Bifurcated hydrogen bond in rare sugar by computational study

Kotena, Zahrabatoul Mosapour; Mohamad, Saharuddin Bin

doi:10.1080/15421406.2017.1283920

Cited by 6 publications

(6 citation statements)

References 33 publications

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“…Also, vibration frequency of the HO 4 in β-idose sugar at 3631 cm −1 was shifted to 3554 cm −1 as well as it for HO 1 at 3653 cm −1 was shifted to 3594 cm −1. [31] These results were in good agreement with previous results from Desiraju et al [37] The strength of intermolecular interactions is reflected in melting points of the crystals; more favorable interactions give rise to higher melting point. Also, H-…”

supporting

confidence: 91%

“…The existence of bifurcated H-bond in rare sugar and also C-H … O bonds in guanosine was investigated using computational calculations. [30,31] The strength of intermolecular interactions is reflected in melting points of the crystals. The strength of these H-bonds allows for strong resistance to thermal distortion of the structure at room temperature, which is about a magnitude higher than kT.…”

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confidence: 99%

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Influence of H‐bonds on acidity of deoxy‐hexose sugars

Kotena

Fattahi

2020

J of Physical Organic Chem

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The unusual monosaccharaides such as deoxy‐hexose sugars, including methyl‐pentose and aldo‐pentose, are promising and important sugars in life science. However, little research on H‐bond interactions in these systems has been reported. The aldo‐pentose has a proton instead of the CH2OH group on C5; conversely, methyl‐pentose has a CH3 group on C5. The aim of the present study is to investigate the role and nature of intramolecular H‐bonds on acidity of CH3‐pentose sugars (L‐fucose and L‐rhamnose) and aldo‐pentose sugars (D‐xylose, L‐lyxose, D‐ribose, and L‐arabinose) using B3LYP/6‐311++G (d, p) level. The calculated acidity values (ΔHacid) of these Dexoy‐hexose were found to be from 343 to 369 kcal.mol−1, indicating they are stronger acid than ethanol and 2‐propanol with the acidity values of 378.3 and 375.1 kcal.mol−1, respectively. This is related to the stabilization of the conjugate bases of these sugar through intramolecular H‐bonds, which were analyzed in this study using atoms in molecules (AIM) and natural bonding orbital (NBO) methods. AIM and NBO analyses indicate the presence of one bifurcated intramolecular H‐bond in the conjugate bases of L‐lyxose and L‐arabinose and two bifurcated H‐bonds in conjugate base of D‐ribose, whereas the conjugate bases of L‐fucose, L‐rhamnose, and D‐xylose present one normal intramolecular H‐bond. According to the topological parameters and charge transfer data, existence of normal and bifurcated intramolecular H‐bonds could greatly increase acidity of deoxy‐hexose sugars. The H‐bond strength in the conjugate bases of aldo‐pentose sugars is higher than that in the conjugate bases of methyl‐pentose sugars including CH3 group on C5, making aldo‐pentose sugars stronger acid than methyl‐pentose sugars.

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confidence: 91%

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confidence: 99%

Influence of H‐bonds on acidity of deoxy‐hexose sugars

Kotena

Fattahi

2020

J of Physical Organic Chem

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“…(kcal.mol -1 ). These values are in good agreement with our previous results for glucose and idose sugars [25].…”

Section: Resultssupporting

confidence: 93%

“…It is clear that the O2…HO4-O4 bond in talose with the energy of EHB=11.73 kcal.mol -1 has the lowest frequency of 3360 cm -1 (see Table 2,4) which is comparable with the previous resul of Desiraju et al [55] and is in excellent agreement with our previous study for glucose and idose sugars [25]. The change of the X-H bond length is related to the charge transfer.…”

Section: Infrared Spectroscopysupporting

confidence: 91%

“…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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Computational insight into networking H‐bonds in open and cyclic forms of glucose

Kotena

Fattahi

2021

J of Physical Organic Chem

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We have studied the intramolecular H‐bonds existing in cyclic and open forms of glucose using B3LYP/6‐311++G(d,p) level, AIM, and NBO methods. The theoretical results indicated that based on acidity values, (ΔHacid), glucose in the open form is more acidic than cyclic form. The acidity values for open and cyclic glucose (332 and 338 kcal/mol) exhibit significantly lower values (i.e., stronger acid) than the reported acidity values for α‐/ß‐anomers of D‐glucopyranose and simple alcohols. Because their conjugate bases are more stabilized through trifurcated and bifurcated intramolecular H‐bonds. AIM analysis showed normal H‐bonds in the conjugate bases of open glucose (O‐Glc), bifurcated, and normal H‐bonds in the conjugate base of cyclic glucose. In the conjugate base of glucose, the O–H···O bonds are categorized as mostly electrostatic and strong, whereas multiple interactions including C–H···O, C–H···H–C (dihydrogen bonding), C–H···C–H, and C=O···H are categorized as weak H‐bonds. The NBO results confirm that the O–H···O intramolecular H‐bonds should be the strongest among all H‐bonds existing within glucose.

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Bifurcated hydrogen bond in rare sugar by computational study

Cited by 6 publications

References 33 publications

Influence of H‐bonds on acidity of deoxy‐hexose sugars

Influence of H‐bonds on acidity of deoxy‐hexose sugars

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

Computational insight into networking H‐bonds in open and cyclic forms of glucose

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