1,720,976 research outputs found
Is the equilibrium composition of mechanochemical reactions predictable using computational chemistry?
Get PDFThe ability of computational methods to predict the structures and energetics that determine the equilibrium of solid state mechanochemical reactions has been assessed. Two previously characterised base catalysed metathesis reactions between aromatic disulfides are studied using crystal structure prediction methods and 10 lattice energy calculations that combine molecular electronic structure methods with anisotropic atom-atom potentials. We find that lattice energy searches locate three of the six crystal structures as global minima on their respective crystal energy landscapes. The remaining structures are less successfully predicted, due to problems 15 modelling relative conformational energies due to limitations of the density functional theory method for calculating intramolecular energies. Prediction of the overall reaction energies proves challenging for current methods, but the results show promise as a base on which to build more accurate and reliable approaches
A computational and experimental search for polymorphs of parabanic acid – a salutary tale leading to the crystal structure of oxo-ureido-acetic acid methyl ester
No full textA computational search to predict the crystal structure of parabanic acid produced the known P21/c crystal structure as the global minimum in the lattice energy. However, there are many hypothetical structures only 2–6 kJ mol?1 less stable than the known form, which are within the energy range of possible polymorphism and have reasonable mechanical properties and relative growth rates. The harmonic intermolecular frequencies and the attachment energy estimate of relative growth rates suggest that the known polymorph is thermodynamically and kinetically favoured, but the possibility of other polymorphs cannot be excluded. A simultaneous experimental search for new polymorphs found crystals with a new morphology and X-ray powder pattern when a solution of parabanic acid in methanol was left to evaporate. Eventually, the structure was shown by single crystal X-ray diffraction to be that of oxo-ureido-acetic acid methyl ester. Thus, under the conditions of recrystallisation from methanol, parabanic acid had undergone a previously unreported ring-opening reaction, and had not crystallised as a new polymorph as had seemed likely prior to single crystal characterisation. The combination of the experimental and theoretical studies indicates that new polymorphs of parabanic acid are unlikely to be found readil
A study of the known and hypothetical crystal structures of pyridine: why are there four molecules in the asymmetric unit cell?
No full textThe oldest crystal structure of pyridine is unusually complex, with four molecules in the asymmetric unit cell of Pna21 symmetry. In an attempt to understand why pyridine crystallises with 16 molecules in the unit cell, we have considered its thermodynamic stability relative to hypothetical pyridine structures. These were generated by a search for minima in the lattice energy of pyridine amongst the more common space groups, using the crystal structure prediction procedure MOLPAK followed by lattice energy minimisation using a distributed multipole-based intermolecular potential. We find over two dozen distinct crystal structures in the energy gap of less than 6 kJ mol?1 between the corresponding models for the observed and most stable (hypothetical) structure. Adding harmonic phonon estimates of the intermolecular zero point energy and entropy at the melting point of pyridine slightly improves the relative stability of the observed Z = 16 structure. Several of these hypothetical structures can be eliminated as only just mechanically stable, or because the growth rate of the crystal is estimated to be very slow by the attachment energy model. Nevertheless, there are still over a dozen structures that appear competitive with the known structure as polymorphs of pyridine. Following these predictions, an intense experimental search has found a new polymorph of perdeutero-pyridine (form II), which was not found in the search. This structure is also predicted to be metastable with a similar energy to form I. Although there is some evidence for kinetic factors favouring the observed structures, the metastable Z = 16 structure and the new form II remain a challenge for our understanding of crystallisatio
Sensitivity of morphology prediction to the force field: paracetamol as an example
No full textThe growth morphology of paracetamol is known to show a strong supersaturation dependence. Most morphology prediction methods, like the attachment energy method, cannot include this dependence in their prediction. Monte Carlo simulations are able to use the supersaturation as an input parameter and can also include the growth mechanism. This makes the Monte Carlo technique a powerful tool to study the growth of organic crystals. Some studies in the literature show that the attachment energy method is only weakly influenced by the force field used to calculate the attachment energies. The present paper presents the sensitivity of the Monte Carlo simulation results to the force field and charge set using paracetamol as a case study. The force field and atomic point charges are found to influence the results to a large extent. This is due to subtle differences in step energies that determine the growth rates of the crystal faces
Dynamics in crystals of rigid organic molecules: contrasting the phonon frequencies calculated by molecular dynamics with harmonic lattice dynamics for finidazole and 5-azauracil
No full textMolecular dynamics simulations have been performed on crystalline imidazole at 100?K and 5-azauracil at 310?K with a model intermolecular potential that includes a distributed multipole representation of the molecular charge distribution using the program DL_MULTI. The anisotropic atom–atom electrostatic model enabled the experimental crystal structures to be reproduced well in a constant pressure simulation and the simulations showed a physically reasonable thermal expansion relative to the minimum in the static lattice energy. The rigid-body molecular motions in a subsequent constant volume simulation were analysed to obtain the k?=?0 frequencies corresponding to different symmetry representations, via the translational and rotational velocity autocorrelation functions. These frequencies were contrasted with the corresponding harmonic lattice modes calculated with the same molecular model and intermolecular potential. The agreement was good, with most, but not all, modes decreasing in frequency in the finite temperature simulation, by generally less than 5?cm?1 in the case of imidazole (reducing the rms error in comparison with experimental frequencies to 18.8?cm?1) and by less than 20?cm?1 for 5-azauracil. Quasi-harmonic calculations using experimental unit cell parameters and analyses of the modes in terms of the different hydrogen bonding motifs were unable to give any clear insight into the causes of the significant variations in the effects of temperature on the different motions
Understanding the influence of polymorphism on phonon spectra: lattice dynamics calculations and terahertz spectroscopy of carbamazepine
No full textRigid molecule atomistic lattice dynamics calculations have been performed to predict the phonon spectra of the four polymorphs of carbamazepine, and these calculations predict that there should be differences in the spectra of all four forms. Terahertz spectra have been measured for forms I and III, and there are clearly different features between polymorphs' spectra, that are accentuated at low temperature. While carbamazepine adopts the same hydrogen bonded dimers in all of its known polymorphs, the calculations show that differences in packing arrangements of the dimers lead to changes in the frequency ranges for each type of hydrogen bond vibration, giving a physical explanation to the observed differences between the spectra. Although the agreement between calculated and observed spectra does not allow a definitive characterization of the spectra, it is possible to make tentative assignments of many of the observed features in the terahertz region for the simpler form III; we can only make some tentative assignments of specific modes in the more complex spectrum of form I. While harmonic rigid molecule lattice dynamics shows promise for understanding the differences in spectra between polymorphs of organic molecules, discrepancies between observed and calculated spectra suggest areas of improvement in the computational methods for more accurate modeling of the dynamics in molecular organic crystals
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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