Universal prediction of intramolecular hydrogen bonds in organic crystals.

A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB.

[1]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[2]  Alan Agresti,et al.  Categorical Data Analysis , 2003 .

[3]  Peter T. A. Galek,et al.  Knowledge-based H-bond prediction to aid experimental polymorph screening , 2009 .

[4]  Frank H. Allen,et al.  Hydrogen-bond directionality at the donor H atom—analysis of interaction energies and database statistics , 2009 .

[5]  Peter T. A. Galek,et al.  Persistent hydrogen bonding in polymorphic crystal structures. , 2009, Acta crystallographica. Section B, Structural science.

[6]  Jacqueline C. Hargis,et al.  Short intramolecular hydrogen bonds: derivatives of malonaldehyde with symmetrical substituents. , 2008, Journal of the American Chemical Society.

[7]  Xu-Hong Yang,et al.  3-(2-Aminoethyl)-2-(4-fluoroanilino)quinazolin-4(3H)-one , 2008, Acta crystallographica. Section E, Structure reports online.

[8]  S. Price,et al.  Computational prediction of organic crystal structures and polymorphism , 2008 .

[9]  C. Macrae,et al.  Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures , 2008 .

[10]  Anthony Nicholls,et al.  What do we know and when do we know it? , 2008, J. Comput. Aided Mol. Des..

[11]  Peter T. A. Galek,et al.  Knowledge-based model of hydrogen-bonding propensity in organic crystals. , 2007, Acta crystallographica. Section B, Structural science.

[12]  E. Cavalli,et al.  Synthesis, characterization, crystal structure and luminescence properties of phosphinic silver(I) complexes with thiourea derivatives , 2007 .

[13]  B. Sridhar,et al.  Voriconazole, an anti­fungal drug , 2007 .

[14]  S. Hitchcock,et al.  Structure-brain exposure relationships. , 2006, Journal of medicinal chemistry.

[15]  Jason C. Cole,et al.  DASH: a program for crystal structure determination from powder diffraction data , 2006 .

[16]  J. Yin,et al.  2‐[3‐(4‐Bromophenyl)‐1,2,4‐oxadiazol‐5‐yl]phenol , 2006 .

[17]  W. D. Sam Motherwell,et al.  An Experiment in Crystal Structure Prediction by Popular Vote , 2006 .

[18]  Henrik G Kjaergaard,et al.  Influence of intramolecular hydrogen bond strength on OH-stretching overtones. , 2006, The journal of physical chemistry. A.

[19]  M. Mandado,et al.  A scheme estimating the energy of intramolecular hydrogen bonds in diols , 2006 .

[20]  R. Mosquera,et al.  Do small carboxylic acids present intramolecular hydrogen bond , 2006 .

[21]  G. Buemi.  Intramolecular Hydrogen Bonds. Methodologies and Strategies for Their Strength Evaluation , 2006 .

[22]  A. Thakkar,et al.  Clusters of glycolic acid with three to six water molecules. , 2005, The Journal of chemical physics.

[23]  James A. Chisholm,et al.  COMPACK: a program for identifying crystal structure similarity using distances , 2005 .

[24]  F. Zuccarello,et al.  DFT study of the intramolecular hydrogen bonds in the amino and nitro-derivatives of malonaldehyde , 2004 .

[25]  W. Kaminsky,et al.  Study of the sulfur atom as hydrogen bond acceptor in N(2)-pyridylmethyl-N′-arylthioureas , 2004 .

[26]  V. Rybakov,et al.  2-(5-Methyl-4-phenyl-1,3-thia­zol-2-yl)-1-phenyl­ethanol , 2003 .

[27]  J. Simons,et al.  Protonated neurotransmitters in the gas-phase: clusters of 2-aminoethanol with phenol , 2003 .

[28]  R. Klein.  Electron density topological analysis of hydrogen bonding in glucopyranose and hydrated glucopyranose. , 2002, Journal of the American Chemical Society.

[29]  A. Thakkar,et al.  Hydrogen bonding in the glycolic acid dimer , 2002 .

[30]  Robin Taylor,et al.  New software for searching the Cambridge Structural Database and visualizing crystal structures. , 2002, Acta crystallographica. Section B, Structural science.

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

[32]  Roger A. Klein,et al.  Ab initio conformational studies on diols and binary diol‐water systems using DFT methods. Intramolecular hydrogen bonding and 1:1 complex formation with water , 2002, J. Comput. Chem..

[33]  E. Lukevics,,et al.  Addition of Me3SiCN to trifluoromethyl derivates of N‐(pyridylmethylidene) anilines catalyzed by Lewis acids , 2001 .

[34]  S. J. Grabowski.  An estimation of strength of intramolecular hydrogen bonds — ab initio and AIM studies , 2001 .

[35]  Luis Fernández Pacios,et al.  Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine , 2001, J. Comput. Chem..

[36]  Valerio Bertolasi,et al.  Evidence for Intramolecular N−H···O Resonance-Assisted Hydrogen Bonding in β-Enaminones and Related Heterodienes. A Combined Crystal-Structural, IR and NMR Spectroscopic, and Quantum-Mechanical Investigation , 2000 .

[37]  F H Allen,et al.  Intramolecular hydrogen bonds: common motifs, probabilities of formation and implications for supramolecular organization. , 2000, Acta crystallographica. Section B, Structural science.

[38]  Christer B. Aakeröy,et al.  Crystal engineering : Strategies and architectures , 1997 .

[39]  Frank H. Allen,et al.  Hydrogen-Bond Acceptor and Donor Properties of Divalent Sulfur (Y-S-Z and R-S-H) , 1997 .

[40]  Gerhard Klebe,et al.  What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs? , 1996 .

[41]  F. Zanardi,et al.  X-ray crystal and molecular structure of 2,3-dideoxy-4-thio-d-arabino-heptonic acid 1,4-lactone: a key intermediate for syntheses of 2′, 3′-dideoxy-4′-thio-l-nucleosides , 1996 .

[42]  Gautam R. Desiraju,et al.  Supramolecular Synthons in Crystal Engineering—A New Organic Synthesis , 1995 .

[43]  V. Bertolasi,et al.  Evidence for resonance-assisted hydrogen bonding. 4. Covalent nature of the strong homonuclear hydrogen bond. Study of the O-H--O system by crystal structure correlation methods , 1994 .

[44]  R. Bader,et al.  The definition of a chemical bond, of molecular structure and of its change as exemplified by the structure diagram for C4H7+ , 1992 .

[45]  Professor Dr. George A. Jeffrey,et al.  Hydrogen Bonding in Biological Structures , 1991, Springer Berlin Heidelberg.

[46]  R. Bader,et al.  A quantum theory of molecular structure and its applications , 1991 .

[47]  Margaret C. Etter,et al.  Hydrogen bonds as design elements in organic chemistry , 1991 .

[48]  D. Kuck,et al.  Synthesis and structure of tricarbonylchromium mono-, bis- and tris-complexes of 10-methyltribenzotriquinacene , 1991 .

[49]  R. Bader.  Atoms in molecules : a quantum theory , 1990 .

[50]  D. Hosmer,et al.  Applied Logistic Regression , 1991 .

[51]  R. Cramer,et al.  Validation of the general purpose tripos 5.2 force field , 1989 .

[52]  C. Brock,et al.  Systematic effects of crystal-packing forces: biphenyl fragments with hydrogen atoms in all four ortho positions , 1989 .

[53]  W. Rowe,et al.  Microwave spectroscopic study of malonaldehyde (3-hydroxy-2-propenal). 2. Structure, dipole moment, and tunneling , 1981 .

[54]  M. C. Etter,et al.  Solid-state transformations and crystal structure analysis of α- and β-o-acetamidobenzamide , 1981 .

[55]  H. Azuma,et al.  PHARMACOLOGICAL PROPERTIES OF N‐(3′,4′‐DIMETHOXYCINNAMOYL) ANTHRANILIC ACID (N‐5′), A NEW ANTI‐ATOPIC AGENT , 1976, British journal of pharmacology.

[56]  Jan Kroon,et al.  O-H · O Hydrogen bonds in molecular crystals a statistical and quantum-chemical analysis , 1975 .

[57]  H. A. Levy,et al.  Glycolic acid: direct neutron diffraction determination of crystal structure and thermal motion analysis , 1971 .

[58]  W. Pijper.  The molecular and crystal structure of glycollic acid , 1971 .