Hirshfeld surface analysis
TL;DR: In the last few years, the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity as mentioned in this paper, which represents an attempt to venture beyond the current paradigm of nuclear distances and angles, crystal packing diagrams with molecules represented via various models, and to view molecules as organic wholes.
Abstract: In the last few years the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to venture beyond the current paradigm—internuclear distances and angles, crystal packing diagrams with molecules represented via various models, and the identification of close contacts deemed to be important—and to view molecules as “organic wholes”, thereby fundamentally altering the discussion of intermolecular interactions through an unbiased identification of all close contacts.
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TL;DR: CrystalExplorer is a native cross-platform program for the visualization and investigation of molecular crystal structures and its successor, CrystalExplorer 2, is available for iOS and Android.
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.
1,096 citations
TL;DR: The accurate and efficient CE-B3LYP and CE-HF model energies for intermolecular interactions in molecular crystals are extended to a broad range of crystals by calibration against density functional results for molecule/ion pairs extracted from 171 crystal structures.
704 citations
Cites methods from "Hirshfeld surface analysis"
...…PIXEL methodology (Gavezzotti, 2005) and symmetry-adapted perturbation theory to compute intermolecular energies, Hirshfeld surface analysis (Spackman & Jayatilaka, 2009) and periodic DFT calculations, as well as mapping the molecular electrostatic potential (ESP) on molecular Hirshfeld…...
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...…paradigm identified by Desiraju, and to view molecules as ‘organic wholes’, thereby fundamentally altering the discussion of intermolecular interactions through the use of a variety of novel computational and graphical tools (Spackman, 2013; Turner et al., 2011; Spackman & Jayatilaka, 2009)....
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TL;DR: This code, a greatly improved version of the previous critic program, can find critical points of the electron density and related scalar fields such as the electron localization function, integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), and generate relevant graphical representations.
452 citations
Cites background from "Hirshfeld surface analysis"
...The NCI domains have been linked to Pauli repulsion regions andhence to intermolecular attraction [40], an important feature to look for when examining close contacts in crystal packing [41]....
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TL;DR: This approach is applied to a sample of organic molecular crystals with known bending, shearing and brittle behaviour, to illustrate its use in rationalising their mechanical behaviour at a molecular level.
442 citations
333 citations
References
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TL;DR: The Cambridge Structural Database now contains data for more than a quarter of a million small-molecule crystal structures, and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.
Abstract: The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.
9,865 citations
TL;DR: Mercury as discussed by the authors is a crystal structure visualization tool that allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns, as well as the ability to perform packing similarity calculations between structures containing the same compound.
Abstract: The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.
7,879 citations
TL;DR: In this article, a general and natural choice is to share the charge density at each point among the several atoms in proportion to their free-atom densities at the corresponding distances from the nuclei.
Abstract: For quantitative description of a molecular charge distribution it is convenient to dissect the molecule into well-defined atomic fragments. A general and natural choice is to share the charge density at each point among the several atoms in proportion to their free-atom densities at the corresponding distances from the nuclei. This prescription yields well-localized bonded-atom distributions each of which closely resembles the molecular density in its vicinity. Integration of the atomic deformation densities — bonded minus free atoms — defines net atomic charges and multipole moments which concisely summarize the molecular charge reorganization. They permit calculation of the external electrostatic potential and of the interaction energy between molecules or between parts of the same molecule. Sample results for several molecules indicate a high transferability of net atomic charges and moments.
5,234 citations
TL;DR: In this article, a least square representation of Slater-type atomic orbitals as a sum of Gaussian-type orbitals is presented, where common Gaussian exponents are shared between Slater−type 2s and 2p functions.
Abstract: Least‐squares representations of Slater‐type atomic orbitals as a sum of Gaussian‐type orbitals are presented. These have the special feature that common Gaussian exponents are shared between Slater‐type 2s and 2p functions. Use of these atomic orbitals in self‐consistent molecular‐orbital calculations is shown to lead to values of atomization energies, atomic populations, and electric dipole moments which converge rapidly (with increasing size of Gaussian expansion) to the values appropriate for pure Slater‐type orbitals. The ζ exponents (or scale factors) for the atomic orbitals which are optimized for a number of molecules are also shown to be nearly independent of the number of Gaussian functions. A standard set of ζ values for use in molecular calculations is suggested on the basis of this study and is shown to be adequate for the calculation of total and atomization energies, but less appropriate for studies of charge distribution.
3,723 citations
TL;DR: In this paper, a two-dimensional mapping of the Hirshfeld surfaces of a molecular molecule is presented, which summarizes quantitatively the nature and type of intermolecular interaction experienced by a molecule in the bulk, and presents it in a convenient graphical format.
Abstract: We have recently described a remarkable new way of exploring packing modes and intermolecular interactions in molecular crystals using a novel partitioning of crystal space. These molecular Hirshfeld surfaces reflect intermolecular interactions in a novel visual manner, offering a hitherto unseen picture of molecular shape in a crystalline environment. The surfaces encode information about all intermolecular interactions simultaneously, but sophisticated interactive graphics are required in order to extract the information most efficiently. To overcome this we have devised a two-dimensional mapping which summarizes quantitatively the nature and type of intermolecular interaction experienced by a molecule in the bulk, and presents it in a convenient graphical format. The mapping takes advantage of the triangulation of the Hirshfeld surfaces, and plots the fraction of points on the surface as a function of the closest distances from the point to nuclei inside and outside the surface.
In this manner all interaction types (for example, hydrogen bonding, close and distant van der Waals contacts, C–H⋯π interactions, π–π stacking) are readily identifiable, and it becomes a straightforward matter to classify molecular crystals by the nature of interactions, and to rapidly identify similarities and differences which can become obscured when examining crystal packing diagrams. These plots are a novel visual representation of all the intermolecular interactions simultaneously, and are unique for a given crystal structure and polymorph. Applications to a wide variety of molecular crystals and intermolecular interactions are presented, including polymorphic systems, as well as crystals where Z′ > 1.
2,646 citations