Subroutines |
CSA calculations
Gaussian94 ab initio CSA calculations:
It is possible to calculate the chemical shift tensors of macromolecular
building blocks using the Gauge Including
Atomic Orbital (GIAO) method as implimented
in Gaussian94. Shown below are a list of the execution script and input files
used to generate the chemical shift tensors included in YARM.
Note that the molecular coordinates listed in the input file is different from
the molecular coordinates listed by Gaussian94 in the output file. The molecular
coordinates listed in the output file describe the frame in which the
calculation is performed. The difference between the molecular cordinates
listed in the input and output files arises from a trivial rotation as
Gaussian94 initializes the calculation looking for symmetry elements within the
molecule. This does not effect the orientation or magnitude of the CSA tensor.
Shown in Table 1 below, is a comparison of calculated and
experimental isotropic shifts for 5'-AMP. The calculated shifts are considered
in good agreement with the experimental shifts despite discrepancies larger than
10 ppm in the aromatic shifts. These large differences are likely due to the
fact that all Gaussian94 calculations are performed in vacuum the experimental
shifts are determined in water, a highly polar solvent.
| Atom
| Calculated (ppm)
| Experimental (ppm)
| Difference (ppm)
|
| C2
| 147.2
| 151.8
| +4.6
|
| C4
| 164.9
| 148.0
| -16.9
|
| C5
| 134.7
| 117.7
| -17.0
|
| C6
| 149.8
| 154.2
| +4.4
|
| C8
| 158.5
| 139.6
| -18.9
|
| C1'
| 93.7
| 87.4
| -6.3
|
| C2'
| 80.3
| 74.7
| -5.6
|
| C3'
| 69.2
| 70.3
| +1.1
|
| C4'
| 78.7
| 83.8
| +5.1
|
| C5'
| 57.3
| 64.3
| +7.0
|
Table 1: Comparison table of calculated and experimentally
determined 13C isotropic chemical shifts for 5'-AMP. Calculated
shifts were obtained using Gaussian94 under the GIAO method with 6-311G* basis
set and B3LYP density functional. The calculated shifts are refernced to ca
clculated TMS reference of 186.4 ppm. The experimental shifts are referenced
to TMS external at 25 C.
YARM Implimentation:
Chemical shift tensors are provided in YARM through a lookup table containing
calculated shift tensors for nucleotides of DNA and RNA. The chemical shift
tensors were calculated using the GIAO method as implimented in Gaussian94. The
6-311G* basis set was used, and electron correlation was treated using the B3LYP
density functional.