Bottom-up coarse-grained (CG) models accurately describe the structure of homogeneous systems but sometimes provide limited transferability and a poor description of thermodynamic properties. Consequently, inhomogeneous systems present a severe challenge for bottom-up models. In this work, we examine bottom-up CG models for interfaces and inhomogeneous systems. We first analyze the effect of external fields upon the many-body potential of mean force. We also demonstrate that the multiscale CG (MS-CG) variational principle for modeling the external field corresponds to a generalization of the first Yvon-Born-Green equation. LDC195943 RNA Synthesis inhibitor This provides an important connection with liquid state theory, as well as physical insight into the structure of interfaces and the resulting MS-CG models. We then develop and assess MS-CG models for a film of liquid methanol that is adsorbed on an attractive wall and in coexistence with its vapor phase. While pair-additive potentials provide unsatisfactory accuracy and transferability, the inclusion of local-density (LD) potentials dramatically improves the accuracy and transferability of the MS-CG model. The MS-CG model with LD potentials quite accurately describes the wall-liquid interface, the bulk liquid density, and the liquid-vapor interface while simultaneously providing a much improved description of the vapor phase. This model also provides an excellent description of the pair structure and pressure-density equation of state for the bulk liquid. Thus, LD potentials hold considerable promise for transferable bottom-up models that accurately describe the structure and thermodynamic properties of both bulk and interfacial systems.We have studied the structure of cetyltrimethylammonium bromide-DNA complexes using small angle x-ray diffraction and elemental analysis. These complexes exhibit a two-dimensional hexagonal phase. The diffraction data have been analyzed using electron density models based on two different structures of these complexes proposed in the literature, which differ in the micelle to DNA stoichiometry. The structure with a 12 micelle-DNA stoichiometry is found to be more consistent with the diffraction data. Furthermore, this structure is also supported by the stoichiometry deduced from elemental analysis. Madelung energies of the two structures, calculated from the electrostatic interaction between their cylindrical constituents, give insight into their relative stability.Vibrational-electronic (vibronic) resonance and its possible role in energy and charge transfer have been experimentally and theoretically investigated in several photosynthetic proteins. Using a dimer modeled on a typical photosynthetic protein, we contrast the description of such excitons provided by an exact basis set description, as opposed to a basis set with reduced vibrational dimensionality. Using a reduced analytical description of the full Hamiltonian, we show that in the presence of vibrational excitation both on electronically excited as well as unexcited sites, constructive interference between such basis states causes vibronic coupling between excitons to become progressively stronger with increasing quanta of vibrational excitation. This effect leads to three distinguishing features of excitons coupled through a vibronic resonance, which are not captured in basis sets that restrict ground state vibrations (1) the vibronic resonance criterion itself, (2) vibronically assisted perfect delocalization between sites even though purely electronic mixing between the sites is imperfect due to energetic disorder, and (3) the nuclear distortion accompanying vibronic excitons becoming increasingly larger for resonant vibronic coupling involving higher vibrational quanta. In terms of spectroscopically observable limitations of reduced basis set descriptions of vibronic resonance, several differences are seen in absorption and emission spectra but may be obscured on account of overwhelming line broadening. However, we show that several features such as vibronic exciton delocalization and vibrational distortions associated with electronic excitations, which ultimately dictate the excited state wavepacket motions and relaxation processes, are fundamentally not described by basis sets that restrict ground state vibrations.Photo-induced relaxation processes leading to excimer formations or other traps are in the focus of many investigations of optoelectronic materials because they severely affect the efficiencies of corresponding devices. Such relaxation effects comprise inter-monomer distortions in which the orientations of the monomer change with respect to each other, whereas intra-monomer distortions are variations in the geometry of single monomers. Such distortions are generally neglected in quantum chemical investigations of organic dye aggregates due to the accompanied high computational costs. In the present study, we investigate their relevance using perylene-bisimide dimers and diindenoperylene tetramers as model systems. Our calculations underline the importance of intra-monomer distortions on the shape of the potential energy surfaces as a function of the coupling between the monomers. The latter is shown to depend strongly on the electronic state under consideration. In particular, it differs between the first and second excited state of the aggregate. Additionally, the magnitude of the geometrical relaxation decreases if the exciton is delocalized over an increasing number of monomers. For the interpretation of the vibronic coupling model, pseudo-Jahn-Teller or Marcus theory can be employed. In the first part of this paper, we establish the accuracy of density functional theory-based approaches for the prediction of vibrationally resolved absorption spectra of organic semiconductors. These investigations underline the accuracy of those approaches although shortcomings become obvious as well. These calculations also indicate the strength of intra-monomer relaxation effects.Hydrated calcium ion clusters have received considerable attention due to their essential role in biological processes such as bone development, hormone regulation, blood coagulation, and neuronal signaling. To better understand the biological role of the cation, the interactions between the Ca2+ ions and water molecules have been frequently investigated. However, a quantitative measure for the intrinsic Ca-O (ion-solvent) and intermolecular hydrogen bond (solvent-solvent) interactions has been missing so far. Here, we report a topological electron density analysis and a natural population analysis to analyze the nature of these interactions for a set of 14 hydrated calcium clusters via local mode stretching force constants obtained at the ωB97X-D/6-311++G(d,p) level of theory. The results revealed that the strength of inner Ca-O interactions for Ca(H2O)n2+ (n = 1-8) clusters correlates with the electron density. The application of a second hydration shell to Ca(H2O)n2+ (n = 6-8) clusters resulted in stronger Ca-O interactions where a larger electron charge transfer between lp(O) of the first hydration shell and the lower valence of Ca prevailed.