80 different push-pull type organic chromophores which possess Donor-Acceptor (D-A) and Donor-Thiophene-Acceptor-Thiophene (D-T-A-T) structures have been systematically investigated by means of density functional theory (DFT) and time-dependent DFT (TD-DFT) at the B3LYP/6-311G* level. The introduction of thiophene (T) in the chain has allowed us to monitor the effect of π-spacers. Benchmark studies on the methodology have been carried out to predict the HOMO and LUMO energies and optical band gaps of the D-A systems accurately. The HOMO and LUMO energies and transition dipoles are seen to converge for tetrameric oligomers, and the latter have been used as optimal chain length to evaluate various geometrical and optoelectronic properties such as bond length alternations, distortion energies, frontier molecular orbital energies, reorganization energies and excited-state vertical transition of the oligomers. Careful analysis of our findings has allowed us to propose potential donor-acceptor couples to be used in organic photovoltaic cells.

Linear and nonlinear optical properties of a series of bis(E-dimesitylborylethenyl)-substituted arenes have been modeled by high-level computational protocols. The former compounds show a remarkable interest as infrared two-photon absorbers and hence may be used in the field of optical active and smart materials or for energy storage purposes. Excited state topologies, absorption and emission spectra, excited state metrics, natural transition orbitals and two-photon absorption cross-section of a series of chromophores have been computed by means of density functional theory (DFT) and timedependent DFT (TD-DFT). An extended benchmark test on the performance of different functionals had been performed. Dynamic and vibronic effects on absorption and emission spectra have been taken into account by sampling the conformational space by means of Wigner distribution and the former have been evidenced as rather important in order to recover absorption maxima and spectral band shape. Important infrared two photon absorption cross sections involving transitions to the second excited state have been observed. In particular, thiophene bridges have been evidenced as the most beneficial to increase TPA efficiency leading to cross-section exceeding 1000 GM.

Understanding atomistic and molecular aspects of chemical reactions is one of the cornerstones in chemistry and biology. Characterizing reactions in time and space is challenging due to the different length-and time-scales on which the nuclear dynamics takes place [1]. For example, typical reaction times for the Claisen rearrangement [2] in solution are on the order of seconds [3] or milliseconds (in the protein) [4]. However, the chemical step (i.e. C-C bond formation and C-O bond breaking) [5] occurs on the femtosecond time scale. In other words, during 10 9 to 10 15 vibrational periods energy is redistributed in the system until sufficient energy has accumulated along the relevant 'progression coordinate' for the reaction to occur. Because the 'chemical step' is so rapid and the system concentration at the transition state is negligible, direct experimental characterization of the transition state and the dynamics between reactant and product is extremely challenging even with current state-of-the art methods, including NMR, [6] IR, [7] or x-ray [8,9] spectroscopies.Atomistic simulations have shown to provide molecular-level insight into the energetics and dynamics of chemical reactions for systems ranging from small (triatomic) molecules to proteins in the condensed phase [1,[10][11][12][13]]. An essential requirement for a meaningful contribution of computer-based work to characterize chemical reactions is a correct description of the intermolecular interactions along the entire reaction path including the degrees of freedom orthogonal to it. This involves regions around the reactants, products and the transition state(s). Intermolecular interactions in molecular systems are often represented as a Born-Oppenheimer

S-Nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification that can alter the function of various proteins. The structural dynamics and vibrational spectroscopy of S-nitrosylation in the condensed phase are investigated for the methyl-capped cysteine model system and for myoglobin. Using conventional point charge and physically more realistic multipolar force fields for the −SNO group, it is found that the SN- and NO-stretch and the SNO-bend vibrations can be located and distinguished from the other protein modes for simulations of MbSNO at 50 K. The finding of stable cis- and trans-MbSNO agrees with experimental findings on other proteins as is the observation of buried −SNO. For MbSNO the observed relocation of the EF loop in the simulations by ∼3 Å is consistent with the available X-ray structure, and the conformations adopted by the −SNO label are in good overall agreement with the X-ray structure. Despite the larger size of the −SNO group compared with −SH, MbSNO recruits more water molecules in the first two hydration shells due to stronger electrostatic interactions. Similarly, when comparing the hydration between the A- and H-helices, they differ by up to 30% between WT and MbSNO. This suggests that local hydration can also be significantly modulated through nitrosylation.

One of the major challenges in rationalizing the intrinsic influences of molecular fine tuning on charge transport in organic semiconductors is due to changes in molecular packing. Thus, it is, to a limited extent, desirable to elaborate materials to exhibit similar packing arrangements that slightly differ in their molecular structures. A molecular system, consisting of a heterocyclic core flanked by phthalimide end-capping units, is promising to overcome this issue. Previous XRD measurements have revealed that, when the bithiophene (bi-T) core was replaced by bifuran (bi-F), the molecular packing was largely maintained, while the resulting difference in charge transport was substantial, substituting bi-T with bi-F results in more than 1 order of magnitude increase in hole mobility (i.e., 1.7 × 10–3 vs 2.6 × 10–2 cm2/(V s)) with a loss in electron mobility (i.e., 0.21 vs 0.0 cm2/(V s)). The calculated hole mobilities with the MPW1K/TZ2P methodology are found to be lower for bi-T, as the reorganization energies of bi-T are noticeably higher than those of bi-F due to the nonplanarity of bi-T. MD simulations have shown that the disordered hole mobility predictions are in good agreement with the experimental measurements, for which T → F substitution results in an increase in hole mobility. In contrast, the difference in electron mobilities with T → F substitution is predicted to be insignificant, most likely due to the lower average electronic coupling of bi-F. The discrepancy between calculated and experimental electron mobility may originate from macroscopic effects, such as the organic field effect transistor (OFET) device configuration which was not taken into consideration in this study.