Charged hydrogen bonds

Stronger hydrogen bonds usually involve charged molecules. Several reports on charged hydrogen-bonded systems of biological relevance were studied using the KS formal-... 

It is the sequence and types of amino acids and the way that they are folded that provides protein molecules with specific structure, activity, and function. Ionic charge, hydrogen bonding capability, and hydrophobicity are the major determinants for the resultant three-dimensional structure of protein molecules. The a-chain is twisted, folded, and formed into globular structures, a-helicies, and P-sheets based upon the side-chain amino acid sequence and weak intramolecular interactions such as hydrogen bonding between different parts of the peptide... 

SPECIFICITY in the association of two proteins or a protein and a small molecule results from the requirement that the two interacting molecules must be complementary—complementary in charge, hydrogen bonding, and hydrophobic patches as well as shape. If any of the possible interactions are not satisfied, the strength of the interaction suffers. 

The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical transformations. It is formed in the three-dimensional structure by a collection of different amino acids (active-site residues) that may or may not be adjacent in the primary sequence. The interactions between the active site and the substrate occur via the same forces that stabilize protein structure hydrophobic interactions, electrostatic interactions (charge-charge), hydrogen bonding, and van der Waals interactions. Enzyme active sites do not simply bind substrates they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction. 

The dipolar nature of water causes molecules to mutually attract each other by virtue of the linking of opposite charges (hydrogen bonding). 

Methods based on physicochemical properties of amino acid residues (Lim, 1974) such as volume, exposure, hydrophobicity/hydrophilicity, charge, hydrogen bonding potential, and so on. 

CIRCLES MAY BE positive or negative charges, hydrogen bond donors or acceptors, lipophilicity centres, and so on... 

Kienhofo-, A. Kast, R Hilvert, D. Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor, J. Am. Chem. Soc. 2003, 125, 3206-3207. 

Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and reactivity are com-... 

D and 3D autocorrelation vectors [70] represent intramolecular 2D topologies or 3D distances within particular molecules. An autocorrelation coefficient is a sum over all atom pair properties separated by a predefined number of bonds (2D) or distance (3D), while the entire vector represents a series of coefficients for all topological or Cartesian distances. Atomic properties involve hydrophobicity [71], partial atomic charges, hydrogen bonding potential and others. Again, a PCA is often used to reduce the number of variables. 3D autocorrelation vectors of properties based on distances calculated from 3D molecular surfaces [72] have also been applied to visually assess the diversity of different libraries [73]. 

---