Aqueous proton transport plays a key role in acid-base neutralization, and energy transport through biological membranes and hydrogen fuel cells. Extensive experimental and theoretical studies have resulted in a highly detailed elucidation of one of the underlying microscopic mechanisms for aqueous excess proton transport, known as the von Grotthuss mechanism, involving different hydrated proton configurations with associated high fluxional structural dynamics. Hydroxide transport, with approximately two-fold lower bulk diffusion rates than those of excess protons, has received much less attention. We present femtosecond UV/IR pump-probe experiments and ab initio molecular dynamics simulations of different proton transport pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ) in water-methanol mixtures. For 7HQ solvent-dependent photoacidity, free energy-reactivity correlation behaviour and QM/MM trajectories point to a dominant OH-/CH3O- transport pathway, for all water-methanol mixing ratios investigated. This provides conclusive evidence for the hydrolysis/methanolysis acid-base neutralization pathway formulated by Manfred Eigen half a century ago.

Femtosecond UV/IR pump-probe experiments and ab initio molecular dynamics simulations of 7-hydroxyquinoline in water-methanol mixtures demonstrate an unexpectedly dominant OH-/CH3O- transport pathway but consistent with a solvent-dependent photoacidity free energy-reactivity correlation behaviour.

Charge transport in organic semiconductors (OSCs) depends on a number of molecular properties, one of which is the electronic coupling matrix element for charge transfer between the molecules forming the material. They are the off-diagonal elements of the electronic Hamiltonian in the charge-localised (or diabatic) basis. The focus of this work is on the development of a method for a fast calculation of these matrix elements for OSCs. After addressing the different methods of their calculation, I present a program to estimate the off-diagonal elements of the Hamiltonian with a fast yet accurate semi-empirical method. This model approximates the off-diagonal elements of the Hamiltonian to be proportional to the overlap between the orbitals of the molecules, which are projected onto a very small basis set. The analytical results are in a reasonable agreement with accurate ab initio and fragment orbital DFT calculations and the speed-up is up to six orders of magnitude compared to DFT calculations. Following on from this, the analytic overlap method was implemented in two programs for charge carrier propagation, one based on Kinetic Monte Carlo simulation of charge carrier hopping (presented here), the other on surface hopping non-adiabatic molecular dynamics. I also show that the analytic overlap method can be used to estimate non-adiabatic coupling vectors very efficiently, which is an important quantity in surface hopping simulations.

We explored structural details of fibrils formed by a mutated amyloid β (Aβ(1-40)) peptide carrying a Phe19 to Lys19 mutation, which was shown to completely abolish the toxicity of the molecule. Computer models suggest that the positively charged Lys19 side chain is expelled from the hydrophobic fibril interior upon fibrillation. This can be accommodated by either a 180° flip of the entire lower β-strand (model M1) or local perturbations of the secondary structure in the direct vicinity of the mutated site (model M2). This is accompanied by the formation of a new salt bridge between Glu22 and Lys28 in model M1. Experimentally, a novel contact between Phe20 and Leu34 as well as the significant structural perturbation of residues 20-23 could be confirmed. However, the mutated fibrils do not show the formation of any salt bridges. This demonstrates that although morphologically very robust, local perturbations of the Aβ(1-40) sequence lead to moderate structural alterations with tremendous impact on the physiological importance of these aggregates, which may suggest alternative strategies for the development of a remedy against Alzheimer's disease.

A quantum-chemistry based protocol, termed MOSS-DFT, is presented for the prediction of 13C and 1H NMR chemical shifts of a wide range of organic molecules in aqueous solution, including metabolites. Molecular motif-specific linear scaling parameters are reported for five different density functional theory (DFT) methods (B97-2/pcS-1, B97-2/pcS-2, B97-2/pcS-3, B3LYP/pcS-2, and BLYP/pcS-2), which were applied to a large set of 176 metabolite molecules. The chemical shift root-mean-square deviations (RMSD) for the best method, B97-2/pcS-3, are 1.93 and 0.154 ppm for 13C and 1H chemical shifts, respectively. Excellent results have been obtained for chemical shifts of methyl and aromatic 13C and 1H that are not directly bonded to a heteroatom (O, N, S, or P) with RMSD values of 1.15/0.079 and 1.31/0.118 ppm, respectively. This study not only demonstrates how NMR chemical shift in aqueous environment can be improved over the commonly used global linear scaling approach, but also allows for motif-specific error estimates, which are useful for an improved chemical shift-based verification of metabolite candidates of metabolomics samples containing unknown components.

The photophysics of 7-hydroxyquinoline (7HQ) in protic media results from an interplay of acid-base chemistry, prompted by the effects of photoacidity of the hydroxyl group and photobasicity of the nitrogen atom in the quinoline aromatic system. With ultrafast IR spectroscopic measurements, we follow the proton transfer dynamics of 7HQ in its four possible charged forms in methanol solution. Using deuterated methanol as solvent, we determine deuteron transfer rates from the neutral to the zwitterionic form to be 330 ps, those from the cationic form to the zwitterionic form to be 170 ps, and those from the anionic form to the zwitterionic form to be 600 ps. We compare the observed IR-active fingerprint marker patterns in the electronic ground state and the first electronically excited 1Lb-state with those calculated using density functional theory and time-dependent density functional theory, respectively, and find good correspondence between experimental and calculated transitions. The calculations provide insight into the nature of electronic excitation of these four different charged forms of 7HQ, suggesting the key role of electronic charge distribution changes upon electronic excitation of 7HQ and hydrogen bond changes at the donor hydroxyl and acceptor nitrogen moieties.

We elucidate the characteristic proton pathways and the transient infrared signatures of intermediate complexes during the first picoseconds of photoinduced protonation dynamics of a photoacid (N-methyl-6-hydroxyquinolinium) in aqueous solution from first-principles molecular dynamics simulations. Our results indicate that the typical latency time between photoexcitation and proton dissociation ranges from 1 ps to longer time time scales (∼100 ps). The rate-limiting step for the actual dissociation of the proton into the solvent is the solvation structure of the first accepting water molecule. The nature of the proton pathway in water (stepwise or concerted) is not unique but determined by the coordination number of the accepting water molecules along the hydrogen bond chain. We find a characteristic uncommon infrared mode at ∼1300 cm(-1) of the transient photobase-Eigen cation complex immediately after photodissociation that we predict to be observable experimentally in time-resolved IR spectroscopy. A broad continuous absorption band from 1500 to 2000 cm(-1) arises from the acidic proton imminently before dissociation.

We introduce a database (HAB11) of electronic coupling matrix elements (H(ab)) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute H(ab) values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Simulation of charge transport in organic semiconducting materials requires the development of strategies for very fast yet accurate estimation of electronic coupling matrix elements for electron transfer between organic molecules (transfer integrals, Hab). A well-known relation that is often exploited for this purpose is the approximately linear dependence of electronic coupling with respect to the overlap of the corresponding diabatic state wave functions for a given donor-acceptor pair. Here we show that a single such relation can be established for a large number of different π-conjugated organic molecules. In our computational scheme the overlap of the diabatic state wave function is simply estimated by the overlap of the highest singly occupied molecular orbital of donor and acceptor, projected on a minimum valence shell Slater-type orbital (STO) basis with optimized Slater decay coefficients. After calibration of the linear relation, the average error in Hab as obtained from the STO orbital overlap is a factor of 1.9 with respect to wave function-theory validated DFT calculations for a diverse set of π-conjugated organic dimers including small arenes, arenes with S, N, and O heteroatoms, acenes, porphins, and buckyballs. The crucial advantage of the scheme is that the STO orbital overlap calculation is analytic. This leads to speedups of 6 orders of magnitude with respect to reference DFT calculations, with little loss of accuracy in the regime relevant to charge transport in organics.