<i>Tormat</i>: a program for the automated structural alignment of molecular conformations

Weng, Ze F.; Motherwell, W. D. S.; Cole, Jacqueline M.

doi:10.1107/s002188980802308x

Cited by 18 publications

(18 citation statements)

References 16 publications

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“…The r.m.s.d.s in the two studies seem to have been calculated in the same way, i.e. using the procedure of Weng et al (2008).…”

Section: Counting Molecular Conformations and Orientationsmentioning

confidence: 99%

High-Z′ structures of organic molecules: their diversity and organizing principles

Brock

2016

Acta Crystallogr B Struct Sci Cryst Eng Mater

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Synopsis: (text) 1. Re: Structures found in the Z'  4 searches (1 pg.; pg. 3). 2. Re: The rejected structures (6 pp.; starts on pg. 4). 3. Re: XY, X = I, Br, Cl; Y = N, O interactions (3 pp.; starts on pg. 10). 4. Re: Complications (4 pp.; starts on pg. 13). 5. Re: Molecular conformations vary little (2 pp.; starts on pg. 17). 6. Re: Two or more H-bonding patterns (3 pp.; starts on pg. 19). 7. Re: Distortions from higher symmetry without an accompanying modulation are uncommon (4 pp.; starts on pg. 22). 8. Re: Sohncke groups are more frequent (1 pg.; pg. 26). 9. Re: There are usually several structural features that each double or triple Z' (2 pp.; starts on pg. 27). 10. Re: Packing units (2 pp.; starts on pg. 29). 11. Re: Ordered faults (5 pp.; starts on pg. 31). 12. Re: Phase sequences (5 pp.; starts on pg. 36). 13. Illustration of an intermediate, hybrid, phase (1 pg.; pg. 41). 14. Re: Polymorphs (7 pp.; starts on pg. 42). 15. Literature citations for the 284 structures in the final list (15 pp.; starts on pg. 49).

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“…The r.m.s.d.s in the two studies seem to have been calculated in the same way, i.e. using the procedure of Weng et al (2008).…”

Section: Counting Molecular Conformations and Orientationsmentioning

confidence: 99%

High-Z′ structures of organic molecules: their diversity and organizing principles

Brock

2016

Acta Crystallogr B Struct Sci Cryst Eng Mater

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“…For this study a novel automated algorithm was developed. The Tormat program, which locates the optimal pair-wise associated atom sets and provides a visual and graphical comparison of matched molecules, is fully described by Weng et al (2008). In summary:…”

Section: Conformational Matchingmentioning

confidence: 99%

“…N tor , or on chemical or crystal structure type. Obviously, in developing the complex automated procedure described in x2, numerous spot checks have been performed using the programs Mercury (Macrae et al, 2006) and Tormat (Weng et al, 2008). The following subsections summarize some immediate observations, but more complete analyses are currently in progress and will be presented for publication in the near future.…”

Section: Patterns Of Conformational Changementioning

confidence: 99%

Conformational variability of molecules in different crystal environments: a database study

Weng

Motherwell

Allen

et al. 2008

Acta Crystallogr Sect B

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A methodology is described for analysing the Cambridge Structural Database (CSD) in terms of molecular conformations. Molecular species that have more than a single occurrence across the complete CSD are identified, either as the sole crystal component or co-crystallized with other components. Cluster analysis, based on a root-mean-square fit of coordinates and chemical connectivity, is performed to identify conformational variance for each molecule. Results are analysed in terms of the number of discrete conformations observed versus the number of crystal environments and number of acyclic torsion angles in the molecule. Special subsets of environments are also analysed, namely polymorphs, co-crystals and solvates. In general, conformational diversity increases with an increasing number of different crystal environments and with an increasing number of flexible torsion angles. Overall, molecules with one or more acyclic flexible torsion angle are observed to exist in more than one conformation in ca 40% of cases. There is evidence that solvated molecules exhibit more conformational flexibility on average, compared with polymorphs and co-crystals.

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“…The overall conformational change in molecular structure, upon transitioning from the S 0 ground-state to triplet T 1 photo-induced state was quantified via RMSD of 0.245 Å. 41,42 As expected, the largest individual bond perturbation is associated with the two Ir-N bonds, which manifest contractions of 0.050Å and 0.052 Å from S 0 T 1 (SI , Table S14). Given the experimental error associated with the experimentally-derived Ir-N bond-lengths in the ground state is 0.003 Å, an average photo-induced Ir-N bond contraction of 0.051(3) Å should be readily observable.…”

Section: Photo-excited Intramolecular Charge-transfer and Optical Banmentioning

confidence: 77%

Material Profiling for Photocrystallography: Relating Single-Crystal Photophysical and Structural Properties of Luminescent Bis-Cyclometalated Iridium-Based Complexes

Cole

Bowes

Clark

et al. 2013

Crystal Growth & Design

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The photophysical properties of seven luminescent iridium complexes are characterised in their single-crystal form and the photo-activity is related to their molecular structures. Specifically, solid-state optical emission spectra and associated lifetimes are determined from single crystals of iridium complexes containing three bidentate ligands: two variously substituted 2phenylbenzothiazoles and either a 2,4-pentadione (acetylacetone) or 2-pyridinecarboxylic (picolinic) acid. All complexes studied exhibit emissive behaviour in the solid-state which originates from 3 * and metal-to-ligand-charge-transfer (MLCT) electronic transitions; this is supported by density functional theory. Phosphorescence is observed in all cases with microsecond lifetimes, ranging from 0.30-2.4 s at 298K and 1.4-4.0 µs at 100 K. Structureproperty relationships are established which are relevant to the potential solid-state application of this series of luminescent complexes as organic light emitting diodes (OLED) material components. In addition, these materials are assessed for their suitability to time-resolved pump-probe photocrystallography experiments, which will reveal their photo-excited-structure. Accordingly, the design process by which materials are selected, and technical parameters are defined, for a photocrystallography experiment is illustrated. This family of complexes presents a case study for this photocrystallography material profiling. Results show that the time-resolved photo-excited state structure, featuring the MLCT transition is, in principle at least, viable for two of these complexes.

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Tormat: a program for the automated structural alignment of molecular conformations

Cited by 18 publications

References 16 publications

High-Z′ structures of organic molecules: their diversity and organizing principles

High-Z′ structures of organic molecules: their diversity and organizing principles

Conformational variability of molecules in different crystal environments: a database study

Material Profiling for Photocrystallography: Relating Single-Crystal Photophysical and Structural Properties of Luminescent Bis-Cyclometalated Iridium-Based Complexes

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