Which conformations make stable crystal structures? Mapping crystalline molecular geometries to the conformational energy landscape

The ability to anticipate the shape adopted by flexible molecules in the solid state is crucial for engineering and predicting crystal packing and, hence, properties. In this study, the conformations adopted by flexible molecules in their crystal structures are assessed in terms of their relationship to the calculated global conformational landscape. The study quantifies the limits on molecular strain that can be induced by intermolecular interactions in single-component crystal structures of molecules with no intramolecular hydrogen bonding, demonstrating that some molecules are distorted by up to 20 kJ mol−1 by crystal packing forces. Furthermore, we find that crystallisation often selects high energy conformers, but only when the high energy conformer is more extended than the lower energy options, allowing for greater intermolecular stabilisation. Based on these observations, we propose that the crystallisability of conformers is assessed in terms of their energies and surface areas. We formulate this as a parameterised pseudo-energy related to molecular surface area, which leads to a dramatic improvement in our ability to predict the conformations adopted by molecules in their crystal structures.

[1]  C S Adjiman,et al.  Efficient Handling of Molecular Flexibility in Lattice Energy Minimization of Organic Crystals. , 2011, Journal of chemical theory and computation.

[2]  C. Lipinski Lead- and drug-like compounds: the rule-of-five revolution. , 2004, Drug discovery today. Technologies.

[3]  G. Day,et al.  Crystal packing predictions of the alpha-amino acids: methods assessment and structural observations , 2010 .

[4]  Sarah L. Price,et al.  Quantifying intermolecular interactions and their use in computational crystal structure prediction , 2004 .

[5]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[6]  T. C. Lewis,et al.  A third blind test of crystal structure prediction. , 2005, Acta crystallographica. Section B, Structural science.

[7]  G. Day,et al.  Predicting inclusion behaviour and framework structures in organic crystals. , 2009, Chemistry.

[8]  E. Pidcock,et al.  A database survey of molecular and crystallographic symmetry. , 2003, Acta crystallographica. Section B, Structural science.

[9]  Graeme M. Day,et al.  Current approaches to predicting molecular organic crystal structures , 2011 .

[10]  B. Civalleri,et al.  Periodic density functional theory calculations for 3-dimensional polyacetylene with empirical dispersion terms. , 2010, Physical chemistry chemical physics : PCCP.

[11]  G. Day,et al.  Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals. , 2010, Physical chemistry chemical physics : PCCP.

[12]  F. Allen The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[13]  Tejender S. Thakur,et al.  Significant progress in predicting the crystal structures of small organic molecules--a report on the fourth blind test. , 2009, Acta crystallographica. Section B, Structural science.

[14]  Marcus A. Neumann,et al.  Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations , 2010, Acta crystallographica. Section B, Structural science.

[15]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[16]  Geoff G. Z. Zhang,et al.  The curious case of (caffeine)·(benzoic acid): how heteronuclear seeding allowed the formation of an elusive cocrystal , 2013 .

[17]  M. Frisch,et al.  Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .

[18]  Claire S. Adjiman,et al.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test , 2011, Acta crystallographica. Section B, Structural science.

[19]  István Kolossváry,et al.  Low‐mode conformational search elucidated: Application to C39H80 and flexible docking of 9‐deazaguanine inhibitors into PNP , 1999 .

[20]  Sarah L Price,et al.  Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted? 2. Crystal Structure Prediction. , 2009, Journal of chemical theory and computation.

[21]  F. Leusen,et al.  Towards ab initio screening of co-crystal formation through lattice energy calculations and crystal structure prediction of nicotinamide, isonicotinamide, picolinamide and paracetamol multi-component crystals , 2013 .

[22]  Bartolomeo Civalleri,et al.  CRYSTAL: a computational tool for the ab initio study of the electronic properties of crystals , 2005 .

[23]  S. Price,et al.  A strategy for producing predicted polymorphs: catemeric carbamazepine form V. , 2011, Chemical communications.

[24]  E. Salager,et al.  Powder crystallography of pharmaceutical materials by combined crystal structure prediction and solid-state 1H NMR spectroscopy. , 2013, Physical chemistry chemical physics : PCCP.

[25]  P. Charifson,et al.  Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. , 2004, Journal of medicinal chemistry.

[26]  William Jones,et al.  Molecular Polarization Effects on the Relative Energies of the Real and Putative Crystal Structures of Valine. , 2008, Journal of chemical theory and computation.

[27]  M. D. King,et al.  Prediction of the Unknown Crystal Structure of Creatine Using Fully Quantum Mechanical Methods , 2011 .

[28]  G. Day,et al.  A strategy for predicting the crystal structures of flexible molecules: the polymorphism of phenobarbital. , 2007, Physical chemistry chemical physics : PCCP.

[29]  Sarah L Price,et al.  Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction. , 2011, International journal of pharmaceutics.

[30]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[31]  Marc-Antoine Perrin,et al.  Energy ranking of molecular crystals using density functional theory calculations and an empirical van der waals correction. , 2005, The journal of physical chemistry. B.

[32]  G. Day,et al.  Predicting stoichiometry and structure of solvates. , 2010, Chemical communications.

[33]  C. Adjiman,et al.  The polymorphs of ROY: application of a systematic crystal structure prediction technique. , 2012, Acta crystallographica. Section B, Structural science.

[34]  A. Bond Why do crystal structures waste molecular inversion symmetry , 2010 .

[35]  William Jones,et al.  Database guided conformation selection in crystal structure prediction of alanine , 2007 .