A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule

Journal of Molecular Modeling
Mariana KozlowskaPawel Rodziewicz

Abstract

Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H⋯O, N-H⋯N, C-H⋯O, C-H⋯N and N-H⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car-Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.

References

Feb 1, 1993·Chemico-biological Interactions·T L ChingA Bast
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Nov 25, 1985·Physical Review Letters·R Car, M Parrinello
Dec 6, 2001·Journal of the American Chemical Society·B J van der VekenP Hobza
Jun 22, 2005·Journal of Pharmaceutical and Biomedical Analysis·Magdalene Xenou KokoletsiMichael Tsiaganis
Jun 22, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Pawel RodziewiczAleksander Koll
Jan 31, 2006·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Ying GaoErkang Wang
Jan 13, 2009·Environment International·Marina IsidoriFabio Temussi
Jan 15, 2010·Fundamental & Clinical Pharmacology·Amirhossein AhmadiSeyed Soheil Saeedi Saravi
Aug 13, 2011·The Journal of Physical Chemistry. a·Sławomir J Grabowski

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.