A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities.

Recently we reported a combined QM/MM approach to estimate condensed-phase values of atomic polarizabilities for use in (bio)molecular simulation. The setup relies on a MM treatment of the solvent when determining atomic polarizabilities to describe the response of a QM described solute to its external electric field. In this work, we study the effect of using alternative descriptions of the solvent molecules when evaluating atomic polarizabilities of a methanol solute. In a first step, we show that solute polarizabilities are not significantly affected upon substantially increasing the MM dipole moments towards values that are typically reported in literature for water solvent molecules. Subsequently, solute polarization is evaluated in the presence of a QM described solvent (using the frozen-density embedding method). In the latter case, lower oxygen polarizabilities were obtained than when using MM point charges to describe the solvent, due to introduction of Pauli-repulsion effects.

M(O)V(I)P(AC): vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations.

We present the software package M(O)V(I)P(AC) for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. M(O)V(I)P(AC) unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add-ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta-program design, M(O)V(I)P(AC) focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode- and Intensity-Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π-helix consisting of 20 (S)-alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α- and 3(10)-helical analogs.

PyADF--a scripting framework for multiscale quantum chemistry.

Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications.

Selective calculation of high-intensity vibrations in molecular resonance Raman spectra.

We present an intensity-driven approach for the selective calculation of vibrational modes in molecular resonance Raman spectra. The method exploits the ideas of the mode-tracking algorithm [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] for the calculation of preselected molecular vibrations and of Heller's gradient approximation [Heller et al., J. Phys. Chem. 86, 1822 (1982)] for the estimation of resonance Raman intensities. The gradient approximation allows us to construct a basis vector for the subspace iteration carried out in the mode-tracking calculation, which corresponds to an artificial collective motion of the molecule that contains the entire intensity in the resonance Raman spectrum. Subsequently, the algorithm generates new basis vectors from which normal mode approximations are obtained. It is then possible to provide estimates for (i) the accuracy of the normal mode approximations and (ii) the intensity of these modes in the final resonance Raman spectrum. This approach is tested for the examples of uracil and a structural motif from the E colicin binding immunity protein Im7, in which a few aromatic amino acids dominate the resonance Raman spectrum at wavelengths larger than 240 nm.

Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory.

The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other biomolecular systems provide a route to calculate the electron densities of proteins efficiently and further make it possible to focus on specific parts. Here, we evaluate and extend the 3-partition frozen-density embedding (3-FDE) scheme [Jacob, C. R.; Visscher, L. J. Chem. Phys.2008, 128, 155102] for this purpose. In particular, we have extended this scheme to allow for the treatment of disulfide bridges and charged amino acid residues and have introduced the possibility to employ more general partitioning schemes. These extensions are tested both for the prediction of full protein electron densities and for focusing on the electron densities of a selected protein site. Our results demonstrate that 3-FDE is a promising tool for the fully quantum-chemical treatment of proteins.

Topological analysis of electron densities from Kohn-Sham and subsystem density functional theory.

In this study, we compare the electron densities for a set of hydrogen-bonded complexes obtained with either conventional Kohn-Sham density functional theory (DFT) calculations or with the frozen-density embedding (FDE) method, which is a subsystem approach to DFT. For a detailed analysis of the differences between these two methods, we compare the topology of the electron densities obtained from Kohn-Sham DFT and FDE in terms of deformation densities, bond critical points, and the negative Laplacian of the electron density. Different kinetic-energy functionals as needed for the frozen-density embedding method are tested and compared to a purely electrostatic embedding. It is shown that FDE is able to reproduce the characteristics of the density in the bonding region even in systems such as the F-H-F(-) molecule, which contains one of the strongest hydrogen bonds. Basis functions on the frozen system are usually required to accurately reproduce the electron densities of supermolecular calculations. However, it is shown here that it is in general sufficient to provide just a few basis functions in the boundary region between the two subsystems so that the use of the full supermolecular basis set can be avoided. It also turns out that electron-density deformations upon bonding predicted by FDE lack directionality with currently available functionals for the nonadditive kinetic-energy contribution.