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              Department of Chemistry & BiochemistryUniversity of Maryland,  College Park, MD 20742    

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General info:

  
  • Users of X-ray diffractometers (powder XRD and SAXS) may request access to the X-ray lab and permission to work on x-ray equipment. This however reqiers to pass Radiation Safety traning and then training on specific instrument.
  • There are two levels of the lab access. Supervised (Individual) user is allowed to work on the instrument only under the supervision of XCC staff, an unsupervised user or the crystallographer (PI). Unsupervised (Authorized) user is one who can access lab anytime and is allowed work on the instrument independently.

  • You should consider to get trained on the XRD instrument if you planning to use machine often as it involve time and cost. If you need to use XRD only occasionally, you could submit samples and XCC stuff with perform experiment and basic analysis. In this case you will be referred as Submitting user.

     

How to become XCC User:

  
  1. In order to operate X-ray systems you have to be trained but first you should pass "Radiation Safety Training for Use of X-ray Devices" online (start here) and request and obtain radiation safety certificate; for more see Radiation safety office web site.
  2. Bring/Email copy of radiation safety certificate and User Registration Form.

  3. Schedule 2 session training on the specific instrument which with RA (Timothy Diethrich tjd5@umd.edu) or any unsupervised user using your own samples and on completion final 3rd session with PI.

  4. For each training you should bring 2-3 samples and Sample Submission Form and for final 3rd* training you also need to bring Lab Acces Form.
     

Note: For training on SAXS use different SAXS submission form and contact Dr. Wonseok Hwang whwang@umd.edu.

  • On the completeing of training you will become supervised user working under supervision of me, TA or any unsupervised user during normal working hours. You will be granted access to the lab and online reservation system.

  • After 3 month of experience, You can apply to unsupervised user status who can work independently with 24/7 access. It could be experience obtained previously.

  • Feel free to stop by if you want to discuss measurements or training. My office is next to XCC lab in the basement of wing 1 in Chemistry building, office hours 1pm 5pm, email: pzavalij@umd.edu, phone: 5-1861.

     

Submiting Samples for Analysis:

  
  • Single Crystals for Crystal Structure Determiantion has to be submitted to the X-ray lab along with Single Crystal Sample Submission Form (Word) [Apex2] which has to be signed by PI/advisor.
  • Samples for Powder Diffraction have to be submitted along with Powder Sample Submission Form [D8, C2, X'pert] to the PI, RA (Timothy Diethrich tjd5@umd.edu).

  • SAXS samples have to be submitted along wirh SAXS submision Form (Word) [Xeuss] to the PI, RA. (Dr. Wonseok Hwang whwang@umd.edu).
     

  • In cases when sample has to be stored under certain conditions, only the form may be submitted and the user will be asked to bring the sample when experiment is scheduled.
     

  • First time users are strongly encouraged to discuss experiemnt with RA or PI first, expecially SAXS samples.

  • Internal users have to drop off samples at the lab or give them to RA or PI, DO NOT mail samples by internal mail

  • External users may send sample by mail along with corresponding Sample Submission Forms.
     
     

Managing Data Files and Folders:

 

Data Folders:

  • ALL FILES (raw experimental and reduced data) should be placed only in the directory "C:\FRAMES\<PI>*", where <PI> is name assigned for each group (usually PI is Advisor last name or last name & initials).

  • It is advised that each user creates his/her own subdirectory <UserName> in the <PI> directory, especially when there are several users from the same group/advisor.

  • It is also strongly recommended to create sub-subdirectory for each project (set of samples). When another project is stored in the same directory, it will be impossible to use original raw data from the first project as the instrumental parameter file will be overwritten with newer one that could be different.

  • Sub-directory name could be for example <date+project-name, so that full path looks like:
    - On D8 Advance   - C:\_Data\<PI>\<UserName>\<Date-Project>\
    - On C2 Disvcover - C:\FRAMES\<PI>\<UserName>\<Date-Project>\
    - On PANalytical
        - C:\XRD data\<PI>\<UserName>\<Date-Project>\

  • SAXS data files are stored on Linux box in subdirectory inside directory external, for example:
    - Xeuss Linux PC - \\...\external\YYYY-MM-DD_Adisor-UserName\
    Details on how to create and organize files are provided during training an can be found in log book.
     

 Storing data files:

  • Data folders and files are automatically archived/backed-up to manager PC on daily basis and less often (weekly and monthly) they are copied to external disk and university server.

  • Nevertheless it is strongly recommended to users to make their own copy of data.

  • All data are stored on the instrument computers at least for 3 year and then may be deleted in case of large raw data files, e.g. *.gfrm frames on C2. Yet all data are stored indefinitely on external hard drive and university server and can be requested anytime.
     

Results sent to Users, Final Reports & Data Retrieval :

Powder Data are provided to users (who has no access to the lab):

 
  • Text file (.xy) with powder diffraction pattern containing two columns: 2-theta and Intensity that can be imported in any spreadsheet.

  • Power Point slide(s) with diffraction pattern and (if performed) with identified phases and their approximate quantities.

  • Sample image, copy of original experimental data (frames), powder diffraction pattern in other formats available on request.
     

Single Crystal data are usually provided in ready for publication form:

 
  • The final results are always checked for chemical sense and consistency. Nevertheless it is strongly recommended that user double check geometry, charge balance, compare similar distances, angles, and especially amount of H atoms and their position, and H-bonds.

  • In non-trivial cases, during the crystal structure determination/refinement user could be asked about additional information or supplied with preliminary structure for checking or in order to resolve problems/questions that arise and to determine necessity of finalizing the structure if it is not what was expected.

Final structure is checked using Check-CIF procedure from Platon software (or online from IUCr site) and the final results are supplied in the following files named by 4-digit lab crystal number:

  • Crystallographic Information File (.CIF) containing variety of crystallographic and experimental information. Planes and dihedral angles between them are refined per request and added in CIF file in _geom_special_details section.

  • In case of substantial disorder often included is also cif file *DRAW.CIF (or *ORDERD.CIF) with removed alternative orientation of disordered species.

  • Final report file (.HTML) containing 5 to 8 tables with crystal data, experimental conditions, atomic parameters, bond length, valence and torsion angles, occupation factors and H-bonds. Description of crystal, experimental setup and brief refinement details are also included. The final report includes useful ellipsoid plot (unlabeled) and sometimes packing diagram.

  • ShelX coordinate file (.RES) and final refinement output file (LST) are provided if requested. These files contain information which can be used to evaluate quality of the refinement and experimental data, e.g. largest peaks and holes from the residual difference Fourier map.

  • Reflection data file (.FCF) containing list of unique observed reflections and their observed and calculated intensities. This file is required by some journal as supporting materials. This file is e-mailed on the user request.

  • Note: new ShelXL version embeds .RES and .FCF files inside .CIF and therefore they are not provided separately.

  • Platon output files (.lis) with various geometric calculation and Check-CIF warning are generated by sent only when requested.

  • Full final data set contains much more files including original files from the integration, crystal snapshots, structure drawing (usually included in the final report), and all refinement files. These data are compressed in ####.zip file and can be furnished per request.