Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.
The results of the fifth blind test of crystal structure prediction, which show important success with more challenging large and flexible molecules, are presented and discussed.
The concept of intrinsic motivation has been considered to lie at the heart of the user engagement created by digital games. Yet despite this, educational software has traditionally attempted to harness games as extrinsic motivation by using them as a sugar-coating for learning content. This paper tests the concept of intrinsic
Many people believe that educational games are effective because they motivate children to actively engage in a learning activity as part of playing the game. However, seminal work by Malone (1981), exploring the motivational aspects of digital games, concluded that the educational effectiveness of a digital game depends on the way in which learning content is integrated into the fantasy context of the game. In particular, he claimed that content which is intrinsically related to the fantasy will produce better learning than that which is merely extrinsically related. However, this distinction between intrinsic and extrinsic (or endogenous and exogenous) fantasy is a concept that has developed a confused standing over the following years. This paper will address this confusion by providing a review and critique of the empirical and theoretical foundations of endogenous fantasy, and its relevance to creating educational digital games. Substantial concerns are raised about the empirical basis of this work and a theoretical critique of endogenous fantasy is offered, concluding that endogenous fantasy is a misnomer, in so far as the "integral and continuing relationship" of fantasy cannot be justified as a critical means of improving the effectiveness of educational digital games. An alternative perspective on the intrinsic integration of learning content is described, incorporating game mechanics, flow and representations.
Isonicotinamide (INA) co-crystallizes with carbamazepine (CBZ), as do nicotinamide (NA) and benzamide. The structure of CBZ-INA form II is solved from powder and is shown to be isostructural with CBZ-NA. However picolinamide (PA), despite its similarity to the other pyridine carboxamides in the homologous series, does not appear to form a co-crystal with CBZ. We compare and contrast the use of computed crystal energy landscapes and binary and ternary phase diagrams to explain this behavior. Two 1:1 co-crystal structures of CBZ and INA were predicted to have lower or comparable lattice energies than the sum of the pure component lattice energies. These structures corresponded to the known co-crystal structures. On the other hand, lattice energies of predicted CBZ-PA co-crystal structures were less stable than the pure component lattice energies, implying that CBZ and PA would not form a co-crystal. This is consistent with the experimental evidence. Examination of the hypothetical crystal structures for CBZ-INA and for CBZ-PA explains this in terms of intermolecular hydrogen-bonding capability. Thus computed crystal energy landscapes are more reliable than simple crystal engineering concepts in understanding co-crystal formation, and can provide a useful complement to experimental co-crystal screening.
A key step in many approaches to crystal structure prediction (CSP) is the initial generation of large numbers of candidate crystal structures via the exploration of the lattice energy surface. By using a relatively simple lattice energy approximation, this global search step aims to identify, in a computationally tractable manner, a limited number of likely candidate structures for further refinement using more detailed models. This paper presents an effective and efficient approach to modeling the effects of molecular flexibility during this initial global search. Local approximate models (LAMs), constructed via quantum mechanical (QM) calculations, are used to model the conformational energy, molecular geometry, and atomic charge distributions as functions of a subset of the conformational degrees of freedom (e.g., flexible torsion angles). The effectiveness of the new algorithm is demonstrated via its application to the recently studied 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY) molecule and to two molecules, β-D-glucose and 1-(4-benzoylpiperazin-1-yl)-2-(4,7-dimethoxy-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione, a Bristol Myers Squibb molecule referenced as BMS-488043. All three molecules present significant challenges due to their high degree of flexibility.
Modelling of disorder in organic crystals is highly desirable since it would allow thermodynamic stabilities and other disorder-sensitive properties to be estimated for such systems. Two disordered organic molecular systems are modeled using a symmetry-adapted ensemble approach, in which the disordered system is treated as an ensemble of the configurations of a supercell with respect to substitution of one disorder component for another. Computation time is kept manageable by performing calculations only on the symmetrically inequivalent configurations. Calculations are presented on a substitutionally disordered system, the dichloro/dibromobenzene solid solution, and on an orientationally disordered system, eniluracil, and the resultant free energies, disorder patterns, and system properties are discussed. The results are found to be in agreement with experiment, when some physically implausible configurations are removed from the ensemble average for eniluracil, highlighting the dangers of a completely automated approach to organic crystal thermodynamics which ignores the barriers to equilibration once the crystal has been formed.
Microfluidic devices for spatially localised heating of microchannel environments were designed, fabricated and tested. The devices are simple to implement, do not require complex manufacturing steps and enable intra-channel temperature control to within +/-0.2 degrees C. Ionic liquids held in co-running channels are Joule heated with an a.c. current. The nature of the devices means that the internal temperature can be directly assessed in a facile manner.
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