A third blind test of crystal structure prediction

The polymorphs of ROY: application of a systematic crystal structure prediction technique

We investigate the ability of current ab initio crystal structure prediction techniques to identify the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, also known as ROY because of the red, orange and yellow colours of its polymorphs. We use a methodology combining the generation of a large number of structures based on a computationally inexpensive model using the CrystalPredictor global search algorithm, and the further minimization of the most promising of these structures using the CrystalOptimizer local minimization algorithm which employs an accurate, yet efficiently constructed, model based on isolated-molecule quantum-mechanical calculations. We demonstrate that this approach successfully predicts the seven experimentally resolved structures of ROY as lattice-energy minima, with five of these structures being within the 12 lowest energy structures predicted. Some of the other low-energy structures identified are likely candidates for the still unresolved polymorphs of this molecule. The relative stability of the predicted structures only partially matches that of the experimentally resolved polymorphs. The worst case is that of polymorph ON, whose relative energy with respect to Y is overestimated by 6.65 kJ mol(-1). This highlights the need for further developments in the accuracy of the energy calculations.

First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

We demonstrate that the intrinsic aqueous solubility of crystalline druglike molecules can be estimated with reasonable accuracy from sublimation free energies calculated using crystal lattice simulations and hydration free energies calculated using the 3D Reference Interaction Site Model (3D-RISM) of the Integral Equation Theory of Molecular Liquids (IET). The solubilities of 25 crystalline druglike molecules taken from different chemical classes are predicted by the model with a correlation coefficient of R = 0.85 and a root mean square error (RMSE) equal to 1.45 log10S units, which is significantly more accurate than results obtained using implicit continuum solvent models. The method is not directly parametrized against experimental solubility data, and it offers a full computational characterization of the thermodynamics of transfer of the drug molecule from crystal phase to gas phase to dilute aqueous solution.

Constrained evolutionary algorithm for structure prediction of molecular crystals: methodology and applications

Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of well defined molecular units. The main feature of this new approach is that each unit is treated as a whole body, which drastically reduces the search space and improves the efficiency, but necessitates the introduction of new variation operators described here. To increase the diversity of the population of structures, the initial population and part (~20%) of the new generations are produced using space-group symmetry combined with random cell parameters, and random positions and orientations of molecular units. We illustrate the efficiency and reliability of this approach by a number of tests (ice, ammonia, carbon dioxide, methane, benzene, glycine and butane-1,4-diammonium dibromide). This approach easily predicts the crystal structure of methane A containing 21 methane molecules (105 atoms) per unit cell. We demonstrate that this new approach also has a high potential for the study of complex inorganic crystals as shown on examples of a complex hydrogen storage material Mg(BH(4))(2) and elemental boron.

Study of the single-crystal X-ray diffuse scattering in paracetamol polymorphs

Single-crystal diffuse X-ray scattering from paracetamol polymorphs is successfully calculated with Monte Carlo (MC) models that are used to simulate the crystals. In order to obtain the correct model appropriate force constants are required that describe the interatomic potentials used in the MC algorithm. Coefficients for an empirical `Buckingham'-type formula are used to determine these force constants. These coefficients are subsequently refined using the least-squares method and are found to converge on similar values for both polymorphic forms. An investigation of the correlation space generated from each model provides what would be expected given that strong displacive correlations exist between the molecules comprising the densely hydrogen-bonded layers. More disordered motions between these layers are present in the model for form (II) as opposed to form (I). An investigation into the peculiarities of librational disorder was also conducted, however, correlation values turn out to be so small that any structural information concerning librational correlation is inconclusive. The purpose of this experiment was to identify if the diffuse scattering features could provide further insight into understanding the physical reasoning behind the metastability of form (II). The form (II) → (I) phase transition is also not currently well understood and usually phase transitional information can be obtained from pronounced diffuse scattering features. Since the diffuse scattering is modelled adequately using harmonic potentials it is our conjecture that the `diffuse' is essentially thermal in origin and does not afford any extra information about the form (II) → (I) phase transition.

Hydrogen-bonded assembly in six closely related pyrazolo[3,4-b]pyridine derivatives; a simple chain, three types of chains of rings and a complex sheet structure

Six closely related pyrazolo[3,4-b]pyridine derivatives, namely 6-chloro-3-methyl-1,4-diphenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(20)H(14)ClN(3)O, (I), 6-chloro-3-methyl-4-(4-methylphenyl)-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(21)H(16)ClN(3)O, (II), 6-chloro-4-(4-chlorophenyl)-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(20)H(13)Cl(2)N(3)O, (III), 4-(4-bromophenyl)-6-chloro-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(20)H(13)BrClN(3)O, (IV), 6-chloro-4-(4-methoxyphenyl)-3-methyl-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(21)H(16)ClN(3)O(2), (V), and 6-chloro-3-methyl-4-(4-nitrophenyl)-1-phenylpyrazolo[3,4-b]pyridine-5-carbaldehyde, C(20)H(13)ClN(4)O(3), (VI), which differ only in the identity of a single small substituent on one of the aryl rings, crystallize in four different space groups spanning three crystal systems. The molecules of (I) are linked into a chain of rings by a combination of C-H···N and C-H···π(arene) hydrogen bonds; those of (II), (IV) and (V), which all crystallize in the space group P ̅1, are each linked by two independent C-H···O hydrogen bonds to form chains of edge-fused rings running in different directions through the three unit cells; the molecules of (III) are linked into complex sheets by a combination of two C-H···O hydrogen bonds and one C-H···π(arene) hydrogen bond; finally, the molecules of (VI) are linked by a single C-H···O hydrogen bond to form a simple chain.

Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories - a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.

Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations

Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis.

A perspective on synthetic and solid-form enablement of inhalation candidates

The administration of compounds by a dry-powder inhaler presents significant challenges to the development and discovery chemist, owing to the stringent requirements placed upon the physical characteristics of the active pharmaceutical ingredient and the high complexity of the molecules concerned. The current state of synthetic chemistry technology is such that commercial syntheses of these compounds are demanding but achievable. While synthetic chemistry will remain a major component of the development of inhaled therapies, the main challenge facing practitioners in this area is the early identification of a suitable solid form. Further advances in the prediction of solid-form properties would significantly enable this field and may allow triage of molecules to be carried out at the design stage of projects.

Temperature-accelerated method for exploring polymorphism in molecular crystals based on free energy

The ability of certain organic molecules to form multiple crystal structures, known as polymorphism, has important ramifications for pharmaceuticals and high energy materials. Here, we introduce an efficient molecular dynamics method for rapidly identifying and thermodynamically ranking polymorphs. The new method employs high temperature and adiabatic decoupling to the simulation cell parameters in order to sample the Gibbs free energy of the polymorphs. Polymorphism in solid benzene is revisited, and a resolution to a long-standing controversy concerning the benzene II structure is proposed.

Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction

The range of target structures in the fifth international blind test of crystal structure prediction was extended to include a highly flexible molecule, (benzyl-(4-(4-methyl-5-(p-tolylsulfonyl)-1,3-thiazol-2-yl)phenyl)carbamate, as a challenge representative of modern pharmaceuticals. Two of the groups participating in the blind test independently predicted the correct structure. The methods they used are described and contrasted, and the implications of the capability to tackle molecules of this complexity are discussed.

Examination of the α-chitin structure and decrystallization thermodynamics at the nanoscale

Chitin is the primary structural material of insect and crustacean exoskeletons and fungal and algal cell walls, and as such it is the one of the most abundant biological materials on Earth. Chitin forms linear polymers of β1,4-linked-N-acetyl-D-glucosamine (GlcNAc), and in Nature, enzyme cocktails deconstruct chitin to GlcNAc. The mechanism of chitin deconstruction, like that of cellulose deconstruction, has been under investigation due to its importance in the global carbon cycle and in production of renewable and sustainable products from biological matter. To further understand the nanoscale properties of chitin, here we simulate crystals of α-chitin, which is the most prevalent form in Nature. We find excellent agreement with the recently reported crystal structure and we report the salient features of the simulations related to crystalline stability. We also compute the thermodynamic work required to peel individual chains from α-chitin surfaces, which a chitinase enzyme must conduct to deconstruct chitin. Compared with previous simulations of native plant cellulose Iβ, α-chitin exhibits higher decrystallization work for chains in the middle of surfaces and similar work for chains on the edges of crystals. Unlike cellulose, the free energy profile is dominated by a single bifurcated hydrogen bond between chains formed by the GlcNAc side chains and the O6 atoms on the primary alcohol group. This study highlights the molecular features of chitin that make it such a tough, recalcitrant material, and provides a key thermodynamic parameter in our quantitative understanding of how enzymes contribute to the turnover of carbohydrates in the biosphere.

Agent-based modeling for the 2D molecular self-organization of realistic molecules

We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.

Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.1(11,15).0(2,6).0(16,20))triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C(24)H(30)N(6)) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z', density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z' = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30-40 kJ mol(-1). These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones

The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize inP21/c,Z= 2, the dichloro derivative in P\bar 1,Z= 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes inP21/c,Z= 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom–atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom–atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph.

Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials

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.

Molecular shape and medicinal chemistry: a perspective

The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for "decoration" with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose prediction, or active site description. Computing power has facilitated this evolution by allowing shape to be handled precisely without the need to reduce down to point descriptors or approximate metrics, and the diversity of resultant applications argues for this being an important step forward. Certainly, it is encouraging that as computation has enabled our intuition, molecular shape has consistently surprised us in its usefulness and adaptability. The first Aurelius question, "What is the essence of a thing?", seems well answered, however, the third, "What do molecules do?", only partly so. Are the topics covered here exhaustive, or is there more to come? To date, there has been little published on the use of the volumetric definition of shape described here as a QSAR variable, for instance, in the prediction or classification of activity, although other shape definitions have been successful applied, for instance, as embodied in the Compass program described above in "Shape from Surfaces". Crystal packing is a phenomenon much desired to be understood. Although powerful models have been applied to the problem, to what degree is this dominated purely by the shape of a molecule? The shape comparison described here is typically of a global nature, and yet some importance must surely be placed on partial shape matching, just as the substructure matching of chemical graphs has proved useful. The approach of using surfaces, as described here, offers some flavor of this, as does the use of metrics that penalize volume mismatch less than the Tanimoto, e.g., Tversky measures. As yet, there is little to go on as to how useful a paradigm this will be because there is less software and fewer concrete results.Finally, the distance between molecular shapes, or between any shapes defined as volumes or surfaces, is a metric property in the mathematical sense of the word. As yet, there has been little, if any, application of this observation. We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive.

Precursor effects of the orthorhombic to monoclinic phase transition in benzocaine form (II) revealed by X-ray diffuse scattering

We described the development of a Monte Carlo computer model for the room-temperature form (II) polymorph of benzocaine that incorporates, on a local scale, structural features derived from the low-temperature form (III) polymorph. The introduction of this extra information convincingly reproduces those observed diffraction features that an earlier harmonic model was unable to achieve. In both form (I) and form (II) the hydrogen-bonded chains of molecules that extend along the respective a axes tend to slide backward and forward along their lengths. While in form (I) the motion is well modelled by a harmonic potential in form (II) there is a degree of anharmonicity that means that some intermolecular contact vectors, which are identical in the average structure, are distributed bimodally with either longer or shorter vectors being preferred to the average. Moreover there is a tendency for these deviations from average to be correlated to give short-range ordered domains that are the precursors of the two twinned variants of the long-range ordered low-temperature form (III) structure.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential.

Pigment Orange 5: crystal structure determination from a non-indexed X-ray powder diagram

Pigment Orange 5, also known as “Dinitroaniline Orange”, is an industrially produced azo pigment. The structure was solved from routinely measured lab X-ray powder data without indexing, by means of a newly developed combination of lattice energy minimization and simultaneous fit to the X-ray powder diagram. Finally, the structure was refined by Rietveld methods using restraints. Pigment Orange 5 crystallizes in space group P21/a with a = 16.365(5) Å, b = 12.874(4) Å, c = 6.924(2) Å, β = 100.143(2)°, Z = 2. The molecules are almost planar and form stacks along the c axis.

An artificial intelligence approach for modeling molecular self-assembly: agent-based simulations of rigid molecules

Agent-based simulations are rule-based models traditionally used for the simulations of complex systems. In this paper, an algorithm based on the concept of agent-based simulations is developed to predict the lowest energy packing of a set of identical rigid molecules. The agents are identified with rigid portions of the system under investigation, and they evolve following a set of rules designed to drive the system toward the lowest energy minimum. The algorithm is compared with a conventional Metropolis Monte Carlo algorithm, and it is applied on a large set of representative models of molecules. For all the systems studied, the agent-based method consistently finds a significantly lower energy minima than the Monte Carlo algorithm because the system evolution includes elements of adaptation (new configurations induce new types of moves) and learning (past successful choices are repeated).

VARICELLA: a variable-cell direct space method for structure determination from powder diffraction data

A direct space method for structure determination from powder diffraction data is proposed. Employing a hybrid Monte Carlo algorithm for generating the random conformations of a flexible molecular model, and sampling in a modified multicanonical statistical ensemble, it allows for variable cell parameters during an iterative search process. The acceptance-rejection criterion involves both a disagreement factor between the calculated and the experimental diffraction profiles and a modified crystal energy so that the space of tentative solutions can be widely explored while maintaining some physical meaningfulness of the proposals. Allowing the cell to be variable requires the zero shift to be treated as an optimizing parameter; this, in turn, requiring the disagreement factor to be based on the Fourier transform of the spectrum. The algorithm is presented in both a serial and a parallel version, the latter presenting several advantages, such as the possibility to probe different structures at a time while keeping them far from each other in the space defined by suitable order parameters. The method is built up and carefully tested by using, as a case study, a crystal of 3-ethyl 2,3-exo-disyndiotactic norbornene heptamer recently determined by single crystal x-ray diffraction techniques.

An investigation of KS-DFT electron densities used in atoms-in-molecules studies of energetic molecules

The atoms-in-molecules (AIM) theory has been proposed as a method to understand chemical stability through stationary properties of the electron density. To assess the applicability of this method for establishing such correlations with various performance and vulnerability properties of energetic materials, we calculated the Kohn-Sham density functional theory (KS-DFT) wavefunctions and their subsequent AIM data for representative materials, including hexanitrobenzene (HNB), pentaerythritol tetranitrate (PETN), pentanitroaniline (PNA), 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), ethylenedinitramine (EDNA), 1,1-diamino-2,2-dinitroethylene (FOX-7), 3-nitro-1,2,4-triazol-5-one (NTO), nitroguanidine (NQ), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), and the TATB dimer using the B3LYP, PBE, and PW91 potentials as well as Hartree-Fock (HF). For the HNB and HMX molecules and the TATB dimer, the number of critical points in the low-density regions of the density gradient vector field varied, sometimes dramatically, with basis set and potential even at their individually optimized geometries. Adding ghost atoms in the low-density regions also affected the existence of critical points. The variation was seen in results generated with three separate AIM software packages, AIMPAC, AIMAll, and InteGriTy. This inconsistency implies that KS-DFT wave-functions can have significant variation in the topology of the electron density to such an extent that these calculations cannot be used to justify the existence or absence of low-density critical points. Therefore, predictions of the stability of a molecule based solely on properties of low-density bond critical points generated from a single DFT calculation are questionable.

Binding mechanisms in supramolecular complexes

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.