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Galek P.T.A.,Cambridge Crystallographic Data Center
CrystEngComm | Year: 2011

A new method is presented to compare crystal packing based on moments of inertia tensors. The approach allows any two crystal structures to be compared irrespective of chemical connectivity. Moreover, the strictly real-space method offers significant ease of interpretation of structural comparisons. The approach allows packing similarity to be identified in otherwise disparate compounds and has the potential to lead to new insight into the influences driving molecular aggregation, crystallisation and polymorphism. The packing relationships between several examples from the Cambridge Structural Database are discussed. © 2011 The Royal Society of Chemistry. Source


Motherwell W.D.S.,Cambridge Crystallographic Data Center
CrystEngComm | Year: 2010

The relationship between molecular shape and packing patterns in molecular crystals has been investigated using the Cambridge Structural Database (CSD). The methodology for molecular shape uses the enclosing box based on the principal axes of inertia, with some descriptors of the amount of void space between the van der Waals surface and the faces of the rectangular box. The ratio of the molecular volume to the volume of the box, and some counts of atom types describing chemical character were also found useful. Packing descriptors are based on the molecular coordination shell of neighbours in contact with a reference molecule, usually 14-16. A set of 16 vectors between molecular centres are sorted by magnitude and stored in tabular form for a set of 133448 CSD entries, together with other descriptors such as unit cell, space group, H-bonds, etc. A computer program was written to search the table file by molecular shape within specified tolerance ranges. This allows one to select a set of molecules most similar in shape to a given target molecule, and cluster the packing patterns. Cluster analysis on the sets of 16 sorted coordination distances often shows visually recognisable structural patterns. Methods for detection of 1D and 2D substructures are discussed. There is broad correlation of packing patterns and molecular shapes classed as rods, discs and spheres and packing patterns based on partition of the 14 distances by largest gap. Case studies showing clustering of packing patterns are presented, using sets of molecules judged most similar to target CSD molecules. © 2010 The Royal Society of Chemistry. Source


Cruz-Cabeza A.J.,Cambridge Crystallographic Data Center | Cruz-Cabeza A.J.,University of Amsterdam
CrystEngComm | Year: 2012

Differences in the predicted aqueous pK a values (ΔpK a) have been calculated for 6465 crystalline complexes containing ionised and non-ionised acid-base pairs in the Cambridge Structural Database. A linear relationship between ΔpK a and the probability of proton transfer between acid-base pairs has been derived for crystalline complexes with ΔpK a between -1 and 4. The pK a rule is validated and quantitated. This journal is © The Royal Society of Chemistry 2012. Source


Schmidt M.F.,University of Cambridge | Korb O.,Cambridge Crystallographic Data Center | Abell C.,University of Cambridge
ACS Chemical Biology | Year: 2013

As microRNA silencing processes are mediated by the protein Argonaute 2 and for target RNA binding only a short sequence at the microRNA's 5′ end (seed region) is crucial, we report a novel inhibitor class: the microRNA-specific Argonaute 2 protein inhibitors that not only block this short recognition sequence but also bind to the protein's active site. We developed a model for rational drug design, enabling the identification of Argonaute 2 active site binders and their linkage with a peptide nucleic acid sequence (PNA), which addresses the microRNA of interest. The designed inhibitors targeting microRNA-122, a hepatitis C virus drug target, had an IC50 of 100 nM, 10-fold more active than the simple PNA sequence (IC50 of 1 μM), giving evidence that the strategy has potential. Due to their lower molecular weight, these inhibitors may show better pharmacokinetic properties than reported oligonucleotide inhibitors, enabling them for potential therapeutic use. © 2013 American Chemical Society. Source


Taylor R.,Cambridge Crystallographic Data Center
CrystEngComm | Year: 2014

The tendency for an interaction to occur in crystal structures is not a simple function of its calculated energy in vacuo. This was shown by ranking intermolecular atom⋯atom interactions in organic crystal structures on the ratio (RF) of their observed frequency of occurrence to the frequency expected at random, i.e. if determined solely by the exposed surface areas of atoms. The study was based on line-of-sight interactions in structures taken from the Cambridge Structural Database. Only one interaction per atom was included in the analysis, the one with the smallest value of d-V, where d is the interatomic distance and V the sum of the atoms' van der Waals radii. 95% confidence intervals were determined for each RF value, enabling identification of interactions that occur significantly more often than expected by chance. Strong hydrogen bonds have the highest RF values, followed by two halogen-bonding interactions, I⋯N and I⋯O. These strong interactions typically occur 3 to 10 times more often than would be expected by chance. Although comparatively weak in energetic terms, C-H⋯F and C-H⋯Cl have RF values significantly in excess of the random expectation value of 1, and higher, for example, than those of Br⋯O and Cl⋯O. RF values clearly reveal the effects of polarisation on the propensity for C-halogen groups to form halogen bonds and C-H groups to form hydrogen bonds to oxygen, and highlight the dramatic differences between the interactions of phenyl and pentafluorophenyl. This journal is © the Partner Organisations 2014. Source

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