Spatial Orientation Of Molecules Research Articles

Three-dimensional descriptors for aminergic GPCRs: dependence on docking conformation and crystal structure

Three-dimensional descriptors are often used to search for new biologically active compounds, in both ligand- and structure-based approaches, capturing the spatial orientation of molecules. They frequently constitute an input for machine learning-based predictions of compound activity or quantitative structure–activity relationship modeling; however, the distribution of their values and the accuracy of depicting compound orientations might have an impact on the power of the obtained predictive models. In this study, we analyzed the distribution of three-dimensional descriptors calculated for docking poses of active and inactive compounds for all aminergic G protein-coupled receptors with available crystal structures, focusing on the variation in conformations for different receptors and crystals. We demonstrated that the consistency in compound orientation in the binding site is rather not correlated with the affinity itself, but is more influenced by other factors, such as the number of rotatable bonds and crystal structure used for docking studies. The visualizations of the descriptors distributions were prepared and made available online at http://chem.gmum.net/vischem_stability, which enables the investigation of chemical structures referring to particular data points depicted in the figures. Moreover, the performed analysis can assist in choosing crystal structure for docking studies, helping in selection of conditions providing the best discrimination between active and inactive compounds in machine learning-based experiments.Graphical abstract

The influence of temperature on optical properties of merocyanine dye thin films

Merocyanine dye thin films have been investigated using optical microscopy methods. The films were deposited using the method of thermal evaporation. The influence of substrate type and temperature on optical properties and spatial orientation of molecules in the above films has been studied. The influence of annealing on structural reorientation of molecules in thermally deposited dye films has been determined.

In situ SERS spectroelectrochemical analysis of antioxidants deposited on copper substrates: What is the effect of applied potential on sorption behavior?

The detection of p-coumaric acid and ferulic acid using a combined in situ electrochemical and surface-enhanced Raman scattering spectroscopic technique in specially made electrode cell is described. New in situ spectroelectrochemical cell was designed as the three-electrode arrangement connected via positioning device to fiber-optic probe of Raman spectrometer Dimension P2 (excitation wavelength 785nm). In situ SERS spectra of p-coumaric acid and ferulic acid were recorded at varying applied negative potentials to copper substrates. The spectral intensities and shapes of bands as well as spatial orientation of molecules on the surface depend significantly on varying values of the applied electrode potential. The change of electrode potential influences analyte adsorption/desorption behavior on the surface of copper substrates, affecting the reversibility of the whole process and overall spectral enhancement level. Principal component analysis is used to distinguish several stages of spectral variations on potential changes.

Formation mechanisms of equilibrium component composition of molecular layers of polymethine dyes

We study the concentration dependences for the absorption spectra and component composition of molecular layers from three homologous series of symmetric polymethine dyes of different electron-donating ability of their terminal heterocyclic groups. We find that a change in the layer thickness leads to a change in the width and position of the spectrum due to a change in the number of absorption bands. The number of bands of monomers increases with increasing chain length and electron-donating ability. The concentration ratio of monomers and associated forms depends on the spatial orientation of molecules in the layer. The electron-donating ability of terminal groups affects the angle between the chromophores of molecules that form a dimer and the intensity ratio between the short- and long-wavelength absorption bands of dimers. We conclude that the effect of the thickness of the layer on its spectral parameters is determined by the degree of intramolecular electron asymmetry that arises as a result of the interaction of chemically symmetric molecules with charges of the substrate surface and upon intermolecular interaction. This asymmetry leads to changes in free energies of ground states of monomeric molecules and, as a consequence, to an increase in equilibrium concentrations of cis-stereoisomeric forms in the layer.

Orienting molecules via an ir and uv pulse pair: Implications for coherent Raman spectroscopy

Spatial orientation of molecules is a pervasive issue in chemical physics and, by breaking inversion symmetry, has major consequences in nonlinear optics. In this paper, we propose and analyze an approach to molecular orientation. This extracts from an ensemble of aligned diatomic molecules equally AB and BA, relative to the E vector a subensemble that is oriented mostly AB or BA. Subjecting an aligned molecule to a tailored infrared ir laser pulse creates a pair of coherent wave packets that correlate vibrational phase with the AB or BA orientation. Subsequent, suitably phased ultraviolet uv or visible pulses dissociate one of these vibrational wave packets, thereby “weeding out” either AB or BA but leaving intact the other orientation. Molecular orientation has significant implications for coherent Raman spectroscopy. In the absence of orientation, coherence between vibrational levels is generated by a pair of laser pulses off which a probe pulse is scattered to produce a signal. Orientation allows direct one-photon ir excitation to achieve in principle maximal Raman coherence.

The absolute orientation of a molecule in space: Extension of the 'CIP' system

A scheme for denoting the absolute spatial orientation of molecules and molecular fragments is presented; this is based on three angular deviations — one for each spatial dimension — with respect to a reference orientation, which is itself defined with the help of certain features of the Cahn-Ingold-Prelog stereochemical notation. The new scheme helps in reconstructing the three-dimensional characteristics of molecules from purely verbal descriptors, and may thus find application in various information storage and retrieval processes (e.g. encrypting holograms, etc.).

Spatial orientation of molecules by a heat flux

An effect of spatial orientation of molecules by a heat flux is predicted. Under typical experimental conditions the magnitude of the constant electric field arising due to static polarization of a gas of oriented molecules can reach values ∼10−4 V/cm.

Spatial orientation of molecules in strong electric fields and evidence for pendular states

IN typical collisional or spectroscopic experiments, molecules rotate freely with random spatial orientations. The resulting isotropic averaging obscures or suppresses much stereodynamical information and has remained a recalcitrant problem. The only practical means for orienting a molecule itself, rather than just its axis of rotation, has been electric field focusing1,2. But this is applicable only to certain rotational states of symmetric top molecules (or equivalent) that exhibit a first-order Stark effect. Orientation of molecules other than symmetric tops has long been considered to be quite unfeasible3. Recently, however, it has been pointed out4,5 that by exploiting the extreme rotational cooling that can occur in supersonic molecular beams, substantial orientation of diatomic, linear or asymmetric top molecules should become possible at accessible field strengths. The anisotropy of the Stark effect allows molecules in the lowest few rotational states to be trapped in 'pendular states' and thereby confined to librate (oscillate about the field axis) over a limited angular range. Here we describe an experiment which demonstrates that oriented pendular states can be obtained for a diatomic molecule with modest field strengths. With anticipated improvements, this technique should become widely applicable.