Dihedral angles, and

The OPLS atom types are a superset of the AMBER united atom types and the bonding parameters are just those of AMBER, supplemented where needed by the OPLS developers. The bond stretch, angle bending, dihedral angle and improper dihedral angle terms are identical to those of AMBER. Unlike AMBER, different combination rules are used for the van der Waals parameters, no hydrogen bonding term is used and no lone pairs are used. 

Infrared, uv, nmr spectra (66), and photoelectron spectra have been reviewed (67). Physical properties of siHcon peroxides are summarized in Reference 43. Other physical properties, eg, dipole moments, dihedral angles, and heats of combustion ate Hsted in Reference 68. The oxygen—oxygen bond strengths of various diaLkyl peroxides have been reported (69). 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

The relative eonfiguration at C-7 and C-8 eannot be established from the HH eoupling eonstants for five-membered rings the relationships between dihedral angles and eoupling eonstants for cis... 

Figure 14.4 The four main types of O2-M geometry. The bridging modes Ib and lib appear superficially similar but differ markedly in dihedral angles and other bonding properties. See also footnote to Table 14.5 for the recently established unique /Lt.rj -superoxide bridging mode.

We refer to models where we write the total potential energy in terms of chemical endties such as bond lengths, bond angles, dihedral angles and so on as valence force field models. 

Molecular mechanics (MM) calculations have been employed for determining dihedral angles and to establish a comparison with values calculated from coupling constants, during conformational studies of tricyclic and tetracyclic quinolizidine alkaloids. The MM results had to be treated with care, as they sometimes predicted ring conformations different to those supported by experimental data <1999JST215>. 

The structure of a second polymorph of 4,5-diphenyl- lH-imidazole has been discussed, with the new form exhibiting significantly different phenyl/imidazole dihedral angles and mode of crystal packing relative to the known form [53], A new triclinic polymorph of 1,4-dibenzoyl-butane was found, differing from the monoclinic form in the torsional angles of the central chain [54], Two polymorphs of diphenyl-(4-pyridyl)methyl methacrylate have been found, where the molecules in the two forms contain weak C—H— n and C—H O/N contacts that lead to the existence of different conformations [55]. 

It is noted that st-20 also has a similar double-well potential curve at about P 160° and M 200° dihedral angles and the global minimum M is slightly... 

The computational requirement of the aBB algorithm depends on the number of variables on which branching occurs. The most important variables are those variables that substantially influence the nonconvexity of the surface and the location of the global minimum. In the protein-folding problem, the backbone dihedral angles ( and ip) are the most influential variables. Therefore, in very large problems, to further reduce the dimensions of the problem, only these variables were involved in the optimization. 

In their study of the conformations of oligosilanes with methyl and ethyl substituents,9 Michl and co-workers pinpointed the specific substituent-substituent interactions in tetrasilanes responsible for inducing C, Z), and A conformations, allowing a prediction of backbone dihedral angle and direction of twist, given a specific arrangement of ethyl groups. 

Fig. 6.8 Correlation of experimental and theoretical residual dipolar couplings calculated using the structural data obtained from restrained molecular dynamics with NOEs, dihedral angle and RDCs-...

Fig. 7. Plot of main chain dihedral angles and (see Fig. 5 for definition) experimentally determined for approximately 1000 nonglycine residues in eight proteins whose structures have been refined at high resolution (chosen to be representative of all categories of tertiary structure).

Now that about 70 different disulfides have been seen in proteins and more than 20 of those have been refined at high resolution, it is possible to examine disulfide conformation in more detail, as it occurs in proteins. Many examples resemble the left-handed small-molecule structures extremely closely Fig. 46 shows the Cys-30-Cys-115 disulfide from egg white lysozyme. The x > Xs and x dihedral angles and the Ca-Ca distance can be almost exactly superimposed on Fig. 45 the only major difference is in Xi All of the small-molecule structures have Xi close to 60°. Figure 47 shows the Xi values for halfcystines found in proteins. The preferred value is -60° (which puts S-y trans to the peptide carbonyl), while 60° is quite rare since it produces unfavorable bumps between S-y and the main chain except with a few specific combinations of x value and backbone conformation. 

Figure 34. Gations, dihedral angles, and symmetry of the tetrachlorocuprates complexes at ambient pressure. The d orbital calculated structures (A-D) reported in the lower section correspond to the different geometries of the CuCl complex.

---