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Molecular Structure Laboratory

Resources


Molecular Structure Laboratory / Resources Updated: October 25, 2016

  • Collaborators
  • Laboratories
  • Publications
  • Societies
  • Software
  • Idealized Geometry Library
  • Solid-G
  • In-house Programs
  • Vendors

Recent collaborators outside University of Wisconsin-Madison in alphabetical order (number of joint publications).

Dr. Arderne, Charmaine. University of Johannesburg, Johannesburg, South Africa. (2).

Dr. Bakac, Andreja, Iowa State University, Ames, IA, USA. (3).

Dr. Bikzhanova, Galina, Covance, Madison, WI, USA (6).

Prof. Choi, Soo Hyuk, Yonsei University, Seoul, Republic of Korea. (13).

Prof. Czerwinski, Curtis J. University of Wisconsin-La Crosse, La Crosse, USA. (7).

Prof. Darkwa, James, University of Johannesburg, Johannesburg, South Africa. (75).

Dr. Dolomanov, Oleg V. Olexsys, Durham, UK.(2)

Dr. Fukin Georgy, Razuvaev Institute of Organometallic Chemistry, Russian Federation. (3).

Prof. Gerasimchuk, Nikolay, Missouri State University, Springfield, MO, USA. (1).

Prof. Guino-o, Marites. University of St. Thomas, MN, USA. (1).

Prof. Han, Baocheng, University of Wisconsin-White Water, White Water, WI, USA. (1)

Dr. Ivanov, Sergei A., Center for Integrated Nanotechnologies, MPA-CINT, Los Alamos National Lab, USA (5).

Prof. Larsen, Anna, Ithaca College, Ithaca, NY, USA. (1).

Prof. McGaff, Robert, University of Wisconsin-La Crosse, La Crosse, USA. (10).

Prof. Minelli, Martin, Grinnell College, Grinnell, IA, USA. (6).

Dra. Paz Sandoval, Angeles, Centro de Investigación y de Estudios Avanzados (Cinvestav), Mexico City, Mexico. (5).

 

 

 

 

Low temperature technique compilation (the file contains publications by Dietmar Stalke (Georg-August-Universität Göttingen), Sean Parkin (University of Kentucky) and Håkon Hope (University of California-Davis) power point by Vic Young (University of Minnesota), comments by Maren Pink (Indiana University), Khalil Abboud (University of Florida), Dima Yufit (Durham University), Ilia Guzei (University of Wisconsin-Madison), and publication by J.W. Pflugrath (Rigaku).

Site with resources on structures containing several independent molecules in the asymmetric unit.

Awesome wrapped in awesome: guidelines on how to prepare an Impactful Scientific Poster.

 

Bruker-AXS - Programs distributed by my favorite X-ray equipment vendor.

Coot - A new excellent Crystallographic Object-Oriented Toolkit for macromolecular refinement.

Diamond - Crystal and Molecular Structure Visualization Tool (PC only). Our Chemistry Department has a site license.
Installation instructions:

  1. Download and install Diamond 3.1 (Diamond Demo Version 3.1).
  2. Download the license file and put it into the Diamond program directory, usually "C:\Program Files\Diamond". The license file download requires a name and password available from the Director of the X-ray Laboratory.
  3. (Optional but recommended). Download and install POV-Ray (free) in order to create visually striking (artistic) images with Diamond.

 

OLEX2 - is a program for the determination, visualisation and analysis of molecular crystal structures. Currently (August 2014) it is my favorite skin for working up crystal structures. Of course it utilizes George Sheldrick's programs, but the graphics interface is wonderful. Read my notes on OLEX2 that will take you beyond the basics.

PLATON. A versatile crystallographic program implementing a large variety of standard geometrical calculations, tests, utilities, graphics and several filters.

ROTAX for Windows twinning software (Determine Twin Matrix from Fo/Fc Data) by Simon Parsons and Bob Gould.

SHELXTL - the latest versions of the programs written by Prof. George Sheldrick are available with a password. The public domain SHELX package programs have full functionality. SHELXL home page.

International Union of Crystallography has recently released program publCIF that is exceptionally valuable in preparation of manuscripts for Acta Cryst. C and E: go to http://www.iucr.org/, select Acta Cryst. C, Author Services, How to Prepare Your Paper, publCIF.

The Idealized Molecular Geometry Library has migrated to a different page integrated with OLEX2.

To access the database from OLEX2 select Tools->Disorder->Ilia's Fragment Library.

 

Program Solid-G

Solid-G is a PC program that allows fascile computation of ligand solid angles in organometallic compounds. The solid angles are converted to percentages (G-values) that illustrate the extent to which each ligand shields the central metal. In the second column there are three figures. The top one is the scheme of a Mg complex and the animated GIF below represents the steric behavior by the two ligands - each ligand and its shadow are assigned a color. The bottom figure demonstrates that Solid-G can handle quite complex compounds and measure steric interaction among ligands.

The program is free to use (at your own risk), but the paper by I.A.Guzei, M. Wendt.  Dalton Trans., 2006, 3991–3999 must be referenced.

The principles implemented in the program are described in
I.A.Guzei, M. Wendt.  Dalton Trans., 2006, 3991–3999.

The 79 papers mentioning solid angle computations with Solid-G are listed on a separate page (as of February 8, 2016).

movie

The zip file contains all the info you need. 

Create
c:\SolidAngle\
directory and extract all the files into it.  Then run Solid-G.exe.  The instructions on how to use the program (quite simple really) are displayed via the "Manual" button. 

The file with extension .xyz is an example input file.

You can Open the xyz file and then go from one activated button to the next.  The blue progress bar can sometimes get stuck but the calculations will continue regardless.  In my experience the program has never hung during normal operation.  The input coordinates should be Cartesian rather than fractional. 

If you want a smooth picture in the visualizer (Start Viewer button) use
view->define bound sphere->granularity
and set it to a multiple of 180.  900 works well. Then you can copy and paste pictures into other programs.

complex

BondComparerDOS - A program for comparing values with standard deviations. Run it from the command line.

G1 estimates the molecular volume, linear absorption coefficient, and conducts elemental analysis.

G4_fcf_filter - this crystallographic program reads CIF and FCF files, suggests outlier reflections, and can create a new INS file. The reference for the general approach is Prince, E., Nicholson, W.L. (1983) Acta Cryst A39, 407-410. For the suggested value for the cutoff see Rollett J.S. (1988) Crystallographic Computing 4, 149-166, Oxford University Press.

The latest CIF for instrument Bucky. Updated August 9, 2016.

The latest CIF for instrument Gromit. Updated August 9, 2016.

Software references for the programs used in the Molecular Structure Laboratory. Updated January 12, 2015.

X-ray diffraction system manufacturers

Bruker-AXS | Oxford Diffraction | Rigaku

Low temperature device manufacturers

CryoIndustries of America | Oxford Cryosystems

Crystallographic supplies

Hamptom Research | MiTeGen



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