Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy

Biswal, Himansu S.

doi:10.1007/978-3-319-14163-3_2

Cited by 48 publications

(45 citation statements)

References 173 publications

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“…Although its earliest conception considered only highly electronegative atoms like O, F, and N as donor and acceptors [1][2][3] , this picture has broadened considerably over recent years [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . For example, despite some early resistance to the idea, the S atom is now recognized as a legitimate proton donor atom [18][19][20][21][22][23] . Also among those atoms which are now known to serve as proton donor is C, despite its nominally low electronegativity [24][25][26][27][28][29][30][31][32][33][34] .…”

Section: Introductionmentioning

confidence: 98%

Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds

Scheiner

2015

J. Phys. Chem. A

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The ability of neutral and charged S-compounds to form different sorts of noncovalent bonds is examined by ab initio calculations. Neutrals are represented by CH3SH and fluoro-substituted FSCH3; cations are (CH3)3S(+), CH3SH2(+), and FHSCH3(+). Each is paired with N-methylacetamide (NMA) whose O atom serves as a common electron donor. Charged species engage in much stronger noncovalent bonds than do the neutral molecules, by as much as an order of magnitude. The strongest noncovalent bond for any system is a O···SF chalcogen bond wherein the O lies directly opposite a S-F covalent bond, amounting to as much as 39 kcal/mol. Second in binding energy is the SH···O H-bond, which can be as large as 34 kcal/mol. Somewhat weaker is the O···SC chalcogen bond, followed by the CH···O H-bond and finally the O···C tetrel bond, which has the appearance of a trifurcated H-bond. Any CH group that participates in a CH···O H-bond shifts its NMR signal downfield by an amount roughly proportional to the strength of the H-bond. This situation is clearly distinguishable from that in a O···S chalcogen or SH···O H-bond wherein the methyl protons are shifted upfield.

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Section: Introductionmentioning

confidence: 98%

Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds

Scheiner

2015

J. Phys. Chem. A

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“…Interestingly, hydrogen bonds involving sulfur atoms were also evident in the structures of both the intermediate and product ions. A combination of laser spectroscopy and quantum mechanical calculations has suggested the sulfur centric hydrogen bonds are as strong as conventional hydrogen bonds . Table provides the energy differences between the intermediate and product ions of the anticipated fragmentation pathways of Scheme .…”

Section: Resultsmentioning

confidence: 99%

Electron transfer dissociation of synthetic and natural peptides containing lanthionine/methyllanthionine bridges

Dolle

Jagadeesh

Bhaumik

et al. 2018

Rapid Comm Mass Spectrometry

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ETD successfully cleaves the lanthionine/methyllanthionine bridges of synthetic and natural lantipeptides. Diagnostic fragment ions of ETD cleavage of lanthionine/methyllanthionine bridges are the N-terminal cysteine/methylcysteine thiyl radical and C-terminal dehydroalanine. Detection of the cysteine/methylcysteine thiyl radical and dehydroalanine in combined ETD-CID-MS may be used for the rapid identification of lantipeptide natural products.

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“…The complex structures were solved by the molecular replacement method with Phaser (McCoy et al, 2007) using the PNA structure as a search model (PDB code 2PEL, Banerjee et al, 1996). The structures were refined with Buster (Bricogne et al, 2011) and manually built with Coot (Emsley et al, 2010). Ligand coordinates were generated with HyperChem TM Professional 7.51, Hypercube Inc. (USA).…”

Section: Structure Resolution Model Building and Refinementmentioning

confidence: 99%

“…4b and Table 3). Additionally, it should be noted that sulfur hydrogen bonds are usually weaker than O-mediated interactions (Biswal, 2015).…”

Section: Binding Of the S-linked Glycoclusters Beyond The Galactose Mmentioning

confidence: 99%

Crystal structures of peanut lectin in the presence of synthetic β-N- and β-S-galactosides disclose evidences for the recognition of different glycomimetic ligands

Cagnoni

Primo

Klinke

et al. 2020

Preprint

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ORCID:https://orcid.org/0000-0002-5448-5483. # equally contributed to this work Keywords Carbohydrate−protein interactions, peanut agglutinin, glycoclusters, multivalent ligands, lectin structure, X-ray crystallography, isothermal titration calorimetry, molecular dynamics. AbstractCarbohydrate−lectin interactions are involved in important cellular recognition processes, including viral and bacterial infections, inflammation, and tumor metastasis. Hence, the structural studies of lectin-synthetic glycan complexes are essential for understanding the lectin recognition processes and the further design of promising chemotherapeutics that interfere with sugar-lectin interactions.Plant lectins are excellent models for the study of the molecular recognition process. Among them, peanut lectin (PNA) is highly relevant in the glycobiology field, because of its specificity for β-galactosides, showing high affinity towards the Thomsen-Friedenreich (TF) antigen, a well-known tumor-associated carbohydrate antigen. Given this specificity, PNA is one of the most frequently used molecular probes for the recognition of tumor cell-surface O-glycans. Thus, it has been extensively used in glycobiology for inhibition studies with a variety of βgalactoside and β-lactoside ligands. Herein, crystal structures of PNA are reported in complex with six novel synthetic hydrolytically stable β-N-and β-S-galactosides. These complexes, along with computational simulations, disclosed key molecular binding interactions of the different sugars to PNA at the atomic level, revealing the role of specific water molecules in the protein-ligand recognition. Furthermore, binding affinity studies measured by isothermal titration calorimetry showed dissociation constant values in the micromolar range, as well as a positive glycoside cluster effect in terms of affinity in the case of the divalent compounds. Taken together, this work provides qualitative structural rationale for the upcoming synthesis of optimized glycoclusters, designed for the study of lectinmediated biological processes. The understanding of the recognition of β-N-and β-Sgalactosides with PNA represents a benchmark in protein-carbohydrate interactions since they are novel synthetic ligands not belonging to the family of O-linked glycosides.

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Hydrogen Bonds Involving Sulfur: New Insights from ab Initio Calculations and Gas Phase Laser Spectroscopy

Cited by 48 publications

References 173 publications

Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds

Comparison of CH···O, SH···O, Chalcogen, and Tetrel Bonds Formed by Neutral and Cationic Sulfur-Containing Compounds

Electron transfer dissociation of synthetic and natural peptides containing lanthionine/methyllanthionine bridges

Crystal structures of peanut lectin in the presence of synthetic β-N- and β-S-galactosides disclose evidences for the recognition of different glycomimetic ligands

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