Pattern recognition strategies for molecular surfaces. II. Surface complementarity

Fuzzy logic based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. Therein, the overlapping surface patches defined in article I1 of this series are used. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Standard technologies can then be used for further optimization of the resulting complex structures. The algorithms are applied to 33 biomolecular complexes. After the optimization with a downhill simplex method, for all these complexes one structure was found, which is in very good agreement with the experimental results.     

WavePacket: A Matlab package for numerical quantum dynamics. III. Quantum-classical simulations and surface hopping trajectories

WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I (Schmidt and Lorenz, Comput. Phys. Commun. 2017, 213, 223] and Part II (Schmidt and Hartmann, Comput. Phys. Commun. 2018, 228, 229] which dealt with quantum dynamics of closed and open systems, respectively, the present Part III adds fully classical and mixed quantum-classical propagation techniques to WavePacket. There classical phase-space densities are sampled by trajectories which follow (diabatic or adiabatic) potential energy surfaces. In the vicinity of (genuine or avoided) intersections of those surfaces, trajectories may switch between them. To model these transitions, two classes of stochastic algorithms have been implemented: (1) Tully's fewest switches surface hopping and (2) Landau–Zener-based single switch surface hopping. The latter one offers the advantage of being based on adiabatic energy gaps only, thus not requiring nonadiabatic coupling information any more. The present work describes the MATLAB version of WavePacket 6.1.0, which is essentially an object-oriented rewrite of previous versions, allowing to perform fully classical, quantum-classical and quantum-mechanical simulations on an equal footing, that is, for the same physical system described by the same WavePacket input. The software package is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics are available. © 2019 Wiley Periodicals, Inc.     

Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory

A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as the electrostatic potential, the local lipophilicity/hydrophilicity, and the hydrogen bond density on the surface for characterization. The definition and the calculation method for these properties are reviewed shortly. The surface is segmented into overlapping patches with similar molecular properties. These patches can be used to represent the characteristic local features of the molecule in a way that is beyond the atomistic resolution but can nevertheless be applied for the analysis of partial similarities of different molecules as well as for the identification of molecular complementarity in a very general sense. The patch representation can be used for different applications, which will be demonstrated in subsequent articles.     

Inherent complexities of trace detection by surface-enhanced Raman scattering.

Surface-enhanced Raman scattering (SERS) and surface-enhanced resonance Raman scattering (SERRS) are powerful optical scattering techniques used in such frontier areas of research as ultrasensitive chemical analysis, the characterization of nanostructures, and the detection of single molecules. However, measuring and, most importantly, interpreting SERS/SERRS spectra can be incredibly challenging. This is the result of modifications to the measured spectra that are due to of a variety of instabilities and contributions. These interferences and modifications arise from the nature of the enhancement itself, as well as the conditions used to attain SERS spectra. The present report is an attempt to collect in one place the analytical interferences that are most commonly found during the collection of SERS/SERRS spectra.     

Hydrogen electrocatalysis.

A selection of recent theoretical and experimental studies on electrolytic hydrogen evolution is presented. It is demonstrated with well-defined model surfaces that this reaction is a very structure-sensitive process. Crystallographic orientation, defect density and surface composition are parameters that determine the local geometric and electronic surface structure, and are thus crucial for the electrocatalytic activity as characterised by the exchange current density. The observed trends can be understood within a recent theory by J. K. N?rskov et al., which is based on density functional calculations and which emphasises the impact of hydrogen chemisorption energies on the reaction rate, that is, on the exchange current density. The particular electrocatalytic activities of ultrathin metal films and of nanostructures are addressed.     

Constructing spin-adiabatic states for the modeling of spin-crossing reactions. I. A shared-orbital implementation

In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a “transition state” structure, where the spin crossing occurs. In this work, we report the implementation of a fully-variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions (predissociation of N₂O, singlet-triplet conversion in CH₂, and CO addition to Fe(CO)₄), the spin-crossing points were obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (ie, a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces.     

Physical modifications of propylene/ethylene–propylen–diene–monomer rubber surfaces. I. Determination of surface composition and surface order by fourier transform infrared–attenuated total reflectance

The aim of this study was to introduce a new method for determining the surface composition and surface order of PP/EPDM (propylene/ethylene–diene–monomer rubber) blends, based on surface-enhanced infrared spectroscopy. PP/EPDM blends were characterized by Fourier transfer IR–attentuated total reflectance (FTIR-ATR) using two different internal reflection elements, Ge and KRS-5. These elements provide information at different depths and show differences in relative band intensities. A linear relationship between the ratio of the bands at 2850 and 2920 cm^?1 EPDM content was obtained when well-defined compositions of PP and EPDM mixtures were used. Changes in crystallinity were measured by the ratio of the bands at 2959 and 2951 cm^?1. For comparison, bands in the lower region of the spectrum and DSC and WAXS measurments were used. It was shown by two calibration methods that FTIR-ATR can provide information on surface composition and surface crystallinity at very low penetration depths. This new method indicates that injection-molded sample show a lower surface order and lower EPDM content at the surface than is seen in bulk. © 1993 John Wiley & Sons, Inc.