ABSTRACT
CrystalExplorer is a native cross-platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum-mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.
ABSTRACT
In toluene fullerene C(70) forms 2:1 complexes with p-benzylcalix[5]arene (1) and p-phenylcalix[5]arene (2), [C(70) subset1(2)].6(C(7)H(8)) and [C(70) subset2(2)].7(C(7)H(8)). The fullerene molecules are completely shrouded by two calix[5]arenes in addition to terminal benzyl groups from other supermolecules, [C(70) subset1(2)], and solvent. Within the capsule-like supermolecules the calixarenes have distinctly different arrangements relative to the principal axis of the fullerene; for [C(70) subset1(2)].6(C(7)H(8)) the oxygen planes of the two calixarenes are skewed by 37.0 and 47.5 degrees , whereas in [C(70) subset2(2)].7(C(7)H(8)) the principal axes of the fullerene and the two encapsulating calixarenes are more closely aligned with the corresponding angles at 9.7 and 8.6 degrees , and features a pentaphenyl inter-calixarene embrace. The Hirshfeld surfaces of these two complexes have been investigated for a detailed understanding of the orientation and nature of interactions of C(70) with the cavitand-type molecules and toluene.
Subject(s)
Calixarenes/chemistry , Fullerenes/chemistry , Models, MolecularABSTRACT
Enhancements to the properties based on Hirshfeld surfaces enable quantitative comparisons between contributions to crystal packing from various types of intermolecular contacts.
Subject(s)
Acetaminophen/chemistry , Heterocyclic Compounds/chemistry , Models, Chemical , Oxalic Acid/chemistry , Computer Simulation , Crystallization , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Quantum Theory , Surface PropertiesABSTRACT
Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.
Subject(s)
Electrons , Molecular Mimicry , Crystallization , Formamides/chemistry , Glycine/chemistry , Models, Molecular , Molecular Structure , Static Electricity , Urea/chemistryABSTRACT
Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.
ABSTRACT
A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.
