The Crystallographic

Overview of this Lecture

Information File (CIF)
Description and Usage • An Overview of the Status of Single Crystal
X-Ray Structure Determination

Ton Spek,
• The What, Why and How of CIF
Bijvoet Center for
Biomolecular Research
• CIF Usage and Applications
Utrecht University
Leiden, 27-Jan.-2009.

A Single Crystal X-Ray Study

Crystal Requirements
Involves
• A Structure Query (What did I make?) • Preferably a single crystal
• Needed: A Single Crystal (0.2 mm) (Sharp Extinctions under Polarized Light)
• Collection of X-Ray Diffraction Data
• Block rather than slim long needle
• Solution of the Phase Problem
(To get a Preliminary Model) • Fresh from mother liquor
• Structure Model Parameter Refinement • Unstable crystals covered with inert oil
• Interpretation of the Result/Geometry Analysis Data collection under cold N2 stream.
• Validation of the Analysis • Twins and split crystals possible but best avoided
• Report and (Co)Publication when possible.

Example of an Oil-mounted Crystal

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 H,K,L, I
Short History of Data Collection
• 1912 – von Laue et al. Experiment – X-ray Film
• 1913 – Bragg – Diffractometer + Detector
• Tot ~ 1965 Film (Weissenberg, etc.)
• ~1960-1995 – Serial Detector Diffractometer
~ 50 datasets / year
• 1995 – present – Image plate/ CCD Detectors
a few hours Collection Time for a Routine Structure
• ~2007 – Digital Detectors (AXIOM, Pilatus etc.)
new options: shutterless, low noise etc.

Diffraction Pattern of a crystal rotated over 1 degree

LNT

X-ray CCD - Detector

Crystal

Goniometer

X-Ray source, Goniometer & Serial Detector X-ray source, goniometer + crystal, N2-cooling and CCD Detector

Central Formulae Solution of the Phase Problem

• Diffraction Spots: 2dhkl sinθhkl = nλ • Early Method: Trial & Error (Salts such as NaCl,
• Electron Density Map (3D Fourier Map) Silicates etc.)
ρx,y,z = 1/V Σhkl Fhkl exp{-2πi(hx + ky + lz)} • Patterson Methods (Heavy Atom)
• Structure Factor (Model) • Direct Methods (SHELXS, DIRDIF, SIR)
Fhkl(calc) = Σj fj Tj,hkl exp{2πi(hxj+kyj+lzj)} • New: Charge Flipping (Ab-initio)
• Least Squares Model Refinement
Minimize: Σhkl [whkl(|Fhkl(obs)|2-|Fhkl(calc)|2)]2 • Phase Problem Solved! Given reasonable data.
• Convergence Criteria: R1, wR2, S

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 3D-Fourier Map

• Given the Diffraction Data and (Approximate)

Phases a 3D Electron Density Map can be
Calculated.
ρx,y,z = 1/V Σhkl Fhkl exp{-2πi(hx + ky + lz)}

Fhkl = |Fhkl|exp(φhkl)

• Following is a section through such a map

Interpretation in Terms of Atoms

• Position of highest density => Position x,y,z
• Deviation of the density shape from the ideal
atomic electron density => Thermal motion
parameters:
• Isotropic: U(iso) or
• Anisotropic: U11,U12,U13,U22,U23,U33
(Displacement Parameters) => ORTEP
Note: ORTEP does NOT represent the electron
distribution.

Interpretation in Terms of Bonds Display Options

• Bonds between atoms of type A and B are • Ball-and-Stick
assigned on the basis of atomic covalent Simpel but may hide problems with a
radii with: d < R(A) + R(B) + 0.4 structure.
• ‘Crystallographic Bonds’ are not • ORTEP
necessarily Chemical Bonds. Often preferred because it visualizes most
• Van der Waals Radii are used to detect model parameters and possible problems.
isolated molecular species or short contacts. • CPK
Spacefilling PLOT illustrating the shape etc

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 A pretty picture, but what
about the numbers …

Parameter Model Refinement

• Translate the 3D electron density in terms
of position and temperature parameters
• Non- Lineair Least Squares Method
Min: Σhkl [whkl(|Fhkl(obs)|2-|Fhkl(calc)|2)]2
• Time consuming: disorder, weak data

Analysis Computing in the Past

Interpretation (geometry, intermolecular • University Mainframe
interactions etc.) • Mainly Batch Mode (Long Waits)
• Structure Validation • Storage on Magnetic Tape
• (Co)Publikation • Piles of Lineprinter Output
• Primitive Computer Graphics
• Results to Cambridge Crystallographic
• No Internet
Database CSD (~500000)

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 16kW
Operator

Plotter Output Input

Console
~1966, Electrologica X8 ALGOL60 ‘Mainframe’ (<1MHz)
Flexowriter for the creation and editing of programs and data

Archival of Model Parameters

Data Storage in the Past
in a Publication (Acta Cryst.)

Direct Methods ALGOL60 Program AUDICE on Papertape

Archival of Reflection Data in

Computing Today
a Publication (Acta Cryst.)
• Personal Workstation (MS-Windows or
Linux)
• No queues for Computing Facilities
• Good graphics & Hardcopy
• Unlimited Disc Storage
• Internet (exchange, information)
• Automation

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 Announced Aug 2007: Tabletop
Problems Around 1990
‘Black Box’ – Smart X2S
Mount crystal and load • Multiple Data Storage Types
• No Standard Computer Readable Format
• Data Entry of Published data via Retyping.
• No easy numerical checking for referees
etc.
Structure ?
• CSD Database Archival by Retyping from
the paper
• Multiple typo’s in Published Data

Solution What is CIF ?

From: http://ww1.iucr.org/cif/index.html
• CIF-Standard Proposal
• S.R. Hall, F.H. Allen, I.D. Brown (1991).
Acta Cryst. A47, 655-685.
• Pioneered and Adopted by the International
Union for Crystallography
• Adopted by the author of the most used
software package SHELXL
(G.M.Sheldrick)

Official Entry Point for

Definition and Details Practical Approach
• We ignore here the scary details that are not
relevant in the current context
• We will Discuss the File structure
• We will look at its relevance for publication
• We will discuss software to edit and check
the CIF file
• We will look at software that uses CIF as
Input.

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 File Structure Constructs
• Both Computer and Human Readable Ascii • data_name
encoded file where name the choosen identifier of the data
• Data associations e.g.
• Free Format _ cell_length_a 16.6392(2)
• Mostly 80 colums wide • Repetition (loop)
loop_
• Parsable in units
__symmetry_equiv_pos_as_xyz
• Data Order Flexible ‘x, y, z’
• Dataname and Value associations ‘-x, y+1/2, -z’

Construct for Text

• Text can be included between semi-columns
• Used for Acta Cryst. Section C & E
• Example
_publ_section_comment
;
Dictionary Lookup Example
This paper presents the first example
of a very important compound.
;

CIF Example File

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 CIF Completion
• CIF Files are created by the refinement
program (e.g. SHELXL)
• Missing Date can be added with a Text
Editor, enCIFer (from the CCDC) or
publCIF (From the IUCr).
• The Syntax can be checked with a locally
installed version of the program enCIFer
(Freely Available: www.ccdc.cam.ac.uk)

PROGRAM
enCIFer

Missing Data

Note on Editing the CIF CIF Applications

• The Idea of editing the CIF is to add • Data Archival
missing information to the CIF. • Deposition to the CSD (=> CSD number)
• Supplementary Material for Publication
• Some Acta Cryst. authors have been found
• Input for Geometry and Graphics Software
to polish away less nice numerical values.
e,g. Mercury (from CCDC) and PLATON
This leaves traces and is generally detected
• Standard Format for publications (Structure
by the validation software and not good for Communications) in Acta Cryst. Sections C &
the career of the culprit… E.
• Structure Validation

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Naked Silver ? Angew. Chem. 47 (2008) 9462
Mystery solved on the basis of the deposited CIF

Reflection CIF (FCF)

Calculations on Published Structures
• CIF data for a published structure can be obtained
from the CCDC
• FCF Data are generally only retrievable from the
IUCr website for Acta Cryst. Papers
• PLATON has a tool to re-create .ins and .hkl files
for re-refinement with SHELXL
• Useful to investigate difference maps for more
details.

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 Structure Validation Why Crystal Structure Validation
• Pioneered by the IUCr • The explosion of structure determinations
• An analyses of the nearly 500000 structures in the
• Currently most journals have implemented a CSD learns that a significant number are in error
validation scheme. • Many analyses are done today by non-specialists
• Papers: • Limited number of experts to detect pitfalls
• A.L.Spek (2003). J. Appl. Cryst. 36, 7-13. • Validation provides a list of issues that need
special attention of the analyst, specialist and
• A.L.Spek (2009). Acta Cryst. D65, 148- referee.
155. • Validation sets quality standards.

VALIDATION QUESTIONS How is Validation Implemented

Single crystal validation addresses three • Computer readable structure analysis results in
CIF format (Syd Hall & George Sheldrick)
simple but important questions:
• A file (Check.def) defines the issues that are tested
with levels of severity and associated explanation
1 – Is the reported information complete? and advise.
2 – What is the quality of the analysis? • The tests are executed by the program PLATON
3 – Is the Structure Correct? • The tests can be executed both in-house or through
the WEB-based IUCr CHECKCIF server.

ALERT LEVELS
CheckCif Report in terms of a list of ALERTS

• ALERT A – Serious Problem

• ALERT B – Potentially Serious Problem
• ALERT C – Check & Explain
• ALERT G – Verify or Take Notice

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 ALERT TYPES
1 - CIF Construction/Syntax errors,
Missing or Inconsistent Data.
2 - Indicators that the Structure Model
may be Wrong or Deficient.
3 - Indicators that the quality of the results
may be low.
4 - Cosmetic Improvements, Queries and
Suggestions.

EXAMPLE OF
PLATON GENERATED
ALERTS FOR A RECENT
PAPER PUBLISHED IN
Which Key Issues are Addressed
J.Amer.Chem.Soc. (2007)

• Missed symmetry (“being Marshed”)

• Wrong chemistry (Misassigned atom types)
Attracted special attention
in Chemical and
• Too many, too few or misplaced H-atoms
Engineering News
• Missed solvent accessible voids in the structure
• Missed Twinning
(Referees obviously
did not Bother)
• Absolute structure
• Data quality and completeness

FCF-VALIDATION Examples
Forthcoming: • Following are some examples of the type of
Automatic twinning detection as part of the problems addressed.
IUCr CheckCif procedure
- Detection of ignored twinning
- Detection of Applied Twinning Correction
without being reported
(Already available via PLATON/Check)

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 Published with Wrong Composition
Acta Cryst. (2007), E63, m1566.

BORAX ! O
B [Sn(IV)(NO3)4(C10H8N2)2]

THE STABLE PENTAMETHYLCYCLOPENTADIENYL CATION

J.B.Lambert et al. Angew. Chem. Int. Ed. 2002, 41, 1429-1431

1.601 Ang.

Missing H in bridge & Sn(IV) => Lanthanide(III)

WRONG SPACEGROUP CORRECTLY REFINED STRUCTURE

P-1, Z=2
J.A.C.S. (2000),122,3413 – P1, Z = 2

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 HOT STRUCTURE – FAST LANE PUBLICATION
Pentamethylcyclopentadienyl
Common Anionic Form “New” Cationic Form

Cp*

Assigned Bond types

Enthusiastic Last Paragraph of NOT SO HOT AFTER ALL !!

C&E-News Editors Note in the next issue of Angewandte Chemie

… The Northwestern chemists are now

exploring the reactivity of C5Me5+. “You
can sit down and write lots of interesting
reactions on paper,” Lambert says, and it
will be interesting to see if the molecule
reacts as expected. But Considering this
cation’s track record, it might be safer to
expect more surprises. [!!]

Strange Bond Pattern and Ring pucker

Corrected Structure
J.N. Jones et al.,Chem. Comm. 2002,1520-1521
Additional
H-Atoms

D
Double
o Bond ?
D
PACKING EFFECTS ??

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 Concluding Remarks
• The CIF standard makes it possible to easily
do follow-up calculations for published
structures
• The available information is more complete
• http://www.cryst.chem.uu.nl for more
information

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