Excited states of the double-stranded DNA model (A)12.(T)12 were calculated in the framework of the Frenkel 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 pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300 cm(-1) for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases.

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.

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) n SH (where n = 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 even FSAMs were more wettable than the odd ones for both types of liquids. However, an inverse odd–even trend was observed for polar protic liquids: odd FSAMs were more wettable than even. 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.

We have investigated the effect of solvation and confinement on an artificial photosynthetic material, carotenoid-porphyrin-C(60) 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.

Resonance Raman (RR) spectroscopy and density functional theory (DFT) calculations of oxochromium(IV,V) derivatives of 5,10,15-tris(pentafluorophenyl)corrole (tpfpc) are shown to provide useful information about the relative strength of the metal-oxo bond in high-valent Cr(IV) versus Cr(V) corroles. Isotope labeling of the terminal oxo group with (18)O revealed that the Cr(V)-oxo (perchromyl) stretch of (tpfpc)Cr(V)O vibrates at a frequency of 986 cm(-1) in carbon disulfide, consistent with a triply bonded Cr(V)[triple bond]O unit. In contrast, an acetonitrile solution produced RR scattering that rapidly changed with the number of scans collected and eventually became dominated by an (18)O-sensitive vibration at a significantly higher frequency of 1002 cm(-1). On the basis of DFT calculations and the observed (18/16)O isotopic shift, we assigned this new RR band at 1002 cm(-1) in acetonitrile as the Cr(IV)-oxo (chromyl) stretch of the autoreduced [(tpfpc)Cr(IV)O](-) product, which previously has been shown to form only during the course of the oxygen atom transfer (OAT) reaction with triphenylphosphine in acetonitrile or in the presence of a reducing chemical (cobaltocene) and electrochemical agents in other solvents. Consequently, RR observations indicate that the pi-bonding character of the chromyl bond is actually increased relative to that of the perchromyl bond, which is of interest if the beneficial role of acetonitrile in OAT catalysis by high-valent oxochromium(IV,V) corroles is to be elucidated.

The direction and magnitude of surface dipoles directly affect the interfacial properties and can be tuned through molecular design. This article examines the effect of a hydrocarbon−fluorocarbon, "HC−FC", dipole on the structural and interfacial properties of self-assembled monolayers (SAMs) as the dipole is buried into the film. A series of selectively fluorinated alkanethiols with a progressively extended alkyl chain atop six fluorocarbons and an alkyl spacer of 11 hydrocarbons, H(CH 2 ) n (CF 2 ) 6 (CH 2 ) 11 SH, where n = 1−7 (HnF6H11SH) were prepared and used to generate SAMs on evaporated gold, allowing for the systematic burying of the HC−FC dipole into the film. Structural analyses of the films revealed well-ordered films with slight disorder/loose packing in the top alkyl chains. In addition, odd−even effects were observed in the orientation and wettability of the SAMs corresponding to the number of carbon atoms in the top alkyl chain, leading to the conclusion that the fluorinated segment behaves as a surrogate surface. As for the effect of the dipole on the wetting behavior of the films, the effect appears to be minimized after three methylene units; however, the structural features of the monolayers were also found to influence the wettability of the films.

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