P. Partovi-Azar

Hydration strongly affects the molecular and electronic structure of membrane phospholipids

We investigate the structure and electronic properties of phosphatidylcholine (PC) under different degrees of hydration at the single-molecule and monolayer type level by linear scaling ab initio calculations. Upon hydration, the phospholipid undergoes drastic long-range conformational rearrangements which lead to a sickle-like ground-state shape. The structural unit of the tilted gel-phase PC appears to be a water-bridged PC dimer. We find that hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids and consequently guides the interactions of the lipids with other molecules and the communication between cells.

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations

The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

Interfacial water facilitates energy transfer by inducing extended vibrations in membrane lipids.

We report the complete assignment of the vibrational spectrum of dipalmitoylphosphatidylcholine (DPPC), which belongs to the most ubiquitous membrane phospholipid family, phosphatidylcholine. We find that water hydrating the lipid headgroups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. The emergence of spatially extended vibrational modes upon hydration, underlies this phenomenon. Our findings illustrate the importance of collective molecular behavior of biomembranes and reveal that hydrated lipid membranes can act as efficient media for the transfer of vibrational energy.

Stone–Wales defects can cause a metal–semiconductor transition in carbon nanotubes depending on their orientation

It has been shown that the two different orientations of Stone-Wales (SW) defects, i.e. longitudinal and circumferential SW defects, on carbon nanotubes (CNTs) result in two different electronic structures. Based on density functional theory we have shown that the longitudinal SW defects do not open a bandgap near the Fermi energy, while a relatively small bandgap emerges in tubes with circumferential defects. We argue that the bandgap opening in the presence of circumferential SW defects is a consequence of long-range symmetry breaking which can spread all the way along the tube. Specifically, the distribution of contracted and stretched bond lengths due to the presence of defects, and hopping energies for low-energy electrons, i.e. the 2p(z) electrons, show two different patterns for the two types of defects. Interplay between the geometric features and the electronic properties of the tubes have also been studied for different defect concentrations. Considering π-orbital charge density, it has also been shown that the deviations of bond lengths from their relaxed length result in different doping for two defect orientations around the defects-electron-rich for a circumferential defect and hole-rich for a longitudinal one. We have also shown that, in the tubes having both types of defects, circumferential defects would dominate and impose their electronic properties.

Nonlinear conductance in finite-length armchair single-wall carbon nanotubes with one single impurity

We investigate theoretically the nonlinear quantum conductance of finite single-wall carbon nanotubes (SWCNTs) due to the presence of a single impurity. To take the length of the tube into account and retain the periodicity of the SWCNT along its axis, a particle-in-a-box model is employed. The dependence of the differential conductance on the gate voltage as well as its sensitive dependence on the position of the possible impurity in the tube is studied. Results suggest a promising method for spectroscopy of electronic energy levels in a SWCNT.

Efficient “On-the-Fly” calculation of Raman Spectra from Ab-Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second‐generation Car‐Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed‐up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite‐temperature Raman spectra “on‐the‐fly” by means of ab‐initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.

The effect of the orientation of the Stone–Wales defects on the bands structure of carbon nanotubes

We have studied the effect of orientation of Stone–Wales (SW) defects formed on the armchair single-wall carbon nanotubes (SWCNTs) on their metal-semiconductor behaviour by means of the density functional formalism. It has been shown that two third of possible orientations of SW defects, at high concentrations, open a ≈ 40 meV gap at Fermi level while in the other one third orientations tube remains metallic.