Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder.

Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI-DNA interactions.

Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles.

Self-replication at the molecular level is often seen as essential to the early origins of life. Recently a mechanism of self-replication has been discovered in which replicator self-assembly drives the process. We have studied one of the examples of such self-assembling self-replicating molecules to a high level of structural detail using a combination of computational and spectroscopic techniques. Molecular Dynamics simulations of self-assembled stacks of peptide-derived replicators provide insights into the structural characteristics of the system and serve as the basis for semiempirical calculations of the UV-vis, circular dichroism (CD) and infrared (IR) absorption spectra that reflect the chiral organization and peptide secondary structure of the stacks. Two proposed structural models are tested by comparing calculated spectra to experimental data from electron microscopy, CD and IR spectroscopy, resulting in a better insight into the specific supramolecular interactions that lead to self-replication. Specifically, we find a cooperative self-assembly process in which ß-sheet formation leads to well-organized structures, while also the aromatic core of the macrocycles plays an important role in the stability of the resulting fibers.

Chiral supramolecular organization and cooperativity in DNA-templated assemblies of ZnII-chromophore complexes.

Templated cooperative binding induced assembly of chromophores is achieved via interactions between Zn-complexes and the DNA phosphodiester backbone. The chromophores are organized in left-handed (M)-helices via double-zipper assembly with the DNA templates.

Tuning the nature and stability of self-assemblies formed by ester benzene 1,3,5-tricarboxamides: the crucial role played by the substituents.

As the benzene 1,3,5-tricarboxamide (BTA) moiety is commonly used as the central assembling unit for the construction of functionalized supramolecular architectures, strategies to tailor the nature and stability of BTA assemblies are needed. The assembly properties of a library of structurally simple BTAs derived from amino dodecyl esters (ester BTAs, 13 members) have been studied, either in the bulk or in cyclohexane solutions, by means of a series of analytical methods (NMR, DSC, POM, FT-IR, UV-Vis, CD, ITC, high-sensitivity DSC, SANS). Two types of hydrogen-bonded species have been identified and characterized: the expected amide-bonded helical rods (or stacks) that are structurally similar to those formed by BTAs with simple alkyl side chains (alkyl BTAs), and ester-bonded dimers in which the BTAs are connected by means of hydrogen bonds linking the amide N-H and the ester C[double bond, length as m-dash]O. MM/MD calculations coupled with simulations of CD spectra allow for the precise determination of the molecular arrangement and of the hydrogen bond pattern of these dimers. Our study points out the crucial influence of the substituent attached on the amino-ester α-carbon on the relative stability of the rod-like versus dimeric assemblies. By varying this substituent, one can precisely tune the nature of the dominant hydrogen-bonded species (stacks or dimers) in the neat compounds and in cyclohexane over a wide range of temperatures and concentrations. In the neat BTAs, stacks are stable up to 213 °C and dimers above 180 °C whilst in cyclohexane stacks form at c* > 3 × 10-5 M at 20 °C and dimers are stable up to 80 °C at 7 × 10-6 M. Ester BTAs that assemble into stacks form a liquid-crystalline phase and yield gels or viscous solutions in cyclohexane, demonstrating the importance of controlling the structure of these assemblies. Our systematic study of these structurally similar ester BTAs also allows for a better understanding of how a single atom or moiety can impact the nature and stability of BTA aggregates, which is of importance for the future development of functionalized BTA supramolecular polymers.

Charge dissociation at interfaces between discotic liquid crystals: the surprising role of column mismatch.

The semiconducting and self-assembling properties of columnar discotic liquid crystals have stimulated intense research toward their application in organic solar cells, although with a rather disappointing outcome to date in terms of efficiencies. These failures call for a rational strategy to choose those molecular design features (e.g., lattice parameter, length and nature of peripheral chains) that could optimize solar cell performance. With this purpose, in this work we address for the first time the construction of a realistic planar heterojunction between a columnar donor and acceptor as well as a quantitative measurement of charge separation and recombination rates using state of the art computational techniques. In particular, choosing as a case study the interface between a perylene donor and a benzoperylene diimide acceptor, we attempt to answer the largely overlooked question of whether having well-matching donor and acceptor columns at the interface is really beneficial for optimal charge separation. Surprisingly, it turns out that achieving a system with contiguous columns is detrimental to the solar cell efficiency and that engineering the mismatch is the key to optimal performance.

An Effective Two-Orbital Quantum Chemical Model for Organic Photovoltaic Materials.

We present a coarse-grained quantum chemical model of organic photovoltaic materials, which is based on the classic idea that the main physical processes involve the electrons occupying the frontier orbitals (HOMO and LUMO) of each molecule or "site". This translates into an effective electronic Hamiltonian with two electrons and two orbitals per site. The on-site parameters (one- and two-electron integrals) can be rigorously related to the ionization energy, electron affinity, and singlet and triplet first excitation energies of that site. The intersite Hamiltonian parameters are introduced in a way that is consistent with classical electrostatics, and for the one-electron part, we use a simple approximation that could be refined using information from atomistic quantum chemical calculations. The model has been implemented within the GAMESS-US package. This allows the exploration of the physics of these materials using state-of-the art quantum chemical methods on relatively large systems (hundreds of electron-donor and electron-acceptor sites). To illustrate this point, we present ground- and excited-state calculations on dimers and two-dimensional arrays of sites using the Hartree-Fock, configuration interaction, and coupled-cluster methods. The calculations provide evidence for the possibility of low-energy, long-range electron transfer in donor-acceptor heterojunctions characterized by a moderate degree of disorder.

Impact of Interaction Strength and Surface Heterogeneity on the Dynamics of Adsorbed Polymers.

We present molecular dynamics simulations of bead-and-spring polymer chains on chemically heterogeneous, energetically disordered surfaces at near-monolayer coverages. The surfaces consist of random mixtures of weakly (W) and strongly (S) attractive sites. We explore systematically the effect of surface composition on the diffusive dynamics of the chains. The polymer diffusion coefficients have a near-Arrhenius temperature dependence, with activation energies which have a nonmonotonic dependence on the fraction of S sites. In other words, we see a nonmonotonic dependence of the interfacial polymer dynamics on its affinity with the surface, when the latter involves some heterogeneity. The maximum activation energy belongs to the surface containing 75% S and 25% W sites, which combines near-maximum average polymer-surface interactions with near-maximum spread or disorder in these interactions. Our results have interesting implications for polymer adhesion and friction and structure-property relationships in polymer nanocomposites.

Tuning the Interfacial Electronic Structure at Organic Heterojunctions by Chemical Design.

Quantum-chemical techniques are applied to assess the electronic structure at donor/acceptor heterojunctions of interest for organic solar cells. We show that electrostatic effects at the interface of model 1D stacks profoundly modify the energy landscape explored by charge carriers in the photoconversion process and that these can be tuned by chemical design. When fullerene C60 molecules are used as acceptors and unsubstituted oligothiophenes or pentacene are used as donors, the uncompensated quadrupolar electric field at the interface provides the driving force for splitting of the charge-transfer states into free charges. This quadrupolar field can be either enhanced by switching from a C60 to a perylene-tetracarboxylic-dianhydride (PTCDA) acceptor or suppressed by grafting electron-withdrawing groups on the donor.

Supramolecular organization and charge transport properties of self-assembled π-π stacks of perylene diimide dyes.

Molecular dynamics (MD) simulations have been coupled to valence bond/Hartree-Fock (VB/HF) quantum-chemical calculations to evaluate the impact of diagonal and off-diagonal disorder on charge carrier mobilities in self-assembled one-dimensional stacks of a perylene diimide (PDI) derivative. The relative distance and orientation of the PDI cores probed along the MD trajectories translate into fluctuations in site energies and transfer integrals that are calculated at the VB/HF level. The charge carrier mobilities, as obtained from time-of-flight numerical simulations, span several orders of magnitude depending on the relative time scales for charge versus molecular motion. Comparison to experiment suggests that charge transport in the crystal phase is limited by the presence of static defects.