Atom deviations from planes

Figure 8.66 Projection along c showing the nearly planar guanidinium-carbonate (1 1) rosette network II at z = 1/2 in the crystal structure of 35. The atom types are differentiated by size and different grey scales, and N-H- O hydrogen bonds are represented by dotted lines. The layer is composed of independent carbonate ions [labeled by their central carbon atoms C(1) and C(3)[ andguanidinium ions [C(2) and C(4)[ in equal numbers. Note Mean atomic deviation from plane of one rosette = 0.36 A, and mean atomic deviation from plane of ribbon fragment [C(1), C(2), C(3), C(4)[ = 0.44 A]. Symmetry transformation a (1 — x, I + y, 1 - z)...

Figure 15.6 Various representations of the molecular structure of ryclc-Si2 showing S atoms in three parallel planes. I he idealized point group symmetry is and the mean dihedral angle is 86.1 5.5 . In the crystal the symmetry is slightly distorted to C21, and the central group of 6 S atoms deviate from eoplanarily by 14pm.

The 6-6-5 membered ring of the IQ system assumes a planar conformation All carbon or nitrogen atoms deviate from the plane, but no more than 0.028 A, from the... 

JOM(400)149 96BSCF33]. The complex 164 is the first known t] -phospholyl species. The tungsten atoms have a coordination number of 9, and the carbon atoms of the phospholyl ring are coplanar. The phosphorus atom deviates from the plane of carbon atoms by 0.015 nm. The basic difference between the Ti -cyclopentadienyl and ri -phospholyl complexes is the existence of a low-lying LUMO localized mainly at the phosphorus atom. 

Ti -Cyclopentadienyl(triphenylphosphine)cobalt reacts with phosphites and forms complexes of 1-alkoxyphosphole oxides 251 (R = Me, Et, Ph) through a step involving (ri -cyclopentadienyl)(phosphite)cobalt (80JA4363). (ri -Cp)Co(PF3)2 reacts with hexafluorobut-2-yne and 252 is formed, which hydrolyzes into 253 (X = OH) [73JCS(CC)583 75JCS(D)197]. The five-member ring has the envelope conformation, in which the carbon atoms are coplanar, and the phosphorus atom deviates from this plane in the direction opposite to the cobalt atom. The heterocycle is a four-electron donor relative to the metal center. 

In the molecule of 4-methylene-3-borahomoadamantane derivative 79, the structure of which was determined by X-ray analysis, the six carbon atoms of the triene system, the two boron and two silicon atoms all lie in one plane within experimental error (mean deviation 1.4 pm). The boron atoms deviate from the trigonal-planar geometry, since the sum of bond angles around the atoms is only 355.8° instead of 360°, as usually encountered in triorganoboranes. Considerable distortions of the bond angles at the terminal C-C double bond occurs in the vicinity of the boron atoms B-C(4)-C(ll) 130.60(19)° and B-C(4)-C(5) 107.38(17)° <2002CEJ1537>. 

In six-membered cyclic nitronates (e.g., in (85)) adopting a half-chair conformation, the C-6 and C-5 atoms deviate from the plane of four atoms in the opposite directions, the deviation of the C-6 atom being substantially larger (the deviation of the C-5 atom. The latter is generally at most 0.05 A). It should be noted that one six-membered cyclic nitronate adopts a half-boat conformation (data from the Cambridge Structural Database, see also Fig. 3.2 and its discussion). 

Stereodynamics of Cyclic Nitronates From general considerations and according to X-ray diffraction data (263a), molecules of hve-membered cyclic nitronates should adopt an envelope conformation with the C-5 atom deviating from the plane. This atom fluctuates together with its substituents (R4 and R5) (Scheme 3.83, process a). 

In the last complex of Table 6, however, the metal atom deviates from the plane of the ring and the arrangement about P-1 is pyramidal with a sum of angles equal to 348°. This situation is described by bonding mode (2) <89NJC353>. It also applies to the 1-alkyl triphosphole with a sum of angles around P-1 of 342° <95CCl6ll>. 

The product 13 was subjected to a crystal structure analysis, and its structure is depicted in Fig. 9, and selected bond lengths are included in Table Y. The overall geometry is a distorted TBP, with one chlorine atom at the apical and one at the equatorial position. The apical Si-Cl bond is significantly longer than the equatorial bond. Table Y shows that 13 has relatively short Si-O and relatively long Si-Cl apical bonds, and hence that this is another rare case of Cl -> Si coordination. In accord with Cl Si coordination the silicon atom deviates from the equatorial plane toward the oxygen atom.41... 

The cluster core, Pt4(CH3COO)4, has >2d symmetry if the Pt4 core is strictly square-planar. But the core structures found in X-ray analysis of Pt4 clusters are distorted, more or less, towsird the tetrahedral in most cases, giving S4 symmetry. The Pt atoms deviate from the Pt4 best plane by 0.2-0.3 A. Steric repulsion between two parallel out-of-plane acetates seems to be responsible for the twisting of the cluster core. 

In contrast to the neptunyl nitrate complex with Bipy, the structure of [Np02(N03)(Terpy)(H20)] (16) represents the monodentate coordination of the nitrate which provides one oxygen as donor in the equatorial plane of Np. The remaining equatorial positions are occupied by the nitrogen atoms of Terpy molecule and a water molecule (Fig. 16) [90]. The Np-N distances have moderate values, 2.580(5)-2.602(5) A. The largest atomic deviation from the least-squares equatorial plane is 0.360 A. 

A), strain is probably present in the dimer. The complex is also puckered, with the oxygen atoms deviating from the equatorial plane by up to 0.14 A. Two dmap molecules are linked to each dimer by N-H-O hydrogen bonds the N atom derives from the pyridine ring, the oxygen from a carboxylate group, (N-O distance 2.819 A). 

Special parameterization is needed to prevent atoms bound to sp2 carbons with three substituents to deviate from planarity. Many implementations apply an energy term Eoop that increases the energy when one of the atoms deviates from the plane defined by the three others. Several functions have been implemented, e.g., improper torsions or Hooke s law functions [22,23]. 

---