Biomedical subjects

D Sebastiani

Publications and source records attributed to D Sebastiani.

5 recordsLinked to original sources

PubMed2006

Bulk chemical shifts in hydrogen-bonded systems from first-principles calculations and solid-state-NMR.

We present an analysis of bulk (1)H NMR chemical shifts for a series of biochemically relevant molecular crystals in analogy to the well-known solvent NMR chemical shifts. The term bulk shifts denotes the change in NMR frequency of a gas-phase molecule when it undergoes crystallization. We compute NMR parameters from first-principles electronic structure calculations under full periodic boundary conditions and for isolated molecules and compare them to the corresponding experimental fast magic-angle spinning solid-state NMR spectra. The agreement between computed and experimental lines is generally very good. The main phenomena responsible for bulk shifts are packing effects (hydrogen bonding and pi-stacking) in the condensed phase. By using these NMR bulk shifts in well-ordered crystalline model systems composed of biologically relevant molecules, we can understand the individual spectroscopic signatures of packing effects. These local structural driving forces, hydrogen bonding, pi-stacking, and related phenomena, stand as a model for the forces that govern the assembly of much more complex supramolecular aggregates. We show to which accuracy condensed-phase ab initio calculations can predict structure and structure-property relationships for noncovalent interactions in complex supramolecular systems.

Journal Article↗

PubMed2006

Diffusion in binary gas mixtures studied by NMR of hyperpolarized gases and molecular dynamics simulations.

The dependence of the individual mean square displacement of rare gases in binary mixtures is studied by a combined experimental and theoretical approach. We show that the diffusion constant can be varied in a considerable range by changing the molar fractions of the mixtures. On the experimental side, NMR diffusion measurements are done on hyperpolarized 3He and 129Xe, mixed with several inert buffer gases, in the presence of a magnetic field gradient. The results are compared to diffusion coefficients obtained from atomistic molecular dynamics simulations based on Lennard-Jones type potentials of the corresponding gas mixtures, and to appropriate analytical expressions, yielding very good mutual agreement. This study is the first quantitative validation of the effects of the mutual interactions between gas particles on the individual diffusion properties. It is shown that the dependency of gas phase diffusion properties on the local chemical environment may not be neglected, e.g. in diffusion-controlled chemical reactions.

Complex Mixtures↗

PubMed2005

Anomalous temperature dependence of nuclear quadrupole interactions in strongly hydrogen-bonded systems from first principles.

We present an analysis of the effect of finite temperatures on the deuteron nuclear quadrupole coupling constants in a strongly hydrogen-bonded molecular crystal by means of first-principles Car-Parrinello molecular-dynamics simulations. Our findings agree well with experiments and provide a microscopic explanation of the anomalous increase of the quadrupole coupling in this class of systems. We show that a simple model based on the anharmonicity of the hydrogen bond potential fails to describe the temperature dependence of the couplings even qualitatively. Instead, the inclusion of fluctuations and disorder in terms of atomic motion of the surrounding molecules turns out to be important to obtain the correct magnitude of the temperature effect.

Journal Article↗

PubMed2001

Accurate total energies without self-consistency.

We present a new way of calculating approximate but accurate total energies within the framework of density functional theory. Our technique is based on an expansion of the energy functional to second order and does not require self-consistent iterations of the total density. The functional can be minimized by using the same techniques as developed for variational density functional perturbation theory. The method is ideally suited to systems composed of weakly interacting fragments, but it can also be applied to semiconductors and insulators. We show the versatility of our approach in a variety of examples exhibiting different types of chemical bonding.

Journal Article↗

PubMed2001

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site.

A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).

Aspartic Acid↗