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Rearrangement of \(A_{iso}\)/\(a_{iso}\) from the Gaussian & ORCA Computations

Source: R/rearrange_aAiso.R
rearrange_aAiso_QCHorgau.Rd

Providing table, specifically from Gaussian (version > G.09) or ORCA (version > 6.0) output text files to summarize the \(A_{iso}\)/\(a_{iso}\) mean values (including the sign) of groups with equivalent nuclei, according to proposed molecular structure/symmetry (see also the rearrange_aAiso_QCHcomp).

Usage

rearrange_aAiso_QCHorgau(
  path_to_QCHoutput,
  nuclei.list.slct,
  origin = "gaussian",
  output.text.origin = FALSE,
  output.text.path = NULL
)

Arguments

path_to_QCHoutput

Character string, corresponding to path of Gaussian or ORCA output text files.

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. In order to figure out the indices of the atoms/nuclei to be selected, user may try to open the output file (e.g. .log, .out, .txt) by any text/code editor like Sublimetext, Zed or Notepad++ or use GUI molecular editors like Avogadro2, Jmol or Gabedit.

origin

Character string, pointing to origin of (DFT) EPR calculation parameters <=> which software package was used. Only two values are available => "gaussian" (default) or "orca".

output.text.origin

Logical, whether to write a text file containing the extracted \(A_{iso}\)/\(a_{iso}\) values from the the original output file defined by the path_to_QCHoutput. Default: output.text.origin = FALSE.

output.text.path

Character string, setting the path to file containing the extracted \(A_{iso}\)/\(a_{iso}\) values from the original output file defined by the path_to_QCHoutput. See also the previous argument.

Value

Data frame/Table of \(A_{iso}\)/\(a_{iso}\) mean values (including the \(\pm\) signs), corresponding to groups of proposed equivalent nuclei within the structure/symmetry constructed directly from Gaussian or ORCA output text files.

See also

Other Evaluations and Quantum Chemistry: eval_gFactor_QCHcomp(), rearrange_aAiso_QCHcomp()

Examples

## built-in file and path
gauss.file.path <-
  load_data_example(file = "TMPDAradCatEPRa.inp.log.zip")
gauss.file <- unzip(gauss.file.path)
symmetry.As.df <-
  rearrange_aAiso_QCHorgau(gauss.file,
    nuclei.list.slct =
    list(c(7, 8), ## 2 x 14N
         c(13, 14, 15, 16), ## 4 x 1H (aromatic)
         c(17, 18, 19, 20,
           21, 22, 23, 24,
           25, 26, 27, 28) ## 12 x 1H (methyl groups)
         )
     )
#
## preview
knitr::kable(
  symmetry.As.df,
  caption = "DFT computed hyperfine couplings(Aiso)/splittings(aiso) for the TMPD radical cation."
)
#> 
#> 
#> Table: DFT computed hyperfine couplings(Aiso)/splittings(aiso) for the TMPD radical cation.
#> 
#> |NuclearGroup                                  | Aiso_MHz| aiso_mT|
#> |:---------------------------------------------|--------:|-------:|
#> |12 x 1H (17,18,19,20,21,22,23,24,25,26,27,28) |    20.25|    0.72|
#> |2 x 14N (7,8)                                 |    17.52|    0.63|
#> |4 x 1H (13,14,15,16)                          |    -5.24|   -0.19|