Oligo calculations

Fig. 3. Formal potentials of oligo(dihexylferrocenylene)s 13 (O) (60,76), those calculated from the first neighboring site interaction (A) with u, = 15 kJ mol-1 and u2 = 4.5 kJmol-1, and those calculated from both first and second neighboring-site interaction (V) with u, = 15kJmol u2 = 4.5 kJ mol 1, and oxr = -3.8 kJ mol-1 (77).

For comparison, the calculated linear and 2D spectra using ft = 12.3 cm-1 and 6 = 52°, which correspond to an a-helical structure (see the contour plot Fig. 19) for the isotopomer Ala -Ala-Ala are shown in Figure 21. The observed spectra for Ala -Ala-Ala are strikingly different from the calculated spectra for a molecule in an a-helical conformation. We emphasize here an important point In contrast to the NMR results on oligo(Ala), in which averaging of different backbone conformations might be present because measurements are made on a time scale that is slow compared to that of conformational motions, these vibrational spectroscopy results are detected on a very fast time scale (Hamm et al, 1999 Woutersen and Hamm, 2000, 2001). This rules out conformational averaging. 

Dissolve a 5 -sulfhydryl-modified oligonucleotide in water or lOmM EDTA at a concentration of 0.05-25 pg/pi. Calculate the total nmoles of oligo present based upon its molecular weight. 

Prepare SPDP-activated alkaline phosphatase in 50 mM sodium phosphate, 0.15M NaCl, lOmM EDTA, pH 7.2. Add to the oligo solution, an amount of the activated enzyme representing a 10-fold molar excess over the calculated amount of DNA present. 

Fio. 47. Retention factors of pteroyl-oliso-yL-glutamates as a ftinction of the eluent pH. The solid lines were calculated as diKussed in Bush et at. (204). Data were obtained for folic acid (FA) and oligo yglutainates containing one (Ft Glu,), three (Ft GIU ). hve (Ft GtU ), and seven (Ft Glur) utamyl residues. The data were obtained on 5 Partisil ODS-2 with 0.1 M phosphate buffers containing 696 (v/v) acetonitrile as eluent, 4S C, with detection at 254 nra. Reprinted with permission from Bush rf a/. (204). 

Roberfroid, M., Gibson, G.R., and Delzenne, N., The biochemistry of oligo-fructose, a nondigestible fiber an approach to calculate its caloric value, Nutr. Rev., 51, 137-146, 1993. 

Golinske, D. and Voss, J. (2005) Electroreduction of organic compounds, 35. Quantum chemical calculations of reaction pathways for the cathodic dehalogenation of chloro-dibenzo-furans and oligo-chlorobenzenes. Zeit. Natur. B Chem. Sci. 60, 780-786. 

A protocol combining molecular dynamics and NMR spectroscopy gave excellent agreement between calculated and experimental nuclear Overhauser effect (NOE) buildup curves of 2,5-oligo(2-thienyl)furans <2002PCA1277>. 

Table TDDFT(B3LYP) calculated excitation energies (eV) for oligo(cyclopentadiene)s, oligo(pyrrole)s, oligo(phosphole)s (Ph) ollgo(thlophene)s (Th)n, and the corresponding polymers (DFT HOMO-LUMO gaps in parentheses)...

Huige and Hezemans179 180 have performed extensive molecular mechanics calculations using the consistent force-field method on various oligo- and polyisocyanides. The hexadecamer of ferf-butyl isocyanide was calculated to have a helical middle section and disordered ends. The dihedral angle N=C—C=N in the middle section was found to be 78.6°, and the number of repeat units per helical turn was 3.75. The latter number is in agreement with circular dichroism calculations using Tinoco s exciton theory (3.6—4.6) and De Voe s polarizability theory (3.81). The molecular mechanics calculations further predicted that the less bulky polymers 56 and 57 form helical polymers as well, whereas a disordered structure was calculated for poly(methyl isocyanide) (55). 

---