scholarly journals Supramolecular Stark Effect in Host-Guest Complexes via Charge Density Analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C674-C674
Author(s):  
Sajesh Thomas ◽  
Rebecca Fuller ◽  
Alexandre Sobolev ◽  
Philip Schauer ◽  
Simon Grabowsky ◽  
...  

The effect of an electric field on the vibrational spectra, the Vibrational Stark Effect (VSE), has been utilized extensively to probe the local electric field in the active sites of enzymes [1, 2]. For this reason, the electric field and consequent polarization effects induced by a supramolecular host system upon its guest molecules attain special interest due to the implications for various biological processes. Although the host-guest chemistry of crown ether complexes and clathrates is of fundamental importance in supramolecular chemistry, many of these multicomponent systems have yet to be explored in detail using modern techniques [3]. In this direction, the electrostatic features associated with the host-guest interactions in the inclusion complexes of halogenated acetonitriles and formamide with 18-crown-6 host molecules have been analyzed in terms of their experimental charge density distribution. The charge density models provide estimates of the molecular dipole moment enhancements which correlate with the simulated values of dipole moments under electric field. The accurate electron density mapping using the multipole formalism also enable the estimation of the electric field experienced by the guest molecules. The electric field vectors thus obtained were utilized to estimate the vibrational stark effect in the nitrile (-C≡N) and carbonyl (C=O) stretching frequencies of the guest molecules via quantum chemical calculations in gas phase. The results of these calculations indicate remarkable elongation of C≡N and C=O bonds due to the electric fields. The electronic polarization in these covalent bonds induced by the field manifests as notable red shifts in their characteristic vibrational frequencies. These results derived from the charge densities are further supported by FT-IR experiments and thus establish the significance of a phenomenon that could be termed as the "supramolecular Stark effect" in crystal environment.

Author(s):  
Ayoub Nassour ◽  
Maciej Kubicki ◽  
Jonathan Wright ◽  
Teresa Borowiak ◽  
Grzegorz Dutkiewicz ◽  
...  

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen–Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O—H...O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C—C=C—OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.


2016 ◽  
Vol 15 (06) ◽  
pp. 1650050
Author(s):  
Yanjiao Qi ◽  
Yaming Zhao ◽  
Xiaoe Wang ◽  
Huining Lu ◽  
Nengzhi Jin

Molecular docking and charge density analysis were carried out to understand the geometry, charge density distribution and electrostatic properties of one of newly synthesized 4-substituted-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylates (PDE), which is regarded as the best [Formula: see text]-Glucosidase inhibitor among the hydropyridine dicarboxylate derivatives. The different bonding models of the PDE molecule in the active sites of proteins Human serum albumin (HSA) and Saccharomyces cerevisiae [Formula: see text]-glucosidase (SAG) are firstly compared, which is important to understand the different intermolecular interactions between drug-transport protein and drug-target protein. The deformation density maps suggest that the electron densities of the PDE molecule are redistributed when it presents in the active sites. When the molecule presents in the active site of the SAG, it is evident to find that the negative region does not appear at the vicinity of the oxygen atoms on one of the carboxylic acid dimethyl ester group. Frontier molecular orbital density distributions for the PDE molecule are similar in all forms. The highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energy gaps in the active sites are higher than that of the molecule in pure solution phase. It is generally noticed that all of the orientations of the dipole moment vectors are reoriented in both active sites. These fine details at electronic level allow to better understand the exact drug-transport protein and drug-target protein interactions.


2008 ◽  
Vol 120 (6) ◽  
pp. 613-620 ◽  
Author(s):  
Reji Thomas ◽  
Shrinwantu Pal ◽  
Ayan Datta ◽  
Mariusz K. Marchewka ◽  
Henryk Ratajczak ◽  
...  

2020 ◽  
Author(s):  
Yufan Wu ◽  
Stephen Fried ◽  
Steven Boxer

<div><p>Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI’s intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems. <br></p></div>


2014 ◽  
Vol 525 ◽  
pp. 170-176
Author(s):  
Zhao Xu Liu ◽  
Jun Zhu ◽  
Si Hua Ha

The quantum-confined Stark effect on the optical absorption of intersubband transitions in an asymmetric AlxGa1-xN/In0.3Ga0.7N/GaN quantum wells is investigated by means of the density matrix formulism. The built-in electric field generated by the piezoelectric and spontaneous polarizations competing against to the external electric fields is considered. As the result, the influences of the built-in and external electric fields on the energy potentials and the eigen stares are discussed in detail. When the positive external electric field is applied, the peak values of the absorption coefficients from 3-2, 2-1 and 3-1 transitions are reduced and moved to the lower photon energy levels. With the negative field, the exactly opposite results can be obtained. Moreover, it is indicated that the results of the wavelengths from the 3-2, 2-1 and 3-1 transitions are reduced by the positive external electric field and increased by the negative field.


2007 ◽  
Vol 17 (06) ◽  
pp. 845-876 ◽  
Author(s):  
PATRICK CIARLET ◽  
SAMIR KADDOURI

We are interested in computing the charge density and the electric field at the rounded tip of an electrode of small curvature. As a model, we focus on solving the electrostatic problem for the electric potential. For this problem, Peek's empirical formulas describe the relation between the electric field at the surface of the electrode and its curvature radius. However, it can be used only for electrodes with either a purely cylindrical, or a purely spherical, geometrical shape. Our aim is to justify rigorously these formulas, and to extend it to more general, two-dimensional, or three-dimensional axisymmetric, geometries. With the help of multiscaled asymptotic expansions, we establish an explicit formula for the electric potential in geometries that coincide with a cone at infinity. We also prove a formula for the surface charge density, which is very simple to compute with the Finite Element Method. In particular, the meshsize can be chosen independently of the curvature radius. We illustrate our mathematical results by numerical experiments.


1989 ◽  
Vol 160 ◽  
Author(s):  
K. Gibb ◽  
C. Lacelle ◽  
A.P. Roth ◽  
B. Soucail ◽  
N. Dupuis ◽  
...  

AbstractWe have used photoluminescence excitation and photocurrent spectroscopy to investigate the electronic properties of InxGa1-xAs/GaAs strained layer quantum wells and superlattices. In quantum wells, sharp excitonic transitions between discrete energy levels are observed both in excitation and near flatband photocurrent spectra whereas superlattices show heavy-hole to conduction miniband transitions at the Brillouin mini-zone centre and edge, directly giving the electron miniband width. Applying a longitudinal electric field to the quantum wells produces a red shift of the excitons due to the quantum confined Stark effect, while in superlattices, photocurrent spectra at finite applied electric fields show for the first time in this system, the effects of Wannier-Stark quantization. The analysis of the spectra provides a precise determination of the band offset.


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