CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems
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.
About: This article is published in IUCrJ.The article was published on 2017-09-01 and is currently open access. It has received 704 citations till now. The article focuses on the topics: Intermolecular force & Open shell.
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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: This contribution highlights tools for this analysis such as Crystal Explorer and NCIPLOT, which are used to evaluate the nature, i.e. attractive/weakly attractive/repulsive, of specific contacts.
Abstract: The analysis of atom-to-atom and/or residue-to-residue contacts remains a favoured mode of analysing the molecular packing in crystals. In this contribution, additional tools are highlighted as methods for analysis in order to complement the `crystallographer's tool', PLATON [Spek (2009). Acta Cryst. D65, 148–155]. Thus, a brief outline of the procedures and what can be learned by using Crystal Explorer [Spackman & Jayatilaka (2009). CrystEngComm 11, 19–23] is presented. Attention is then directed towards evaluating the nature, i.e. attractive/weakly attractive/repulsive, of specific contacts employing NCIPLOT [Johnson et al. (2010). J. Am. Chem. Soc. 132, 6498–6506]. This is complemented by a discussion of the calculation of energy frameworks utilizing the latest version of Crystal Explorer. All the mentioned programs are free of charge and straightforward to use. More importantly, they complement each other to give a more complete picture of how molecules assemble in molecular crystals.
323 citations
TL;DR: A tutorial review aimed at both the novice and the seasoned solid-state chemist provides a succinct overview of key findings that have, over the last half century, advanced our ability to make molecular crystals with targeted structures and desired properties.
Abstract: This Tutorial Review, aimed at both the novice and the seasoned solid-state chemist, provides a succinct overview of key findings that have, over the last half century, advanced our ability to make molecular crystals with targeted structures and desired properties. The article critically evaluates the efficiency and reliability of the well-established guidelines used by experimentalists in crystal engineering and highlights statistical and computational tools that are both advantageous to crystal design and accessible to experimental solid-state chemists.
193 citations
TL;DR: The CSD's value in the design of biologically active molecules and the solid forms in which they are delivered is demonstrated and its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics.
Abstract: The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
150 citations
TL;DR: The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen, which have been grouped into the four themes: fundamentals, beyond the halogen bond, characterisation, and applications.
Abstract: The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen. This article is based upon my Closing Remarks Lecture at the 203rd Faraday Discussion meeting on Halogen Bonding in Supramolecular and Solid State Chemistry, held in Ottawa, Canada, on 10-12th July, 2017. The Discussion included papers on fundamentals and applications of halogen bonding in the solid state and solution phase. Analogous interactions involving main group elements outside group 17 were also examined. In the closing lecture and in this article these contributions have been grouped into the four themes: (a) fundamentals, (b) beyond the halogen bond, (c) characterisation, and (d) applications. The lecture and paper also include a short reflection on past work that has a bearing on the Discussion.
135 citations
References
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TL;DR: A new density functional of the generalized gradient approximation (GGA) type for general chemistry applications termed B97‐D is proposed, based on Becke's power‐series ansatz from 1997, and is explicitly parameterized by including damped atom‐pairwise dispersion corrections of the form C6 · R−6.
Abstract: A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.
23,058 citations
"CrystalExplorer model energies and ..." refers background in this paper
...The dispersion energy term, E0dis, is Grimme’s D2 dispersion correction (Grimme, 2006) summed over all intermolecular atom pairs....
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Book•
01 Jan 1990
TL;DR: In this article, the quantum atom and the topology of the charge desnity of a quantum atom are discussed, as well as the mechanics of an atom in a molecule.
Abstract: List of symbols 1. Atoms in chemistry 2. Atoms and the topology of the charge desnity 3. Molecular structure and its change 4. Mathematical models of structural change 5. The quantum atom 6. The mechanics of an atom in a molecule 7. Chemical models and the Laplacian of the charge density 8. The action principle for a quantunm subsystem Appendix - Tables of data Index
11,853 citations
"CrystalExplorer model energies and ..." refers methods in this paper
...Although the resulting energy estimates from this approach have been shown to be unreliable, and for a very wide range of interactions (Spackman, 2015), they are commonly reported in current studies, for example, by Zhurov & Pinkerton (2015) as part of their experimental charge–density analysis of 2-nitrobenzoic acid, and by Landeros-Rivera et al. (2016), who examined intermolecular interactions in crystalline arene– perhaloarene adducts by QTAIM methods, ESP mapping and noncovalent index (NCI) surfaces (Johnson et al., 2010), as well as energies from Gavezzotti’s PIXEL method for selected molecular pairs....
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...Hirshfeld surface analysis, ESP mapping and Quantum Theory of Atoms in Molecules (QTAIM) (Bader, 1990) topological analysis of theoretical and experimental electron densities were employed by Pyziak et al. (2015) as part of their experimental charge–density investigation of intermolecular interactions, including chalcogen bonding, in 4-[[4-(methoxy)-3-quinolinyl]thio]-3-thiomethylquinoline, and by Lai et al. (2016) in a study comparing -piroxicam with piroxicam monohydrate....
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...Hirshfeld surface analysis, ESP mapping and Quantum Theory of Atoms in Molecules (QTAIM) (Bader, 1990) topological analysis of theoretical and experimental electron densities were employed by Pyziak et al. (2015) as part of their experimental charge–density investigation of intermolecular…...
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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
"CrystalExplorer model energies and ..." refers methods in this paper
...Mercury (Macrae et al., 2008) was used to add H atoms for a small number of structures and, as before, all X—...
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TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.
Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
6,313 citations
"CrystalExplorer model energies and ..." refers background in this paper
...HF/3-21G monomer calculations also failed to converge for some openshell molecules/ions [Cambridge Structural Database (CSD; Groom et al., 2016) refcodes ACACCR07, ACACVO04, CPNDYV07, IGACEC, JIYKEH, AFATAE and AGEFEX], and those structures were not included in the determination of scale factors…...
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TL;DR: This work develops an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives, which provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids.
Abstract: Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
5,731 citations
"CrystalExplorer model energies and ..." refers methods in this paper
...…acid, and by Landeros-Rivera et al. (2016), who examined intermolecular interactions in crystalline arene– perhaloarene adducts by QTAIM methods, ESP mapping and noncovalent index (NCI) surfaces (Johnson et al., 2010), as well as energies from Gavezzotti’s PIXEL method for selected molecular pairs....
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