Rearrangement of \(A_{iso}\)/\(a_{iso}\) from Quantum Chemical (QCH) Computations

Providing table, based on Gaussian/ORCA/...etc. output text files in order to summarize the mean \(A_{iso}\)/\(a_{iso}\) values of groups with equivalent nuclei, according to proposed molecular structure/symmetry.

Usage

rearrange_aAiso_QCHcomp(path_to_ASC, col.names, nuclei.list.slct)

Arguments

path_to_ASC: Character string, pointing to path of ASCII file (txt,csv...etc, it may be also provided by file.path). The file must include characteristic \(A_{iso}\) or \(a_{iso}\) values.
col.names: Character string vector, containing names of all columns from QCH computational output, for the names see the example in Details, they must contain atomic/structure number, isotopic value with element label (nucleus characterization) and \(A\) in MHz as well as \(a\) in Gauss.
nuclei.list.slct: List of numeric values for the rearrangement of selected atoms/nuclei according to symmetry, e.g. nuclei.list.slct <- list(3,c(21,22),c(20,23),c(24,25),c(27,26)) where the numbers correspond to indices of proposed equivalent nuclei in the ASCII text file.

Value

Data frame/Table of \(A_{iso}\)/\(a_{iso}\) mean values corresponding to groups of equivalent nuclei within the structure/symmetry.

Details

The \(A_{iso}\)/\(a_{iso}\) values are computed for each atom/nucleus (with its corresponding atomic number within the structure as well as with the characteristic isotopic number/value), such an entire table can be copied e.g. from Gaussian output (after 'Isotropic Fermi Contact Couplings' line) or can be constructed from ORCA (or any other) output, example for such a file structure (from Gaussian):

No_atom	Atom_Nucleus	MegaHertz	Gauss	1e-4_cm-1
1	N(14)	0.00643	0.00229	0.00214
17	N(14)	13.99707	4.9945	4.66892
28	H(1)	16.34971	5.83398	5.45368

The input table/data frame, like the previous one, must include following columns: atomic/nucleus number, atom/nucleus notation, hyperfine coupling constant in MHz and finally hyperfine splitting constant in G. These columns/variables are essential for the evaluation.

Examples

if (FALSE) { # \dontrun{
rearrange_aAiso_QCHcomp(
"./iso_values_Gaussian.txt",
c("No","Nucleus","au","Megahertz","Gauss","10^n4_cm^n1"),
list(3,c(21,22),c(20,23),c(24,25),c(27,26))
)
} # }