Fundamentals of Modern Peptide Synthesis
Mesut Karahan in Synthetic Peptide Vaccine Models, 2021
Significant delocalization of the lone pair of electrons on the nitrogen atom gives the group a partial double bond character. The partial double bond renders the amide group planar, occurring in either the cis or trans-isomers. The geometry and dimensions of the peptide bonds are given in Figure 3.2. The peptide bond length is given in the Angstrom unit, the bond angles – in degrees. In the unfolded time of the proteins, the peptides are isomerized, and after folding this structure appears as a single isomer (at each position of the protein). Most peptide bonds exist in trans and genus and there are transitions between them alternately. For most peptide bonds (roughly 1000:1 ratio in trans cis populations) conversion is overwhelmingly preferred. However, this symmetry between the Cα and Cδ atoms of proline (Pro) in the peptide groups can make the cis and trans isomers nearly equal in energy (they tend to have a roughly 30:1 ratio) (Raven et al. 2014; Reece et al. 2011).The geometry and dimensions of the peptide bonds. (Source: WillowW at the English language Wikipedia https://en.wikipedia.org/wiki/File:Cis_trans_isomerization_kinetics_X_Pro_peptide_bonds.png.)
DFT based QSAR study on quinolone-triazole derivatives as antibacterial agents
Published in Journal of Receptors and Signal Transduction, 2022
Niloofar Ghasedi, Shahin Ahmadi, Sepideh Ketabi, Ali Almasirad
Considering the structures, it seems that the presence of a phenyl ring with an electron-withdrawing group on the para position is an adequate substitution on triazole's N1, which has resulted in a more negative partial charge on this nitrogen atom. The partial atomic charge (Q) for C7 atom of the quinolone nucleus shows a positive contribution, indicating a more positive charge and low electron density on this atom is favorable. The presence of a substitute with electronegative atoms attached to C7 carbon and electronegative and electron-withdrawing groups such as halogens or nitrogen at the 6 and 8 positions of the quinolone nucleus can help lower the electron density on C7. According to the structures, piperazine or aminopyrrolidine substitutions on C7 have significantly increased the positive partial charge on this atom. Bond length is one of the geometrical descriptors attributed to the 3 D structures of molecules [49].
10H-1,9-diazaphenothiazine and its 10-derivatives: synthesis, characterisation and biological evaluation as potential anticancer agents
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2019
Beata Morak-Młodawska, Krystian Pluta, Małgorzata Latocha, Małgorzata Jeleń, Dariusz Kuśmierz, Kinga Suwińska, Aleksander Shkurenko, Zenon Czuba, Magdalena Jurzak
The bond angles on heteroatoms in the central ring C1a–N10–C10a and C4a–S5–C5a are 118.74(12)° and 98.19(7)°, respectively. The thiazine nitrogen atom (N10) showed pyramidal configuration as a sum of three bond angles around this atom is 353.12°. The N10–C bond lengths in the thiazine ring are 1.406–1.409 Å, being significantly longer than the azine N–C bonds (1.331–1.349 Å). The N10–CH3 bond length is the longest at 1.463(2) Å due to the sp3 hybridisation of the carbon atom. The molecule interacts with the neighbouring four molecules with four non-classical C–H…N hydrogen bonds (the molecule is an acceptor of two and a donor of two others H-bonds) forming 2D layers perpendicular to the c crystallographic axis. Consequently, a layer-type structure was observed.
Nanocarrier for levodopa Parkinson therapeutic drug; comprehensive benserazide analysis
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2018
Mehdi Yoosefian, Elham Rahmanifar, Nazanin Etminan
To get deeper insight into the characteristics of intramolecular HBs, wide spectrum of HBs within the species have been analysed [24–27]. The optimized structures of title compounds are shown in Figures 1–4 with numbering of the atoms. The optimized structure parameters of studied molecules are listed in Table 1 in accordance with the atom numbering given in Figures 1–4. Table 1 shows O–H bond lengths of the most stable conformer (CT4), are detected in the range of 0.98–0.99 Ǻ, the H···O contacts are of about 1.98–2.13 Ǻ and H···N contacts are about 2.17–2.35 Ǻ. In the case of N–H bond the electron density at the corresponding BCP amounts to 0.3138 Å and for H···N interaction such electron density amounts to 0.024 Å. Besides, the corresponding Laplacian values of the O···H and N···H interaction contacts are positive. The positive Laplacian is the topological evidence of the noncovalency of closed-shell interactions [28–30]. A very well-known relationship between the proton-donating bond length and the proton-acceptor distance often found for studied conformers. It indicates that the greater the elongation of hydrogen donor bond is the shorter the hydrogen acceptor contact is which means the stronger is the interaction. The electron density at the corresponding bond length reflects the strength of any pair interactions: this density is greater for shorter distances. Figure 5 presents the molecular graph of the most stable conformer.
Related Knowledge Centers
- Atom
- Methane
- Molecular Geometry
- Molecule
- Atomic Nucleus
- X-Ray Crystallography
- Microwave Spectroscopy
- Chloromethane
- Orbital Hybridisation
- Steric Effects