants. The agreement can be improved by fitting the Lennard-Jones constants which has not been attempted.

Although the calculations are performed at infinite dilution and entropy effects are not included, the results bring insight to the behavior of molecules in highly restricted environments such as in tight pores. Similar simplified calculations can be used to close the gap between highly idealized molecular simulations and complicated systems common in real applications.     

The determination of the kinetics of polysaccharide thermal degradation using high temperature viscosity measurements

Information about the thermal degradation of the polysaccharides sodium alginate, carrageenan and carboxymethyl cellulose has been obtained from the time dependence of the viscosity at high temperatures measured using a slit viscometer. The viscosity is related to the molecular weight using previously-published relations between the zero shear specific viscosity and the coil overlap parameter in conjunction with the appropriate Mark-Houwink equation. It is found that alginate is much less stable than carboxymethyl cellulose and carrageenan. Activation energies for depolymerisation obtained from Arrhenius plots in the presence of oxygen ranged from 50 kJ/mol for alginate to 105 kJ/mol for κ-carrageenan.     

Studies on the isothermal crystallization of D-glucose and cellulose oligosaccharides by differential scanning calorimetry.

Isothermal crystallization from the glassy state of D-glucose and cellulose oligosaccharides (e.g., cellobiose, cellotriose, and cellotetraose) has been studied by differential scanning calorimetry. The crystallization of amorphous D-glucose and oligosaccharides was very difficult in the absence of traces of water. Amorphous cellobiose and cellotetraose crystallized far more rapidly than amorphous D-glucose and cellotriose. The activation energy for the crystallization of cellobiose and cellotetraose was approximately 10-12 kJ. mol(-1), while that for D-glucose and cellotriose was approximately 1-2 kJ. mol(-1). An odd-even effect seemed to be associated with the crystallization process of these saccharides.     

Carboxylate binding modes in zinc proteins: A theoretical study

The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second-sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, approximately 6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70-100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK(a) of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8-9.     

Thermal degradation mechanisms of wood under inert and oxidative environments using DAEM methods

The pyrolytic behavior of wood is investigated under inert and oxidative conditions. The TGA experiment is given a temperature variation from 323 to 1173 K by setting the heating rate between 5 and 40 K/min. The results of DTG curves show that the hemicellulose shoulder peak for birch is more visible under inert atmosphere due to the higher content of reactive xylan-based hemicellulose (mannan-based for pine). When oxygen presents, thermal reactivity of biomass (especially the cellulose) is greatly enhanced due to the acceleration of mass loss in the first stage, and complex reactions occur simultaneously in the second stage when char and lignin oxidize. A new kinetic model is employed for biomass pyrolysis, namely the distributed activation energy model (DAEM). Under inert atmosphere, the distributed activation energy for the two species is found to be increased from 180 to 220 kJ/mol at the solid conversion of 10-85% with the high correlation coefficient. Under oxidative atmosphere, the distributed activation energy is about 175-235 kJ/mol at the solid conversion of 10-65% and 300-770 kJ/mol at the solid conversion of 70-95% with the low correlation coefficient (below 0.90). Comparatively, the activation energy obtained from established global kinetic model is correspondingly lower than that from DAEM under both inert and oxidative environments, giving relatively higher correlation coefficient (more than 0.96). The results imply that the DAEM is not suitable for oxidative pyrolysis of biomass (especially for the second mass loss stage in air), but it could represent the intrinsic mechanism of thermal decomposition of wood under nitrogen better than global kinetic model when it is applicable.     

Thermodynamic and kinetic processes during the unfolding of BSA in the presence of the mycotoxin patulin

The effects of the mycotoxin patulin on the thermodynamics and kinetics of the transition of bovine serum albumin (BSA) in aqueous solution were studied by Differential Scanning Calorimetry and Photoluminescence methods. Results show that in the presence of patulin, the free enthalpy change during the transition of BSA was decreased by an average of ～ 46 kJ/mol, the free energy change was decreased by ～ 4 kJ/mol, and the activation energy fell from ～ 1546 to ～ 840 kJ/mol. These results indicate that the bioactivity of patulin is based on the kinetic rather than on the thermodynamic properties of the transition. This is the first evidence of the direct interaction of patulin with the free thiol-containing BSA, a process which could contribute to the adverse cyto- and genotoxic effects induced by patulin.     

Kinetics and apparent activation energy of the reaction of the fluorogenic reagent 5-furoylquinoline-3-carboxaldehyde with ovalbumin

Incomplete labeling of proteins by a derivatizing reagent usually results in the formation of a large number of products, which can produce unacceptable band broadening during electrophoretic analysis. In this paper, we report on the reaction of the fluorogenic reagent 5-furoylquinoline-3-carboxaldehyde (FQ) with the lysine residues of ovalbumin. Mass spectrometry was first used to determine the distribution in the number of labels attached to the protein. At room temperature, 3.6+/-1.9 labels were attached after 30 min. The reaction rate and number of labels increased at elevated temperatures. At 65 degrees C, 6+/-2.5 labels were attached after 5 min. The apparent activation energy for this reaction is estimated as 48+/-17 kJ/mol. Based on the mass spectrometry study, the labeling reaction was assumed to consist of two steps. In the first, the protein unfolds to make lysine residues accessible. In the second, the reagents react with the epsilon -amine of the lysine residues. To test this hypothesis, submicellar capillary electrophoresis and laser-induced fluorescence were used to characterize the reaction mixture. The apparent activation energy was measured for the labeling reaction; the apparent activation energy was 57+/-12 kJ/mol for reaction performed in the separation buffer. Denaturing agents were added to the reaction mixture. The addition of 2 M thiourea with 6 M urea to the reaction resulted in a modest decrease in the apparent activation energy to 42+/-2 kJ/mol. The addition of 2.5 M or higher concentration of ethanol decreased the apparent activation energy to 32+/-2 kJ/mol. We conclude that the apparent activation energy for protein labeling is dominated by denaturation of the protein, and that the addition of suitable denaturing reagents can eliminate this contribution to the reaction chemistry.     

The promotion of collagen polymerization by lanthanide and calcium ions.

Ca2+ (1-5 mM) and lanthanide (20-250 microM) ions enhance the rate of polymerization of purified calf skin collagen (1.5 mg/ml) at pH 7.0 in the presence of 30mM-Tris/HCl and 0.2 M-NaCl. Both the nucleation phase and the growth phase of polymerization are accelerated. The activation energy of the growth phase, 239.3 +/- 24.3 kJ/mol (57.2 +/- 5.8 kcal/mol), is decreased to 145.6 +/- 9.6 kJ/mol (34.8 +/- 2.3 kcal/mol) by 5 mM-Ca2+ and to 75.3 +/- 4.6 kJ/mol (18.0 +/- 1.1 kcal/mol) by 25 microM-Sm3+. In contrast, the activation energy of the nucleation phase, 191.6 +/- 23.4 kJ/mol (45.8 +/- 5.6 kcal/mol), is only slightly decreased by Ca2+ or Sm3+. Collagen fibrils formed in the presence of Sm3+ are thinner than control fibrils, and more thermoresistant.     

Analysis of coals and biomass pyrolysis using the distributed activation energy model

The thermal decomposition of coals and biomass was studied using thermogravimetric analysis with the distributed activation energy model. The integral method resulted in Datong bituminous coal conversions of 3-73% at activation energies of 100-486 kJ/mol. The corresponding frequency factors were e(19.5)-e(59.0)s(-1). Jindongnan lean coal conversions were 8-52% at activation energies of 100-462 kJ/mol. Their corresponding frequency factors were e(13.0)-e(55.8)s(-1). The conversion of corn-stalk skins were 1-84% at activation energies of 62-169 kJ/mol with frequency factors of e(10.8)-e(26.5)s(-1). Datong bituminous coal, Jindongnan lean coal and corn-stalk skins had approximate Gaussian distribution functions with linear ln k(0) to E relationships.     

Study on the binding of Arsenazo-TB to human serum albumin by Rayleigh light scattering technique and FT-IR

The interaction between Arsenazo-TB and human serum albumin (HSA) was studied by Rayleigh light scattering (RLS) technique and Fourier transformed IR (FT-IR). The binding parameters of Arsenazo-TB with HSA were studied at different temperature of 288, 298, 308, 318 K under the optimum conditions. It is indicated by the Scatchard plots that the binding constant K decreased from 5.03 x 10(7) to 7.13 x 10(6) and the maximum binding number N reduced from 53 to 36 with the increasing of the temperature. The binding process was exothermic, enthalpy driven and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction. The free energy change deltaG0, the enthalpy change deltaH0 and the entropy change deltaS0 of 288 K were calculated to be -42.46 kJ/mol, -49.17 kJ/mol and 318.15 J/mol K, respectively. The alterations of protein secondary structure in the presence of Arsenazo-TB in aqueous solution were quantitatively calculated from FT-IR spectroscopy with reductions of alpha-helix from 57% to 40% and with increases of beta-sheet from 36% to 39%, beta-turn from 7% to 21%.     

Ab initio molecular dynamics simulations of the adsorption of the methylguanidine or methylguanidinium on Ag(111)

A density-functional and Car–Parrinello molecular dynamics methods were employed to study the adsorption of the methylguanidine or methylguanidinium on Ag(111) surface with Vanderbilt pseudopotentials and PBE functional. The geometry, interacting energy, vibrational frequency, Mayer bond order and electrostatic fit charges were calculated. The results show that the methylguanidine interacts with the Ag(111) surface mainly through the interaction between the sp² hybridisation imine nitrogen and its nearest silver atom on top site, assisted with the Ag???H interaction, with the most stabilising interacting energy ?78.83 kJ/mol. The Car–Parrinello molecular dynamics results at 293.15 or 300.00 K indicate that the Ag???N interaction exists stably for more than 6 ps and the Mayer bond order analysis shows that it is the main interaction in adsorption. For the methylguanidinium on Ag(111) surface, the weak interaction between N?H and its neighbour silver atoms, with the energy of ?40.73–?42.68 kJ/mol and the interacting time of 0.2–0.3 ps at 300 K, could not keep it steady on Ag(111). The CP dynamics results show that only the methylguanidine could adsorb on Ag(111) at the room temperature.     

Probing the molecular mechanism of action of co-repressor in the E. coli methionine repressor-operator complex using surface plasmon resonance (SPR).

We have studied quantitatively the effect of the corepressor, S-adenosylmethionine (SAM), on the interaction between the E. coli methionine repressor, MetJ, and an idealised operator fragment, by recording measurements of surface plasmon resonance using a BIAcore instrument. We have recorded kinetic binding data in the presence of SAM, which carries a net positive charge, and two corepressor analogues, adenosylornithine (AO) and aza-SAM, which differ in the location of the atom carrying the positive charge. Our data support the hypothesis that the effect of the corepressor is electrostatic in origin. The difference in electrostatic interaction energy between the SAM- and AO-repressor-operator complexes of approximately 3.5 kJ/mol calculated from the known three-dimensional structure is within the range of our experimentally determined values of 2.8-4.3 kJ/mol. These results illustrate the potential of SPR measurements for studying protein-nucleic acid interactions.     

Comparative thermodynamic analysis of DNA--protein interactions using surface plasmon resonance and fluorescence correlation spectroscopy

We report a kinetic and thermodynamic analysis of interactions between ssDNA and replication protein A (RPA) using surface plasmon resonance (SPR) and fluorescence correlation spectroscopy (FCS) at variable temperature. The two methods yield different values for the Gibbs free energy but nearly the same value for the reaction enthalpy of ssDNA-RPA complex formation. The Gibbs free energy was determined by SPR and FCS to be -62.6 and -54.7 kJ/mol, respectively. The values for the reaction enthalpy are -64.4 and -66.5 kJ/mol. It is concluded that the difference in Gibbs free energy measured by the two methods is due to different reaction entropies. The entropic contribution to the free energy at 25 degrees C is -1.8 kJ/mol for SPR and -11.8 kJ/mol for FCS. In SPR, the reaction is restricted to two dimensions because of immobilization of the DNA molecules to the sensor surface. In contrast, FCS is able to follow complex formation without spatial restrictions. In consequence, the reaction entropy determined from SPR experiments is lower than for FCS experiments.     

Interactions of sodium pentobarbital with D-glucose and L-sorbose transport in human red cells.

Pentobarbital acts as a mixed inhibitor of net D-glucose exit, as monitored photometrically from human red cells. At 30 degrees C the Ki of pentobarbital for inhibition of Vmax of zero-trans net glucose exit is 2.16+/-0.14 mM; the affinity of the external site of the transporter for D-glucose is also reduced to 50% of control by 1. 66+/-0.06 mM pentobarbital. Pentobarbital reduces the temperature coefficient of D-glucose binding to the external site. Pentobarbital (4 mM) reduces the enthalpy of D-glucose interaction from 49.3+/-9.6 to 16.24+/-5.50 kJ/mol (P<0.05). Pentobarbital (8 mM) increases the activation energy of glucose exit from control 54.7+/-2.5 kJ/mol to 114+/-13 kJ/mol (P<0.01). Pentobarbital reduces the rate of L-sorbose exit from human red cells, in the temperature range 45 degrees C-30 degrees C (P<0.001). On cooling from 45 degrees C to 30 degrees C, in the presence of pentobarbital (4 mM), the Ki (sorbose, glucose) decreases from 30.6+/-7.8 mM to 14+/-1.9 mM; whereas in control cells, Ki (sorbose, glucose) increases from 6.8+/-1.3 mM at 45 degrees C to 23.4+/-4.5 mM at 30 degrees C (P<0.002). Thus, the glucose inhibition of sorbose exit is changed from an endothermic process (enthalpy change=+60.6+/-14.7 kJ/mol) to an exothermic process (enthalpy change=-43+/-6.2 7 kJ/mol) by pentobarbital (4 mM) (P<0.005). These findings indicate that pentobarbital acts by preventing glucose-induced conformational changes in glucose transporters by binding to 'non-catalytic' sites in the transporter.