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Protein Folding01:22

Protein Folding

Overview
Polyprotic Acids03:38

Polyprotic Acids

Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:
Globular and Fibrous Proteins02:21

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Basicity of Aliphatic Amines01:21

Basicity of Aliphatic Amines

Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates higher...
Basicity of Heterocyclic Aromatic Amines01:25

Basicity of Heterocyclic Aromatic Amines

Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).

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Related Experiment Video

Updated: Jun 23, 2026

Determination of the Gas-phase Acidities of Oligopeptides
11:00

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Polyglycine conformational analysis: calculated vs experimental gas-phase basicities and proton affinities.

Alice Chung-Phillips1

  • 1Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA. philliac@muohio.edu

The Journal of Physical Chemistry. A
|July 13, 2006
PubMed
Summary

Density functional theory calculations reveal that intramolecular hydrogen bonding drives polyglycine stability and determines preferred protonation sites. This research clarifies experimental gas-phase basicity and proton affinity measurements for peptides.

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Area of Science:

  • Computational Chemistry
  • Peptide Structure and Stability
  • Quantum Chemistry

Background:

  • Polyglycines (Gly(n)) are fundamental peptides whose conformational behavior and protonation energetics are crucial for understanding peptide chemistry.
  • Previous studies lacked detailed structural insights into the various conformations and protonation states of small polyglycines.
  • Experimental methods for determining gas-phase basicity (GB) and proton affinity (PA) can yield differing results, necessitating theoretical validation.

Purpose of the Study:

  • To computationally determine the stable structures of neutral and protonated polyglycines (Gly(n) and Gly(n)H(+), n=1-6) near global energy minima.
  • To elucidate the driving forces behind polyglycine conformational stability and identify preferred protonation sites.
  • To calculate ab initio gas-phase basicity (GB) and proton affinity (PA) values and compare them with experimental data.

Main Methods:

  • Density functional theory (DFT) calculations using B3LYP functional with 6-311++G** and 6-31+G** basis sets.
  • Conformational analysis of 93 structures to identify stable neutral and protonated polyglycine geometries.
  • Calculation of electronic energies and thermal corrections to Gibbs free energy and enthalpy for GB and PA determination.

Main Results:

  • Polyglycine structures range from open chains to multiple rings, with intramolecular hydrogen bonding identified as the key factor for stability.
  • Preferred protonation sites are the terminal nitrogen atom and the adjacent amide oxygen.
  • Calculated GB and PA values show good agreement with kinetic method (KM) experimental data, while reaction bracketing (RB) results are systematically lower.

Conclusions:

  • Intramolecular hydrogen bonding dictates polyglycine conformation and protonation preferences.
  • DFT calculations provide reliable ab initio GB and PA values, supporting the interpretation of experimental data.
  • The kinetic method (KM) primarily samples high-population, thermally equilibrated structures, whereas reaction bracketing (RB) favors sterically accessible sites.