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. Tonto is an object oriented system for computational chemistry. This paper focuses mainly on the Foo, the object oriented language used to implement Tonto. Foo currently translates into Fortran 95. It offers almost all the features of the coming Fortran 2000 except for dynamic types. It goes beyond the Fortran standard in that parameterised types and template-like inheritance mechanisms are provided. Since the method is based on textual inclusion, it generates code which is easy for the compiler and human to understand. Example code is given, and possible future work on the language is discussed.
An experimental wavefunction is one that has an assumed form and that is also fitted to experimental measurements according to some well defined procedure. In this paper, the concept of extracting wavefunctions from experimental data is critically examined and past efforts are reviewed. In particular, the importance of scattering experiments for wavefunction fitting schemes is highlighted in relation to the more familiar model, the Hamiltonian paradigm. A general and systematically improvable method for fitting a wavefunction to experimental data is proposed. In this method, the parameters in a model wavefunction are determined according to the variational theorem but subject to an imposed constraint that an agreement statistic between the calculated and observed experimental data has a certain acceptable value. Advantages of the method include the fact that any amount of experimental data can be used in the fitting procedure irrespective of the number of parameters in the model wavefunction, the fact that a unique answer is obtained for a given choice of the model wavefunction, and the fact that the method can be used to model different experiments simultaneously. The wavefunction fitting method is illustrated by developing the theory for extracting a single-determinant wavefunction for a fragment of a molecular crystal, using data obtained from elastic X-ray scattering data. Effects due to thermal motion of the nuclei, secondary extinction of the X-ray scattering and different choices for the crystal fragment are treated.
The constrained Hartree-Fock method using experimental X-ray diffraction data is extended and applied to the case of noncentrosymmetric molecular crystals. A new way to estimate the errors in derived properties as a derivative with respect to added Gaussian noise is also described. Three molecular crystals are examined: ammonia [NH(3)], urea [CO(NH(2))(2)], and alloxan [(CO)(4)(NH)(2)]. The energetic and electrical properties of these molecules in the crystalline state are presented. In all cases, an enhancement of the dipole moment is observed upon application of the experimental constraint. It is found that the phases of the structure factors are robustly determined by the constrained Hartree-Fock model, even in the presence of simulated noise. Plots of the electron density, electrostatic potential, and the electron localization function for the molecules in the crystal are displayed. In general, relative to the Hartree-Fock model, there is a depletion of charge around hydrogen atoms and lone pair regions, and a build-up of charge within the molecular framework near nuclei, directed along the bonds. The electron localization function plots reveal an increase in the pair density between vicinal hydrogen atoms.
Constrained Hartree–Fock calculations have been performed to obtain wavefunctions that reproduce experimental X‐ray structure‐factor magnitudes for crystalline NH3 to within the limits of experimental error. Different model densities using both a single molecule and clusters of NH3 in the calculation of X‐ray structure‐factor magnitudes have been examined. The effects of the crystalline lattice on the experimental wavefunction of the NH3 unit can be reproducibly recovered. The construction of structure‐factor magnitudes based on normally distributed random perturbations of the experimental values has also been used to gauge the accuracy of integrated atomic properties obtained from the wavefunctions, the point at which the constraint procedure should be terminated, and the approximate error in the experimental values.
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