AIM and NBO analyses on hydrogen bonds formation in sugar-based surfactants (α/β-<scp>d</scp>-mannose and <i>n-</i>octyl-α/β-<scp>d</scp>-mannopyranoside): a density functional theory study

Kotena, Zahrabatoul Mosapour; Behjatmanesh–Ardakani, Reza; Hashim, Roslan

doi:10.1080/02678292.2014.886731

Cited by 21 publications

(7 citation statements)

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“…for deoxy-hexose sugars [26]; 2.17-2.19 (Å) for α/β-D-mannose [24]; and 1.85-2.11 (Å) for α/β-Dglucopyranose and α/β-D-galactopyranose [45]. Accordingly, our calculated results are comparable with those reported in the references [24,26,[44][45][46].…”

Section: Resultssupporting

confidence: 88%

“…Several theoretical methods have been used to investigate the structural and electronic properties of carbohydrate sugars to understand the nature of H-bonds interactions [24][25][26][27][28]. The present study aims to investigate the H-bonds formation and the orientation effects of five hydroxyl groups in the four rare sugars theoretically.…”

Section: Introductionmentioning

confidence: 99%

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Theoretical Study of Hydrogen Bond Formation in Four Rare Sugars: Gulose, Allose, Altrose, and Talose

Kotena¹,

Razi²,

Ahmadi³

2021

Preprint

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Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including; gulose, allose, altrose and talose are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The DFT, AIM, and, NBO calculations were used to probe the probability of formation of internal H-bonds in four rare sugars. The AIM analysis identified that altrose and talose can form three predominantly intramolecular H-bonds, whereas gulose and allose revealed one and two H-bonds, respectively and these normal intramolecular H-bonds are mostly closed-shell interactions. The theoretical calculated O-H stretching FT-IR vibrational frequencies confirmed that the intramolecular H-bonds shifted toward low frequencies in comparison to the free hydroxyl group, which caused the red-shift. Also, the lowest IR frequency in each sugar was related to the structure with the highest stabilization energy and the most strongest intramolecular H-bonds.

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Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Theoretical Study of Hydrogen Bond Formation in Four Rare Sugars: Gulose, Allose, Altrose, and Talose

Kotena¹,

Razi²,

Ahmadi³

2021

Preprint

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“…Mannose and galactose are important natural products mainly found in plant sources, , and they both are C-2 and C-4 epimers of glucose, respectively, where the OH group is axially positioned at C-2 in the former and at C-4 in the latter. From density functional theory calculations, the intramolecular HBs of these epimerically related glycolipids define conventional HBs which were reported to be more stable than the nonconventional ones. , α-Man-OC 8 , with two conventional HBs, is more stable and has a higher T C value than α-Glc-OC 8 . On the other hand, the galactoside with an axial OH on C-4 has only one conventional intramolecular HB and subsequently has the smallest T C value .…”

Section: Resultsmentioning

confidence: 99%

“…It would seem that despite the many apparent OH sites in the sugar headgroup available for water molecules in the lyotropic state to bond with, at most only two water molecules are actually observed to bind to the headgroup, the α-/β-anomers. The understanding for this rather surprising situation could be found in the computational computer simulation work conducted on these systems with and without water. ,, There is strong hydrogen bonding between neighboring headgroups within the layer (intralayer hydrogen bonding) which contribute greatly toward the stability of the layers in these systems by holding the assembly together. There is also hydrogen bonding across the bilayer (interlayer hydrogen bonding) which comes into play when the layers interact with water in the lyotropic systems.…”

Section: Resultsmentioning

confidence: 99%

Probing n-Octyl α-d-Glycosides Using Deuterated Water in the Lyotropic Phase by Deuterium NMR

et al. 2021

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The lyotropic phase behavior of four common and easily accessible glycosides, n-octyl α-D-glycosides, namely, α-Glc-OC 8 , α-Man-OC 8 , α-Gal-OC 8 , and α-Xyl-OC 8 , was investigated. The presence of normal hexagonal (H I ), bicontinuous cubic (V I ), and lamellar (L α ) phases in α-Glc-OC 8 and α-Man-OC 8 including their phase diagrams in water reported previously was verified by deuterium nuclear magnetic resonance ( 2 H NMR), via monitoring the D 2 O spectra. Additionally, the partial binary phase diagrams and the liquid crystal structures formed by α-Gal-OC 8 and α-Xyl-OC 8 in D 2 O were constructed and confirmed using small-and wide-angle X-ray scattering and 2 H NMR. The average number of bound water molecules (n b ) per headgroup in the L α phase was determined by the systematic measurement of the quadrupolar splitting of D 2 O over a wide range of molar ratio values (glycoside/ D 2 O), especially at high glucoside composition. The number of bound water molecules bound to the headgroup was found to be around 1.5−2.0 for glucoside, mannoside, and galactoside, all of which possesses four OH groups. In the case of xyloside, which has only three OH groups, the bound water content is ∼2.0. Our findings confirmed that the bound water content of all n-octyl α-Dglycosides studied is lower compared to the number of possible hydrogen bonding sites possibly due to the fact that most of the OH groups are involved in intralayer interaction that holds the lipid assembly together.

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“…high ellipticity value signifies unstable bonds. 74 The ellipticity of the carbapenem-LdtMt2 Table 3. The other carbapenem-LdtMt2 complexes also exhibited the strongest stabilization energies in HB1 interactions.…”

Section: Qtaim Analysismentioning

confidence: 99%

Molecular insight on the non-covalent interactions between carbapenems and l,d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

Ntombela

Fakhar

Ibeji

et al. 2018

J Comput Aided Mol Des

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Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. L,D-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both D,D- and L,D-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit D,D-transpeptidases, while L,D-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of Ldt complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of Ldt (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards Ldt. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of Ldt. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and Ldt were also assessed. To further examine the nature of intermolecular interactions for carbapenem-Ldt complexes, AIM and NBO analysis were performed for the QM region (carbapenems and the active residues of Ldt) of the complexes. These analyses revealed that the hydrogen bond interactions and charge transfer from the bonding to anti-bonding orbitals between catalytic residues of the enzyme and selected ligands enhances the binding and stability of carbapenem-Ldt complexes. The two-layered ONIOM (B3LYP/6-31+G(d): Amber) model was used to evaluate the efficacy of FDA approved carbapenems antibiotics towards Ldt.

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AIM and NBO analyses on hydrogen bonds formation in sugar-based surfactants (α/β-d-mannose and n-octyl-α/β-d-mannopyranoside): a density functional theory study

Cited by 21 publications

References 50 publications

Theoretical Study of Hydrogen Bond Formation in Four Rare Sugars: Gulose, Allose, Altrose, and Talose

Theoretical Study of Hydrogen Bond Formation in Four Rare Sugars: Gulose, Allose, Altrose, and Talose

Probing n-Octyl α-d-Glycosides Using Deuterated Water in the Lyotropic Phase by Deuterium NMR

Molecular insight on the non-covalent interactions between carbapenems and l,d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study

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