Features

You will be able to measure the bond distance, the angles and the dihedrals of your 3d structures; working with different conformers, at different temperaturesor with the same population when the energy is constant.

Mspin can be ran on a desktop or laptop computer, whether the user is running Windows, Mac or Linux. Just select the OS you need and download it.

The Mspin Graphical User Interface (GUI) consists of a plugin selector (J Coupling, NOE and RDC), an OpenGL based molecular visor, some buttons for general actions and the interface of the loaded  plugin.  It  is important to note that each plugin carries on its own GUI, which is independent of the main program. This interface is activated by clicking on the correspondent
icon inside the plugin selector box.

Currently, Mspin supports the following molecular formats:

• PDB
• XYZ
• Mol / SDF
• MacroModel / Maestro
• Gaussian98/03
• Gaussian Input
• Gaussian Archive
• Gamess US
• NW Chem

You can export the 3D molecule structures as Raster (*.bmp, *.jpeg) or as Vector graphics (*.eps, *.svg, *.pdf) just by using the Mspin interface.

JCoupling

Scalar coupling constants, in particular vicinal (3J) couplings, are widely used in NMR for the determination of relative stereochemistry and preferred conformation of molecules.

Use this feature to find out more about the skeleton of your compound by computing 2Js and 3Js by using a wide variety of Karplus like equations (Karplus, Altona, Diez-Donders) for both homonuclear (H-H) or heteronuclear (H-N, H-F, etc) couplings on small molecules, peptides and glycosides.

NOE.

The NOE (nuclear Overhauser effect) experiment is also extensively used, primarily, to define the stereochemistry within a molecule. Unlike scalar couplings, its mode of operation relies on the direct, through-space interaction between nuclei, and is independent of the presence of through-bond couplings.

This module computes NOE, TOE, NOESY and ROESY experiment intensities from phenomenological equations by using full relaxation matrix method (CORMA) to calculate NOE intensities from internuclear distances.

RDC

Residual dipolar coupling (RDC) is able to provide global orientations between remote internuclear vectors, and thus gives a potential solution to these limitations. RDC's have been widely used for the analysis of proteins and nucleic acids, but to a lesser extent in the small molecules area.

Fortunately, recent research results considerably extended the applications of RDCs to small molecules as new alignment media for organic solvents, either liquid crystal type as PBLG, or mechanically stretched cross-linked polymer gels such as poly(methyl methacrylate) gel (PMMA) or polydimethylsiloxane (PDMS) are available.

The use of RDCs in small molecule structural determination is typically based on the determination of the alignment tensor, a 3x3 matrix, which contains the information about the probability of the molecule pointing in a particular direction of the space. This matrix can be determined by least squares fitting to the experimental RDCs.