Models energy minimization

Fig. 7. Buildup rate analysis of NOESY spectra at T = 298 K (Xn, = 0.3 s, 0.6 s, 1 s) and T = 233 K (Tm = 10 ms, 20 ms, 30 ms, 40 ms, 80 ms, 160 ms, 320 ms, 640 ms, 1.2 s). Lines are drawn according to eq. (8) with a dynamic matrix from the energy minimized model (table 1). High-temperature data (negative slopes) are linearly fitted according to eq. (30). Low-temperature data (positive slopes) are fitted by eq. (30) only points with aij /ajj < 0.2 were used (inset).

Complete success, however, was not attained in the initial version. The limiting factor was the development of overcurvature in the formed components. This was shown to be due to an incompatibility strain which arises between the formed and not-yet-formed regions on any one pass through the forming machine. Using an energy minimization model, the overcurvature was shown to be inherent to the process. 

Figure 4.18 Energy-minimized models of the tertiary structures of bovine ot8l- (a), / - (b) and k- (c) caseins (from Kumosinski, Brown and Farrell, 1993a, b Kumosinski and Farrell,...

Molecular modeling of the noncovalent interaction between trisphenanthroline metal complexes and DNA has been used to aid in the interpretation of the NMR spectra of these systems12161. The AMBER force field was used to model the DNA, and the metal complex/DNA systems were energy-minimized. Distances from the energy-minimized models were used to calculate relaxation rates and compared with the experimentally determined data12161. 

The model was built and optimized in the absence of inhibitors. Dipeptide inhibitors were docked in the energy-minimized model. The coordinates of the... 

Fig. 3. Stereoviews of the central trinucleotide d(CA G ) d(CTG) of the A G -platinated duplex d(CTCA G CCTC)d(GAGGCTGAG) (2). Top energy-minimized model in which the thymine conserves its Watson-Crick imino hydrogen bond with A, whereas the amino hydrogen bond is disrupted. Bottom energy-minimized model in which the thymine retains its Watson-Crick amino hydrogen bond with A, whereas the imino hydrogen bond is disrupted. The H(2 ) proton of the cytidine of the platinated strand lies in the shielding cone of the five-membered ring of A in both models, which accounts for the strong upfield shift observed for its NMR signal (reproduced from [70] with permission).

Fig. 4. Steroview of an energy-minimized model proposed for the doubly-G G -platinated oligonucleotide d(GACCATATG G TC)2 (reproduced from [72] with permission)...

Consider the related complex with the quinoline ligand replaced by 2-methylqui-noline. Calculate the strain energies of the two isomers of the complex with this ligand and predict which isomer would be preferred. Use the energy minimized models of the two isomers and measure the closest H — H contacts. Calculate the intensities of the expected NOESY crosspeaks arising from these contacts. 

Thus, the application of the ligand field model [178] in combination with the strain energy minimization model [230] makes it possible to calculate with high accuracy the geometrical parameters of sepulchrate and sarcophaginate frameworks. 

Figure 14. (a) Top view of a single antiparallel (t shoe of biosynthesized monodisperse poly(alanylglycine). Fold length is commensurate with the octapeptide periodicity. Vertical dotted lines indicate H-bonds. (b) Arrangement of (t sheels into 3-D crystal. Sheets lie horizontally. Energy-minimized model refined using X-ray data (from ref 87, by permission of the American Chemical Society). 

Fig. 14. Stereo views of space-filling models of (top) the active site of native hen egg white lysozyme (middle) energy-minimized model-built hexamer [(GlcNAc)6] bound to the active site (right-sided mode) and (bottom) lowest-energy hexamer bound to the active site (left-sided mode) [51]...

Measure the CH3, CH3 distance in the energy-minimized model of ds-2-butene and the CHj, H distance in the energy-minimized model of trans-2-butene. In which isomer is the nonbonded interaction strain greater ... 

Measure the C=C—C bond angles in the energy-minimized models of the cis and trans isomers of 2,2,5,5-tetramethyl-3-hexene. In which case is the deviation fromVSEPR predictions greater ... 

Measure the C—C—C and C—C—H bond angles in the energy-minimized model of cyclohexene and compare them with those predicted by VSEPR. Explain any differences. 

Ave. exptl. value or range Ideal value Energy minimized model... 

Energy minimized models may be further optimized by molecular dynamics (MD) simulations, as reported in-depth in section 2.3. 

---