Analysis Tools

VMS Analysis (for All Users)

Spectra Processing

Spectra Processing capabilities of VMS-Draw include derivation, normalization, conversion, smoothing and other manipulations of several spectra at the same time.

VMS can plot spectra for different kind of spectroscopies. If the simulation has been performed without broadening the single vibronic peaks, broadening effects can be added a-posteriori using VMS (Gaussian, Lorentzian and Pseudo-Voigt functions are supported). If broadening effects have been included in the GAUSSIAN computation, VMS plot the spectrum without applying any additional broadening

Plot digitization and Comparison spectra

VMS Draw includes a program to digitize graphs, named Plot Digitizer. It allows you to take a scanned image of a plot (in GIF, JPEG, or PNG format) and quickly digitize values of the plot just by clicking the mouse on each data point.

VMS Draw provides an integrated environment for direct comparison between different types of theoretical and experimental spectra. In order to compare more properly experimental and theoretical results, VMS offers Runtime manipulation of spectra positions and intensities.

Merging spectra and Simulate Mixtures

VMS Draw allows users to merge several spectra to generate a final sum spectrum involving multiple electronic transitions. In addition, it can evaluate a complex molecular mixture varying the contributions of single-components.

Predicted compound color

VMS is able to evaluate the color of a compound from its spectrum in the 380-780 nm regions. This analysis is done by computing the chromaticity coordinates (as defined by the CIE), which are then converted to RGB color model.

Visualization of the spectra with highly customizable plotting functionality

The plots produced by VMS-Draw are highly customizable via user-modifiable settings in order to produce publication quality graphs.

Input Generation

User-friendly graphical tools are developed to better facilitate creating the complex text-based input files for ESCs. Users can construct new structures either atom-by-atom or from fragments (using pre-defined fragments library or load a fragment from their local disk).

VMS-Draw includes a 3D polymerization tool which is able to replicate 3D microstructures. User has to select the repeating unit, the number of replica, the torsion angle of added replica, and the head and tail atoms of the polymer.

The graphical interface allows to set-up all the necessary parameters for the NMR and Rotational spectrum calculation, respectively, using VMS-NMR and VMS-ROT module.

Vibrational Analysis (for Gaussian Users)

Vibrational Modes

VMS Draw can be used for visualizing, animating, and plotting vibrational modes. Arrow size, animation, graphics quality etc. can be adjusted using the Jmol 3D molecular viewer. The vibrations can be displayed clicking on the peak of vibrational spectrum or selecting an element of the vibrational modes list.

Analyzing Gaussian Anharmonic Constants

VMS Draw allows analyzing Gaussian anharmonic constants (X, Y and Cubic Force Constants Matrix. An indicator of the magnitude of the contribution of the higher derivatives to the frequencies is the X Matrix. It can be split into different sub-matrices (containing Coriolis, cubic and quartic terms, respectively) Y Matrix, whose diagonal elements estimate the intrinsic anharmonicity. Speaking of the reduction of the dimensionality of a problem. An analysis of the Kiij force constants is helpful in order to reduce the number of normal modes which have to compute in an anharmonic calculation.

Vibronic Analysis (for Gaussian Users)

Mode Mixing and Huang Rhys Factor

The square of each element of the Duschinsky matrix that provides the overlap between each mode of the initial and final state. Shift Vector represents the displacement vector between the nuclear Cartesian coordinates from the initial to the final state of the loaded spectrum. Finally, VMS shows also the percentage of the actual intensity calculated based on the prescreening scheme with respect to the total intensity defined analytically.

Vibronic Geometries

One photon absorption and emission involve transitions between vibrational energy levels of two different electronic states. In order to visualize geometry changes accompanying electronic excitations, a tool has been set up, which superposes simplified stick and ball models of the equilibrium geometries of ground and excited states drawn in different colors.

3D plot for Resonance Raman spectra

It is possible to visualize both the spectrum and the excitation profile at the same time by employing a 3D plot with a color map to aid visualization.

UV/VIS Analysis (for Gaussian Users)

2D and 3D Molecular Orbitals

With this functionality, users are allowed to analyze molecular orbitals in the output file Gaussian 09 through a 2D diagram molecular orbital and a 3D interactive. The fragments can be defined and their percentage contributions can be displayed with a pie or ring chart for each orbital.

One−electron transitions

VMS Draw provides a tool to visualize the percentages of specific configurations for each overall electronic transition. The user can set manually the number of transitions reported in the histogram (changing Percentage Threshold and Exited States Range) and in the exported file.

PCM Analysis (for Gaussian Users)

PCM Surface

The Polarizable Continuum Model (PCM) using the integral equation formalism variant (IEFPCM) is the default SCRF method. This method creates the solute cavity via a set of overlapping spheres. It was initially devised by Tomasi and coworkers and Pascual-Ahuir and coworkers . PCM Cavity surface can be displayed by VMS DRAW. The user can change colors, transparency, wireframe, fill faces, dots, antialising and control the percentage of the molecule to be displayed based on clipping planes.