A generalized expression for the similarity of spectra: application to powder diffraction pattern classification

Gelder, René de; Wehrens, Ron; Hageman, Jos A.

doi:10.1002/1096-987x(200102)22:3<273::aid-jcc1001>3.0.co;2-0

Cited by 122 publications

(134 citation statements)

References 10 publications

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“…The similarity measure, used in this study for the quantification of the agreement between the calculated, ( ) f ν , and measured, ( ) g ν , IR or VCD spectra, is a fairly straightforward adaptation of a cosine based similarity measure as will be demonstrated in detail below and as was also used by Kuppens et al [13][14][15][16] , following up on work by De Gelder et al [17] for comparing powder diffraction spectra. Instead of such a generalized cosine in a multidimensional vector space, one can also use the arithmetic mean as normalizing term or, in fact, any other similarity measure, including the Tanimoto one as recently used by Shen et al [18] .…”

Section: Neighbourhood Similarity (Ns)mentioning

confidence: 99%

A Confidence Level Algorithm for the Determination of Absolute Configuration Using Vibrational Circular Dichroism or Raman Optical Activity

Debie

Gussem

Dukor³

et al. 2011

ChemPhysChem

200

275

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Spectral comparison is an important part of the assignment of the absolute configuration (AC) by vibrational circular dichroism (VCD), or equally by Raman Optical Activity (ROA). In order to avoid bias caused by personal interpretation, numerical methods have been developed to compare measured and calculated spectra. Using a neighbourhood similarity measure, the agreement between a computed and measured VCD or ROA spectrum is expressed numerically to introduce a novel confidence level measure. This allows users of Vibrational Optical Activity (VOA) techniques (VCD and ROA) to assess the reliability of their assignment of the AC of a compound. To that end, a database of successful AC determinations is compiled along with neighbourhood similarity values between the experimental spectrum and computed spectra for both enantiomers. For any new AC determination, the neighbourhood similarities between the experimental spectrum and the computed spectra for both enantiomers are projected on the database allowing an interpretation of the reliability of their assignment.

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Section: Neighbourhood Similarity (Ns)mentioning

confidence: 99%

A Confidence Level Algorithm for the Determination of Absolute Configuration Using Vibrational Circular Dichroism or Raman Optical Activity

Debie

Gussem

Dukor³

et al. 2011

ChemPhysChem

200

275

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“…Radial distribution functions have been used as a fingerprint to measure the distances between crystal structures, 28,29 as well as methods based on comparison of the calculated powder diffraction patterns. 30,31 In the same spirit, Oganov and Valle 32 used element resolved radial distribution functions as a crystal fingerprint. For a crystal containing one element, only a single function is obtained for the entire system.…”

Section: Introductionmentioning

confidence: 99%

A fingerprint based metric for measuring similarities of crystalline structures

Zhu

Amsler

Fuhrer

et al. 2016

The Journal of Chemical Physics

117

119

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Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures. The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings. C 2016 AIP Publishing LLC. [http://dx

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“…Crystal structure similarity can also be identified by comparing radial distribution functions, as implemented in the Polymorph Predictor program (Verwer & Leusen, 1998;van Eijck & Kroon, 1997), and by comparing computed powder patterns (Karfunkel et al, 1993;de Gelder, 2001).…”

Section: Introductionmentioning

confidence: 99%

COMPACK: a program for identifying crystal structure similarity using distances

2005

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A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

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A generalized expression for the similarity of spectra: application to powder diffraction pattern classification

Cited by 122 publications

References 10 publications

A Confidence Level Algorithm for the Determination of Absolute Configuration Using Vibrational Circular Dichroism or Raman Optical Activity

A Confidence Level Algorithm for the Determination of Absolute Configuration Using Vibrational Circular Dichroism or Raman Optical Activity

A fingerprint based metric for measuring similarities of crystalline structures

COMPACK: a program for identifying crystal structure similarity using distances

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