Calculations of the Exciton Coupling Elements Between the DNA Bases Using the Transition Density Cube Method

Excited states of the of the double-stranded DNA model (A)$_{12}\cdot$(T)_{12} were calculated in the framework of the exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy $\pi\pi^{*}$ excitations of the individual nucleobases obtained from TDDFT calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal-dipole approximation (IDA) methods were found significantly different for the small inter-chromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of the structural fluctuations were incorporated by averaging the properties of the excited states over a large number of conformations obtained from the MD simulations

Quantum Origins of Molecular Recognition and Olfaction in Drosophila

The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled olfactants indicate that there may be a molecular vibration-sensing component to olfactory reception, specifically in the spectral region around 2300 cm$^{-1}$. Here we present a donor-bridge-acceptor model for olfaction which attempts to explain this effect. Our model, based upon accurate quantum chemical calculations of the olfactant (bridge) in its neutral and ionized states, posits that internal modes of the olfactant are excited impulsively during hole transfer from a donor to acceptor site on the receptor, specifically those modes that are resonant with the tunneling gap. By projecting the impulsive force onto the internal modes, we can determine which modes are excited at a given value of the donor-acceptor tunneling gap. Only those modes resonant with the tunneling gap and are impulsively excited will give a significant contribution to the inelastic transfer rate. Using acetophenone as a test case, our model and experiments on D. melanogaster suggest that isotopomers of a given olfactant give rise to different odorant qualities. These results support the notion that inelastic scattering effects play a role in discriminating between isotopomers, but that this is not a general spectroscopic effectComment: 7 pages, 3 figure

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.Comment: Accepted to PLoS Comp Biol, 201

Multiscale Simulation on a Light-Harvesting Molecular Triad

We have investigated the effect of solvation and confinement on an artificial photosynthetic material, carotenoid-porphyrin-C₆₀ molecular triad, by a multiscale approach and an enhanced sampling technique. We have developed a combined approach of quantum chemistry, statistical physics, and all-atomistic molecular dynamics simulation to determine the partial atomic charges of the ground-state triad. To fully explore the free energy landscape of triad, the replica exchange method was applied to enhance the sampling efficiency of the simulations. The confinement effects on the triad were modeled by imposing three sizes of spherocylindrical nanocapsules. The triad is structurally flexible under ambient conditions, and its conformation distribution is manipulated by the choice of water models and confinement. Two types of water models (SPC/E and TIP3P) are used for solvation. When solvated by SPC/E water, whose HOH angle follows an ideal tetrahedron, the structural characteristics of triad is compact in the bulk systems. However, under a certain nanosized confinement that drastically disrupts hydrogen bond networks in solvent, the triad favors an extended configuration. By contrast, the triad solvated by TIP3P water shows a set of U-shaped conformations in the confinement. We have shown that a slight structural difference in the two water models with the same dipole moment can have great distinction in water density, water orientation, and the number of hydrogen bonds in the proximity of a large flexible compound such as the triad. Subsequently, it has direct impact on the position of the triad in a confinement as well as the distribution of conformations at the interface of liquid and solid in a finite-size system

Inverted Surface Dipoles in Fluorinated Self-Assembled Monolayers

The presence of surface dipoles in self-assembled monolayers (SAMs) gives rise to profound effects on the interfacial properties of the films. For example, CF₃-terminated alkanethiolate films are surprisingly more wettable toward polar contacting liquids than analogous hydrocarbon SAMs due to the fluorocarbon-to-hydrocarbon transition (CF₃–CH₂) at the interface (i.e., the presence of a strong “FC–HC” surface dipole). This report explores the converse situation by analyzing partially fluorinated monolayers (FSAMs) in which the polarity of the surface dipole has been inverted through the creation of an “HC–FC” surface dipole. Thus, a new series of methyl-capped partially fluorinated alkanethiols, CH₃(CF₂)₆(CH₂)_<i>n</i>SH (where <i>n</i> = 10–13), were designed and synthesized. Structural analyses of the new films show that these adsorbates give rise to well-ordered monolayers. As for the wetting behavior of various liquids on these FSAMs, the new films proved to be less hydrophobic than both the corresponding CF₃-terminated and hydrocarbon SAMs and more oleophobic than their hydrocarbon counterparts. Furthermore, odd–even trends were observed in the wettability of the nonpolar and polar aprotic liquids on the new films in which the <i>even</i> FSAMs were more wettable than the <i>odd</i> ones for both types of liquids. However, an inverse odd–even trend was observed for polar protic liquids: <i>odd</i> FSAMs were more wettable than <i>even</i>. We attribute this latter effect to the resistance of highly hydrogen-bonded liquid molecules at the liquid–FSAM interface to adopt a more favorable orientation (on the basis of polarity) when in the presence of the inverted HC–FC dipole