Polar hydrogens

Hess H F, Kochanski G P, Doyle J M, Greytak T J, and Kleppner D 1986 Spin-polarized hydrogen maser Phys.Rev. A 34 1602-4... 

Brunger, A. T., Karplus, M. Polar hydrogen positions in proteins Empirical energy placement and neutron diffraction comparison. Proteins Struct. Func. Genet. 4 (1988) 148-156. 

Organic acids are characterized by the presence of a positively polarized hydrogen atom (blue in electrostatic potential maps) and are of two main kinds those acids such as methanol and acetic acid that contain a hydrogen atom bonded to an electronegative oxygen atom (O-H) and those such as acetone (Section 2.5) that contain a hydrogen atom bonded to a carbon atom next to a C=0 bond (Q=C-C-H). 

The model system for these calculations is carboxy-myoglobin starting from the X-ray coordinates (19). The polar hydrogen parameter set PARAM19 (20) was used for all calculations. In this representation there are 1532 atoms. It is not expected that the results of this work would change substantially if a different protein or if a different parameter set were used. 

The examples in the previous section give a comprehensive overview of application areas where molecular rotors have become important fluorescent reporters. Current work on the further development of molecular rotors can broadly be divided into three areas photophysical description, structural modification, and application development. Although a number of theories exist that describe the interaction between a TICT fluorophore and its environment, the detailed mechanism of interaction that includes effects such as polarity, hydrogen bonding, or size and geometry of a hydrophobic pocket are not fully understood. Molecular simulations have recently added considerable knowledge, particularly with... 

A Water is a polar, hydrogen bonding compound. It should mix well with other polar,... 

In non-polar solvents TIN is believed to exist mainly in an intramolecularly hydrogen-bonded form which is non-fluorescent at room temperature (9.12.16). Fluorescence emission (Xmax = 630 nm) from the proton-transferred form of the molecule is observed in low temperature, non-polar glasses (9.10.12.16) and in the crystalline form (15.). In polar, hydrogen-bonding solvents a shorter wavelength fluorescence (Xmax = 400 nm) is observed which is attributed to those molecules which are intermolecularly hydrogen bonded to the solvent and which do not undergo ESIPT (10-12.14.16-19). 

Figure 8.1 Details of the intermolecular interactions from a minimized complex between norepinephrine and a rhodopsin-based model of the aib-AR are shown. As for the amino acid residues (D3.32, S5.42 and F6.51), only the polar hydrogen atoms are shown. Norepinephrine is colored by atom type, whereas the amino acid residues are colored according to their helix location.

Crivori et al. [12] Molecular size, shape, polarity, hydrogen-bonding, and other Volsurf-generated variables... 

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