scholarly journals Charge density analysis of two proton transfer complexes: Understanding hydrogen bonding and determination of in-crystal dipole moments

2008 ◽  
Vol 120 (6) ◽  
pp. 613-620 ◽  
Author(s):  
Reji Thomas ◽  
Shrinwantu Pal ◽  
Ayan Datta ◽  
Mariusz K. Marchewka ◽  
Henryk Ratajczak ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Charge Density ◽  
Dipole Moments ◽  
Density Analysis

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 ◽  
...  
Keyword(s):  
Electric Field ◽  
Charge Density ◽  
Electric Fields ◽  
Active Sites ◽  
Stark Effect ◽  
Dipole Moments ◽  
Covalent Bonds ◽  
Guest Molecules ◽  
Density Mapping ◽  
Density Analysis

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.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

2014 ◽  
Vol 70 (2) ◽  
pp. 331-341 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Hydrogen Bonding ◽  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Bond Critical Point ◽  
Potential Region ◽  
Electrostatic Properties ◽  
Structural And Electronic Properties ◽  
Density Analysis ◽  
Mycobacterial Cell Wall

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed usingCRYSTAL09with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N—N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C—H...N, C—H...O and N—H...N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Exploring the rare S—H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid

2017 ◽  
Vol 73 (4) ◽  
pp. 626-633 ◽  
Author(s):  
Mysore. S Pavan ◽  
Sounak Sarkar ◽  
Tayur N. Guru Row
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Charge Density ◽  
Interaction Energy ◽  
Electron Density ◽  
Type I ◽  
Weak Hydrogen Bond ◽  
Topological Features ◽  
Density Analysis ◽  
Density Study

Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S—H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S—H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. Thepara-substituted mercaptobenzoic acid depicts a type I S...S interaction.

scholarly journals Proton Transfer Equilibria and Critical Behavior of H-Bonding

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
L. Sobczyk ◽  
B. Czarnik-Matusewicz ◽  
M. Rospenk ◽  
M. Obrzud
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Dipole Moments ◽  
Electronic Polarizability ◽  
Bond Properties ◽  
Acid Base ◽  
Definition Of ◽  
Magnetic Resonances ◽  
Very High

The aim of the present paper is an analysis of the hydrogen bond properties for the acid-base systems depending on the ability to the proton transfer in the formulation of the Brönsted approach. After definition of the proton transfer equilibrium expressed by using the equation log KPT=ξΔpKN, various examples of different physical properties, such as dipole moments, IR spectra, and nuclear magnetic resonances, are presented which correlate with the ΔpKN value. In such a way, a critical state of hydrogen bonding can be defined that corresponds to the potential of the proton motion for either single minimum or double minimum with low barrier. A particular attention in this paper found electronic spectra which have not been analysed so far and the quantitative analysis of the vibrational polarizability which can reach very high values of the order of electronic polarizability.

scholarly journals Intra‐ and Inter‐molecular Sulf‐ hydryl Hydrogen Bonding: Facilitating Proton Transfer Events for Determination of pH in Sea Water

2020 ◽  
Author(s):  
Neel Sisodia ◽  
Monica Miranda ◽  
Kay L. McGuinness ◽  
Jay D. Wadhawan ◽  
Nathan S. Lawrence
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Sea Water

scholarly journals Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopentanedione, a compound displaying a resonance-assisted hydrogen bond

2014 ◽  
Vol 70 (2) ◽  
pp. 197-211 ◽  
Author(s):  
Ayoub Nassour ◽  
Maciej Kubicki ◽  
Jonathan Wright ◽  
Teresa Borowiak ◽  
Grzegorz Dutkiewicz ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Density ◽  
Electron Density ◽  
Dipole Moments ◽  
Lone Pair ◽  
Covalent Bonds ◽  
Density Maps ◽  
Structure Factors ◽  
Density Analysis ◽  
Additional Charges

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.

Experimental and theoretical charge-density analysis of hippuric acid: insight into its binding with human serum albumin

2019 ◽  
Vol 75 (4) ◽  
pp. 750-762 ◽  
Author(s):  
Asma Hasil ◽  
Arshad Mehmood ◽  
Maqsood Ahmed
Keyword(s):  
Crystal Structure ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Charge Density ◽  
Human Serum ◽  
Hippuric Acid ◽  
Noncovalent Interactions ◽  
Dipole Moments ◽  
Topological Analysis ◽  
Density Analysis

In order to comprehend the binding of an important metabolite, hippuric acid, with human serum albumin and to understand its chemical and electronic nature, an experimental charge-density analysis has been carried out using high-resolution diffraction data collected under cryogenic conditions, and all the results have been compared with theoretical findings using the B3LYP/6-311++g(2d,2p) level of theory. The structure displays very strong classical hydrogen bonds as well as other noncovalent interactions, which have been fully characterized using Hirshfeld surface analysis and Bader's quantum theory of atoms in molecules. Contact analysis on the Hirshfeld surfaces shows that the O...H, C...H and C...N intermolecular interactions are enriched and gives their relative strengths. Topological analysis of the electron density shows the charge concentration/depletion of hippuric acid bonds in the crystal structure. Electrostatic parameters such as atomic charges and dipole moments were calculated. The mapping of atomic basins and the calculation of respective charges show the atomic volumes of each atom as well as their charge contributions in the hippuric acid crystal structure. The dipole-moment calculations show that the molecule is very polar in nature. Calculations of the electrostatic potential show that the chain part of the molecule has a higher concentration of negative charge than the ring, which might be instrumental in its strong binding with the polar residues of site II of human serum albumin.

Sign in / Sign up

Export Citation Format

Share Document