Biomedical subjects

Donald L Thompson

Publications and source records attributed to Donald L Thompson.

At least 19 recordsLinked to original sources

PubMed2006

Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field.

We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.

Journal Article↗

PubMed2006

Molecular dynamics simulations of surface-initiated melting of nitromethane.

The melting of nitromethane initiated at solid-vacuum interfaces has been investigated using molecular dynamics nvt simulations with a realistic force field [D. C. Sorescu et al., J. Phys. Chem. B 104, 8406 (2000)]. The calculated melting point (251+/-5 K) is in good agreement with experiment (244.73 K) and values obtained previously (approximately 255.5 and 266.5+/-8 K) using other simulation methods [P. M. Agrawal et al., J. Chem. Phys. 119, 9617 (2003)]. Analyses of the molecular orientations and diffusion during the simulations as functions of the distance from the exposed surfaces show that the melting is a direct crystal-to-liquid transition, in which the molecules first gain rotational freedom, then mobility. There is a slight dependence of the melting temperature on the exposed crystallographic face.

Journal Article↗

PubMed2006

Molecular dynamics simulations of melting of perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine.

The melting mechanism of superheated perfect crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (alpha-RDX) has been investigated using molecular dynamics simulations with the fully flexible force field developed by Smith and Bharadwaj [J. Phys. Chem. B 103, 3570 (1999)]. Sequential 50 ps equilibration simulations of the constant stress-constant temperature ensemble were performed at 10 K intervals over the range of 300-650 K, corresponding to a heating rate of 2.0 x 10(11) Ks. A solid-solid phase transition is observed between 480 and 490 K, followed by melting, which occurs between 500 and 510 K. The solid-solid phase transition, both displacive and rotational, is characterized by an abrupt decrease in the lengths of the unit cell edges a and b and an increase of the length of edge c. The molecular conformation in the new phase is AAE, although the axial nitro groups have different changes: one shift is more axial and the other is more equatorial. Phases other than alpha-RDX have been observed experimentally, however, there are insufficient data for comparisons to ascertain that the new phase observed here corresponds to a real phase. At the high heating rate (2.0 x 10(11) Ks) used in the simulations, the melted RDX reaches full orientational disorder at about 540 K and translational freedom at around 580 K. If the simulation at the melting temperature (510 K) is run sufficiently long complete rotational freedom is achieved in a few hundreds of picoseconds, while complete translational freedom requires much longer. These results show that given a sufficiently high heating rate, the system can exist for significant periods of time in a near-liquid state in which the molecules are not as free to rotate and diffuse as in the true liquid state. The bond lengths and bond angles undergo little change upon melting, while there are significant changes in the dihedral angles. The molecular conformation of RDX changes from AAE to EEE upon melting. The ramification of this for formulating force fields that accurately describe melting is that it is important that the torsional motions are accurately described.

Journal Article↗

PubMed2006

On the accuracy of force fields for predicting the physical properties of dimethylnitramine.

The accuracy of three force fields for predicting the physical properties of dimethylnitramine (DMNA) has been investigated by using molecular dynamics simulations. The Sorescu, Rice, and Thompson (SRT) (J. Phys. Chem. B 1997, 101, 798) rigid-molecule, flexible generalized AMBER (J. Comput. Chem. 2004, 25, 1157), and Smith et al. flexible force fields (J. Phys. Chem. B 1999, 103, 705) were tested. The density, lattice parameters, isotherm, and melting point of DMNA are calculated using classical molecular dynamics. Except for the melting point, the predictions of the three force fields are in reasonable agreement with experimental values. The calculated thermodynamic melting points (Tmp) for the SRT, AMBER, and Smith et al. force fields are 380, 360, and 260 K, respectively. The experimental value is 331 K. Modifications of the torsional barriers in the AMBER force field resulted in Tmp = 346 K, in good agreement with the experimental value of 331 K. The calculated lattice parameters and bulk modulus are also improved with the modifications of the AMBER potential. The results indicate that, although not sufficiently accurate without modifications, the general force fields such as AMBER provide the basis for developing force fields that correctly predict the physical properties of nitramines.

Journal Article↗

PubMed2006

Molecular dynamics simulations of p-tert-butylcalix[4]arene with small guest molecules.

Classical molecular dynamics simulations were used to study p-tert-butylcalix[4]arene inclusion compounds with xenon, nitrogen, hydrogen, methane, and sulfur dioxide guest molecules. The calixarene units were taken to be rigid and the intermolecular molecular interactions were modeled as a sum of the van der Waals interactions with parameters from the AMBER force field and electrostatic interactions. Simulations of the high-density alpha phase and low-density beta0 phase of p-tert-butylcalix[4]arene were used to test the force field. The predicted densities of the two phases were found to agree with experimental measurements at 173 K to within 5 %. Simulations were performed with guests placed inside the calixarene cages of the beta0 phase. Guest-host ratios of 1:1 to 1:4 were considered. Changes in the unit-cell volume and density of the phases with the addition of guest molecules and the inclusion energies for the guests were determined. Finally, the dynamics of the guest motion inside the cages were characterized by determining the root-mean-square displacements and velocity autocorrelation functions of the xenon and nitrogen guests.

Journal Article↗

PubMed2006

Molecular dynamics simulations of melting and the glass transition of nitromethane.

Molecular dynamics simulations have been used to investigate the thermodynamic melting point of the crystalline nitromethane, the melting mechanism of superheated crystalline nitromethane, and the physical properties of crystalline and glassy nitromethane. The maximum superheating and glass transition temperatures of nitromethane are calculated to be 316 and 160 K, respectively, for heating and cooling rates of 8.9 x 10(9) Ks. Using the hysteresis method [Luo et al., J. Chem. Phys. 120, 11640 (2004)] and by taking the glass transition temperature as the supercooling temperature, we calculate a value of 251.1 K for the thermodynamic melting point, which is in excellent agreement with the two-phase result [Agrawal et al., J. Chem. Phys. 119, 9617 (2003)] of 255.5 K and measured value of 244.73 K. In the melting process, the nitromethane molecules begin to rotate about their lattice positions in the crystal, followed by translational freedom of the molecules. A nucleation mechanism for the melting is illustrated by the distribution of the local translational order parameter. The critical values of the Lindemann index for the C and N atoms immediately prior to melting (the Lindemann criterion) are found to be around 0.155 at 1 atm. The intramolecular motions and molecular structure of nitromethane undergo no abrupt changes upon melting, indicating that the intramolecular degrees of freedom have little effect on the melting. The thermal expansion coefficient and bulk modulus are predicted to be about two or three times larger in crystalline nitromethane than in glassy nitromethane. The vibrational density of states is almost identical in both phases.

Journal Article↗

PubMed2006

Reproduction in high body condition mares with high versus low leptin concentrations.

Previous results from our laboratory indicated that a majority of mares with high body condition scores (BCS) displayed estrous cycles or had considerable follicular activity during the winter. Among these high BCS mares, about 35% of them exhibited a persistent hyperleptinemia and hyperinsulinemia. The current experiment was designed to compare the reproductive characteristics of high BCS mares with hyperleptinemia to those with normal (low) plasma concentrations of leptin during the winter and the first estrous cycle (or the first full cycle encountered for those already cycling). Light horse mares with high BCS (6-8.5) were assigned to groups based on leptin concentrations (8/group): low (<5 ng/mL) and high (>10 ng/mL). Beginning 7 January, mares were assessed every 3d for follicular activity and then daily once a follicle >25 mm was detected. Mares were subsequently monitored through their first and second ovulations. Leptin concentrations remained higher (P<0.001) in mares in the high leptin group over the duration of the experiment. Also, high leptin mares had greater (P<0.0001) insulin response to glucose infusion and a faster (P<0.05) rate of glucose clearance. One mare with high leptin and three mares with low leptin had progesterone concentrations indicative of the presence of a corpus luteum at the onset of the experiment. Plasma concentrations of LH, FSH, and progesterone did not differ between groups (P>0.1) during the first estrous cycle occurring after 7 January. Date of first ovulation after 7 January and interovulatory interval were similar (P>0.1) for the two groups, as were estimates of follicular numbers on the ovaries (small, medium, and large; P>0.1). It is concluded that the perturbations in leptin and insulin secretion observed in some high BCS mares are not associated with alterations in ovarian activity or the estrous cycle during winter and into the period of vernal transition.

Animals↗

PubMed2006

Molecular dynamics simulations of the melting of 1,3,3-trinitroazetidine.

Physical properties of condensed-phase 1,3,3-trinitroazetidine (TNAZ) have been computed with molecular dynamics (MD) and a nonreactive, fully flexible force field formulated by combining the intramolecular interactions obtained from the Generalized AMBER Force Field and the rigid-molecule force field developed by Sorescu-Rice-Thompson [J. Phys. Chem. B 1997, 101, 798] (AMBER-SRT). The results are compared with MD calculations, using the AMBER force field. The predicted densities of crystalline TNAZ from both force fields are about 10% lower than the experimental value. The calculated thermodynamic melting point at 1 atm from the AMBER-SRT force field is 390 K, in good agreement with the measured value of 374 K, while the AMBER force field predicts a thermodynamic melting point of 462 K. The lattice parameters and the molecular and crystal structures calculated with the AMBER-SRT force field are in excellent agreement with experiment. Simulations with the AMBER-SRT force field were also used to generate the isotherm of TNAZ up to 4 GPa and the bulk modulus and its pressure derivative.

Journal Article↗

PubMed2006

Urea and urea nitrate decomposition pathways: a quantum chemistry study.

Electronic structure calculations have been performed to investigate the initial steps in the gas-phase decomposition of urea and urea nitrate. The most favorable decomposition pathway for an isolated urea molecule leads to HNCO and NH3. Gaseous urea nitrate formed by the association of urea and HNO3 has two isomeric forms, both of which are acid-base complexes stabilized by the hydrogen-bonding interactions involving the acidic proton of HNO3 and either the O or N atoms of urea, with binding energies (D0(o), calculated at the G2M level with BSSE correction) of 13.7 and 8.3 kcal/mol, respectively, and with estimated standard enthalpies of formation (delta(f)H298(o) of -102.3 and -97.1 kcal/mol, respectively. Both isomers can undergo relatively facile double proton transfer within cyclic hydrogen-bonded structures. In both cases, HNO3 plays a catalytic role for the (1,3) H-shifts in urea by acting as a donor of the first and an acceptor of the second protons transferred in a relay fashion. The double proton transfer in the carbonyl/hydrogen bond complex mediates the keto-enol tautomerization of urea, and in the other complex the result is the breakdown of the urea part to the HNCO and NH3 fragments. The enolic form of urea is not expected to accumulate in significant quantities due to its very fast conversion back to H2NC(O)NH2 which is barrierless in the presence of HNO3. The HNO3-catalyzed breakdown of urea to HNCO and NH3 is predicted to be the most favorable decomposition pathway for gaseous urea nitrate. Thus, HNCO + NH3 + HNO3 and their association products (e.g., ammonium nitrate and isocyanate) are expected to be the major initial products of the urea nitrate decomposition. This prediction is consistent with the experimental T-jump/FTIR data [Hiyoshi et al. 12th Int. Detonation Symp., Aug 11-16, San Diego, CA, 2002].

Journal Article↗

PubMed2006

Interpolating moving least-squares methods for fitting potential-energy surfaces: further improvement of efficiency via cutoff strategies.

In standard applications of interpolating moving least squares (IMLS) for fitting a potential-energy surface (PES), all available ab initio points are used. Because remote ab initio points negligibly influence IMLS accuracy and increase IMLS time-to-solution, we present two methods to locally restrict the number of points included in a particular fit. The fixed radius cutoff (FRC) method includes ab initio points within a hypersphere of fixed radius. The density adaptive cutoff (DAC) method includes points within a hypersphere of variable radius depending on the point density. We test these methods by fitting a six-dimensional analytical PES for hydrogen peroxide. Both methods reduce the IMLS time-to-solution by about an order of magnitude relative to that when no cutoff method is used. The DAC method is more robust and efficient than the FRC method.

Journal Article↗

PubMed2006

Molecular dynamics simulations of the melting of aluminum nanoparticles.

Molecular dynamics simulations are performed to determine the melting points of aluminum nanoparticles of 55-1000 atoms with the Streitz-Mintmire [Phys. Rev. B 1994, 50, 11996] variable-charge electrostatic plus potential. The melting of the nanoparticles is characterized by studying the temperature dependence of the potential energy and Lindemann index. Nanoparticles with less than 850 atoms show bistability between the solid and liquid phases over temperature ranges below the point of complete melting. The potential energy of a nanoparticle in the bistable region alternates between values corresponding to the solid and liquid phases. This bistability is characteristic of dynamic coexistence melting. At higher temperatures, only the liquid state is stable. Nanoparticles with more than 850 atoms undergo a sharp solid-liquid-phase transition characteristic of the bulk solid phase. The variation of the melting point with the effective nanoparticle radius is also determined.

Journal Article↗

PubMed2005

Simulations of the solid, liquid, and melting of 1-n-butyl-4-amino-1,2,4-triazolium bromide.

Molecular dynamics simulations are used to study the solid and liquid properties and to predict the melting point of 1-n-propyl-4-amino-1,2,4-triazolium bromide ([patr][Br]) using a force field based on the one developed by Canongia Lopes et al. (J. Phys. Chem. B 2004, 108, 2038) for dialkyl substituted imidazolium salts, which was modified by including terms from the general AMBER force field. Electrostatic charges for the intermolecular interactions were determined from gas-phase ab initio electron structure calculations of the triazolium cation. Simulations of the solid state at 100 K reproduced the experimental density to within 4%. Simulations from 100 K to the melting point and the liquid from 333 to 500 K were performed to determine the temperature dependence of the densities of the two phases. The structures of the solid and liquid phases are characterized with radial distribution functions, which show that there are strong spatial correlations among neighboring ion pairs in liquid [patr][Br]. The dynamic behavior of the ions in the liquid state is also studied by computing velocity autocorrelation functions and the mean-square displacements between the ions. The melting point is determined by simulating void-induced melting. Changes in the density, intermolecular energy, and Lindemann index are used as indicators of the melting transition. The computed melting point is 360 +/- 10 K, which is within 10% of the experimental value 333 K.

Journal Article↗

PubMed2005

Theoretical predictions of the initial decomposition steps of dimethylnitramine.

The structures and energies of the reactants, products, and transition states of the initial steps in the gas-phase decomposition of dimethylnitramine (DMNA) have been determined by quantum chemical calculations at the B3LYP density-functional theory, MP2, and G2 levels. The pathways considered are NO2 elimination, HONO elimination, and nitro-nitrite rearrangement. The NO2 elimination is predicted to be the main channel of the gas-phase decomposition of DMNA in accord with experiment. The values of the Arrhenius parameters, log A=16.6+/-0.5 and Ea=40.0+/-0.6 kcal/mol, for the N-NO2 bond-fission reaction were obtained using a canonical variational theory with B3LYP energies and frequencies. The HONO-elimination channel has the next lowest activation energy of 44.7+/-0.5 kcal/mol (log A=13.6+/-0.5) and is characterized by a five-member transition-state configuration in which a hydrogen atom from one of the methyl groups is transferred to an oxygen atom of NO2. Tunneling contributions to the rate of this reaction have been estimated. The nitro-nitrite rearrangement reaction occurs via a transition state in which both oxygen atoms of NO2 are loosely bound to the central nitrogen atom, for which Rice-Ramsperger-Kassel-Marcus theory predicts log A=14.4+/-0.6 and Ea=54.1+/-0.8 kcal/mol.

Journal Article↗

PubMed2005

Molecular dynamics studies of melting and some liquid-state properties of 1-ethyl-3-methylimidazolium hexafluorophosphate [emim][PF6].

Molecular dynamics simulations are used to study the liquid-state properties and melting of 1-ethyl-3-methylimidazolium hexafluorosphosphate [emim][PF6] using the force field of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] and geometric constants from crystallographic data. The structures of the solid and liquid states are characterized by carbon-carbon, carbon-phosphorous, and phosphorous-phosphorous radial distribution functions. Spatial correlations among the ions are strong in the liquid state. The cohesive energy density and the temperature dependences of the molar volume and density of the liquid have been computed. The melting point is determined by equilibrating the solid-state supercells in which void defects have been introduced to eliminate the free-energy barrier for the formation of a solid-liquid interface. The computed melting point is 375+/-10 K, which is approximately 10% higher than the experimental value of 333 K.

Journal Article↗

PubMed2005

First-principles calculations of the adsorption of nitromethane and 1,1-diamino-2,2-dinitroethylene (FOX-7) molecules on the alpha-Al2O3(0001) surface.

First-principles calculations based on density functional theory (DFT) and the generalized gradient approximation (GGA) have been used to study the adsorption of nitromethane (NM) and 1,1-diamino-2,2-dinitroethylene (FOX-7) molecules on the basal plane of an alpha-Al(2)O(3) crystal. The calculations employ a (2 x 2) supercell slab model and 3D periodic boundary conditions. On the basis of these calculations, we have determined that both NM and FOX-7 molecules can adsorb nondissociatively on the surface with the most stable adsorption configurations parallel to the surface. The binding energies are in the range 25.3-26.0 kcal/mol for NM and 35.6-48.3 kcal/mol for FOX-7 depending on the relative molecular orientation and the surface sites. The minimum energy pathways for NM dissociation have been determined, and a low-energy pathway leading to H-atom elimination with formation of adsorbed CH(2)NO(2) and hydroxyl species has been identified. Additional calculations have focused on adsorption properties of aci-nitromethane tautomers and on description of the energetic pathways connecting adsorbed nitromethane molecule with these tautomers.

Adsorption↗

PubMed2005

Molecular dynamics simulations of the oxidation of aluminum nanoparticles.

The oxidation of aluminum nanoparticles is studied with classical molecular dynamics and the Streitz-Mintmire (Streitz, F. H.; Mintmire, J. W. Phys. Rev. B 1994, 50, 11996) electrostatic plus (ES+) potential that allows for the variation of electrostatic charge on all atoms in the simulation. The structure and charge distributions of bulk crystalline alpha-Al(2)O(3), a surface slab of alpha-Al(2)O(3) with an exposed (0001) basal plane, and an isolated Al(2)O(3) nanoparticle are studied. Constant NVT simulations of the oxidation of aluminum nanoparticles are also performed with different oxygen exposures. The calculations simulate a thermostated one-time exposure of an aluminum nanoparticle to different numbers of surface oxygen atoms. In the first set of oxidation studies, the overall approximate ratios of Al to O in the nanoparticle are 1:1 and 2:1. The nanoparticles are annealed to 3000 K and are then cooled to 500, 1000, or 1500 K. The atomic kinetic energy is scaled during the simulation to maintain the desired temperature. The structure and charge distributions in the oxidized nanoparticles differ from each other and from those of the bulk Al(2)O(3) phases. In the Al(1)O(1) simulation, an oxide shell forms that stabilizes the shape of the particle, and thus the original structure of the nanoparticle is approximately retained. In the case of Al(1)O(0.5), there is insufficient oxygen to form a complete oxide shell, and the oxidation results in particles of irregular shapes and rough surfaces. The particle surface is rough, and the nanoparticle is deformed.

Aluminum↗

PubMed2005

Effects of oral administration of levothyroxine sodium on serum concentrations of thyroid gland hormones and responses to injections of thyrotropin-releasing hormone in healthy adult mares.

OBJECTIVE: To determine the effects of levothyroxine sodium (L-T4) on serum concentrations of thyroid gland hormones and responses to injections of thyrotropin-releasing hormone (TRH) in euthyroid horses. ANIMALS: 12 healthy adult mares. PROCEDURE: 8 horses received an incrementally increasing dosage of L-T4 (24, 48, 72, or 96 mg of L-T4/d) for weeks 1 to 8. Each dose was provided for 2 weeks. Four additional horses remained untreated. Serum concentrations of total triiodothyronine (tT3), total thyroxine (tT4), free T3 (fT3), free T4 (fT4), and thyroid-stimulating hormone (TSH) were measured in samples obtained at weeks 0, 2, 4, 6, and 8; 1.2 mg of TRH was then administered i.v., and serum concentrations of thyroid gland hormones were measured 2 and 4 hours after injection. Serum reverseT3 (rT3) concentration was also measured in the samples collected at weeks 0 and 8. RESULTS: Treated horses lost a significant amount of weight (median, 19 kg). Significant treatment-by-time effects were detected for serum tT3, tT4, fT3, fT4, and TSH concentrations, and serum tT4 concentrations were positively correlated (r, 0.95) with time (and therefore dosage) in treated horses. Mean +/- SD serum rT3 concentration significantly increased in treated horses (3.06 +/- 0.51 nmol/L for week 8 vs 0.74 +/- 0.22 nmol/L for week 0). Serum tT3, tT4, fT3, and TSH concentrations in response to TRH injections differed significantly between treated and untreated horses. CONCLUSIONS AND CLINICAL RELEVANCE: Administration of levothyroxine sodium increased serum tT4 concentrations and blunted responses toTRH injection in healthy euthyroid horses.

Analysis of Variance↗

PubMed2004

Interpolating moving least-squares methods for fitting potential energy surfaces: Analysis of an application to a six-dimensional system.

The basic formal and numerical aspects of different degree interpolated moving least-squares (IMLS) methods are applied to a six-dimensional potential energy surface (PES) of the HOOH molecule, for which an analytic ("exact") potential is available in the literature. The results of systematic investigations of the effects of weight function parameters, the degree and partial degree of IMLS, the number of data points allowed, and the optimal automatic point selection of data points up to full third-degree IMLS fits are reported. With partial reduction of cross terms and automatic point selection the full six-dimensional HOOH PES can be fit over a range of 100 kcal/mol to an accuracy of less than 1 kcal/mol with approximately 1350 ab initio points.

Journal Article↗