Density hydrogen bonding

An important step is to validate the structure, that is, to compare features of the structure to features in known protein structures. This includes localized fit to density, hydrogen bonding patterns, divergence from standard geometry, and much more [12]. Such calculations can highlight where the model requires further improvement. 

S Molecular structure Environment (electron density, hydrogen bonding, solvent effect, hydration etc.)... 

Keywords Bond path Bond critical point Laplacian of the electron density Hydrogen bond Halogen bond Pnicogen bond Lewis acid-Lewis base interaction Quantum Theory of Atoms in Molecules (QTAIM) Natural Bond Orbitals (NBO) method o-hole concept Electrostatic potential... 

F, St-Amant A, I Papai and D R Salahub 1992. Gaussian Density Functional Calculations on Hydrogen-Bonded Systems, journal of the American Chemical Society 114 4391-4400. ter J C1974. Quantum Theory of Molecules and Solids Volume 4 The Self-Consistent Field for Molecules and Solids. New York, McGraw-Hill. 

The crystal stmcture of PPT is pseudo-orthorhombic (essentially monoclinic) with a = 0.785/nm b = 0.515/nm c (fiber axis) = 1.28/nm and d = 90°. The molecules are arranged in parallel hydrogen-bonded sheets. There are two chains in a unit cell and the theoretical crystal density is 1.48 g/cm. The observed fiber density is 1.45 g/cm. An interesting property of the dry jet-wet spun fibers is the lateral crystalline order. Based on electron microscopy studies of peeled sections of Kevlar-49, the supramolecular stmcture consists of radially oriented crystaUites. The fiber contains a pleated stmcture along the fiber axis, with a periodicity of 500—600 nm. 

Upon melting, ice loses its open structure with the "melting" of some fraction of the hydrogen bonds, and so the volume of the Hquid water decreases, reaching a minimum at 4°C above this temperature thermal expansion dominates the density. 

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