scholarly journals Hydrogen Bond Studies in Interact 6-Mercaptopurine with its Receptor Hypoxanthine-Guanine Phosphoribosyltransferase

2020 ◽  
Vol 11 (02) ◽  
pp. 271-275
Author(s):  
Alaa A. Habeeb ◽  
Falah S A Suhail ◽  
Sami W Radhi
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Population Analysis ◽  
Correlation Coefficients ◽  
Density Distributions ◽  
Hydrogen Bonding Interactions ◽  
Anti Cancer ◽  
Substituent Constants ◽  
Hypoxanthine Guanine Phosphoribosyltransferase ◽  
Intramolecular Hydrogen

Objective: The aim of this study was to study some properties of the pharmaceutical compound (6-mercaptopurine) a number of theoretical methods were carried out to calculate their molecular energy, the length of the bonds and angles, in addition to their chemical forms and the binding sites with the enzyme as important anti-cancer inhibitors. Methods: The intramolecular hydrogen bond, molecular structure, and vibrational frequencies of 6- Mercaptopurine have been investigated by means of density functional (DFT and AM1) methods with 6-311++G basis. Results: The nature of these interactions, known as resonance assisted hydrogen bonds, has been discussed. As a geometrical indicator of a local aromaticity, the geometry-based HOMA index has been applied. Additionally, the linear correlation coefficients between substituent constants and selected parameters in R position have been calculated. Conclusion: The results show that the hydrogen bond strength is mainly governed by the resonance variations inside the chelate ring induced by the substituent groups. The topological properties of the electron density distributions for 6- MP H...N intra molecular bridges have been analyzed .Finally, the natural population analysis methods has been used to evaluate the hydrogen bonding interactions.

scholarly journals Application of Hammett equation to intramolecular hydrogen bond strength in para-substituted phenyl ring of trifluorobenzoylacetone and 1-aryl-1,3-diketone malonates

2018 ◽  
Vol 9 (3) ◽  
pp. 213-221 ◽  
Author(s):  
Vahidreza Darugar ◽  
Mohammad Vakili ◽  
Sayyed Faramarz Tayyari ◽  
Fadhil Suleiman Kamounah ◽  
Raheleh Afzali
Keyword(s):  
Hydrogen Bond ◽  
Bond Strength ◽  
Intramolecular Hydrogen Bond ◽  
Density Functional ◽  
Equilibrium Constants ◽  
Density Functional Theory Calculations ◽  
Electronic Effects ◽  
Hydrogen Bond Strength ◽  
Substituent Constants ◽  
Intramolecular Hydrogen

The stability of two stable cis-enol forms in two categories of β-diketones, including para-substituted of trifluorobenzoylacetone (X-TFBA) and 1-aryl-1,3-diketone malonates (X-ADM, X: H, NO2, OCH3, CH3, OH, CF3, F, Cl, and NH2) has been obtained by different theoretical methods. According to our results, the energy difference between the mentioned stable chelated enol forms for the titled compounds is negligible. The theoretical equilibrium constants between the two stable cis-enol of the mentioned molecules are in excellent agreement with the reported experimental equilibrium constant. In addition, the effect of different substitutions on the intramolecular hydrogen bond strength has been evaluated. The correlation between Hammett para-substituent constants, σp. with the theoretical and experimental parameters related to the strength of hydrogen bond in p-X-TFBA and p-X-ADM molecules also investigated by means of density functional theory calculations. The electronic effects of para-substitutions on the intramolecular hydrogen bond strength were determined by NMR and IR data related to intramolecular hydrogen bond strength, geometry, natural bond orbital results, and topological parameters. These parameters were correlated with the Hammett para-substituent constants, σp. Good linear correlations between σp and the several parameters related to the hydrogen bond strength, in this study were obtained.

Crystal structure of osimertinib mesylate Form B (Tagrisso), (C28H34N7O2)(CH3O3S)

2021 ◽  
pp. 1-9
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Emma L. Markun ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Amino Nitrogen ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
Dimethylamino Group ◽  
Intramolecular Hydrogen

The crystal structure of osimertinib mesylate Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Osimertinib mesylate Form B crystallizes in space group P-1 (#2) with a = 11.42912(17), b = 11.72274(24), c = 13.32213(22) Å, α = 69.0265(5), β = 74.5914(4), γ = 66.4007(4)°, V = 1511.557(12) Å3, and Z = 2. The crystal structure is characterized by alternating layers of cation–anion and parallel stacking interactions parallel to the ab-planes. The cation is protonated at the nitrogen atom of the dimethylamino group, which forms a strong hydrogen bond between the cation and the anion. That hydrogen atom also participates in a weaker intramolecular hydrogen bond to an amino nitrogen. There are two additional N–H⋅⋅⋅O hydrogen bonds between the cation and the anion. Several C–H⋅⋅⋅O hydrogen bonds also link the cations and anions. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

scholarly journals Salicylaldehyde Hydrazones: Buttressing of Outer-Sphere Hydrogen-Bonding and Copper Extraction Properties

2017 ◽  
Vol 70 (5) ◽  
pp. 556 ◽  
Author(s):  
Benjamin D. Roach ◽  
Tai Lin ◽  
Heiko Bauer ◽  
Ross S. Forgan ◽  
Simon Parsons ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Outer Sphere ◽  
Copper Extraction ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Oxime Derivatives ◽  
Intramolecular Hydrogen

Salicylaldehyde hydrazones are weaker copper extractants than their oxime derivatives, which are used in hydrometallurgical processes to recover ~20 % of the world’s copper. Their strength, based on the extraction equilibrium constant Ke, can be increased by nearly three orders of magnitude by incorporating electron-withdrawing or hydrogen-bond acceptor groups (X) ortho to the phenolic OH group of the salicylaldehyde unit. Density functional theory calculations suggest that the effects of the 3-X substituents arise from a combination of their influence on the acidity of the phenol in the pH-dependent equilibrium, Cu2+ + 2Lorg ⇌ [Cu(L–H)2]org + 2H+, and on their ability to ‘buttress’ interligand hydrogen bonding by interacting with the hydrazone N–H donor group. X-ray crystal structure determination and computed structures indicate that in both the solid state and the gas phase, coordinated hydrazone groups are less planar than coordinated oximes and this has an adverse effect on intramolecular hydrogen-bond formation to the neighbouring phenolate oxygen atoms.

THE EFFECT OF SUBSTITUTION ON STRUCTURE, INTRAMOLECULAR HYDROGEN BONDING STRENGTH, ELECTRON DENSITY AND RESONANCE IN 3-AMINO 2-IMINOMETHYL ACRYL ALDEHYDE

2012 ◽  
Vol 11 (05) ◽  
pp. 925-939 ◽  
Author(s):  
HEIDAR RAISSI ◽  
MAHDI YOOSEFIAN ◽  
FARIBA MOLLANIA ◽  
FARZANEH FARZAD
Keyword(s):  
Hydrogen Bonding ◽  
Electron Density ◽  
Population Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Analysis Data ◽  
Covalent Character ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bond Strength ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonding Strength

B3LYP/6-311++G** calculations have been carried out to simulate the influence of substitutions in position R1 and R2 of 3-amino 2-iminomethyl acryl aldehyde on intramolecular hydrogen bond strength. The following substituents are taken into considerations: CN, NO2, Cl, F, CH3, CHO, NH2, C2H5, SH, SCH3, CF3 and CH3CO and their vibrational frequencies are calculated at the same level of theory. Quantum theory of "Atoms in Molecules" and Natural Bond Orbitals method were applied to analyzed H-bond interactions. The electron density (ρ) and Laplacian (∇2ρ) properties, estimated by AIM calculations, indicate that N⋯H bond possesses low ρ and positive ∇2ρ values which are in agreement with electrostatic character of the HBs, whereas N–H bonds have covalent character (∇2ρ < 0). Natural population analysis data, the electron density and Laplacian properties, as well as, ν (N-H) and γ (N-H) have been used to evaluate the hydrogen bonding interactions.

scholarly journals Crystal structure of trirubidium citrate monohydrate from laboratory X-ray powder diffraction data and DFT comparison

2017 ◽  
Vol 73 (2) ◽  
pp. 227-230 ◽  
Author(s):  
Alagappa Rammohan ◽  
James A. Kaduk
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Three Dimensional ◽  
Powder Diffraction Data ◽  
Hydrogen Bond Donor ◽  
X Ray ◽  
Intramolecular Hydrogen

The crystal structure of the title compound, 3Rb+·C6H5O73−·H2O, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The hydroxy group participates in an intramolecular hydrogen bond to the deprotonated central carboxylate group with graph-set motifS(5). The water molecule acts as a hydrogen-bond donor to both terminal and central carboxylate O atoms. The three independent rubidium cations are seven-, six- and six-coordinate, with bond-valence sums of 0.84, 1.02, and 0.95, respectively. In the extended structure, their polyhedra share edges and corners to form a three-dimensional network. The hydrophobic methylene groups occupy channels along thebaxis.

Molecular Engineering of β-Substituted Oxoporphyrinogens for Hydrogen-Bond Donor Catalysis

2019 ◽  
Author(s):  
Mandeep K. Chahal ◽  
Daniel Payne ◽  
Yoshitaka Matsushita ◽  
Jan Labuta ◽  
Katsuhiko Ariga ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Molecular Engineering ◽  
Hydrogen Bond Donor ◽  
Conjugate Additions ◽  
Bond Forming ◽  
Michael Additions ◽  
New Class ◽  
Hydrogen Bonding Interactions ◽  
Multiple Hydrogen Bond ◽  
Intramolecular Hydrogen

<p>A new class of bifunctional hydrogen-bond donor organocatalyst using oxoporphyrinogens with increased intramolecular hydrogen-bond donor distances is reported. Oxoporphyrinogens are highly non-planar rigid macrocycles containing a multiple hydrogen bond forming binding site. In this work we report the first example of non-planar OxPs as hydrogen-bond donor catalysts. The introduction of β-substituents is key to the catalytic activity and the catalysts are able to catalyze 1,4-conjugate additions and sulfa-Michael additions, as well as, Henry and aza-Henry reactions at low catalyst loadings (≤ 1 mol%) under mild conditions. Preliminary mechanistic studies have been carried out and a possible reaction mechanism has been proposed based on the bi-functional activation of both substrates through hydrogen-bonding interactions.</p>

Crystal structure of vardenafil hydrochloride trihydrate, C23H33N6O4SCl (H2O)3

2018 ◽  
Vol 33 (4) ◽  
pp. 319-326
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Strong Hydrogen Bond ◽  
Water Molecules ◽  
Ring Nitrogen ◽  
Intramolecular Hydrogen

The crystal structure of vardenafil hydrochloride trihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Vardenafil hydrochloride trihydrate crystallizes in space group C2/c (#15) with a = 34.78347(16), b = 11.56752(4), c = 14.69308(5) Å, β = 93.3410(4), V = 5901.839(30) Å3, and Z = 8. The fused ring system and the phenyl ring are nearly co-planar; the interplanar angle between them is 6.0°. Two intramolecular hydrogen bonds help determine this conformation. These planes stack along the c-axis. The side chains of these ring systems have a large Uiso and are neighbors in the stacks. Along the a-axis, these stacks are separated by hydrophilic layers of chloride, water molecules, and the positively charged nitrogen atoms of the vardenafil cation. Hydrogen bonds are prominent in the crystal structure. The protonated nitrogen atom forms a strong hydrogen bond to the chloride anion. The water molecules form a hexagon, making hydrogen bonds with themselves, as well as the C1 and a ring nitrogen atom. These discrete hydrogen bonds form a cluster, and there is no extended hydrogen bond network. There are many C–H⋯Cl, C–H⋯O, and C–H⋯N hydrogen bonds, which (although individually weak) contribute significantly to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1620.

MAGNETIC COUPLING CONSTANTS AND SPIN DENSITY DISTRIBUTIONS FOR CYANO-BRIDGED Gd(III)-Fe(III) AND Gd(III)-Cr(III) COMPOUNDS: BROKEN-SYMMETRY AND DENSITY FUNCTIONAL THEORY CALCULATIONS

2005 ◽  
Vol 19 (15n17) ◽  
pp. 2538-2543 ◽  
Author(s):  
YI QUAN ZHANG ◽  
CHENG LIN LUO ◽  
ZHI YU
Keyword(s):  
Density Functional Theory ◽  
Spin Density ◽  
Spin Polarization ◽  
Density Functional ◽  
Population Analysis ◽  
Magnetic Coupling ◽  
Coupling Constants ◽  
Broken Symmetry ◽  
Functional Theory ◽  
Density Distributions

Magnetic coupling constants J for the complete structures of [ Gd(capro) 2( H 2 O )4 Cr(CN) 6]• H 2 O (capro represents caprolactam) (a) and trans-[ Fe(CN) 4(μ- CN )2 Gd ( H 2 O )4 (bpy) ]•4 H 2 O •1.5 bpy (b) have been calculated using hybrid density functional theory (DFT) B3LYP combined with a modified broken symmetry approach (BS). The calculated J value of -0.24 cm-1 for a is very close to the experimental -0.33 cm-1. They both show the antiferromagnetic interaction between Gd(III) and Cr(III) . For b, although the sign of the calculated J value of 4.24 cm-1 is different from that of the experimental -0.38 cm-1, the two values both show the weak magnetic coupling interaction between Gd(III) and Fe(III) . The spin density distributions are discussed on the basis of Mulliken population analysis. For complexes a and b, both transition metal ( Fe(III) or Cr(III) ) and rare earth Gd(III) display a spin polarization effect on the surrounding atoms, where a counteraction of the opposite polarization effects leads to a low spin density on the bridging ligand C1N1 . For the compounds Gd(III) - Cr(III) (a) and Gd(III) - Fe(III) (b) in the HS states, Cr(III) has stronger spin polarization influence on the bridging atoms than Fe(III) even causing the positive spin population on the bridging atom N1 .

Sign in / Sign up

Export Citation Format

Share Document