Computational structure

This work has been supported by the U.S. National Science Foundation (grant MCB-9314854) and the U.S. National Institutes of Health s National Center for Research Resources (grant RR08102 to the UNC/Duke Computational Structural Biology Resource). 

The estimated intensities of the various reflections are indicated by the abbreviations vs, very strong s, strong ms, medium strong m, medium mw, medium weak w, weak vw, very weak vvw, very very weak a, absent. The number placed below the estimated intensity for each plane gives the computed structure-factor. 

We study three different approximations for removing unlinked diagrams in EOM-CC and show that these models provide second-order properties and transition probabilities that are close to those provided by CCLR in isolated molecular systems, but in a more convenient computational structure. 

Buhl, M. 1998, NMR Chemical Shift Computation Structural Applications , in Encyclopedia of Computational Chemistry, Schleyer, P. v. R. (Editor-in-Chief), Wiley, Chichester. 

Levitt M (2001) The birth of computational structural biology. Nat Struct Biol 8(5) 392-393... 

Since the phase angles cannot be measured in X-ray experiments, structure solution usually involves an iterative process, in which starting from a rough estimate of the phases, the structure suggested by the electron density map obtained from Eq. (13-3) and the phase computed by Eq. (13-1) are gradually refined, until the computed structure factor amplitudes from Eq. (13-1) converge to the ones observed experimentally. 

The terms involving the subscript j represents the contribution of atom j to the computed structure factor, where nj is the occupancy, fj is the atomic scattering factor, and Ris the coordinate of atom i. In Eq. (13-4) the thermal effects are treated as anisotropic harmonic vibrational motion and U =< U U. > is the mean-square atomic displacement tensor when the thermal motion is treated as isotropic, Eq. (13-4) reduces to ... 

Shown below are snapshots of structures from our simulations of native RT with Sustiva and nevirapine. No crystal structure had been reported for RT with Sustiva when the calculations were performed however, confidence in the computed structure comes from the quantitative accord for the inhibition penalties and because Matador yielded docked structures for nevirapine, MKC-442, and 9-C1-TIBO that are virtually identical to the crystal structures.57 Sustiva hydrogen bonds with the backbone of K101, as do MKC-442 and 9-chloro-TIBO, and it has hydrophobic interactions in the Y181-Y188 pocket, also typical of NNRTIs. 

A crystal structure for the Sustiva/RT complex was subsequently reported and fully confirmed the correctness of the computed structure.58... 

The optimal styx pattern of three ctbb, ten Tbbb, and twelve OBH(t) bonds requires a total of 2(3 + 10 + 12) = 50 electrons, whereas a neutral (BH)i2 framework provides only 12(3 + 1) = 48 valence electrons. Hence, two additional electrons must be added to form the B12H122- anion that achieves the idealized icosahedral bonding pattern (3.259). Figure 3.111 depicts the computed structure of Bi2Hi22, which indeed optimizes to perfect icosahedral symmetry with each B—B = 1.787 A (experimental 1.77 A) and B—H = 1.202 A. 

As anticipated by its ML2X2 formulation (Table 4.52), the computed structure of singlet nickelocene approximates a square-planar di-allylic coordination mode. We can deconstruct each r 3-Cp to Ni interaction into an electron-pair bond (M—X) with the radical carbon and a dative interaction (M—L) with the 7icc bond, symbolized as shown below with a half-filled circle ( >) to represent the radical site and a filled circle ( ) to represent the dative 7t-bond site ... 

Computed structures for model /V-acyloxy-/V-alkoxyamides, X-ray diffraction data for a number of congeners, as well as spectroscopic evidence fully support these qualitative arguments. 

It is also common practice to integrate the pressures and impulses, over the surface areas, to obtain average values, rather than try and compute structural response to spatially-varying, as well as time-varying loads. But, this averaging procedure should be used cautiously for long walls or ceilings, because it can lead to serious underprediction of shock loads for part of the surface. 

Figure 3. Computed structure of vinyl cation 8a. (B3LYP/6-31G(d), bond lengths in picometer). 

Figure 10. Computed structure of vinyl cation 20 (underlined MP2/6-31G(d), italic B3LYP/6-31G(d)). Additional bond angles Si2-(f-C+= 112.3. 118.0 S/y-C -C+= /33.J. /27.d.

Similarly the experimental dynamic structure factor also seems to be in disagreement with the latest and most extensive coarse grained MD-simula-tions by Putz et al. [79]. Figure 3.26 compares the computed structure factors... 

Selected computed structural data at the B3LYP/aug-cc-pvTZ level of theory are given in Figure 31. With respect to resonance stabilization, it is interesting to compare the C-N distances. Two things are worthy of discussion (i) the C—NO distance is always smaller compared to the C—NO2 (e.g. NNtM 1.320 vs. 1.399 DNNtM 1.342 vs. 1.489 NDNtM 1.318 vs. 1.399/1.476 A), and (ii) the smallest C—N distance is found in DNNtM, displaying the best resonance along the ON—C—NO unit (cf. DNM). 

Selected computed structural data on the three tautomeric forms of protonated NNtM, DNNtM and NDNtM are depicted in Figure 33. Only the most stable oxime isomers are presented. As long as only two functional groups are attached to the central methanide carbon, the entire molecule remains planar due to resonance stabilization, whereas introduction of a third group, either NO or NO2, results in rotation of at least one group, preferably the nitro group. Flowever, the CN3 moiety in the nonplanar species remains... 

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