Computer modelling of the thermal decomposition of solids
- Authors: De la Croix, Annemarie
- Date: 1996
- Subjects: Solids -- Thermal properties -- Computer simulation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4302 , http://hdl.handle.net/10962/d1004960 , Solids -- Thermal properties -- Computer simulation
- Description: Decompositions of solids are typically of the form: A(s) ----> B(s) + gases. Symmetry-controlled routes (based on known and hypothetical crystal structures) for transforming the solid reactant into the solid product were devised as possible decomposition pathways. Lattice energies of the reactants, of the postulated transient intermediate structures and of the final solid products were then estimated by crystal modelling procedures. Profiles of lattice energy changes during the proposed decomposition routes were constructed and any energy barriers were compared with experimental activation energies reported for the thermal decompositions. The crystal modelling was performed with the computer program WMIN. Calculation of the lattice energies involved the development of a model potential for the perfect lattice and the evaluation of the interatomic parameters. The potential was based on the Born model of ionic solids using the Buckingham potential (Ø(r)= Ae⁻r/p - C/r⁶) to describe the short-range energy contribution. Empirical fitting was used to establish reliable interatomic energy parameters. The reliability of the interatomic potentials was assessed by calculating crystal structures and lattice energies (which were not included in the fitting). The particular reactions selected for modelling were the decompositions of the alkaline-earth metal (Ca, Sr, Ba) peroxides and carbonates: M0₂(s) ---> MO(s) + ¹/₂0₂(g) MC0₃(s) ---> MO(s) + CO₂(g)The lattice energies calculated for the known structures were in good agreement with reported values, (except for Ba0₂ and BaC0₃) which provided support for the adequacy of the potential model used. Activation energies calculated for the decomposition of the carbonates were in the correct order but hlgher than experimental values, i. e., 422, 422, 465 and 499 kJ mol̄̄⁻¹ compared to the experimental values of 205, 87(?), 222 and 283 kJ mol̄̄⁻¹ for CaC0₃ (calcite), CaC0₃(aragonite), SrC0₃ and BaC0₃. The values calculated for the peroxides (91 and 100 kJ mol⁻¹ compared to the experimental values of 119 and 185 kJ mol⁻¹ for Sr0₂ and Ba0₂ respectively) were less satisfactory but could be a reflection of the poor structural data used for the peroxides. The significance of this approach to the modelling of solid decompositions is discussed.
- Full Text:
- Date Issued: 1996
- Authors: De la Croix, Annemarie
- Date: 1996
- Subjects: Solids -- Thermal properties -- Computer simulation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4302 , http://hdl.handle.net/10962/d1004960 , Solids -- Thermal properties -- Computer simulation
- Description: Decompositions of solids are typically of the form: A(s) ----> B(s) + gases. Symmetry-controlled routes (based on known and hypothetical crystal structures) for transforming the solid reactant into the solid product were devised as possible decomposition pathways. Lattice energies of the reactants, of the postulated transient intermediate structures and of the final solid products were then estimated by crystal modelling procedures. Profiles of lattice energy changes during the proposed decomposition routes were constructed and any energy barriers were compared with experimental activation energies reported for the thermal decompositions. The crystal modelling was performed with the computer program WMIN. Calculation of the lattice energies involved the development of a model potential for the perfect lattice and the evaluation of the interatomic parameters. The potential was based on the Born model of ionic solids using the Buckingham potential (Ø(r)= Ae⁻r/p - C/r⁶) to describe the short-range energy contribution. Empirical fitting was used to establish reliable interatomic energy parameters. The reliability of the interatomic potentials was assessed by calculating crystal structures and lattice energies (which were not included in the fitting). The particular reactions selected for modelling were the decompositions of the alkaline-earth metal (Ca, Sr, Ba) peroxides and carbonates: M0₂(s) ---> MO(s) + ¹/₂0₂(g) MC0₃(s) ---> MO(s) + CO₂(g)The lattice energies calculated for the known structures were in good agreement with reported values, (except for Ba0₂ and BaC0₃) which provided support for the adequacy of the potential model used. Activation energies calculated for the decomposition of the carbonates were in the correct order but hlgher than experimental values, i. e., 422, 422, 465 and 499 kJ mol̄̄⁻¹ compared to the experimental values of 205, 87(?), 222 and 283 kJ mol̄̄⁻¹ for CaC0₃ (calcite), CaC0₃(aragonite), SrC0₃ and BaC0₃. The values calculated for the peroxides (91 and 100 kJ mol⁻¹ compared to the experimental values of 119 and 185 kJ mol⁻¹ for Sr0₂ and Ba0₂ respectively) were less satisfactory but could be a reflection of the poor structural data used for the peroxides. The significance of this approach to the modelling of solid decompositions is discussed.
- Full Text:
- Date Issued: 1996
Continuous-flow dynamic dialysis and its application to collagen-ligand interactions
- Authors: Sparrow, Neil Arthur
- Date: 1983
- Subjects: Collagen Ligands (Biochemistry) Ligand binding (Biochemistry) Protein-protein interactions Tannins
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4297 , http://hdl.handle.net/10962/d1004617
- Description: Studies undertaken to investigate the binding of low molecular mass analogues of polyphenolic vegetable tannins to collagen have prompted the development of a new method to investigate protein-ligand interactions. This method, the continuous-flow dynamic dialysis method (CFDD), differs from conventional dialysis procedures used for protein-ligand binding studies. In this method, the ligand concentration in the diffusate is monitored automatically at successive closely spaced time intervals while being continuously eluted from the dialysis cell. The primary data obtained by this method consists of a series of spectrophotometric absorbance measurements representing the ligand concentration in the sink compartment of a dialysis cell. This primary data is recorded by means of a data logging device onto a punched paper tape for subsequent computer processing. Two original methods are presented for analysing the primary data to extract the protein-ligand binding isotherm. The first of these is a direct analysis which relies on Fick's first law of diffusion. In this method it is necessary to establish, by means of a control experiment, a value for the ligand permeation constant. This is used in a subsequent analysis to establish a relationship between the measured rate of diffusion of the ligand from a protein-ligand mixture and the concentration of unbound ligand which is in equilibrium with the protein-ligand complex. The protein-ligand binding isotherm is obtained from parametric equations which give the quantity of ligand bound to the protein and the concentration of unbound ligand in the sample compartment as functions of time. The second method, which is more general, utilizes the same primary data but is based on establishing a system transfer function to characterise the dialysis and eluting processes. This analysis depends on the linearity of the system and utilizes numerical laplace transforms of the primary data sets obtained from control and protein-ligand dialyses. Laplace transforms are used to effect a deconvolution of the transfer function from the primary data and yield the concentration of ligand in equilibrium with the protein-ligand complex. This procedure yields, simultaneously, both the total ligand concentration and the concentration of unbound ligand in the protein compartment of the dialysis cell. These quantities are used to establish the binding isotherm for the protein ligand system. Numerical inversion of the laplace transforms in this analysis is effected by their reduction to Fourier series. The experimental reliability of the continuous-flow dynamic dialysis method, and validity of the two analytical methods used to derive a binding isotherm from dialysis data are evaluated from studies of the binding of phenol red to bovine serum albumin (BSA) at 15⁰, 20⁰ and 25⁰ C, as well as from simulated binding curves generated by the numerical solution of the differential equations used to describe the dialysis and elution process in terms of a two-site Scatchard binding model. The method is used to investigate the binding to collagen of a series of low molecular mass phenolic compounds which can be isolated from Wattle and Quebracho vegetable tannin extracts. These compounds can be considered as monomeric precursor analogues of the polymeric vegetable tannins. The binding of these ligands to collagen is shown to be characterised by high capacity, low affinity binding in which the uptake of ligand by the protein increases linearly with increasing ligand concentration. Collagen exhibits no indication of site saturation for these ligands over the experimentally accessible concentration ranges investigated.
- Full Text:
- Date Issued: 1983
- Authors: Sparrow, Neil Arthur
- Date: 1983
- Subjects: Collagen Ligands (Biochemistry) Ligand binding (Biochemistry) Protein-protein interactions Tannins
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4297 , http://hdl.handle.net/10962/d1004617
- Description: Studies undertaken to investigate the binding of low molecular mass analogues of polyphenolic vegetable tannins to collagen have prompted the development of a new method to investigate protein-ligand interactions. This method, the continuous-flow dynamic dialysis method (CFDD), differs from conventional dialysis procedures used for protein-ligand binding studies. In this method, the ligand concentration in the diffusate is monitored automatically at successive closely spaced time intervals while being continuously eluted from the dialysis cell. The primary data obtained by this method consists of a series of spectrophotometric absorbance measurements representing the ligand concentration in the sink compartment of a dialysis cell. This primary data is recorded by means of a data logging device onto a punched paper tape for subsequent computer processing. Two original methods are presented for analysing the primary data to extract the protein-ligand binding isotherm. The first of these is a direct analysis which relies on Fick's first law of diffusion. In this method it is necessary to establish, by means of a control experiment, a value for the ligand permeation constant. This is used in a subsequent analysis to establish a relationship between the measured rate of diffusion of the ligand from a protein-ligand mixture and the concentration of unbound ligand which is in equilibrium with the protein-ligand complex. The protein-ligand binding isotherm is obtained from parametric equations which give the quantity of ligand bound to the protein and the concentration of unbound ligand in the sample compartment as functions of time. The second method, which is more general, utilizes the same primary data but is based on establishing a system transfer function to characterise the dialysis and eluting processes. This analysis depends on the linearity of the system and utilizes numerical laplace transforms of the primary data sets obtained from control and protein-ligand dialyses. Laplace transforms are used to effect a deconvolution of the transfer function from the primary data and yield the concentration of ligand in equilibrium with the protein-ligand complex. This procedure yields, simultaneously, both the total ligand concentration and the concentration of unbound ligand in the protein compartment of the dialysis cell. These quantities are used to establish the binding isotherm for the protein ligand system. Numerical inversion of the laplace transforms in this analysis is effected by their reduction to Fourier series. The experimental reliability of the continuous-flow dynamic dialysis method, and validity of the two analytical methods used to derive a binding isotherm from dialysis data are evaluated from studies of the binding of phenol red to bovine serum albumin (BSA) at 15⁰, 20⁰ and 25⁰ C, as well as from simulated binding curves generated by the numerical solution of the differential equations used to describe the dialysis and elution process in terms of a two-site Scatchard binding model. The method is used to investigate the binding to collagen of a series of low molecular mass phenolic compounds which can be isolated from Wattle and Quebracho vegetable tannin extracts. These compounds can be considered as monomeric precursor analogues of the polymeric vegetable tannins. The binding of these ligands to collagen is shown to be characterised by high capacity, low affinity binding in which the uptake of ligand by the protein increases linearly with increasing ligand concentration. Collagen exhibits no indication of site saturation for these ligands over the experimentally accessible concentration ranges investigated.
- Full Text:
- Date Issued: 1983
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