scholarly journals Specific energy contributions associated with competing hydrogen bond motifs

2014 ◽  
Vol 70 (a1) ◽  
pp. C542-C542
Author(s):  
Thomas Gelbrich ◽  
Ulrich Griesser
Keyword(s):  
Crystal Packing ◽  
Lattice Energy ◽  
Model System ◽  
Dispersion Forces ◽  
Interaction Energies ◽  
Individual Contributions ◽  
Small Set ◽  
N Form ◽  
The Difference ◽  
Small Clusters

The semi-classical density sums (SCDS-Pixel) method [1] was used to study the intermolecular interaction energies in six polymorphs of phenobarbital, a model system for the barbiturate class of compounds.[2] Barbiturates display a rigid pyrimidinetrione ring whose two N–H and three C=O functions can be employed in H-bonding. The ensuing intermolecular N–H···O=C interactions result in a small set of standard H-bonded chain, layer and framework motifs.[3] Even though the average number of N–H···O=C bonds per molecule is always two, the standard barbiturate H-bond motifs differ in the number of intermolecular two-point and one-point N–H···O=C connections per molecule, i.e. (1; 0), (½; 1), (0; 2). For each polymorph (I, II, III, V, VI, X), cumulated Pixel energies, E(n), were calculated for the first n (n = 1, 2, 3, ...) interactions associated with the highest individual contributions to the lattice energy. The obtained sets of E(n) values were compared to one another to establish the differences associated with the formation of the alternate N–H···O=C motifs. Those polymorphs whose N–H···O bonded structures are dominated by two-point connections have superior E(n) values for small clusters of molecules (low n). However, this advantage diminishes gradually if larger clusters of molecules are considered and is completely compensated at n = 8. This indicates that crystal packing on the basis of one-point connection N–H···O=C motifs is viable only because the latter enable the formation of more advantageous weaker interactions which are dominated by dispersion forces. This case illustrates that an assessment of competing H-bond motifs cannot be restricted to just those molecules that are directly involved in H-bond interactions. Rather, the complete crystal packing has to be taken into account. [Figure: Evolution of the difference between E(n) (form V; one-point connections) and E(n)' (form III; two-point connections) with n].

The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contact

2010 ◽  
Vol 66 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Angelo Gavezzotti
Keyword(s):  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Minimum Energy ◽  
Lattice Energy ◽  
Interaction Force ◽  
Coordination Shell ◽  
Geometrical Parameters ◽  
Interaction Energies ◽  
Organic Salts

A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule–molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ∼ 9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom–atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care.

Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid

2013 ◽  
Vol 69 (11) ◽  
pp. 1238-1242 ◽  
Author(s):  
Sofiane Saouane ◽  
Gernot Buth ◽  
Francesca P. A. Fabbiani
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Lattice Energy ◽  
Interaction Energies ◽  
Energy Calculations ◽  
X Ray ◽  
Carboxylate Groups ◽  
Dimensional Network ◽  
Complementary Analysis

The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by thePIXELmethod brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure,PIXELlattice energy calculations confirm the predominance of the Coulombic term (−379.1 kJ mol−1) ahead of the polarization (−141.4 kJ mol−1), dispersion (−133.7 kJ mol−1) and repulsion (266.3 kJ mol−1) contributions.

scholarly journals Towards computer-guided tuning of the crystal packing of porous organic cages

2014 ◽  
Vol 70 (a1) ◽  
pp. C667-C667
Author(s):  
Angeles Pulido ◽  
Ming Liu ◽  
Paul Reiss ◽  
Anna Slater ◽  
Sam Chong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Molecular Sieves ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Aromatic Aldehydes ◽  
Lattice Energy ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Computational Techniques

Among microporous materials, there has been an increasing recent interest in porous organic cage (POC) crystals, which can display permanent intrinsic (molecular) and extrinsic (crystal network) porosity. These materials can be used as molecular sieves for gas separation and potential applications as enzyme mimics have been suggested since they exhibit structural response toward guest molecules[1]. Small structural modifications of the initial building blocks of the porous organic molecules can lead to quite different molecular assembly[1]. Moreover, the crystal packing of POCs is based on weak molecular interactions and is less predictable that other porous materials such as MOFs or zeolites.[2] In this contribution, we show that computational techniques -molecular conformational searches and crystal structure prediction- can be successfully used to understand POC crystal packing preferences. Computational results will be presented for a series of closely related tetrahedral imine- and amine-linked porous molecules, formed by [4+6] condensation of aromatic aldehydes and cyclohexyl linked diamines. While the basic cage is known to have one strongly preferred crystal structure, the presence of small alkyl groups on the POC modifies its crystal packing preferences, leading to extensive polymorphism. Calculations were able to successfully identify these trends as well as to predict the structures obtained experimentally, demonstrating the potential for computational pre-screening in the design of POCs within targeted crystal structures. Moreover, the need of accurate molecular (ab initio calculations) and crystal (based on atom-atom potential lattice energy minimization) modelling for computer-guided crystal engineering will be discussed.

Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing

2014 ◽  
Vol 70 (4) ◽  
pp. 681-696 ◽  
Author(s):  
Piyush Panini ◽  
K. N. Venugopala ◽  
Bharti Odhav ◽  
Deepak Chopra
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Biologically Active ◽  
Two Dimensional ◽  
Energy Calculations ◽  
X Ray ◽  
Fingerprint Plots

A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (AandB) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N—H]+...Cl−and [C—H]+...Cl−hydrogen bonds mainly stabilizes the crystal packing in both formsAandB, while in the case ofB·H2O [N—H]+...Owaterand Owater—H...Cl−hydrogen bonds along with [N—H]+...Cl−and [C—H]+...Cl−provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case ofA, form (I) (monoclinic) is more stable whereas forBit is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms ofAandBand its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. TheR/E(distance–energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organicR+and Cl−) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case ofA) or the hydrates (in the case ofB) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms ofAandBand its hydrate were observed to be different.

On the cubic and hexagonal close-packed lattices

1955 ◽  
Vol 227 (1171) ◽  
pp. 447-465 ◽  
Keyword(s):  
Solid Helium ◽  
Zero Point ◽  
Lattice Energy ◽  
Close Packing ◽  
Inert Gases ◽  
Zero Point Energy ◽  
Point Energy ◽  
Hexagonal Close Packed ◽  
The Difference ◽  
Central Forces

The present paper was stimulated by the discovery by Dugdale & Simon (1953) of a polymorphic transition in solid helium. A discussion is given of the relative stability of the cubic and hexagonal close-packed lattices assuming central forces of the Mie—Lennard-Jones type. Taking static lattice energy alone into account the usual laws of force favour the hexagonal close-packed lattice, the difference in energy being about 0·01%. However, lattice dynamics indicates that the equivalent Debye Θ at the absolute zero is smaller for the cubic lattice, the difference being about 1%. Hence, ignoring zero-point energy, we should expect a transition to occur from hexagonal to cubic at an elevated temperature. The estimated temperature and energy of the transition are of the same order of magnitude as those observed experimentally in solid helium. An estimate is made of the effect of zero-point energy; the results can be applied with confidence to the heavier inert gases, but can only be considered as giving a qualitative indication for helium, since anharmonic effects are of great importance in this case. For the other inert gas solids it is concluded that the experimentally observed cubic close-packing at all temperatures must be due to non-central forces.

scholarly journals Insight from energy surfaces: structure prediction by lattice energy exploration

2014 ◽  
Vol 70 (a1) ◽  
pp. C28-C28
Author(s):  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Organic Crystals ◽  
Crystal Structure Prediction ◽  
Stability Order ◽  
The Stability ◽  
Solid Form ◽  
Energy Surfaces

A long-standing challenge for the application of computational chemistry in the field of crystallography is the prediction of crystal packing, given no more than the chemical bonding of the molecules being crystallised. Recent years have seen significant progress towards reliable crystal structure prediction methods, even for traditionally challenging systems involving flexible molecules and multi-component solids [1]. These methods are based on global searches of the lattice energy surface: a search is performed to locate all possible packing arrangements, and these structures are ranked by their calculated energy [2]. One aim of this lecture is to provide an overview of advances in methods for crystal structure prediction, focussing on molecular organic crystals, and highlighting strategies that are being explored to extend the reach of these methods to more complex systems. A second aim is to discuss the range applications of crystal structure prediction calculations, which have traditionally included solid form screening, particularly of pharmaceutically active molecules, and structure determination. As energy models become more reliable at correctly ranking the stability order of putative structures, and the timescale required for structure searching decreases, crystal structure prediction has the potential for the discovery of novel molecular materials with targeted properties. Prospects for computer-guided discovery of materials will be discussed.

scholarly journals Two Extra Components in the Brier Score Decomposition

2008 ◽  
Vol 23 (4) ◽  
pp. 752-757 ◽  
Author(s):  
D. B. Stephenson ◽  
C. A. S. Coelho ◽  
I. T. Jolliffe
Keyword(s):  
Sea Surface ◽  
Brier Score ◽  
Sea Surface Temperatures ◽  
Seasonal Forecasts ◽  
Multimodel Ensemble ◽  
Probability Score ◽  
Small Set ◽  
Generalized Resolution ◽  
Probability Forecasts ◽  
The Difference

Abstract The Brier score is widely used for the verification of probability forecasts. It also forms the basis of other frequently used probability scores such as the rank probability score. By conditioning (stratifying) on the issued forecast probabilities, the Brier score can be decomposed into the sum of three components: uncertainty, reliability, and resolution. This Brier score decomposition can provide useful information to the forecast provider about how the forecasts can be improved. Rather than stratify on all values of issued probability, it is common practice to calculate the Brier score components by first partitioning the issued probabilities into a small set of bins. This note shows that for such a procedure, an additional two within-bin components are needed in addition to the three traditional components of the Brier score. The two new components can be combined with the resolution component to make a generalized resolution component that is less sensitive to choice of bin width than is the traditional resolution component. The difference between the generalized resolution term and the conventional resolution term also quantifies how forecast skill is degraded when issuing categorized probabilities to users. The ideas are illustrated using an example of multimodel ensemble seasonal forecasts of equatorial sea surface temperatures.

Can we predict lattice energy from molecular structure?

2003 ◽  
Vol 59 (5) ◽  
pp. 676-685 ◽  
Author(s):  
Carole Ouvrard ◽  
John B. O. Mitchell
Keyword(s):  
Organic Compounds ◽  
Crystal Packing ◽  
Correlation Coefficients ◽  
Lattice Energy ◽  
Enthalpy Of Sublimation ◽  
Final Model ◽  
Wide Range ◽  
Independent Test ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
Enthalpies Of Sublimation

By using simply the numbers of occurrences of different atom types as descriptors, a conceptually transparent and remarkably accurate model for the prediction of the enthalpies of sublimation of organic compounds has been generated. The atom types are defined on the basis of atomic number, hybridization state and bonded environment. Models of this kind were applied firstly to aliphatic hydrocarbons, secondly to both aliphatic and aromatic hydrocarbons, thirdly to a wide range of non-hydrogen-bonding molecules, and finally to a set of 226 organic compounds including 70 containing hydrogen-bond donors and acceptors. The final model gives squared correlation coefficients of 0.925 for the 226 compounds in the training set and 0.937 for an independent test set of 35 compounds. The success of such a simple model implies that the enthalpy of sublimation can be predicted accurately without knowledge of the crystal packing. This hypothesis is in turn consistent with the idea that, rather than being determined by the particular features of the lowest-energy packing, the lattice energy is similar for a number of hypothetical alternative crystal structures of a molecule.

scholarly journals AIE Stereoisomers with Huge Differences in Luminescence Behavior and Biomedical Activity

2020 ◽  
Author(s):  
Xuewen He ◽  
Ryan Tsz Kin Kwok ◽  
Jacky W. Y. Lam ◽  
Ben Zhong Tang
Keyword(s):  
Room Temperature ◽  
Molecular Motion ◽  
Crystal Packing ◽  
Process Analysis ◽  
Luminescence Properties ◽  
Void Space ◽  
Pronounced Difference ◽  
Conversion Rates ◽  
The Difference ◽  
High Fluorescence

Stereoisomers that differ only in spatial orientation of their atoms could exhibit distinctive properties and have attracted immense interest in drug development and material science. Herein, a series of AIE-featured stereoisomers with pronounced difference in luminescent and biomedical activities were efficiently synthesized and easily purified. One of the isomers in the E/Z pair is emissive with high fluorescence quantum yield at room temperature, while the other one is nearly non-emissive. As the isomers could transform between each other under UV irradiation, the light-up cell imaging was successfully demonstrated using the non-emissive isomer as a turn-on probe via isomerization process. Analysis of crystal packing patterns illustrated that the contrasts in void space possibly caused the difference in molecular motion and thus led to their distinct luminescence properties. Further, the E/Z isomers displayed remarkable difference in enzymatic conversion rates and cellular toxicities for several cancer cell lines. The distinctive luminescence properties of the isomeric pair provided a powerful tool to image those divergencies in biomedical activity, holding great potential for visualizable drug screening and development.

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