Biomedical subjects

Daniel Borgis

Publications and source records attributed to Daniel Borgis.

4 recordsLinked to original sources

PubMed2006

Quantized time correlation function approach to nonadiabatic decay rates in condensed phase: application to solvated electrons in water and methanol.

A new, alternative form of the golden rule formula defining the nonadiabatic transition rate between two quantum states in condensed phase is presented. The formula involves the quantum time correlation function of the energy gap, of the nonadiabatic coupling, and their cross terms. Those quantities can be inferred from their classical counterparts, determined via molecular dynamics simulations. The formalism is applied to the problem of the nonadiabatic p-->s relaxation of an equilibrated p-electron in water and methanol. We find that, in both solvents, the relaxation is induced by the coupling to the vibrational modes and the quantum effects modify the rate by a factor of 2-10 depending on the quantization procedure applied. The resulting p-state lifetime for a hypothetical equilibrium excited state appears extremely short, in the sub-100 fs regime. Although this result is in contrast with all previous theoretical predictions, we also illustrate that the lifetimes computed here are very sensitive to the simulated electronic quantum gap and to the strongly correlated nonadiabatic coupling.

Journal Article↗

PubMed2005

Density functional theory of solvation and its relation to implicit solvent models.

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.

Chemistry, Physical↗

PubMed2004

A semi-implicit solvent model for the simulation of peptides and proteins.

We present a new model of biomolecules hydration based on macroscopic electrostatic theory, that can both describe the microscopic details of solvent-solute interactions and allow for an efficient evaluation of the electrostatic hydration free energy. This semi-implicit model considers the solvent as an ensemble of polarizable pseudoparticles whose induced dipole describe both the electronic and orientational solvent polarization. In the presented version of the model, there is no mutual dipolar interaction between the particles, and they only interact through short-ranged Lennard-Jones interactions. The model has been integrated into a molecular dynamics code, and offers the possibility to simulate efficiently the conformational evolution of biomolecules. It is able to provide estimations of the electrostatic solvation free energy within short time windows during the simulation. It has been applied to the study of two small peptides, the octaalanine and the N-terminal helix of ribonuclease A, and two proteins, the bovine pancreatic trypsin inhibitor and the B1 immunoglobin-binding domain of streptococcal protein G. Molecular dynamics simulations of these biomolecules, using a slightly modified Amber force field, provide stable and meaningful trajectories in overall agreement with experiments and all-atom simulations. Correlations with respect to Poisson-Boltzmann electrostatic solvation free energies are also presented to discuss the parameterization of the model and its consequences.

Algorithms↗

PubMed2002

Density functional theory of solvation in a polar solvent: extracting the functional from homogeneous solvent simulations.

In the density functional theory formulation of molecular solvents, the solvation free energy of a solute can be obtained directly by minimization of a functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the direct correlation function of the pure solvent. To obtain that function as exactly as possible for a given atomistic solvent model, we propose the following approach: first to perform molecular simulations of the homogeneous solvent and compute the position and angle-dependent two-body distribution functions, and then to invert the Ornstein-Zernike relation using a finite rotational invariant basis set to get the corresponding direct correlation function. This rather natural scheme is proved, for the first time to our knowledge, to be valuable for a dipolar solvent involving long range interactions. The resulting solvent free-energy functional can then be minimized on a three-dimensional grid around a solute to get the solvent particle and polarization density profiles and solvation free energies. The viability of this approach is proven in a comparison with "exact" molecular dynamics calculations for the simple test case of spherical ions in a dipolar solvent.

Journal Article↗