Biomedical subjects

Jeffery B Klauda

Publications and source records attributed to Jeffery B Klauda.

6 recordsLinked to original sources

PubMed2006

Dynamical motions of lipids and a finite size effect in simulations of bilayers.

Molecular dynamics (MD) simulations of dipalmitoylphosphatidylcholine bilayers composed of 72 and 288 lipids are used to examine system size dependence on dynamical properties associated with the particle mesh Ewald (PME) treatment of electrostatic interactions. The lateral diffusion constant Dl is 2.92 x 10(-7) and 0.95 x 10(-7) cm2/s for 72 and 288 lipids, respectively. This dramatic finite size effect originates from the correlation length of lipid diffusion, which extends to next-nearest neighbors in the 288 lipid system. Consequently, diffusional events in smaller systems can propagate across the boundaries of the periodic box. The internal dynamics of lipids calculated from the PME simulations are independent of the system size. Specifically, reorientational correlation functions for the slowly relaxing phosphorus-glycerol hydrogen, phosphorus-nitrogen vectors, and more rapidly relaxing CH vectors in the aliphatic chains are equivalent for the 72 and 288 lipid simulations. A third MD simulation of a bilayer with 72 lipids using spherical force-shift electrostatic cutoffs resulted in interdigitated chains, thereby rendering this cutoff method inappropriate.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2006

Simulation-based methods for interpreting x-ray data from lipid bilayers.

The fully hydrated liquid crystalline phase of the dimyristoylphosphatidycholine lipid bilayer at 30 degrees C was simulated using molecular dynamics with the CHARMM potential for five surface areas per lipid (A) in the range 55-65 A(2) that brackets the previously determined experimental area 60.6 A(2). The results of these simulations are used to develop a new hybrid zero-baseline structural model, denoted H2, for the electron density profile, rho(z), for the purpose of interpreting x-ray diffraction data. H2 and also the older hybrid baseline model were tested by fitting to partial information from the simulation and various constraints, both of which correspond to those available experimentally. The A, rho(z), and F(q) obtained from the models agree with those calculated directly from simulation at each of the five areas, thereby validating this use of the models. The new H2 was then applied to experimental dimyristoylphosphatidycholine data; it yields A = 60.6 +/- 0.5 A(2), in agreement with the earlier estimate obtained using the hybrid baseline model. The electron density profiles also compare well, despite considerable differences in the functional forms of the two models. Overall, the simulated rho(z) at A = 60.7 A(2) agrees well with experiment, demonstrating the accuracy of the CHARMM lipid force field; small discrepancies indicate targets for improvements. Lastly, a simulation-based model-free approach for obtaining A is proposed. It is based on interpolating the area that minimizes the difference between the experimental F(q) and simulated F(q) evaluated for a range of surface areas. This approach is independent of structural models and could be used to determine structural properties of bilayers with different lipids, cholesterol, and peptides.

Computer Simulation↗

PubMed2005

A comparative study of nitrogen physisorption on different C70 crystal structures using an ab initio based potential.

Quantum mechanical calculations are performed using the recently developed hybrid method for interaction energies to determine atom site Lennard-Jones potential parameters for the interactions of molecular nitrogen with C(70) molecules. This ab initio based potential is used in grand canonical Monte Carlo simulations to predict surface adsorption properties of N(2) on five known C(70) structures: rhombohedral, fcc, ideal hcp, deformed hcp, and monoclinic crystals. Because of the presence of five-membered carbon rings and the surface curvature of C(70) molecule, the Lennard-Jones potential parameters for nitrogen-carbon interactions obtained from ab initio based calculations are found to be different from that with planar graphite. The simulation results obtained from these two sets of force fields are compared and shown to differ, particularly at low coverage, where the nitrogen-carbon interactions are more important than the nitrogen-nitrogen interactions. The surface area, monolayer capacity, and isosteric heat of adsorption are calculated for various C(70) crystals and found to change appreciably as a result of the shear-induced phase transformation from hcp to rhombohedral lattice.

Crystallography, X-Ray↗

PubMed2005

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis.

High-level ab initio quantum mechanical calculations are used to study various gauche conformational energies of n-pentane to n-decane. The destabilizing "pentane effect" (adjacent gauche states of opposite sign) for alkanes is confirmed, but the energies were found to depend slightly on chain length. In contrast, introducing an adjacent gauche of the same sign requires only 0.22-0.37 kcal/mol, approximately half of the single gauche state energy. This adjacent gauche stabilization should be taken into account when formulating or analyzing rotational isomeric models, carrying out conformational analysis, and developing force fields for alkanes, lipids, and related polymers.

Alkanes↗

PubMed2005

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Energies of 119 conformations of normal alkanes from butane to heptane were calculated at approximately the CCSD(T)/cc-pVQZ level. Energies of gauche (g) conformers relative to trans (t) decrease as chain length increases. In what is termed the "positive pentane effect", adjacent gauche conformers of the same sign are stabilized compared to nonadjacent conformers; e.g., for hexane the energies of tgt, tgg, and gtg are 0.600, 0.930, and 1.18 kcal/mol, respectively. Torsional terms in the CHARMM27 (C27) force field were fit to the calculated QM energies to yield a revised potential, C27r. Molecular dynamics simulations of normal alkanes (heptane, decane, tridecane, and pentadecane) with C27r yield higher populations of gauche states, increased transition rates, and improved agreement with experiment as compared to C27. In addition, C27r simulations of a hydrated DPPC lipid bilayer yield improved agreement with the experimental NMR deuterium order parameters for the aliphatic chain ends.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Hierarchical modeling N2 adsorption on the surface of and within a C60 crystal: from quantum mechanics to molecular simulation.

The adsorption of N(2) on the surface of, and within, a C(60) face-centered cubic crystal has been studied using a hierarchical approach. First, an ab initio potential between N(2) and C(60) is obtained from a recently developed quantum mechanical hybrid method, and then the adsorption behavior is predicted using Monte Carlo simulation. On the crystal surface, N(2) adsorption isotherm at 77.3 K is of type II. The adsorption simulated with the ab initio potential is slightly greater than that with the empirical Steele potential derived from experimental N(2) adsorption on planar graphite, and both are in fairly good agreement with measured results. With increasing pressure, N(2) molecules are found to sequentially occupy three favorable sites: the octahedral sites, the tetrahedral sites, and the top of C(60) molecules. Finally multiple layers form and wetting occurs as the bulk N(2) saturation pressure is reached. The isosteric heat of adsorption exhibits two maxima and finally approaches the enthalpy of vaporization of bulk N(2). Within the crystal, the N(2) adsorption isotherm at 77.3 K is of type I, and the use of ab initio potential leads to significantly greater adsorption than the Steele potential. N(2) molecules are observed to intercalate only the octahedral sites, and the isosteric heat of adsorption is nearly a constant. As in our previous work of N(2) and O(2) adsorption in the C(168) schwarzite (Jiang et al. J. Phys. Chem. B 2004, 108, 9852), this work demonstrates the importance of an accurate adsorbate-adsorbent interaction potential in the determination of gas adsorption behavior.

Journal Article↗