Modeling hydroxyl and water H atoms

Abstract

The coordinates of hydroxyl (alcohol, phenol, etc.) and water H atoms can be easily calculated, within acceptable approximation, by combined geometric and force-®eld calculations on the basis of hydrogen-bonding interactions. To perform this kind of calculation the computer program HYDROGEN has been developed.

Structures and trends of neutral MXxsolvent4−xtetrahedra and anionic [MX4]2−tetrahalometallates of zinc(ii), cadmium(ii) and mercury(ii) with benzopyridine- and benzopyrazine-type N-donor ligands or cations

“…The centroid-to-centroid distance alternates between the BB acridinium pairs comprising the monolayer. The smallest centroid-to-centroid distance of 3.8353 (19) Å is displayed between cations in the BB-units which are hydrogen-bonded to the same tetrahalometallate unit. The inter-unit BB distances are longer, having a value of 5.635(2) Å.…”

“…The hydrogen atoms of the aqua ligand coordinated to the Zn 2+ cation, the isolated water molecule as well as the hydroxyl functionality were generated with the program CALC-OH by Nardelli. 19 The local tetrahedral Zn 2+ coordination sphere is coordinated by three bromido ligands and one water molecule, with ∠(XZnX)s and Zn-X bond distances ranging between 102.50(3)° and 116.894(9)° and 2.3666(2) Å and 2.4012(2) Å, respectively, as collated in Table 6. The rather large variation in tetrahedral bond angles of the inorganic Zn 2+ moiety is ascribed to the difference in steric and electronic requirements of the coordinated ligands, where the angles involving the O(1) atom are smaller.…”

Diaquabis(2,2’-dipyridylamine)M(II) Terephthalate Dihydrates, M(II) = Ni, Co: Synthesis, Crystal Structures, Thermal and Magnetic Properties

“…Water H atoms for O8A and O8B were also found in ΔF maps and refined with O-H distances restrained to 0.85 Å. Positions of water H atoms for O7 were calculated using the program HYDROGEN 26 and added to the structural model before the final cycle of refinement with fixed coordinates and with U iso (H) = 1.5U eq (O). For water H34 atom in 1 and H33 atom in 2 were not possible to identify suitable hydrogen bond acceptors.…”

Synthesis, crystal structure and magnetism of [Cu(cyclam)Ni(NCS)4(H2O)2]n

“…Hydrogen atoms in the cyclam ligand were placed in the calculated positions and allowed to ride on the parent atoms with isotropic thermal parameters tied with the parent atoms (U(H) = 1.2U(CH2), U(H) = 1.2U(N)). Water hydrogen atoms in 1 were located with the program CALC-OH (Nardelli 1999) and their isotropic thermal parameters were tied with the parent oxygen atoms (U(H) = 1.5U(O)). The structural figures were drawn using the Diamond software (Brandenburg 2008).…”