A quantum-topological analysis of noncovalent interactions in secondary polyalanine structures

2016

Molecules

Abstract:The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.

Section: Resultsmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR

2016

Molecules

“…Additional confirmation came from Guo et al in 2009 [172]. In that same year, the C α H··O HB was computed to be stronger than NH··O in dipeptide and tripeptide models of the parallel β-sheet geometry of Ala [173]. In fact, CH··O HBs have shown some propensity to stabilize the α-helix as well [173][174][175].…”

Section: Longer Chainsmentioning

confidence: 67%

“…In that same year, the C α H··O HB was computed to be stronger than NH··O in dipeptide and tripeptide models of the parallel β-sheet geometry of Ala [173]. In fact, CH··O HBs have shown some propensity to stabilize the α-helix as well [173][174][175]. There is also experimental support for the importance of CH··O HBs is β-sheets [176]; the β-pleated sheet structure for β-sulfidocarbonyls [177] contains not only CH··O, but also CH··S HBs.…”

Section: Longer Chainsmentioning

confidence: 99%

The CH‥O H-Bond as a Determining Factor in Molecular Structure

Challenges and Advances in Computational Chemistry and Physics

2015

The factors that affect the strength of CH··O hydrogen bonds (HBs) are enumerated, along with the source of their stability, and the structural and spectroscopic features that signal their presence. Their influence upon a number of chemical and biological processes is discussed. Within the context of proteins, the C α H group of protein residues can engage in CH··O HBs, as can the CH groups of a number of amino acid side chains including aromatic residues. CH··O HBs have the potential to make a major contribution to protein folding, particularly in an aqueous environment. These unconventional HBs may play as important a role in the formation of protein β-sheet structures as do NH··O HBs. The strength of CH··O HBs is magnified several-fold by the presence of positive charge on the proton donor. The implications of these principles are discussed for a number of specific biological and chemical problems, which include the catalytic mechanisms of methyltransferases and serine proteases, and the structural properties of fluoroamides.

“…But a glance at the actual structure in Fig 5 shows that CH groups might also serve this same function, a possibility which had heretofore been completely ignored. Quantum calculations addressed this issue specifically [56] and found quite the opposite: The interstrand CH··O HBs were competitive in strength with NH··O, and serve as an integral component in the stability of the β-sheet, a finding that has since been confirmed by others [57][58][59][60][61][62].…”

Section: Nominally Weak Hbsmentioning

confidence: 95%

Forty years of progress in the study of the hydrogen bond

2019

Struct Chem

The author looks back at developments over the last few decades concerning the H-bond. The list of atoms involved as proton donor and acceptor has broadened dramatically, including most electronegative atoms and even metals. The factors that control the transfer of the proton across the H-bond have been elucidated and show the importance of even minor changes in its geometry. Small stretches can shut down the transfer entirely and certain bends can force a proton to transfer against a pK gradient. Along with recognition that a CHꞏꞏO interaction can represent a true H-bond, and one with strength comparable to more traditional H-bonds, has come an understanding of its contributions to protein structure and function. The replacement of the bridging H by any of a litany of electronegative atoms leads to similarly strong interactions, with many features virtually indistinguishable from a true H-bond. These noncovalent interactions are typically referred to as halogen, chalcogen, pnicogen, and tetrel bonds, depending upon the identity of the substitute bridging atom.