Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

Transferability of fragmental contributions to the octanol/water partition coefficient: an NDDO-based MST study

This study examines the transferability of fragmental contributions to the octanol/water partition coefficient. As a previous step, we report the parameterization of the AM1 and PM3 versions of the MST model for n-octanol. The final AM1 and PM3 MST models reproduce the experimental free energy of solvation and the octanol/water partition coefficient (log P(ow)) with a root-mean-square deviation of around 0.7 kcal/mol and 0.5 (in units of log P), respectively. Based on this parameterization, an NNDO-based procedure is presented to dissect the free energy of transfer between octanol and water in contributions directly associated with specific atoms or functional groups. The application of this procedure to a set of representative molecular systems illustrates the dependence of the log P(ow) fragmental contribution due to electronic, hydrogen bonding, and steric effects, which cannot be easily accounted for in simple additive-based empirical schemes. The results point out the potential use of theoretical methods to refine the fragmental contributions in empirical methods.     

Resonance energy transfer: Beyond the limits

In pursuit of a better understanding of how electronic excitation migrates within complex structures, the concept of resonance energy transfer is being extended and deployed in a wide range of applications. Utilizing knowledge of the quantum interactions that operate in natural photosynthetic systems, wide‐ranging molecular and solid‐state materials are explored in the cause of more efficient solar energy harvesting, while advances in theory are paving the way for the development and application of fundamentally new mechanisms. In this review, an introduction to the underlying processes that cause singlet‐singlet and triplet‐triplet energy transfer leads into a discussion of how a new conception of these fundamental processes has emerged over recent years. Illustrative examples relevant to laser science and photonics are described, including photosynthetic light‐harvesting, light‐activated sensors, processes of cooperative and accretive energy pooling and quantum cutting in rare earth‐doped crystals, and incoherent triplet‐triplet energy upconversion in molecular solutions.     

Towards a molecular scale interpretation of excitation energy transfer in solvated bichromophoric systems. II. The through-bond contribution

In this paper we present a quantum-mechanical investigation on the mechanisms which promote intramolecular EET coupling. This investigation is done by using a new computational strategy in which we combine a configuration-interaction and a linear response approach. The combined use of these two methods allows a direct identification and a quantification of both "direct" (coulomb and exchange) and through-bond (superexchange and charge-transfer) contributions. In addition, solvent effects are introduced using the polarizable continuum model. The method is applied to a family of naphthalene-bridge-naphthalene and naphthalene-bridge-anthracene systems, and the results obtained are compared with experiments. The results found suggest that the through-bond charge-transfer effects are not significant when the EET goes through permitted excitations on distant chromophores (see DN4 and DN6) while they become as important as (or even more important than) the covalent terms for EETs involving weakly allowed excitations (see A6N). By contrast, the presence of a very short bridge (in DN2) allows a very efficient delocalization of the excitation energy which is also largely modified by the presence of a solvent.     

On the Binding of Congo Red to Amyloid Fibrils

Amyloids are characterized by their capacity to bind Congo red (CR), one of the most used amyloid‐specific dyes. The structural features of CR binding were unknown for years, mainly because of the lack of amyloid structures solved at high resolution. In the last few years, solid‐state NMR spectroscopy enabled the determination of the structural features of amyloids, such as the HET‐s prion forming domain (HET‐s PFD), which also has recently been used to determine the amyloid–CR interface at atomic resolution. Herein, we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rationalize CR binding to amyloids. In contrast to a previous assumption on the binding mode, our results suggest that CR binding to the HET‐s PFD involves a cooperative process entailing the formation of a complex with 1:1 stoichiometry. This provides a molecular basis to explain the bathochromic shift in the maximal absorbance wavelength when CR is bound to amyloids.     

Does Förster theory predict the rate of electronic energy transfer for a model dyad at low temperature?

The use of the F?rster model to predict the dynamics of resonant electronic energy transfer (RET) in a model donor-acceptor dyad (a terphenyl-bridged perylene diimide (PDI)-terrylene diimide (TDI) dyad molecule) embedded at low temperature in a PMMA matrix is tested against experiment. The relevant ingredients involved in the F?rster rate for RET, namely electronic coupling, spectral overlap, and screening effects, are accounted for in a quantitative manner. Electronic couplings are obtained from time-dependent density functional theory calculations, and the effect of the PMMA environment is included both on the transition densities and on their interaction through the IEFPCM model. We find that the presence of the terphenyl bridge induces a slight delocalization of the PDI and TDI transition densities over the bridge originating in a 56% increase in the coupling and in the breakdown of the dipole-dipole approximation. The spectral overlap is determined on the basis of a detailed simulation of the homogeneously broadened donor emission and acceptor absorption line shapes determined by fitting the single molecule spectra measured at 1.2 K. The corresponding distribution of spectral overlap throughout the ensemble is then estimated by assuming an uncorrelated inhomogeneous line broadening for the donor and acceptor. Combining the calculated electronic couplings and spectral overlaps sampled from Monte Carlo realizations of the energetic disorder, we obtain a mean RET time (approximately 8 ps) and a distribution in reasonable agreement with experiment.     

How solvent controls electronic energy transfer and light harvesting: toward a quantum-mechanical description of reaction field and screening effects

This paper presents a quantum-mechanical study of electronic energy transfer (EET) coupling on over 100 pairs of chromophores taken from photosynthetic light-harvesting antenna proteins. Solvation effects due to the protein, intrinsic waters, and surrounding medium are analyzed in terms of screening and reaction field contributions using a model developed recently that combines a linear response approach with the polarizable continuum model (PCM). We find that the screening of EET interactions is quite insensitive to the quantum-mechanical treatment adopted. In contrast, it is greatly dependent on the geometrical details (distance, shape, and orientation) of the chromophore pair considered. We demonstrate that implicit (reaction field) as well as screening effects are dictated mainly by the optical dielectric properties of the host medium, while the effect of the static properties is substantially less important. The empirical distance-dependent screening function we proposed in a recent letter (Scholes, G. D.; Curutchet, C.; Mennucci, B.; Cammi, R.; Tomasi, J. J. Phys. Chem. B 2007, 111, 6978-6982) is analyzed and compared to other commonly used screening factors. In addition, we show that implicit medium effects on the coupling, resulting from changes in the transition densities upon solvation, are strongly dependent on the particular system considered, thus preventing the possibility of defining a general empirical expression for such an effect.     

Solvation in octanol: parametrization of the continuum MST model

This study reports the parametrization of the HF/6‐31G(d) version of the MST continuum model for n‐octanol. Following our previous studies related to the MST parametrization for water, chloroform, and carbon tetrachloride, a detailed exploration of the definition of the solute/solvent interface has been performed. To this end, we have exploited the results obtained from free energy calculations coupled to Monte Carlo simulations, and those derived from the QM/MM analysis of solvent‐induced dipoles for selected solutes. The atomic hardness parameters have been determined by fitting to the experimental free energies of solvation in octanol. The final MST model is able to reproduce the experimental free energy of solvation for 62 compounds and the octanol/water partition coefficient (log P_ow) for 75 compounds with a root‐mean‐square deviation of 0.6 kcal/mol and 0.4 (in units of log P), respectively. The model has been further verified by calculating the octanol/water partition coefficient for a set of 27 drugs, which were not considered in the parametrization set. A good agreement is found between predicted and experimental values of log P_o/w, as noted in a root‐mean‐square deviation of 0.75 units of log P. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1180–1193, 2001