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Drug Design, Synthesis, and Development
Published in Nathan Keighley, Miraculous Medicines and the Chemistry of Drug Design, 2020
Ever since the discovery of the atom through Rutherford’s alpha-scattering experiments in 1911, our knowledge and understanding of chemistry has catapulted the development of the subject, which has been instrumental in facilitating many advancements in our modern society. The nature of atoms and understanding how they interact and bond with one another is fundamental to chemistry. Having an appreciation of the three-dimensional properties of molecules is essential to structure and bonding; molecular geometry and isomerism are important features of drug molecules and govern how drug molecules bind to their target through intermolecular interactions.
Biomedical Applications of Raman Scattering
Published in R. Michael Gendreau, Spectroscopy in the Biomedical Sciences, 1986
However, αzz, itself is a function of time. Thus, for small changes in molecular geometry (such as occur when a molecule vibrates), is the static polarizability arising from the equilibrium geometry of the molecule, vvib is the molecular vibrational frequency, and Δq is the maximal change in internuclear configuration which causes the change in polarizability during the vibration of interest. This implies that
Determining and Drawing Molecular Geometry and Polarity
Published in Patrick E. McMahon, Rosemary F. McMahon, Bohdan B. Khomtchouk, Survival Guide to General Chemistry, 2019
Patrick E. McMahon, Rosemary F. McMahon, Bohdan B. Khomtchouk
Lewis structures show the bonding atom connection pattern and number of lone pairs around each atom in a covalent molecule; the structures do not represent any direct information concerning the actual three-dimensional (3-D) shape of the molecule. The three-dimensional (3-D) 3-D shape of a complete molecule, termed the molecular geometry, is based on the arrangement of all electron pairs around each central atom in a complete molecule. The 3-D geometry around a central atom describes the relative positions of each lone electron pair and each bonding electron pair. By extension, the relative positions of the bonding electron pairs must specify the corresponding positions of all atoms, whether central or outside, attached to a central atom.Analysis of 3-D geometry applies only to central atoms in a molecule; the geometry around outside (atoms does not contribute to overall molecular geometry. A minimum of two bonded-atoms is necessary to make central atom positional comparisons relevant to molecular properties.The first analysis of the shape of a complete molecule proceeds through determination of the 3-D geometry of one central atom at time. The shape of each central atom, in turn, produces a starting composite view of the shape of the molecule. A first analysis determines the geometry of the central atoms; the positional relationships between central atoms require further levels of analysis.
Target-based drug discovery through inversion of quantitative structure-drug-property relationships and molecular simulation: CA IX-sulphonamide complexes
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2018
Petar Žuvela, J. Jay Liu, Myunggi Yi, Paweł P. Pomastowski, Gulyaim Sagandykova, Mariusz Belka, Jonathan David, Tomasz Bączek, Krzysztof Szafrański, Beata Żołnowska, Jarosław Sławiński, Claudiu T. Supuran, Ming Wah Wong, Bogusław Buszewski
H6erepresents the H-autocorrelation at a distance of six bonds weighted by Sanderson electronegativity73. It is based on constructing a leverage matrix (H) from three-dimensional molecular geometry for i-j atom pairs at a defined topological distance. Within the H-matrix, only atoms j at a distance of dij bonds have a chance to interact with the i-th atom73. Its elements are multiplied by electronegativity values of individual atoms. This descriptor, thereby, encodes similar structural information as B05[N-Cl], and B05[O-S] descriptors, and it exhibits almost identical multivariate correlation towards logKi and logkw, only of a slightly higher magnitude.
Insights into structures of imidazo oxazines as potent polyketide synthase XIII inhibitors using molecular modeling techniques
Published in Journal of Receptors and Signal Transduction, 2020
Shanthakumar B., Kathiravan M. K.
Molecular structures were drawn from ACD/labs ChemSketch Freeware 2017.2.1 [15]. It was subjected to Open Babel V2.4.1 for converting them to Sybyl mol2 format [16]. Further to obtain a defined 3D molecular geometry and to develop co-ordinates it was subjected to Avogadro V1.2.0. The structures were minimized by molecular mechanic force fields in order to obtain an appropriate conformer possessing the least global minimum energy and to be devoid of strain in the molecular structure. All the optimized structures were subjected to PaDEL Descriptor version 2.20 software to calculate descriptors for 58 compounds [17].
Vesicle formation mechanisms: an overview
Published in Journal of Liposome Research, 2021
To the best of our knowledge, no review article is available which systematically and comprehensively explains the mechanisms involved in thin-film hydration, bulk, and electroformation methods in one place. For example, Lasic et al. (1988) reviewed the thermodynamics in vesicle formation by thin-film and bulk methods, while Guida (2010) provided a general overview of thermodynamic and kinetic aspects in vesicle formation. Moreover, the review on the possible mechanism of liposome electrofomration based on recent research is not yet available. In the present contribution, we have attempted to explain the vesicle formation mechanisms based on theoretical approaches. For this, several recent and past publications have been compiled to achieve insightful ideas about the mechanisms, especially in bulk and electroformation methods. In the current outline, we provide the necessary background information, to be familiar with the factors governing vesicle manufacturing. The fundamental theory behind the self-assembly of lipids into large ordered structures, such as bilayers or vesicles, involves three key points (thermodynamic aspects): (a) the interaction free energy of the lipid molecules, (b) molecular geometry, and (c) elastic properties of the lipid bilayers. These aspects are elaborated in the next section. Sections 3 to 5 deal with vesicle formation mechanisms under different modes of manufacturing [see a recent review by Has and Sunthar (2019), for various vesicle preparation methods], i.e. bulk (Section 3), thin-film hydration (Section 4), and electroformation (Section 5) methods. Various kinetic aspects of vesicle formation are discussed in Section 6. Section 7 discusses some criteria for obtaining unilamellar and multilamellar vesicles. Finally, the key aspects of the overview are summarised in Section 8. It is anticipated that the community involved in liposome research will find this review useful in a better understanding the principles of vesicle formation.