Hydrogen bonds electrostatic potential

Kenny, P.W. (2000) Hydrogen bonding, electrostatic potential, and molecular design. Journal of Chemical Information and Modeling, 49, 1234—1244. 

In biological recognition phenomena, protein-protein interactions are of primary importance. In an attempt to mimic these processes, LaBrenz and Kelly [51] synthesized the peptidic host 64. In this receptor, the dibenzofuran template separates the two peptide units by roughly 10 A and allows for the complexation of a guest peptide (65), as depicted in Fig. 21. The complex first forms a three-stranded, antiparallel /J-sheet that is stabilized by hydrogen bonds, electrostatic interactions, and aromatic-aromatic interactions between the dibenzofuran and the benzamide moieties. This complex can further self associate to form more complex structures. This example shows that structurally defined peptide nanostructures can interfere with biological recognition processes and potentially have therapeutic applications. 

Another AFM-based technique is chemical force microscopy (CFM) (Friedsam et al. 2004 Noy et al. 2003 Ortiz and Hadziioaimou 1999), where the AFM tip is functionalized with specific chemicals of interest, such as proteins or other food biopolymers, and can be used to probe the intermolecular interactions between food components. CFM combines chemical discrimination with the high spatial resolution of AFM by exploiting the forces between chemically derivatized AFM tips and the surface. The key interactions involved in food components include fundamental interactions such as van der Waals force, hydrogen bonding, electrostatic force, and elastic force arising from conformation entropy, and so on. (Dther interactions such as chemical bonding, depletion potential, capillary force, hydration force, hydrophobic/ hydrophobic force and osmotic pressure will also participate to affect the physical properties and phase behaviors of multicomponent food systems. Direct measurements of these inter- and intramolecular forces are of great interest because such forces dominate the behavior of different food systems. 

The relationship between amino acid properties and protein stability revealed that the number of carbon atoms (methyl and methylene groups) that reflects the property hydrophobicity has a strong relationship with protein stability for the mutations in the interior of the protein. Yet, hydrophobic, hydrogen bond, electrostatic, and other polar interactions are important for the stability of mutation at the surface of the protein. The atom pair potentials set up on the basis of chemical nature and connectivity successfully could predict protein stability during amino acid substitution. 

Part of simulation ECEPP/2 vdW + electrostatic, hydrogen bonds, torsional potential e = 2 united-atom + polar hydrogens harmonic force on N, Ca, C, O atoms of terminal residues on x-ray positions... 

Diffusivity (I)) is a temperature-dependent parameter (Equation (2)) that essentially describes the mobility of a penetrating molecule within the stratum corneum. Diffusivity can be affected by a variety of factors, including the physical size of a penetrant and its potential interactions with the stratum corneum (through hydrogen bonding, electrostatic forces, etc.). 

The three-dimensional order of the crystallized solids is expensive in entropy its reason is thus in the maximization of interactions (van der Waals, hydrogen bond, electrostatic, delocalization of the electrons in a metal) between structure elements, considering the geometrical constraints related to the shape of the molecules or the size of the ions. The whole of the sohd thus creates a periodic potential, in particular in space surrounding a stracture element, which at 0 K occupies the position of minimum energy in the perfect solid. 

Knowledge of the spatial dimensions of a molecule is insufficient to imderstand the details of complex molecular interactions. In fact, molecular properties such as electrostatic potential, hydrophilic/lipophilic properties, and hydrogen bonding ability should be taken into account. These properties can be classified as scalar isosurfaces), vector field, and volumetric properties. 

The representation of molecules by molecular surface properties was introduced in Section 2.10. Different properties such as the electrostatic potential, hydrogen bonding potential, or hydrophobicity potential can be mapped to this surface and seiwe for shape analysis [44] or the calculation of surface autocorrelation vectors (refer to Section 8.4.2). 

Examine the electrostatic potential map of H3B THE (borane-tetrahydrofuran complex) on Learning By Modeling How does the electrostatic potential of the hydrogens bonded to boron dif fer from the potential of the hydrogens of the tetrahydrofuran ring" ... 

FIGURE 19 2 Attrac tions between regions of positive (blue) and negative (red) electrostatic potential are responsible for intermo lecular hydrogen bonding between two molecules of acetic acid... 

The exchange repulsion and dispersive attraction com bine in what is referred to as a van der Waals term. Sometimes a potential is added to account for hydrogen bonding explicitly while in other situations this is expected to fall out of ordinary electrostatic interactions. 

The orientational structure of water near a metal surface has obvious consequences for the electrostatic potential across an interface, since any orientational anisotropy creates an electric field that interacts with the metal electrons. Hydrogen bonds are formed mainly within the adsorbate layer but also between the adsorbate and the second layer. Fig. 3 already shows quite clearly that the requirements of hydrogen bond maximization and minimization of interfacial dipoles lead to preferentially planar orientations. On the metal surface, this behavior is modified because of the anisotropy of the water/metal interactions which favors adsorption with the oxygen end towards the metal phase. 

FIGURE 2.4 Valence bond picture of bonding in H2 as illustrated by electrostatic potential maps. The Is orbitals of two hydrogen atoms overlap to give an orbital that contains both electrons of an H2 molecule. 

The S—H bond is less polai than the O—H bond, as is cleaiTy seen in the electrostatic potential maps of Figure 15.7. The decreased polarity of the S—H bond, especially the decreased positive character of the proton, causes hydrogen bonding to be absent in thiols. Thus, methanethiol (CH3SH) is a gas at room temperature (bp 6°C), whereas methanol (CH3OH) is a liquid (bp 65°C). 

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