Hydrogen Bonding: A Theoretical Perspective (Topics in Physical Chemistry)

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We applied the statistical potentials to a larger set of protein-protein complexes. The x-ray and NMR structures of protein-protein complexes with a more flexible threshold of resolution were selected. Metal ions and water molecules were excluded in all analysis.

For each protein complex, the contributions of different interaction types to the total binding energy were calculated as shown in Equation 4 , Equation 4 where z represents a certain type of pair interaction see Table I. Comparisons of energy minimization calculations with and without inclusion of the CH…O hydrogen bonding interaction energies.

A Short History of the Hydrogen Bond

The crystal structures of the protein complexes served as the starting point. In the first one, cycles of the conjugate gradient minimizer CONJ were used until the energy convergence; no atoms were fixed; and the van der Waals and electrostatic interactions were calculated as the non-bonded interactions of atom pairs during the minimization process. In all minimization calculations, the dielectric constant was simply set at 80 to simulate the water medium.

Hydrogen–Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals

The crystal structure was used as the reference structure for the purpose of comparisons. Based on the definition of the five atom types, the distance-dependent potentials were extracted from the training set. In all figures, the symbols are merely connected by smooth curves for visualization, and no smoothing procedure was used. To reflect the trends of the potentials in the range, the dashed line is appended. The calculated energies of the three interactions have very different characterizations: the example of conventional hydrogen bonding interactions has a favorable valley in the distance range from 2.

Based on the new definition of five atom types, different interactions at protein interfaces can be classified easily. We have applied the potentials to the set of protein-protein complexes. The mean value of every interaction percentage was then calculated. In Fig. The y axis represents the number of occurrence.

The protein-protein complexes are denoted by Protein Data Bank codes. The distribution is shown in Fig. The Protein Data Bank codes include 2kin , 2gac , 2bqp , 1pya , 1prt , 1lya , 1kvd , 1fi8 , 1dgw , and 1apy. Only main chain atoms are shown with the conventional color codes: red , oxygen; blue , nitrogen; black , carbon; white , hydrogen. The displayed atoms are at the interface between chains A and B of the dimer. The displayed atoms are at the interface between chains A and B of the heterotetrameric structure of human aspartylglucosaminidase. The displayed atoms are at the interface between chains A and B of the complex.

For other details, refer to the legend to Fig.

How resonance assists hydrogen bonding interactions: An energy decomposition analysis

The analyzed interface is between chains K and Z of the multichain proteinase. Their structural features and characterizations are rather esoteric, so no further surveys were possible. Biological interfaces of protein-protein complexes contain many specific interactions, including hydrogen bonding, water bridging interactions, and nonspecific interactions 32 , The occurrence of each atom pair is sufficiently high in all the statistics. Moreover, we omitted the statistics in the distance shells with low atom pair occurrence to reduce the mistakes of insufficient statistics.

We believe that the details of the potentials obtained which is the basis for the comparison of different interactions are meaningful. Here, using our statistical potentials from the training set of real protein-protein complexes, the calculated free energy has a reasonable potential form, which is similar to the quantum calculation of the ideal model. These nonspecific interactions have an even potential close to zero at longer distances and have a rapidly climbing potential at short distances up to 4.

More importantly, they have no obviously favorable valleys at all distances. Moreover, this shape of potential is similar to that of a conventional hydrogen bond, despite the different strength and optimum distance. Our conclusion is supported by the ab initio quantum calculation of Scheiner et al. First, we quantitatively calculated the energy contribution of different types of interactions at protein-protein interfaces, which indicates the role of different forces at protein-protein interfaces.

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Conventional hydrogen bonding and hydrophobic interactions are generally considered to play important roles in protein associations. The largest contribution of hydrophobic interactions indicates that the large number of hydrophobic atom pairs occur at the protein-protein interface because the energy of each hydrophobic atom pair is less than that of the other pair interactions. It is interesting to note that the structural motif of a bifurcated hydrogen bond is found between the adjacent strands at some representative examples of real protein interfaces Fig.

Moreover, the observed geometrical parameters of all the close contacts are very close to those expected for hydrogen bonds.

Hydrogen bonding (Inter & Intra) -IIT JEE Chemistry

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Add to Wishlist. USD Ship This Item — This item is available online through Marketplace sellers. Temporarily Out of Stock Online Please check back later for updated availability. Overview Because of the importance of the hydrogen bond, there have been scores of insights gained about its fundamental nature by quantum chemical computations over the years. About the Author Southern Illinois University. Table of Contents 1.

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