Recent changes to Home

Home modified by Daniele Licari

Daniele Licari — Sat, 28 Nov 2020 12:51:48 -0000

--- v2
+++ v3
@@ -1,37 +1,38 @@
-Features
-VMS-Draw in a Nutshell
-VMS Draw provides user-friendly access to Gaussian 16, Pickett’s SPFIT/SPCAT, SoSNMR and ESPIRES computational tools (the last only supported by VMS-Draw) with which an organic chemist user is easily able to predict and analyze Ultraviolet–Visible (UV/Vis), fluorescence, infrared (IR), vibrational circular dichroism (VCD), non-resonant Raman (nRR), resonance Raman (RR), Raman optical activity (ROA), resonance Raman optical activity (RROA), microwave, electronic one-photon absorption (OPA) and one-photon emission (OPE), electronic circular dichroism (ECD), circularly polarized luminescence (CPL) and nuclear magnetic resonance (NMR) spectra.
+# ** VMS-Draw in a Nutshell **
+VMS Draw provides user-friendly access to Gaussian 16, Pickett’s SPFIT/SPCAT, and SoS NMR  with which an organic chemist user is easily able to analyze  Ultraviolet–Visible (UV/Vis), fluorescence, infrared (IR), vibrational circular dichroism (VCD), non-resonant Raman (nRR), resonance Raman (RR), Raman optical activity (ROA), resonance Raman optical activity (RROA), microwave, electronic one-photon absorption (OPA) and one-photon emission (OPE), electronic circular dichroism (ECD), circularly polarized luminescence (CPL) and nuclear magnetic resonance (NMR) spectra.
+
+It is designed to be easy to install and use with a clean and intuitive interface. It’s written in Java, works in all platforms, tested in Windows, Linux and Mac OS X.

 Despite a number of graphical interfaces (such as GaussView, Chemissian, GaussSum, and other available competitors) has been already developed, VMS Draw provides the following features that are not available in the current solutions:


-Vibronic
+## Vibronic
 Vibrationally resolved electronic and resonance Raman (RR) spectroscopies are reliable way to simulate electronic spectra and involve transitions among 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 3D models of the equilibrium geometries of ground and excited states drawn in different colors. Furthermore, the RR scattering intensity can be plotted with respect to the energy of either the incident or scattered radiation, analyzing the Raman excitation profile and the Raman spectrum at the same time.

-Vibrational
+## Vibrational
 Besides the possibility of plotting anharmonic vibrational spectra and their vibrational modes, it allows to analyze the anharmonic constants which contain fundamental information regarding the capability of validate the calculation (X and Y matrices) and reduce the dimensionality of a problem (Kiij force constants matrix).

-Microwawe
+## Microwawe
 It includes VMS-ROT module which is the most suitable tool to simulate, interpret and assign a rotational spectrum, because it is actually based on the interplay of theory and experiment, also enabling the user to easily deal with different microwave techniques. It allows for accurately characterizing stable and transient species (ions, radicals, neutral molecules and clusters) in the gas phase and deriving information on their molecular structures and dynamics, information that hardly accessible from other experimental techniques.

-NMR
+## NMR
 It includes the (SoS)NMR module (developed in collaboration with Alfonso Pedone at University of Modena) to simulate NMR spectra which pave the way for the study of amorphous solids (polymers and multi-component inorganic glasses) and molecular crystals having a rich polymorphism and biomolecules.

-Excited state Analysis
+## Excited state Analysis
 VMS Draw is able to provide a plot of one-photon absorption electronic spectra using an Gaussian output of a single-point (SP) TD-DFT calculation. The intensity of the transitions is given by the module of the transition dipole moment.
 It can to analyze molecular orbitals from Gaussian calculations—MO energy and occupancy diagrams. MOs can be visualized as iso-surfaces or biulding the Energy Level Diagram. In addition, it provides a tool to visualize the percentages of specific configurations for each overall electronic.

-PCM Surface
+## PCM Surface
 It can display the solvation cavity used for an SCRF calculation with Gaussian. 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.

-Combining Spectra and Mixture Editor
+## Combining Spectra and Mixture Editor
 Combined and (possibly) weighted spectra data can be summed to obtain the overall spectrum. E.g., it can simulate the overall UV-Vis spectrum by summing the transitions of multiple excited electronic states. There are several possibilities to evaluate the composition of a complex molecular mixture with VMS Draw. A first option is to loaded fully ab initio spectra and scale them with the single contributions estimated from the Boltzmann populations. Alternatively, it is also possible to estimate relative amounts of sub-components by a procedure involving the fitting of theoretical spectra (varying contributions of single-component ones) to the observed experimental data.

-Overlapping and comparing spectra
+## Overlapping and comparing spectra
 It provides a fully integrated environment for direct comparison between different types of theoretical and experimental spectra. A specific module of VMS Draw allows to import experimental data from spectrometers, scanned image and PubChem Database. In order to compare more properly experimental and theoretical results, it offers runtime manipulation of spectra (normalization, unit conversion, broadening simulation, peak detection, smoothing filter, etc.). This feature is crucial to quickly identify the molecule that best fulfils desired properties amongst a series of possible candidates.

-Spectra Color
+## Spectra Color
 It 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.

-Molecular Editor and Polymerization
+## Molecular Editor and Polymerization
 Users can construct new structures either atom-by-atom or from fragments using Jmol Editor (embedded in VMS Draw). In addition, the 3D microstructures can be replicated with a 3D polymerization tool. A polymer can be created selecting the repeating unit, the number of replica, the torsion angle of added replica, and the head and tail atoms of the polymer.

Features modified by Daniele Licari

Daniele Licari — Sat, 28 Nov 2020 12:39:15 -0000

--- v1
+++ v2
@@ -1,8 +1,37 @@
-Welcome to your wiki!
+Features
+VMS-Draw in a Nutshell
+VMS Draw provides user-friendly access to Gaussian 16, Pickett’s SPFIT/SPCAT, SoSNMR and ESPIRES computational tools (the last only supported by VMS-Draw) with which an organic chemist user is easily able to predict and analyze Ultraviolet–Visible (UV/Vis), fluorescence, infrared (IR), vibrational circular dichroism (VCD), non-resonant Raman (nRR), resonance Raman (RR), Raman optical activity (ROA), resonance Raman optical activity (RROA), microwave, electronic one-photon absorption (OPA) and one-photon emission (OPE), electronic circular dichroism (ECD), circularly polarized luminescence (CPL) and nuclear magnetic resonance (NMR) spectra.

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+Despite a number of graphical interfaces (such as GaussView, Chemissian, GaussSum, and other available competitors) has been already developed, VMS Draw provides the following features that are not available in the current solutions:

-The wiki uses [Markdown](/p/vmspectrometer/wiki/markdown_syntax/) syntax.

-[[members limit=20]]
-[[download_button]]
+Vibronic
+Vibrationally resolved electronic and resonance Raman (RR) spectroscopies are reliable way to simulate electronic spectra and involve transitions among 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 3D models of the equilibrium geometries of ground and excited states drawn in different colors. Furthermore, the RR scattering intensity can be plotted with respect to the energy of either the incident or scattered radiation, analyzing the Raman excitation profile and the Raman spectrum at the same time.
+
+Vibrational
+Besides the possibility of plotting anharmonic vibrational spectra and their vibrational modes, it allows to analyze the anharmonic constants which contain fundamental information regarding the capability of validate the calculation (X and Y matrices) and reduce the dimensionality of a problem (Kiij force constants matrix).
+
+Microwawe
+It includes VMS-ROT module which is the most suitable tool to simulate, interpret and assign a rotational spectrum, because it is actually based on the interplay of theory and experiment, also enabling the user to easily deal with different microwave techniques. It allows for accurately characterizing stable and transient species (ions, radicals, neutral molecules and clusters) in the gas phase and deriving information on their molecular structures and dynamics, information that hardly accessible from other experimental techniques.
+
+NMR
+It includes the (SoS)NMR module (developed in collaboration with Alfonso Pedone at University of Modena) to simulate NMR spectra which pave the way for the study of amorphous solids (polymers and multi-component inorganic glasses) and molecular crystals having a rich polymorphism and biomolecules.
+
+Excited state Analysis
+VMS Draw is able to provide a plot of one-photon absorption electronic spectra using an Gaussian output of a single-point (SP) TD-DFT calculation. The intensity of the transitions is given by the module of the transition dipole moment.
+It can to analyze molecular orbitals from Gaussian calculations—MO energy and occupancy diagrams. MOs can be visualized as iso-surfaces or biulding the Energy Level Diagram. In addition, it provides a tool to visualize the percentages of specific configurations for each overall electronic.
+
+PCM Surface
+It can display the solvation cavity used for an SCRF calculation with Gaussian. 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.
+
+Combining Spectra and Mixture Editor
+Combined and (possibly) weighted spectra data can be summed to obtain the overall spectrum. E.g., it can simulate the overall UV-Vis spectrum by summing the transitions of multiple excited electronic states. There are several possibilities to evaluate the composition of a complex molecular mixture with VMS Draw. A first option is to loaded fully ab initio spectra and scale them with the single contributions estimated from the Boltzmann populations. Alternatively, it is also possible to estimate relative amounts of sub-components by a procedure involving the fitting of theoretical spectra (varying contributions of single-component ones) to the observed experimental data.
+
+Overlapping and comparing spectra
+It provides a fully integrated environment for direct comparison between different types of theoretical and experimental spectra. A specific module of VMS Draw allows to import experimental data from spectrometers, scanned image and PubChem Database. In order to compare more properly experimental and theoretical results, it offers runtime manipulation of spectra (normalization, unit conversion, broadening simulation, peak detection, smoothing filter, etc.). This feature is crucial to quickly identify the molecule that best fulfils desired properties amongst a series of possible candidates.
+
+Spectra Color
+It 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.
+
+Molecular Editor and Polymerization
+Users can construct new structures either atom-by-atom or from fragments using Jmol Editor (embedded in VMS Draw). In addition, the 3D microstructures can be replicated with a 3D polymerization tool. A polymer can be created selecting the repeating unit, the number of replica, the torsion angle of added replica, and the head and tail atoms of the polymer.

Home modified by Daniele Licari

Daniele Licari — Wed, 25 Jun 2014 13:24:06 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Daniele Licari (admin)