|Indiana University Molecular Structure Center|
The following information is provided for internal Indiana University Bloomington Campus users of the IUMSC. Collaborators who are not located on the IUB campus should contact firstname.lastname@example.org for details on external use of the facility.
Introduction to facilities.
The IUMSC is a service and research unit of the Department of Chemistry, Indiana University, Bloomington campus. It was established by the department to assist faculty within the department in obtaining structural information using the techniques of X-ray diffraction.
The laboratories of the IUMSC are located on the fourth floor of what is referred to as the "64 addition" of the Chemistry Building complex on the IUB campus. The public entrance to the facility is via. A421, located at the south end of the west corridor. A "tour" of the laboratory is available from the "Virtual Laboratory Tour" page of this site.
The facility is staffed by professionally trained crystallographers who are available to collaborate with researchers with all aspects of X-ray diffraction. A receptionist is available in A421 to answer questions and direct inquires to the appropriate person.
The laboratory is normally open from 8:00AM - 5:00PM on Monday through Friday. Because staff meetings are held Tuesday mornings, the laboratory usually does not open until 11:00AM. If the entry door is unlocked at other times users are welcome to come in, but please try to minimize staff interruptions. Because the laboratory operates on a continuous basis, the professional staff are often present at hours other that those stated above. Researchers who need access to the facility evenings and weekends can be issued keys.
Room A421 contains a variety of computers and other hardware of use to researchers using the facility. A complete description of the computing facilities is given below. The computers available in the IUMSC have all been obtained for specific purposes--crystallographic data manipulation, molecular visualization, etc., and none of the systems are available for "general-purpose" computing (i.e. word-processing, E-mail, etc.).
In addition to the X-ray diffraction and computing facilities, the IUMSC is equipped with microscopes that can be used to examine samples, and molecular model sets are available for use within the laboratory. The copy machine and other "office" equipment in the IUMSC are NOT available for general use (see receptionist if you need copies of crystallographic information in the laboratory)
We strongly encourage all first-time users to visit the facility and speak with the Director or one of the professional staff prior to submitting any samples. Due to the complex nature of crystallography and the safety hazards involved, most of the work performed in the laboratory is assigned to one of the professional staff. Even researchers with extensive crystallographic experience are not familiar with the hardware and computer systems in the IUMSC. It is important that users work with the staff to ensure optimum utilization of the facility and to insure that the results are meaningful and appropriate for the problem being studied.
The IUMSC has made a concerted effort to minimize the need for researchers to have to visit the laboratory (although visitors are always welcome!) except for submitting new samples and picking up samples that have already been examined. Most laboratories in the department that heavily use the facility have been equipped with stereo binocular microscopes for examination of crystals (contact the Director if your laboratory needs a microscope). For occasional users there are microscopes in A423, and researchers are always encouraged to consult with the staff about crystal quality. Users should always ask before using the microscopes in case delicate samples have been left out.
The IUMSC has available several sophisticated software systems designed to aid in the interpretation of crystallographic data. Included are the Cerius2 visualization and modeling system from Molecular Simulations, Inc., the SHELXTL PC system, the locally developed XTEL system for data manipulation, XMView for molecular graphics, and a host of other programs. In addition, the common crystallographic data bases are available via the computers in A421, as well as from other systems attached to the departmental network. The Scintag powder diffraction analysis library is available for researchers who have submitted powder samples for analysis.
Silicon Graphics workstations in A701 are available to all chemistry personnel who need to use the specialized graphics software available. Researchers who need a system for crystallography support (i.e. XMView, accessing CSD data base, etc.) are encouraged to contact the ITG for details. Details on obtaining accounts on the computers is given in the section on Computing Facilities, below.
Arrangements can be made with the Director to utilize the CAVE system maintained by the VR/VE group in Lindley Hall to view results of structural studies using XMView/CMView.
Finally, copies of nearly all of the 2,500+ reports generated by the IUMSC are available on the IUMSC web server (http://www.iumsc.indiana.edu).
The professional staff are always available to visually examine crystals and give advice on crystal quality. In addition, the staff thoroughly understand what data can and can not be obtained with the equipment on hand, as well as what limitations there are. They can help the user to better understand when an absolute structure can be determined, when hydrides can be reliably located, etc. All users are strongly encouraged to consult with the staff at any time. The IUMSC does NOT offer crystallization as a service. There are several readily available resources for those having problems (see, for example, Paul Boyle has some excellent crystal growing tips available from the crystallography facility at North Carolina State University).
In general, samples for single crystal structural analysis should be well-formed with sharp well defined edges and mirror-like faces. Light atom structures (i.e. no atoms heavier than Z = 40) should have a minimum crystal dimension of 0.3 mm. Ideal crystals are equidimensional with few observable imperfections, although poor-looking samples can often yield excellent results. Air sensitive samples should be submitted in several sealed tubes so that accidental exposure will not destroy the entire sample. Slowly-grown crystals are almost always of better quality than those grown rapidly. Do NOT subject crystals to vacuum drying, as solvents of crystallization may be present. If the crystals appear to become opaque upon drying (or show obvious fracture lines), they are undoubtedly losing a solvent of crystallization. In such cases the sample must be kept under the mother liquor at all times, and appropriate notes made on the sample submission sheet.
It is certainly to the advantage of the person submitting the sample to run several simple stability tests on the crystals prior to submitting the sample. It will greatly increase the likelihood of a successful investigation if the staff are aware of any potential problems.
When a suitable sample has been obtained, a "Sample Submission Form" must be completed and left with the sample on the table adjacent to the A423 entry door. Pre-numbered Sample Submission Forms are located in the bin on the sample submission table. The form with the lowest number should be used. This number is used to track the sample in the laboratory, and should immediately be entered into the researchers laboratory notebook. Any questions or requests for information should always be accompanied by this number. DO NOT remove these forms from the laboratory. If itis necessary to withdraw a sample, or if a form is ruined, ask for assistance from the receptionist or a professional staff member. An e-mail note will be sent to the research advisor acknowledging the submission of the sample and requesting verification of the account number.
Many of the samples examined in the IUMSC have special handling needs. As shown in the Annual Reports, 90% of the submitted samples are either oxygen or moisture sensitive, undergo solvent loss, are temperature sensitive or are a combination of the above. Feel free to consult with the staff concerning the special handling requirements for your sample. As stated above, all samples which are "at risk" should be submitted in duplicate containers. Note also that there is a surcharge for special handling requirements.
If there are any "special" risks involved in handling or storing the sample, be certain to not only note this on the Sample Submission Form, but also discuss the problem with one of the staff. If a sample cannot be left in the IUMSC (i.e. it must remain in a laboratory drybox, etc.), it is essential that arrangements be discussed with one of the professional staff. All users should remember that storing a sample in a location other than the IUMSC can lead to delays in examination of the sample.
We are frequently requested by new users from other laboratories to utilize techniques that they, or collaborators they worked with, successfully employed at their previous location. While we are always willing to listen to suggestions and look at alternative methods, it is impractical to modify our special handling techniques for each new user. With over 3000 reactive samples having been examined in the IUMSC, we feel confident that we can handle nearly every situation. It is imperative, however, that users work with the staff so that we fully understand the problems likely to be encountered.
Questions often arise concerning the scheduling of samples. While the general rule is first in-first out, there are exceptions, and many factors will effect when a particular sample is placed on an instrument. With the SMART6000 now in place, most samples will be examined within one week. While the director will have final jurisdiction on scheduling, the following are some of the considerations:
a.) Stable samples with excellent optical properties (i.e. well formed faces and morphologies) may receive higher priority because they maximize the time available to the professional staff and have little impact on available instrument time.
b.) Some samples may wait until a particular staff member has instrument time available. This is especially true for similar samples in a continuing project.
c.) "Urgent" samples will be given priority if sufficient justification is given (unusual).
d.) Samples which are especially reactive or require special handling, especially when only one sample vial is present, may be delayed to maximize the chances of obtaining a suitable crystal. They may also be given priority when prior arrangements have been made.
e.) Environmental conditions (high laboratory humidity, etc.) can lead to delays for certain types of samples.
F: Data and Report Distribution
The traditional IUMSC hard copy Report typically consists of up to 100 pages of numeric and graphic data. It is the intention to continue to make such reports available for as long as they prove useful. We are, however, encouraging all users to switch to strictly electronic access for data and reports. If requested, complete copies of reports will be generated and the user charged copying fees.
The preferred method of obtaining structural data is via the IUMSC Web server. The server is the outgrowth of a New Computing Initiatives grant (Office of Information Technology, IU), and a class project for a Computer Science course (CS490w) at Purdue University. Details of the data format and searching procedure are available. All structures completed after 1990 are now located on the server, and efforts are being made to transfer all remaining structures. If a structure is not available on the web database, it will be added upon request (contact the receptionist). The server also allows users access to most of the crystallography programs used by the IUMSC. Users are encouraged to learn how to use the available software to maximize the usefulness of the crystallographic data.
All users will be kept informed via. e-mail when your crystal is placed on the goniostat, when a preliminary structure is available, and when the final files are posted. All data and results generated in the IUMSC will be posted on the WWW server. Those researchers who desire confidentiality for their data will have password protection applied, and the compressed libraries will be encrypted if desired. Please do not request password protection and encryption unless absolutely necessary, as this adds greatly to the administrative overhead.
G. Powder X-ray Diffraction
Powder diffraction is best known as a "fingerprint" technique used to identify known phases. A uniformly ground sample will yield a spectra characteristic of the compound in a given crystalline form. If the sample has been recorded in a searchable database, it is possible to compare an unknown with the know spectra to identify it. If the single crystal structure is known, it is also possible to calculate the spectra one would obtain for the material in a powdered sample. Thus, not only is powder diffraction an excellent tool for identifying a known common phase, but can be used to insure that the bulk sample is consistent with the spectra based on a single crystal study.
The IUMSC has available (room A423F) an automated Scintag Powder Diffractometer system. The existing system is interfaced using locally developed hardware and software.
The procedures for submitting X-ray powder samples are similar to those for single crystal analysis. Researchers should fill out a "Powder Diffraction Sample Submission Form" and leave it with the sample. As with the single crystal procedure, the form should not be removed, even if the sample is withdrawn. Users are requested to either choose the default conditions for the spectra or to specify the required values. Any single run which requires more than 20 hours must be discussed with the staff.
The IUMSC will work with researchers who have air-sensitive and/or other special needs, but users are cautioned that the existing equipment was not designed for non-ambient experiments. A cold stage is under development to assist users with low temperature needs.
X-ray powder diffraction requires considerably more sample than a single crystal analysis. Users should submit at least 1/2cc of material whenever possible.
IUMSC staff will attempt to identify unknown materials whenever possible, but users are cautioned that, unlike single crystal studies, there are significant chances for misinterpretation. In all cases, the raw data are available for the researcher to draw their own conclusions.
H. Crystallographic Databases Available
In addition to the IUMSC reports available on the IUMSC WWW server, the laboratory has available the following crystallographic databases:
a.) Cambridge Structural Database (CSD). A compilation of over 200,000 organic and organo-metallic compounds reported in the scientific literature as indexed by the Cambridge Crystallographic Data Centre (CCDC). Users can search the database for known compounds, substructures, journal citations, authors, etc. In general, the CSD is a comprehensive database of carefully reviewed crystallographic data. An on-line manual is available for persons wishing to use the CSD. The CSD is available on the Silicon Graphics network, as well as via the UNIX research systems at UITS (University Information Technology Services). In addition a Linux based PC in A423 has the CSD locally installed.
b.) Inorganic Crystal Structure Database (ICSD). A compilation of over 50,000 inorganic structures which are not in the CSD. While the database is not as elegant as the CSD, it allows easy access to many common inorganic compounds and minerals. The ICSD is available via several systems in the IUMSC.
c.) National Institute of Science and Technology (NIST) Crystal Data files. A compilation of the cell parameters and other basic crystallographic data on all reported crystals. Reduced cells are given as well as search programs to compare experimental cells with those in the database.
d.) Protein Data Base (PDB). The PDB is the depository for macromolecular structures. Since 1995 these are searchable via the CSD as well.
All of these databases are available from computer terminals located in A421. In addition when licensing agreements allow, some of the databases may be accessed using properly configured workstations connected to the departmental network.
Information on how to access and use the databases is available on the IUMSC web server.
I. Computing Facilities in the IUMSC
The IUMSC contains primarily Intel based (i.e. IBM PC compatible) workstations and Silicon Graphics workstations. The locally modified Picker X-ray diffractometers are controlled by Intel 80486 IBM compatible PC's, and the SMART6000 frame buffer is a 400MHz Pentium III system. Workstations for the staff consist of pentium systems. Silicon Graphics systems (Idigo, Indigo-Elan, O2) are used for molecular visualization. Data servers for the laboratory include a SG Challenge and gateway 2000 P5-120's.
J. Instruments Available in the IUMSC
The major (non-computer related) instrumentation in the facility consists of:
Specialized X-ray equipment, including
Crystal mounting and handling facilities, including
Additional support equipment in the IUMSC include
K. Security and After-hours Access to the IUMSC
Because of the hazards involved with ionizing radiation (X-rays), and the fact that open beam experiments are necessary, access to the instrument laboratory (A423) is severely restricted. In general, NO keys are issued except in rare instances. The open computing and molecular visualization areas (A421) are generally open during the day, and keys will be issued to this area when a researcher can show a demonstrated need. It should be emphasized that persons issued keys are never to allow entrance to others, and they are to use only those systems for which they have been checked out on. Researchers with justifiable needs for access must undergo a series of safety training sessions prior to being issued a key.
Activity in the laboratory (both A421 and A423) are monitored continuously by video cameras after hours and on weekends.
L. Publication, Authorship, and Ethics
Questions often arise concerning the authorship of papers which include crystallographic results, as well as proper referencing of crystallographic materials.
One often hears the argument that the crystallography required only one week (or less), while the collaborator has spent months, if not years preparing the compound. It should be pointed out that the reason it only took one week is because the professional staff have spent hundreds of hours to develop and implement the equipment and procedures being used. The IUMSC is fortunate in having over 100 man-years of crystallographic expertise on the existing staff. The programs being used have been written, modified, and updated continuously since the IUMSC was established in 1968. The program used to drive the goniostat, for example, has been completely rewritten at least four times in the past twenty years, and consists of over 6000 lines of code.
The counter argument can be made that once all the starting materials and equipment had been gathered for a given synthesis (surely routine technician work), it was kinetics, not the intellectual skill of the chemist, that determined how long it took to synthesize a new compound.
There are several sources which attempt to clarify the question of "ethically correct" authorship of crystallographic results. In general, the following criteria have proven adequate in the IUMSC, and are considered the appropriate way to handle crystallographic results.
1) If the structural information is a major part of the intellectual content of the paper, and if this information has been derived primarily by X-ray diffraction, then the crystallography should be included in the paper and the crystallographer should be considered a co-author. Most papers which include metric parameters (i.e. distances and angles) would fall under this classification. The professional staff who performed the crystallographic portion of the research should assist in the preparation of, and be allowed to review publications which use the structural data.
2) If crystallography is used only to confirm a structure which is well-established by other means (nmr, mass spec, etc.), and if no structural details are given in the paper, only an acknowledgment is necessary. This would occur, for example, when the relative stereochemistry of an intermediate in a complex organic synthesis has been determined. In such cases, the crystallographer should be allowed to publish the structural results of the investigation independently if desired.
A related problem is that of proper citations. With the numerous databases in use, it is important that we properly cite the source. If users have any questions concerning the proper way to cite any of the sources in the IUMSC, they should contact one of the professional staff.