PCSB

NOTE: The valence contribution update now targets specific bond types. No changes are expected in typical organic systems, except for the N-S bond, which is no longer corrected.

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 or Gaussian LOG file 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 the 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 penality function approach to determine improved Cartesian coordinates. To get a better understanding of the method, please check the reference article. To get a flavour of the workflow of the website, please refer to the original article.

PCSB

$$ r_{PCSB} = r(rDSD/3F12-) + \Delta r_{B} $$ $$ \Delta r_{B} = \Delta r^{CVB}_{ij} + \Delta r^{VB}_{ij} $$ $$ \Delta r^{CVB}_{ij} = -k \sqrt{N_iN_j-1} \left ( r_i^{cov} + r_j^{cov} \right ), N_i=min(n_i,3) $$ $$ \Delta r^{VB}_{ij} = \Delta r^{CVB}_{ij} \left[ \sqrt{|BO_{ij} - 2|} - 1\right]\left[ \delta(i,C)\delta(j,S) + \delta(i,S)\delta(j,C) + \sum_{x,y \in \{C,N\}} \delta(i,x)\delta(j,y) \right] $$

DVB correction

2. Upload a molecular structure (XYZ or Gaussian LOG file).

3. Download refined structure and view its properties.

Input Structure

Refined structure

Bond distances

Parent rotational constants