BDPCS3

NOTE: Please, when using this tool in scientific publications cite the following papers:

- Barone, V., Lazzari, F. (2023). Hunting for complex organic molecules in the interstellar medium: the role of accurate low-cost theoretical geometries and rotational constants. The Journal of Physical Chemistry A, 127(49), 10517-10527.

- Uribe, L., Mendolicchio, M., Municio, S., Mato, S., Alonso, E. R., Alonso, J. L., León, I., Barone, V. (2025). From Norbornadiene to Norcamphor and Camphor: Reduced-Cost Semiexperimental Structural Refinement from Limited Isotopologue Data. The Journal of Physical Chemistry Letters, 16, 6523-6532.

Details and instructions

The Pisa Composite Scheme (PCS) in its bond corrected (PCSB) variant applies a set of linear corrections to covalent bonds starting from an initial geometry provided as input. The tool is used in three sequential steps:

Select or deselect the optional valence corrections (on by default).

Upload the starting geometry using an XYZ obtained from a revDSD/3F12- geometry optimization. The 3F12red.gbs file is available here (please remove the .txt extension when using the basis set). A sample input file for g16 software is given below:


%mem=8GB

%nproc=8

#p dsdpbep86

iop(3/125=0079905785,3/78=0429604296,3/76=0310006900,3/74=1004)

empiricaldispersion=gd3bj iop(3/174=0437700,3/175=-1,3/176=0,3/177=-1,3/178=5500000) genecp opt



 H2O



0 1

H

O 1 R1

H 2 R1 1 A1



R1=0.96

A1=104.5



@3F12red.gbs

Visualize the refined molecular structure, view its properties and download the refined XYZ geometry file.

The tool employs the redundant internal coordinates and penalty function approach to determine improved Cartesian coordinates. For more details, see the reference article and the original article.

BDPCS3

$$ r_{BDPCS3} = r(rDSD/3F12-) + \Delta r_{B} $$ $$ \Delta r_{B} = \Delta r^{BCV}_{ij} + \Delta r^{BV}_{ij} $$ $$ \Delta r^{BCV}_{ij} = -0.0011(1+1.1\delta_{CH}) \sqrt{N_iN_j - 1} \left ( r_i^{cov} + r_j^{cov} \right ),\, N_i = \min(n_i,3) $$ $$ \Delta r^{BV}_{ij} = \Delta r^{BCV}_{ij} \left[\sqrt{|BO_{ij} - 2|} - 1\right] \left[ \delta(i,C)\delta(j,S) + \delta(i,S)\delta(j,C) + \sum_{x,y \in \{C,N\}} \delta(i,x)\delta(j,y) + \frac{1}{\Delta r^{BCV}_{ij}}\left[\delta(i,C)\delta(j,F) + \delta(i,F)\delta(j,C)\right] \right]$$

DBV correction

Upload a molecular structure (XYZ file).

Download refined structure and view its properties.

Input Structure

Refined structure

Bond distances

Parent rotational constants