Molecular structure, spectral analysis and hydrogen bonding analysis of ampicillin trihydrate: a combined DFT and AIM approach

2015 ◽  
Vol 39 (12) ◽  
pp. 9800-9812 ◽  
Author(s):  
Eram Khan ◽  
Anuradha Shukla ◽  
Anubha Srivastava ◽  
Shweta Shweta ◽  
Poonam Tandon
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonding ◽  
Spectral Analysis ◽  
Active Sites ◽  
Bonding Analysis ◽  
Ampicillin Trihydrate

The optimized structure and active sites of ampicillin trihydrate calculated using monomeric and dimeric models.

The significance of the Cα substituent in the selective inhibition of matrix metalloproteinases 1 and 9

2011 ◽  
Vol 392 (11) ◽  
Author(s):  
Riyad Domingo ◽  
Kelly Chibale ◽  
Edward D. Sturrock
Keyword(s):  
Hydrogen Bonding ◽  
Matrix Metalloproteinases ◽  
Active Sites ◽  
Unsaturated Compound ◽  
Selective Inhibition ◽  
Acid Group ◽  
Side Chain ◽  
Carboxylic Acid Group ◽  
Lead Compounds ◽  
Hydrogen Bonding Interactions

Abstract Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing Cα substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC50 value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the Cα substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand’s morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P1′ and P2′ may confer selectivity among MMPs and may aid in the search for novel lead compounds.

scholarly journals Relevance of Hydrogen Bonds for the Histamine H2 Receptor-Ligand Interactions: A Lesson from Deuteration

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 196 ◽  
Author(s):  
Mojca Kržan ◽  
Jan Keuschler ◽  
Janez Mavri ◽  
Robert Vianello
Keyword(s):  
Hydrogen Bonding ◽  
Active Sites ◽  
Density Functional ◽  
Receptor Activation ◽  
Histamine H2 Receptor ◽  
Therapeutic Practice ◽  
H2 Receptor ◽  
Ligand Interactions ◽  
Solvent Molecules ◽  
Near Future

We used a combination of density functional theory (DFT) calculations and the implicit quantization of the acidic N–H and O–H bonds to assess the effect of deuteration on the binding of agonists (2-methylhistamine and 4-methylhistamine) and antagonists (cimetidine and famotidine) to the histamine H2 receptor. The results show that deuteration significantly increases the affinity for 4-methylhistamine and reduces it for 2-methylhistamine, while leaving it unchanged for both antagonists, which is found in excellent agreement with experiments. The revealed trends are interpreted in the light of the altered strength of the hydrogen bonding upon deuteration, known as the Ubbelohde effect, which affects ligand interactions with both active sites residues and solvent molecules preceding the binding, thus providing strong evidence for the relevance of hydrogen bonding for this process. In addition, computations further underline an important role of the Tyr250 residue for the binding. The obtained insight is relevant for the therapy in the context of (per)deuterated drugs that are expected to enter therapeutic practice in the near future, while this approach may contribute towards understanding receptor activation and its discrimination between agonists and antagonists.

Synthesis, molecular structure, and spectral analysis of copper(II) complexes derived from pyridinediols

2014 ◽  
Vol 68 (2) ◽  
pp. 206-219 ◽  
Author(s):  
Guillermo M. Chans ◽  
Elizabeth Gómez ◽  
Virginia Gómez-Vidales ◽  
R. Alfredo Toscano ◽  
Cecilio Álvarez-Toledano
Keyword(s):  
Molecular Structure ◽  
Spectral Analysis

scholarly journals Vibrational Resonant Inelastic X-Ray Scattering Inliquid Acetic Acid: A Ruler for Molecular Chain Lengths

2020 ◽  
Author(s):  
Viktoriia Savchenko ◽  
Iulia-Emilia Brumboiu ◽  
Victor Kimberg ◽  
Michael Odelius ◽  
Pavel Krasnov ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonding ◽  
Acetic Acid ◽  
Molecular Chain ◽  
X Ray ◽  
X Ray Scattering ◽  
Localized Excitations ◽  
Vibrational Excitations ◽  
Chain Lengths ◽  
Ray Scattering

Abstract Quenching of vibrational excitations in resonant inelastic X-ray scattering (RIXS) spectra of liquid acetic acid is observed. At the oxygen core resonance associated with localized excitations at the O-H bond, the spectra lack the typical progressionof vibrational excitations observed in RIXS spectra of comparable systems. We interpret this phenomenon as due to strong rehybridization of the unoccupied molecular orbitals as a result of hydrogen bonding. This allows us to address the molecular structure of the liquid, and to determine a lower limit for the average molecular chain length.

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