Molecular dynamics study of crystalline water ices

The behavior of structures of H₂O crystalline ices Ih, Ic, XI, VII, VIII, VI is studied in molecular dynamics experiment using the potential offered by Poltev and Malenkov. The behavior of the system consisting of one of the two identical interpenetrating, but without any common hydrogen bonds, water frameworks comprising the ice VI structure is also simulated. As a result of simulations, the ice VII structure has collapsed, whereas other systems proved to be stable. The reasons of instability of the ice VII and previously studied ice IV structures in molecular dynamics experiments are discussed. Based on the simulation results of the above-mentioned ices and previous simulation of ices II, III, IX, IV, and XII, the general regularities of dynamic properties of water molecules in crystalline water ices are formulated. Unreliability of results obtained by molecular dynamics in the investigation of self-organizing processes in aqueous systems is shown.     

Tailor-made force fields for crystal-structure prediction

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.     

Progress in crystal structure prediction

The results of the application of a density functional theory method incorporating dispersive corrections in the 2010 crystal structure prediction blind test are reported. The method correctly predicted four out of the six experimental structures. Three of the four correct predictions were found to have the lowest lattice energy of any crystal structure for that molecule. The experimental crystal structures for all six compounds were found during the structure generation phase of the simulations, indicating that the tailor-made force fields used for screening structures were valid and that the structure generation engine, which combines a Monte Carlo parallel tempering algorithm with an efficient lattice energy minimiser, was working effectively. For the three compounds for which the experimental crystal structures did not correspond to the lowest energy structures found, the method for calculating the lattice energy needs to be further refined or there may be other polymorphs that have not yet been found experimentally.     

Bioactive saponins and glycosides. XVIII. Nortriterpene and triterpene oligoglycosides from the fresh leaves of Euptelea polyandra Sieb. et Zucc. (2): Structures of eupteleasaponins VI, VI acetate, VII, VIII, IX, X, XI, and XII.

Following the elucidation of eupteleasaponins I, II, III, IV, V, and V acetate, eupteleasaponins VI, VI acetate, VII, VIII, IX, X, XI, and XII were isolated from the fresh leaves of Euptelea polyandra Sieb. et Zucc. The structures of eupteleasaponins VI-XII were determined on the basis of chemical and physicochemical evidence.     

Ab initio crystal structure predictions for flexible hydrogen‐bonded molecules. Part III. Effect of lattice vibrations

In crystal structure predictions possible structures are usually ranked according to static energy. Here, this criterion has been replaced by the free energy at any temperature. The effects of harmonic lattice vibrations were found by standard lattice‐dynamical calculations, including a rough estimate of the effects of thermal expansion. The procedure was tested on glycol and glycerol, for which accurate static energies had been obtained previously (Part II of this series). It was found that entropy and zero‐point energy give the largest contribution to free energy differences between hypothetical crystal structures, adding up to about 3 kJ/mol for the structures with lowest energy. The temperature‐dependent contribution to the energy and the effects of thermal expansion showed less variation among the structures. The overall accuracy in relative energies was estimated to be a few kJ/mol. The experimental crystal structure for glycol corresponded to the global free energy minimum, whereas for glycerol it ranked second at 1 kJ/mol. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 816–826, 2001     

Solid-State NMR-Driven Crystal Structure Prediction of Molecular Crystals: The Case of Mebendazole

Among all possible NMR crystallography approaches for crystal-structure determination, crystal structure prediction – NMR crystallography (CSP-NMRX) has recently turned out to be a powerful method. In the latter, the original procedure exploited solid-state NMR (SSNMR) information during the final steps of the prediction. In particular, it used the comparison of computed and experimental chemical shifts for the selection of the correct crystal packing. Still, the prediction procedure, generally carried out with DFT methods, may require important computational resources and be quite time-consuming, especially if there are no available constraints to use at the initial stage. Herein, the successful application of this combined prediction method, which exploits NMR information also in the input step to reduce the search space of the predictive algorithm, is presented. Herein, this method was applied on mebendazole, which is characterized by desmotropism. The use of SSNMR data as constraints for the selection of the right tautomer and the determination of the number of independent molecules in the unit cell led to a considerably faster process, reducing the number of calculations to be performed. In this way, the crystal packing was successfully predicted for the three known phases of mebendazole. To evaluate the quality of the predicted structures, these were compared to the experimental ones. The crystal structure of phase B of mebendazole, in particular, was determined de novo by powder diffraction and is presented for the first time in this paper.     

Structure prediction, disorder and dynamics in a DMSO solvate of carbamazepine

We have applied crystal structure prediction methods to understand and predict the formation of a DMSO solvate of the anti-convulsant drug carbamazepine (CBZ), in which the DMSO molecules are disordered. Crystal structure prediction calculations on the 1:1 CBZ:DMSO solvate revealed the generation of two similar low energy structures which differ only in the orientation of the DMSO molecules. Analysis of crystal energy landscapes generated at 0 K suggests the possibility of solvent disorder. A combined computational and experimental study of the changes in the orientation of the DMSO within the crystal structure revealed that the nature of the disorder changes with temperature. At low temperature, the DMSO disorder is static whilst at high temperature the DMSO configurations can interconvert by a 180° rotation of the DMSO molecules within the lattice. This 180° rotation of the DMSO molecules drives a phase change from a high temperature dynamically disordered phase to a low temperature phase with static disorder. Crystallisation of a DMSO solvate of the related molecule epoxycarbamazepine resulted in a different degree of DMSO disorder in the crystal structure, despite the similarity of the carbamazepine and epoxycarbamazepine molecules. We believe consideration of disorder and its contribution to entropy and crystal free energies at temperature other than 0 K is fundamental for the accuracy of future energy rankings in crystal structure prediction calculations of similar solvated structures.     

Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

Terpenoids—LXI Conversion of eudesmol to di- and tetrahydrocostol

Dihydro-β-eudesmol (IV), obtained by catalytic hydrogenation of β-eudesmol (II), on pyrolysis via the benzoate gives dihydro-β-selinene (V). Its epoxyderivative (VI) is converted on treatment with acetic acid to the hydroxy acetate (VII), the benzoate of which on pyrolysis, followed by saponification, affords dihydrocostol (XI), converted by hydrogenation to tetrahydrocostol (XII). The alcohol (XI) is not identical with agarol to which the same stereoformula has been assigned previously. These results would necessitate a re-examination of the structure and stereochemistry of agarol which has already been undertaken.     

Reactions with α-substituted cinnamonitriles. A novel synthesis of hexa-substituted pyridines

Whereas acetoacetanilide (II) reacted with α-cyano- and α-benzoylcinnamonitrile derivatives Ia-e to give hexa-substituted pyridines III and V, it reacted with α-carboxamido- and α-thiocarboxamidocinnammonitrile derivatives If-h to afford penta-substituted pyridines VI. One mole of acetonedicarboxylic acid dianilide (VII) reacted with two moles of each of α-cyano- and α-thiocarboxamidocinnamonitriles Ia,b,f,g to yield the dipyridyl ketones VIII and IX, respectively. On the other hand, α-benzoyl- and α-ethoxycarbonylcinnamonitriles Ic,d,i,j reacted with VII in equimolecular ratio to give the pyran derivaties X and XI, respectively. Several schemes were proposed to illustrate reactions steps. The structures of the synthesized compounds were proved by chemical and spectral methods.     

Über in 6-Stellung basisch substituierte Morphanthridine. 8. Mitteilung über siebengliedrige Heterocyclen

Morphanthridines III with a basic substituent in position 6, which show neuroleptic activity, have been synthesised as follows: Chlorination of the lactams I with POCl₃ gave the iminochlorides II, which were converted by bases to the amidines III. The 11-oxo-morphanthridines VI and VII were synthesised using the same procedure, 2-(1-methylpiperazine-4-carbonyl)-2′-amino-benzophenone (XI) was obtained directly from the 6-chloro-11-oxo-morphanthridine (V) or by extended heating of VI with N-methylpiperazine. Reduction of the 11-oxo-compounds VI and VII with NaBH₄ gave the 11-hydroxy-compounds IX and X. 3-(2-aminophenyl)-phtalide (VIII) resulted from the acid hydrolysis of IX.     

Mass spectrometry of hop compounds—III. Mass spectra of substituted 1,3-cyclopentanediones derived from hop constituents

The mass spectra of isohumulones (IV, V), tetrahydroisocohumulones (VI, VII), tetrahydroisohumulones (VIII) neohydroisocohumulones (XI, XII) cohumulinic acid (III), lupuloxinic acid (XV), humulinone (XIV) and related compounds are described. Ions which appear to be diagnostic for particular structures are discussed.     

Crystal structure predictions for acetic acid

Possible crystal structures of acetic acid were generated, considering eight space groups and assuming one molecule in the asymmetric unit. Our grid-search method was compared with a Monte Carlo approach as implemented in the Biosym/MSI Polymorph Predictor. This revealed no sampling deficiencies. A large number of possible crystal structures were found (∼100 within only 5 kJ/mol), including the experimental structure. Energy minimizations were done with a united-atoms force field (GROMOS), an all-atoms force field (AMBER), and a potential that describes the electrostatic interactions with distributed multipoles (DMA). In all cases, the experimental structure had a low lattice energy. The number of hypothetical crystal structures was reduced considerably by removing space-group symmetry constraints, or by a primitive molecular dynamics shake-up. Nevertheless, sufficient structures of equal or lower energy compared with the experimental structure remained to suggest that other factors need to be considered for genuine structure prediction. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 459–474, 1998     

N2分子在UO(100)表面的吸附与解离

运用密度泛函理论中广义梯度近似(GGA)的VWN-BP方法结合周期性平板模型, 研究N2在UO(100)表面的吸附. 研究表明, N2平行吸附在UO(100)表面穴位为最稳定吸附构型, 吸附能为79.0 kJ·mol-1. Mulliken布居分析显示, N2获得电子. 吸附后, N—N伸缩振动频率发生红移, 波数在1770-2143 cm-1之间. 态密度分析表明, U原子将d、f电子转移至N2的2π轨道. 计算所得解离反应的能垒为266.9 kJ·mol-1.     

Metabolism of terniary compounds. V. Decomposition of diincarbonic acids and hydrocarbons in vivo

10,12-Heneicosadiynoic acid (I), 5,7-hexadecadiynoic acid (IV), and 10,12-docosadiynedioic acid (VI) were fed to rats. As metabolites 4,6-undecadiynedioic acid (II), 5,7-dodecadiynedioic acid (V), and 4,6-decadiynedioic acid (VII) respectively were isolated from the urine. 10,12-Heptadecadiynoic acid (III) also yielded metabolite II. Furthermore 9,11-eicosadiyne (X) and for comparison purposes eicosane (XI), hexadecanedioic acid (VIII), and docosanedioic acid (IX) were fed. X and XI were incorporated into depot fat and liver lipids to a cetain degree. The diynes I, II, IV, and X are new compounds.     

Stable structures of oxocarbons and pseudooxocarbons of group VI

Density functional theory has been used to study the geometries, electronic structure and harmonic vibrational frequencies of the oxocarbons and the pseudooxocarbons of group VI. The ability of the maximum hardness principle for predicting the stable structures of oxocarbons and pseudooxocarbons of group VI is tested by analyzing the results of these calculations. To obtain the stable structure, the geometrical parameters and stability of molecules are compared and analyzed. Bond orders of candidate molecules are calculated by using natural bond orbital analysis. Except selenium derivatives, atoms in molecule calculations prove being useful for studying the nature of carbon heteroatom bond. Chemical hardness is also reported. This study reveals that (1) DFT gives very similar geometries and energies to ab-initio methods and (2) the maximum hardness principle (MHP) is not verified for some of these structures. Data for C₆Se₆, which are new, are presented in this work.     

On the Solvent‐free Structure of a Jäger‐type Cobalt(II) N2O2‐Chelate Complex

A combined synchrotron X‐ray and density functional theory (DFT) study on the structure of a Jäger‐type N₂O₂ chelate complex was carried out. The ethoxy‐substituted bis(3‐oxo‐enaminato)cobalt(II) complex ( 1 ) was an original sample from the laboratory of the late Professor Ernst‐G. Jäger (University of Jena, Germany). Single‐crystal X‐ray analysis revealed essentially flat molecules of 1 , which are unsolvated and coordinatively unsaturated. The DFT calculations on the isolated molecule predict a planar structure for the non‐hydrogen atoms, which is a local minimum on the energy surface. The crystal packing is achieved through off‐set stacking (staircase arrangement), resulting in a herringbone pattern in the space group P2₁2₁2₁. The structure of 1 is compared to known structures of related bis(3‐oxo‐enaminato)cobalt(II) complexes ( 2 – 4 ). Original bulk material of 1 was investigated by scanning electron microscopy (SEM), powder X‐ray diffraction (PXRD), melting point determination, and infrared (IR) spectroscopy.     

Relative evaluation of neutron activation,X-ray fluorescence and spark source mass spectrometry for multielement analysis of geothermal waters

To sulfide geothermal waters from the French Pyrenees region and bicarbonate and chloride waters from the French Vosges area, all of the following analysis techniques were applied in order to compose a broad inventory of trace elements: (1) for the dissolved material: neutron activation analysis after a freeze-drying step using a very short cycle (I), short cycle (II) or long cycle (III), neutron activation after co-crystallization on 1-(2-pyridylazo)-2-naphthol (PAN) using a short cycle (IV) or long cycle (V), X-ray fluorescence after co-crystallization on PAN (VI) and spark source mass spectrometry after evaporation on graphite (VII) or preconcentration on PAN, and, (2) for the filtered or suspended material: neutron activation using a very short (VIII), short (IX) or long cycle (X) and X-ray fluorescence (XI). Altogether, on the average some 30 elements could be determined above the detection limit in solution and 15 in suspension. It appeared, however, that for procedures (I), (II), (IV), (VI), (VIII) and (XI) the investment of time and cost had not been efficient enough. Invoking only procedures (III), (V), (IX), (X) and for low salinity geothermal waters only: (VII), the number of elements detected was almost as large.     

Efficient Screening for Ternary Molecular Ionic Cocrystals Using a Complementary Mechanosynthesis and Computational Structure Prediction Approach

The discovery of molecular ionic cocrystals (ICCs) of active pharmaceutical ingredients (APIs) widens the opportunities for optimizing the physicochemical properties of APIs whilst facilitating the delivery of multiple therapeutic agents. However, ICCs are often observed serendipitously in crystallization screens and the factors dictating their crystallization are poorly understood. We demonstrate here that mechanochemical ball milling is a versatile technique for the reproducible synthesis of ternary molecular ICCs in less than 30 min of grinding with or without solvent. Computational crystal structure prediction (CSP) calculations have been performed on ternary molecular ICCs for the first time and the observed crystal structures of all the ICCs were correctly predicted. Periodic dispersion-corrected DFT calculations revealed that all the ICCs are thermodynamically stable (mean stabilization energy=−2 kJ mol⁻¹) relative to the crystallization of a physical mixture of the binary salt and acid. The results suggest that a combined mechanosynthesis and CSP approach could be used to target the synthesis of higher-order molecular ICCs with functional properties.