Vibrational Energy Distribution Analysis (VEDA)

down VEDA 4 (Windows)

author: Michał H. Jamróz, Warsaw

 Once results of the VEDA analysis are to be published, The reference should be cited as follows:

Michal. H. Jamroz, Vibrational Energy Distribution Analysis VEDA 4, Warsaw, 2004-2010

The VEDA computer program optimizes the set of internal coordinates to elucidate the IR and Raman experimental/theoretical spectra. As a result, the theoretical normal modes are represented by internal coordinates giving users a more intuitive view of the molecular movements. Each of the internal coordinates is expressed as a superposition of several local modes of two, three, or four atoms connected by bonds for stretching, bending, or torsional and out-of-plane local modes, respectively.

 

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Vibrational Energy Distribution Analysis (VEDA)

down VEDA 4 (Windows)

down  VEDA 4xx (Windows) Veda version for up to 480 atoms.

author: Michał H. Jamróz, Warsaw

 Once results of the VEDA analysis are to be published, The reference should be cited as follows:

Michal. H. Jamroz, Vibrational Energy Distribution Analysis VEDA 4, Warsaw, 2004-2010

The VEDA computer program is optimizing the set of internal coordinates for elucidation of IR and Raman experimental/theoretical spectra. As a result, the theoretical normal modes are represented by internal coordinates giving users a more intuitive view of the molecular movements. Each of the internal coordinates is expressed as a superposition of several local modes of two, three, or four atoms connected by bonds for stretching, bending, or torsional and out-of-plane local modes, respectively.

The basis of calculations are the following:

 1. Obligatory:

  • geometry of the structure (atom orientation) in cartesian coordinates,
  • force-field (F matrix) in cartesian coordinates.

2. Desirable:

  • calculated frequencies and atom displacement matrix (ADM)

VEDA 4 extracts automatically the necessary data from the Gaussian94/98/03 output files (.log and .fch)

The introductory file containing the set of internal coordinates (.dd2) is generated by VEDA, but the user can defined his own set as well.

VEDA 4 enables three ways to analyse the distribution of vibrational energy:

  • Manual editing of the Base coordinates (with the help of Alternative coordinates),
  • Mixing Modes procedure (optional),
  • Optimization procedure.

 All this ways can be combined.

 

Veda additional informations:

 

1. If .log and .fmu files are corrrect, the .fmv file is generated. The .fmv file is useful in the next start of the analysis. Then the .log and .fmu files are not necessary.

2. When .dd2 file is edited, you can remove the modes assignments.Then Veda automatically generates the new ones.

3. When you add a line (at the end of the file) in the .fmv (.fmu) file: scaling factor = a * x + b (a, b - numbers) then in the .vdf file the scalled freqencies are generated. To easy convert the results to the table in an editor, the | sign as the column separator is added.

4. When Veda finds the .mpo file in the folder, Veda reads it, orthewise the .mpo file is generated.

5. You can renumerate an atom : place in the .fmv (.fmu) file line renumerating atoms, followed by two columns: old number, new number. If the number is the same, it can be ommited. Also you can write two in the reversed order: new number, old number. You can put the renumerated atoms in the .dd2 file, but the renumeration is reversed.

6. When editing the .dd2 file, the definitions can be introduced as follow:name of mode followed by 2 (3, 4) atom numbers, for example: 1 stre 12 15.

7. You can introduce the user coordinates in the .dd2 file. Then the user modes can be omitted in the next optimization by choosing "hide user coordinates" in the control box. Similarly, you can hide the othercoordinates, e.g., stre, bend, tors, out, etc.

8. Linear dependence of the coordinates: sometimes Veda creates a set of coordinates which is linearly dependent. Especially, this may happen for very symmetric structures. Veda offers some ways to deal with such a problem:

a) old version of the .dd2 creation (control box) - it uses another way of the coordinate definitions. This option also helps when the usual .dd2 creation generates too small set of coordinates.

b) test alternative until TED<999 (control box)

c) generate .dd2 without coordinates of the "out" type of the modes "in plane"

d) ring coordinates - for structures with ring

e) echange groups of coordinates - alternative .dd2 button

f) manual edit of coordinates - it can be succesfull for structues with intermolecular bonds.

g) in hopeless cases send me the .fmv file.


Download

VEDA4 program (Windows)

Examp_1 and Examp_2 contain files for exemplary molecules.

Some additional information can be find in veda_use.doc

If Veda not act because of lack of the MSVBVM50.DLL, put MSVBVM50.DLL file into your VEDA folder

 

VEDA4xx Veda version for up to 480 atoms.


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Spesca

Spesca downloadSpesca3 (Windows)

author: Michał H. Jamróz, Warsaw

Spesca3 program for comparison between theoretical and experimental spectra by weighted linear regression.

 

Spesca downloadSpesca4 (Windows)

author: Michał H. Jamróz, Warsaw

Spesca4 program for visualization of the theoretical and experimental spectra.

CHIGRA

down CHIGRA (Windows)

author: Michał H. Jamróz, Warsaw

CHIGRA

The CHIGRA program for PC computers is based on the hypervertex version of the Chiral Graph Theory restricted to the presence of only asymmetric vertices. The graph is introduced in the form of a HGI (cHiral Graph Index) file specific for CHIGRA which is the Protein Data Base PDB file augmented with additional information about the labels of the chiral atoms and the complex number parameters (a and b) assigned to these very atoms. All C and heteroatoms are set up to be identical vertices while the H-atoms are ignored in the calculations. The program considers complex matrices in the form A+iB and realizes matrix calculations on real matrices preserving the rules of the algebra of complex numbers: (A+iB)(A+iB)=A2-B2+i(BA+AB).

We can apply these rules because all considered matrices, except the chiral incidence matrix, are symmetric. The CHIGRA output contains real and imaginary parts of the Wiener, first and second Zagreb, Laplacian and Randiæ indices.

The HGI CHIGRA input files were generated through the PDB files produced by many molecular graphics programs. The PDB files were edited to obtain the HGI files by introducing the labels of the chiral atoms and the parameters of the complex numbers assigned to them.

M. H. Jamróz, CHIGRA - program calculating chiral graph topological indices for molecules with chiral centres based on the hypervertex Chiral Graph Theory, Institute of Nuclear Chemistry and Technology, Warsaw, 2014. The CHIGRA program is available at the http://www.smmg.pl/ web page.

If CHIGRA not act because of lack of the MSVBVM50.DLL, put MSVBVM50.DLL file into your CHIGRA folder

Program should be cited as:

Jan Cz. Dobrowolski, M. H. Jamroz, P. F. J. Lipinski, On Chiral Graph Topological Indices of alpha-Amino Acids, MATCH. Commun.Math. Comput. Chem. 76 (2016) 401-418

Chimea

down Chimea (Windows)

author: Michał H. Jamróz, Warsaw

Chimea

Chimea is a program for determining chirality measures. Chirality measures are described as the distance between a molecule and its mirror image minimized over all its arbitrary orientation-preserving isometries in the R3× Pk Cartesian product of Euclidean and prperties spaces. Following this formalism, different chirality measures can be determined by taking into consideration different sets of atomic properties.
 
The Gaussian log files and also: pdb, .hau (Hauusian), .gjf (Gaussian), .fmu, .fmv (Veda), .chi (Chimea) can be used as input files.
 
Chimea calculates four basic chirality measures:
 
CH0 (only atoms positions)
CH1 (including atom type and connectivity)
CH2 (mass weighted)
CH3 (charge weighted)
 
As an example see the following papers:
1. Michał H. Jamróz, Joanna E. Rode, Sławomir Ostrowski, Piotr F. J. Lipiński, Jan Cz. Dobrowolski, Chirality Measures of α-Amino Acids, J. Chem. Inform. Model., 52(2012)1462-1479.
2. Sławomir Ostrowski, Michal H. Jamróz, Joanna E. Rode, Jan Czeslaw Dobrowolski, On Stability, Chirality Measures, and Theoretical VCD Spectra of the Chiral C58X2 Fullerenes (X=N, B), J. Phys. Chem. A, 116(2012)631–643.
3. Sławomir Ostrowski, Michał H. Jamróz, Jan Czeslaw Dobrowolski, On Stability, Chirality Measures, and Theoretical VCD Spectra of the Heterofullerenes C69X (X = B, Si, Ge, N, P, As), Tetrahedron: Asymmetry, 24 (2013) 1097–1109.

 

 

 

Hauusian

Spesca downloadHauusian (Windows)

Spesca download Hauusian (Windows) version for up to 1920 atoms.

Hauusian program for multi-components structure system generation.

License

Example

Additional information

 author: Michał H. Jamróz, Warsaw