We extend the fragmentation-based double incremental expansion in FALCON coordinates (DIF) and its linear-scaling analogue [C. Konig and O. Christiansen, J. Chem. Phys., 2016, 145, 064105] to dipole surfaces. Thereby, we enable the calculation of intensities in vibrational absorption spectra from these cost-efficient property surfaces. We validate the obtained potential energy and dipole surfaces by vibrational spectra calculations employing damped response theory for correlated vibrational coupled cluster wave functions. Our largest calculation on a hexa-phenyl includes all 180 vibrational degrees of freedom of the system, which illustrates the potential of both the DIF schemes for property surface generation and the use of damped response theory from high-dimensional correlated vibrational wave functions. Generally, we obtain good agreement between the spectra calculated from the DIF property surfaces and the non-fragmented analogues. Moreover, when adopting suitable electronic structure methods, good agreement with respect to the experiment can be obtained, as shown for the example of 5-methylfurfural and RI-MP2. In conclusion, our results illustrate that the presented scheme with linearly scaling surfaces enables high quality spectra, as long as reasonably sized fragments can be defined. With this work, we push the realistic limits of vibrational spectra calculations from vibrational wave function methods and accurate electronic structure calculations to significantly larger systems than currently accessible.

A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

We present a visual exploration environment tailored for large-scale spatio-temporal molecular dynamics simulation data. The environment is referred to as VIA-MD (visual interactive analysis of molecular dynamics) and has been developed in a participatory design process with domain experts on molecular dynamics simulations of complex molecular systems. A key feature of our approach is the support for linked interactive 3D exploration of geometry and statistical analysis using dynamic temporal windowing and animation. Based on semantic level descriptions and hierarchical aggregation of molecular properties we enable interactive filtering, which enables the user to effectively find spatial, temporal and statistical patterns. The VIA-MD environment provides an unprecedented tool for analysis of complex microscopic interactions hidden in large data volumes. We demonstrate the utility of the VIA-MD environment with four use cases. The first two deal with simulation of amyloid plaque associated with development of Alzheimer's, and we study an aqueous solution of 100 probes and an amyloid fibril. The identification of interaction "hotspots" is achieved with the use of combined filter parameters connected with probe molecular planarity and probe-fibril interaction energetics. The third and fourth examples show the wide applicability of the environment by applying it to analysis of molecular properties in material design.

We present a combination of the incremental expansion of potential energy surfaces (PESs), known as n-mode expansion, with the incremental evaluation of the electronic energy in a many-body approach. The application of semi-local coordinates in this context allows the generation of PESs in a very cost-efficient way. For this, we employ the recently introduced flexible adaptation of local coordinates of nuclei (FALCON) coordinates. By introducing an additional transformation step, concerning only a fraction of the vibrational degrees of freedom, we can achieve linear scaling of the accumulated cost of the single point calculations required in the PES generation. Numerical examples of these double incremental approaches for oligo-phenyl examples show fast convergence with respect to the maximum number of simultaneously treated fragments and only a modest error introduced by the additional transformation step. The approach, presented here, represents a major step towards the applicability of vibrational wave function methods to sizable, covalently bound systems.