Biomedical subjects

Saman Alavi

Publications and source records attributed to Saman Alavi.

17 recordsLinked to original sources

PubMed2006

Stability of rare gas structure H clathrate hydrates.

Molecular dynamics simulations are used to study the stability of structure H (sH) clathrate hydrates with the rare gases Ne, Ar, Kr, and Xe. Simulations on a 3 x 3 x 3 sH unit cell replica are performed at ambient pressure at 40 and 100 K temperatures. The small and medium (s+m) cages of the sH unit cell are assigned rare gas guest occupancies of 1 and for large (l) cages guest occupancies of 1-6 are considered. Radial distribution functions for guest pairs with occupancies in the l-l, l-(s+m), and (s+m)-(s+m) cages are presented. The unit cell volumes and configurational energies are studied as a function of large cage occupancy for the rare gases. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at 100 K and 1 bar and 20 kbar pressures. These studies show that the most stable argon clathrate has five guests in the large cages. For krypton and xenon the most stable configurations have three and two guests in the large cages, respectively.

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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.

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PubMed2006

Molecular dynamics simulations of binary structure H hydrogen and methyl-tert-butylether clathrate hydrates.

Binary structure H (sH) hydrogen and methyl-tert-butylether (MTBE) clathrate hydrates are studied with molecular dynamics simulations. Simulations on a 3 x 3 x 3 sH unit cell with up to 4.7 mass % hydrogen gas are run at pressures of 100 bars and 2 kbars at 100 and 273 K. For the small and medium cages of the sH unit cell, H2 guest molecule occupancies of 0, 1 (single occupancy), and 2 (double occupancy) are considered with the MTBE molecule occupying all of the large cages. An increase of the small and medium cage occupancies from 1 to 2 leads to a jump in the unit cell volume and configurational energy. Calculations are also set up with 13, 23, and 89 of the MTBE molecules in the large cages replaced by sets of three to six H2 molecules, and the effects on the configurational energy and volume of the simulation cell are determined. As MTBE molecules are replaced with sets of H2 guests in the large cages, the configurational energy of the unit cell increases. At the lower temperature, the energy and volume of the clathrate are not sensitive to the number of hydrogen guests in the large cages; however, at higher temperatures the repulsions among the H2 guest molecules in the large cages cause an increase in the system energy and volume.

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PubMed2006

Void-induced dissolution in molecular dynamics simulations of NaCl and water.

To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100 ps, in contrast with a much longer time scale of 1 mus expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300 K and 1 atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100 K increase in temperature, and a weak dependence on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.

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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].

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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.

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PubMed2006

Molecular-dynamics simulations of binary structure II hydrogen and tetrahydrofurane clathrates.

The binary structure II hydrogen and tetrahydrofurane (THF) clathrates are studied with molecular-dynamics simulations. Simulations are done at pressures of 120 and 1.013 bars for temperatures ranging from 100 to 273 K. For the small cages of the structure II unit cell, H2 guest molecule occupancies of 0, 16 (single occupancy), and 32 (double occupancy) are considered. THF occupancies of 0-8 in the large cages are studied. For cases in which THF does not occupy all large cages in a unit cell, the remaining large cages can be occupied with sets of four H2 guest molecules. The unit-cell volumes and configurational energies are compared in the different occupancy cases. Increasing the small cage occupancy leads to an increase in the unit-cell volume and thermal-expansion coefficient. Among simulations with the same small cage occupancy, those with the large cages containing 4H2 guests have the largest volumes. The THF guest molecules have a stabilizing effect on the clathrate and the configurational energy of the unit cell decreases linearly as the THF content increases. For binary THF + H2 clathrates, the substitution of the THF molecules in the large cages with sets of 4H2 molecules increases the configurational energy. For the binary clathrates, various combinations of THF and H2 occupancies have similar configurational energies.

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PubMed2005

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides.

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.

DNA↗

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.

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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.

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PubMed2005

A theoretical expression for drying time of thin lumber.

An analytical expression for the drying time of thin lumber is derived, based on a method presented in this study. The laws of moisture content change in wood as function of mass transfer are used for the theoretical approach. The diffusion equation for moisture content is set up for a three-dimensional block of lumber based on the assumption of uniform initial distribution of moisture throughout the specimen. The boundary condition stipulates that the moisture gradient at the boundary is proportional to the deviation of the moisture content of the slab from the equilibrium value at that temperature. These conditions are used to derive an analytical expression for the time required to get from an initial moisture distribution to a desired final moisture content of thin lumber. For a sample calculation, the result of drying time agrees within 10% with the prediction of previously published analytical formulas for the drying curve.

Computer Simulation↗

PubMed2005

NMR shielding constants for hydrogen guest molecules in structure II clathrates.

Proton NMR shielding constants and chemical shifts for hydrogen guests in small and large cages of structure II clathrates are calculated using density-functional theory and the gauge-invariant atomic-orbital method. Shielding constants are calculated at the B3LYP level with the 6-311++G(d,p) basis set. The calculated chemical shifts are corrected with a linear regression to reproduce the experimental chemical shifts of a set of standard molecules. The calculated chemical shifts of single hydrogen molecules in the small and large structure II cages are 4.94 and 4.84 ppm, respectively, which show that within the error range of the method the H2 guest molecules in the small and large cages cannot be distinguished. Chemical shifts are also calculated for double occupancy of the hydrogen guests in small cages, and double, triple, and quadruple occupancy in large cages. Multiple occupancy changes the chemical shift of the hydrogen guests by approximately 0.2 ppm. The relative effects of other guest molecules and the cage on the chemical shift are studied for the cages with multiple occupancies.

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PubMed2005

Molecular-dynamics study of structure II hydrogen clathrates.

Molecular-dynamics simulations are used to study the stability of structure II hydrogen clathrates with different H2 guest occupancies. Simulations are done at pressures of 2.5 kbars and 1.013 bars and for temperatures ranging from 100 to 250 K. For a structure II unit cell with 136 water molecules, H2 guest molecule occupancies of 0-64 are studied with uniform occupancies among each type of cage. The simulations show that at 100 K and 2.5 kbars, the most stable configurations have single occupancy in the small cages and quadruple occupancy in the large cages. The optimum occupancy for the large cages decreases as the temperature is raised. Double occupancy in the small cages increases the energy of the structures and causes tetragonal distortion in the unit cell. The spatial distribution of the hydrogen guest molecules in the cages is determined by studying the guest-water and guest-guest radial distribution functions at various temperatures.

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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.

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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↗

PubMed2004

A molecular-dynamics study of structural and physical properties of nitromethane nanoparticles.

The structural and physical properties of nanoparticles of nitromethane are studied by using molecular dynamics methods with a previously developed force field. [Agrawal et al., J. Chem. Phys. 119, 9617 (2003).] This force field accurately predicts solid- and liquid-state properties as well as melting of bulk nitromethane. Molecular dynamics simulations of nanoparticles with 480, 240, 144, 96, 48, and 32 nitromethane molecules have been carried out at various temperatures. The carbon-carbon radial distribution function, dipole-dipole correlation function, core density, internal enthalpy, and atomic diffusion coefficients of the nanoparticles were calculated at each temperature. These properties were used to characterize the physical phases and thus determine the melting transitions of the nanoparticles. The melting temperatures predicted by the various properties are consistent with one another and show that the melting temperature increases with particle size, approaching the bulk limit for the largest particle. A size dependence of melting points has been observed in experimental and theoretical studies of atomic nanoparticles, and this is a further demonstration of the effect for large nanoparticles of complex molecular materials.

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PubMed2004

Molecular dynamics studies of melting and solid-state transitions of ammonium nitrate.

Molecular dynamics simulations are used to calculate the melting point and some aspects of high-temperature solid-state phase transitions of ammonium nitrate (AN). The force field used in the simulations is that developed by Sorescu and Thompson [J. Phys. Chem. A 105, 720 (2001)] to describe the solid-state properties of the low-temperature phase-V AN. Simulations at various temperatures were performed with this force field for a 4 x 4 x 5 supercell of phase-II AN. The melting point of AN was determined from calculations on this supercell with voids introduced in the solid structure to eliminate superheating effects. The melting temperature was determined by calculating the density and the nitrogen-nitrogen radial distribution functions as functions of temperature. The melting point was predicted to be in the range 445 +/- 10 K, in excellent agreement with the experimental value of 442 K. The computed temperature dependences of the density, diffusion, and viscosity coefficient for the liquid are in good agreement with experiment. Structural changes in the perfect crystal at various temperatures were also investigated. The ammonium ions in the phase-II structure are rotationally disordered at 400 K. At higher temperatures, beginning at 530 K, the nitrate ions are essentially rotationally unhindered. The density and radial distribution functions in this temperature range show that the AN solid is superheated. The rotational disorder is qualitatively similar to that observed in the experimental phase-II to phase-I solid-state transition.

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