How Good Is A Point Charge As A Model For A Hydrogen Bonding Atom?

Clipboard, Search History, and several other advanced features are temporarily unavailable. Skip to main page content

The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation Search: Search Advanced Clipboard Save Email Send to

• Clipboard
• My Bibliography
• Collections
• Citation manager

Display options Display options Format Abstract PubMed PMID

Save citation to file

Format: Summary (text) PubMed PMID Abstract (text) CSV Create file Cancel

Email citation

Email address has not been verified. Go to My NCBI account settings to confirm your email and then refresh this page. To: Subject: Body: Format: Summary Summary (text) Abstract Abstract (text) MeSH and other data Send email Cancel

Add to Collections

• Create a new collection
• Add to an existing collection

Name your collection: Name must be less than 100 characters Choose a collection: Unable to load your collection due to an error Please try again Add Cancel

Add to My Bibliography

• My Bibliography

Unable to load your delegates due to an error Please try again Add Cancel

Your saved search

Name of saved search: Search terms: Test search terms Would you like email updates of new search results? Saved Search Alert Radio Buttons

• Yes
• No

Email: (change) Frequency: Monthly Weekly Daily Which day? The first Sunday The first Monday The first Tuesday The first Wednesday The first Thursday The first Friday The first Saturday The first day The first weekday Which day? Sunday Monday Tuesday Wednesday Thursday Friday Saturday Report format: Summary Summary (text) Abstract Abstract (text) PubMed Send at most: 1 item 5 items 10 items 20 items 50 items 100 items 200 items Send even when there aren't any new results Optional text in email: Save Cancel

Create a file for external citation management software

Create file Cancel

Your RSS Feed

Name of RSS Feed: Number of items displayed: 5 10 15 20 50 100 Create RSS Cancel RSS Link Copy

Actions

CiteCollectionsAdd to Collections

• Create a new collection
• Add to an existing collection

Name your collection: Name must be less than 100 characters Choose a collection: Unable to load your collection due to an errorPlease try again Add Cancel PermalinkPermalinkCopyDisplay options Display options Format AbstractPubMedPMID

Page navigation

• Title & authors
• Abstract
• References
• Publication types
• MeSH terms
• Substances
• LinkOut - more resources

Title & authors Abstract References Publication types MeSH terms Substances LinkOut - more resources CiteDisplay options Display options Format AbstractPubMedPMID

Abstract

In order to design new ligands for protein-binding sites of unknown structure, it would be useful to predict the likely sites of hydrogen bonding of an unknown protein fragment to a known molecule. The positions of maxima and minima in the electrostatic potential at appropriate distances from the van der Waals surface were calculated for various small molecules, nucleic acid bases, peptide units and amino acid side chains containing groups which can form the biologically important N-H...O=C and N-H...N hydrogen bonds. Their ability to predict the positions of H and O/N in hydrogen bonded complexes, as predicted by optimising the electrostatic interactions of pairs of such molecules constrained by the molecular shapes, was assessed. It is shown that extrema in the electrostatic potential around the isolated molecules give worthwhile predictions for the locations of hydrogen binding partners. For molecules bound by a single N-H...O=C hydrogen bond, the electrostatic maximum associated with the H is usually less than 1 A from an acceptor atom, while a C=O electrostatic minimum is generally less than 1.5 A from the hydrogen bond proton. However, a significant number of hydrogen bonds form to the opposite lone pair from the electrostatic minimum, in which case the separation is up to 3.3 A. This reflects the broad electrostatic potential well around a carbonyl oxygen between the lone pair directions. The model predicts when neighbouring atoms drastically change the hydrogen bonding characteristics of an N-H or C=O group. Although the geometries of hydrogen bonded complexes are influenced by the other van der Waals contacts between the molecules, particularly multiple hydrogen bonds, these influences are constant when considering hydrogen bonding to a specific uncharacterised binding site. Hence, the consideration of sterically accessible electrostatic extrema will be useful in the design of new ligands.

PubMed Disclaimer

References

1. 1. J Comput Aided Mol Des. 1995 Feb;9(1):33-43 - PubMed
2. 1. Proc Natl Acad Sci U S A. 1928 Apr;14(4):359-62 - PubMed
3. 1. Protein Eng. 1995 Feb;8(2):109-16 - PubMed
4. 1. J Mol Biol. 1994 Jun 3;239(2):315-31 - PubMed
5. 1. J Mol Biol. 1990 Oct 5;215(3):457-71 - PubMed

Show all 9 references

Publication types

• Research Support, Non-U.S. Gov't Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search

MeSH terms

• Amides / chemistry Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Electrochemistry Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Hydrogen Bonding* Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Models, Chemical Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Models, Molecular Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Molecular Structure Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Oxygen / chemistry Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Static Electricity Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search

Substances

• Amides Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search
• Oxygen Actions
  • Search in PubMed
  • Search in MeSH
  • Add to Search

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.

[x] Cite Copy Download .nbib .nbib Format: AMA APA MLA NLM Send To

• Clipboard
• Email
• Save
• My Bibliography
• Collections
• Citation Manager

[x]

NCBI Literature Resources

MeSH PMC Bookshelf Disclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.