Potential energy surface and orientational disorder in solid fullerene C60

The polymorphism and molecular disorder in crystalline C₆₀ have been studied by modelling the optimum packing of fullerene molecules by the atom-atomic potential method. The study includes the calculation of minima and saddle points of the potential energy surface with sorting out of the most common space symmetry groups. Two models of intermolecular potential for C₆₀ have been checked, one of which assumes effective charges at the centers of C-C bonds. It has been found that the calculated barrier of reorientations is much lower in the case where the concerted character of rotations of different molecules is taken into account. The model of orientational disorder in the face-centered cubic phase is suggested, which is based on consideration of symmetrically arranged equivalent minima separated by low potential barriers.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1466–1469, August, 1995.The work was financially supported by the Russian Foundation for Basic Research (Project No. 94-03-08895).     

New Fluorescence Domain “Excited Multimer” Formed upon Photoexcitation of Continuously Stacked Diaroylmethanatoboron Difluoride Molecules with Fused π‐Orbitals in Crystals

The crystal‐packing structures of seven derivatives of diaroylmethanatoboron difluoride ( 1 a – gBF₂ ) are characterized by no overlap of the π‐conjugated main units of two adjacent molecules (type I), overlap of the benzene ring π‐orbitals of two adjacent molecules (type II), and overlap of the benzene and dihydrodioxaborinine rings π‐orbitals of adjacent molecules (type III). The crystal‐packing structures govern the fluorescence (FL) properties in the crystalline states. The FL domain that is present in type I crystals, in which intermolecular orbital interactions are absent, leads to excited monomer‐like FL properties. In the case of the type II crystals, the presence of intermolecular overlap of the benzene rings π‐orbitals generates new FL domains, referred to as “excited multimers”, which possess allowed S₀–S₁ electronic transitions and, as a result, similar FL lifetimes at longer wavelengths than the FL of the type I crystals. Finally, intermolecular overlap of the benzene and dihydrodioxaborinine ring π‐orbitals in the type III crystals leads to “excited multimer” domains with forbidden S₀–S₁ electronic transitions and longer FL lifetimes at similar wavelengths as that in type I crystals.     

H2 adsorption by noble gas insertion compounds: A computational study

In order to find a solution of energy-related problems, sophisticated hydrogen storing materials are needed as hydrogen is an abundant and environment friendly fuel. We have investigated the hydrogen storage potential of Ng inserted metal acetylide and metal cyanide compounds (metal ​= ​Cu, Ag and Au) at the ωB97X-D/cc-pVTZ-PP level of theory. Due to the difference in electronegativity and formal charge on metal atoms in the insertion compounds, the interaction with the hydrogen molecule is expected to be different. The adsorption energies, the free energy of adsorption, natural charges on atomic centers/moieties are obtained through the natural population analysis, and energy decomposition analysis has also been carried out for nH₂···MNgCCH and nH₂···MNgCN (n ​= ​1–3). The hydrogen adsorption capacity of the strongest and the weakest cases has also been investigated. Both the insertion compounds, MNgCCH and MNgCN, are found to adsorb a maximum of three hydrogen molecules on the metal site. The single H₂ adsorbed minimum energy structures of studied compounds show a “T-shaped” orientation while double H₂ adsorbed minimum energy structures are of “Y- shaped” geometry and those of tricoordinated structures resemble “T_d-like” shape. The negative value of Gibbs free energy change suggests the thermodynamical spontaneity of the hydrogen adsorption process.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

From small structural modifications to adjustment of structurally dependent properties: 1‐methyl‐3,5‐bis[(E)‐2‐thienylidene]‐4‐piperidone and 3,5‐bis[(E)‐5‐bromo‐2‐thienylidene]‐1‐methyl‐4‐piperidone

The molecules of the title compounds, C₁₆H₁₅NOS₂, (I), and C₁₆H₁₃Br₂NOS₂, (II), are E,E‐isomers and consist of an extensive conjugated system, which determines their molecular geometries. Compound (I) crystallizes in the monoclinic space group P2₁/c. It has one thiophene ring disordered over two positions, with a minor component contribution of 0.100 (3). Compound (II) crystallizes in the noncentrosymmetric orthorhombic space group Pca2₁ with two independent molecules in the unit cell. These molecules are related by a noncrystallographic pseudo‐inversion center and possess very similar geometries. The crystal packings of (I) and (II) have a topologically common structural motif, viz. stacks along the b axis, in which the molecules are bound by weak C—H...O hydrogen bonds. The noncentrosymmetric packing of (II) is governed by attractive intermolecular Br...Br and Br...N interactions, which are also responsible for the very high density of (II) (1.861 Mg m⁻³).     

Molecular Shape and Crystal Packing: a Study of C12H12 Isomers,Real and Imaginary

Isomeric C₁₂H₁₂ hydrocarbon molecules with widely different constitution and shape are analysed for their packing ability. Some correspond to known compounds with known crystal structures, but some are invented hypothetical molecules designed to have low packing efficiency. For each isomer, a large number of close‐packed, low‐energy crystal structures was generated by computer, with lattice energies within a range of a few kJ mol⁻¹. Molecules with linear chains, triple bonds and Me groups tend to have larger molecular volume, lower lattice energy and lower crystal density than cyclic or cage isomers. The calculated crystal structures for each isomer show an inverse relationship between packing energy and cell volume. Although the slope dE/dV varies from molecule to molecule, the product of slope and free space stays roughly constant; less efficient crystal packings thus appear to be less sensitive to an increase in cell volume. Lattice‐vibrational frequencies and the corresponding contributions to thermal vibrational entropy were estimated for real and virtual crystal structures. For a given isomer, as expected, a higher entropy goes with a larger cell volume, but different isomers show different entropy/volume relationships. At 300 K, TΔS differences among computational polymorphs may compete with ΔH differences, thus making the lattice‐vibrational entropy estimation a relevant factor in crystal‐structure prediction.     

Molecular electrostatic charge models: A topographical approach

Electrostatic charge models for molecules have been developed by employing the critical topographical features of the molecular electrostatic potential (MESP ) as the “fitting” criterion. These models include one or more spherical Gaussians for incorporating the continuous electron-charge distribution in addition to the positive valued point charges representing the nuclei. The model parameters (point charges, the orbital exponents, and Gaussian centers) are optimized so as to mimic the extremal characteristics of the corresponding quantum chemical MESP . The test cases reported here include methane, ethylene, and methanol molecules. The charge models developed using the present method are seen to satisfactorily reproduce the ab initio MESP and its extremal features. © 1994 John Wiley & Sons, Inc.     

From amorphous solid to defective crystal. A study of structural peculiarities in close packings of hard spheres

The structure of models of close packings of hard spheres is examined, with density of the packings exceeding the maximum value for uniform disordered packings (η = 0.64). High densities are achieved due to regions of the closest packing (η = 0.74) emerging in the models. Spatial geometry of good tetrahedral atomic configurations and of simplest elements of the crystal structure identified by Delaunay simplices was studied using the Voronoi— Delaunay method. Models with a packing coefficient η varying from 0.639 to 0.706 were considered. At smaller densities, a well-known disordered close “Bernal packing” is realized. At η = 0.706 (the greatest density achieved), a unified crystal structure with numerous defects is formed. At intermediate densities, stochastically oriented crystalline nuclei are observed. Specific atomic aggregates — stacks of five-membered rings in good tetrahedral configurations of spheres — are revealed in models having a substantial fraction of crystalline phase (η = 0.664). Such non-trivial structures can occur only in packings that are intermediate between amorphous and crystalline phases.     

Design of crystal packings of styryl heterocycles and regularities of [2+2] photocycloaddition in their single crystals 8. Topochemical [2+2] autophotocycloaddition and back reaction in styryl dye of the benzothiazole series

New styryl dye of the 2-benzothiazole series was synthesized. The new dye contains two methoxy groups in the benzene ring and tosylate counterion. The [2+2] photocycloaddition (PCA) of the dye was studied in the polycrystalline film and in single crystal. Two modifications of the dye cocrystallizate with hydroquinone differed in the ratio of components were obtained, and their ability to enter PCA was studied. According to the X-ray diffraction data, molecular cations of the dye form stack packings either of syn-“head-to-tail” type or relatively isolated stacking dimers. In all cases, the ethylene bonds of the adjacent cations are brought together and antiparallel, favoring PCA to form the centrosymmetric rctt-isomer of 1,2,3,4-tetrasubstituted cyclobutane. In two cases, the PCA reaction proceeded as the “single crystal-to-single crystal” transformation. Hydrogen bonds in crystals including hydroquinone molecules strengthen the crystal packing retarding the PCA. The back photoreaction (retro-PCA) was detected: it occurs without single crystal decomposition and results in the accumulation of the initial styryl dye in crystal consisting of the cyclobutane derivative. This is the first example of such a transformation in single crystals.     

Intermolecular interactions in the acyclic tetraazagold(III) metal complexes

The packings of the crystal structures of the gold(III) iodide, perchlorate, and hexafluorophosphate complexes with the iminate-amine ligand, [Au(C₉H₁₉N₄)]Y₂ (Y = I (I), ClO₄ (II), and PF₆ (III)), are studied in comparison. The packings of structures I–III are similar. They are determined and stabilized by a vast network of intermolecular interactions (hydrogen bonds N-H…A, C-H…A, C-H…Au, and C-H…π and short contacts Au…A (A = I, O, F)). Structures I–III are characterized by cation-cationic and cationanionic infinite chains and closed rings formed by classical and nonclassical hydrogen bonds and contacts. The structures include multicentered hydrogen bonds. The replacement of the anion does not basically change the packing structures.     

The Pyrolysis of Azides in the Gas Phase

The chemistry of the non-metallic elements has in recent years passed through a period of rapid development, often referred to as its “renaissance”. To emphasize just one of the key facets: numerous short-lived molecules containing multiple bonds to elements of the third and higher periods have been discovered, often accompanied by the planned synthesis of derivatives which are sterically shielded by bulky groups and thus kinetically stabilized. Thus today molecules such as silabenzenes H₆C_6?nSi_n and silaethenes H₂Si?CH₂ or R₂Si?CR₂, disilenes R₂Si?SiR₂ and diphosphenes RP?PR, silaphenylisonitrile H₅C₆? N?Si, or methylidyne-phosphanes R? C?P, are all well-known species. Sandwich compounds with P₆ rings or silicon centers demonstrate that there are now hardly any barriers to impede the imagination of the non-metal chemist. In sharp contrast is our lack of knowledge regarding the “microscopic” pathways of chemical reactions: thus apart from information provided for example by molecular beam experiments, or from exact numerical calculations involving species consisting of only a few atoms, it remains largely unknown from which directions medium-sized molecules must approach each other to successfully collide and form a “reaction complex”, in which way their structures are changed in such a process or which role is played by molecular dynamics in the energy transfer.–The pyrolysis of azides X? N₃, i.e. compounds which tend to explode violently when ignited in the condensed phase but can be heated in low-pressure gas flow systems without much risk, illustrates that studies of reactive intermediates are of interest not only because novel molecules may be discovered and isolated, and thereby possibilities for synthesis expanded. Moreover, some aspects of the “microscopic” pathways of these azide pyrolyses can be described satisfactorily on the basis of calculated energy hypersurfaces, and the influence of molecular dynamics becomes experimentally visible in the “chemical activation” of intermediates which leads to their “thermal explosion”.     

Similarities and differences in the structures of 5‐bromo‐6‐hydroxy‐7,8‐dimethylchroman‐2‐one and 6‐hydroxy‐7,8‐dimethyl‐5‐nitrochroman‐2‐one

The title compounds, C₁₁H₁₁BrO₃, (I), and C₁₁H₁₁NO₅, (II), respectively, are derivatives of 6‐hydroxy‐5,7,8‐trimethylchroman‐2‐one substituted at the 5‐position by a Br atom in (I) and by a nitro group in (II). The pyranone rings in both molecules adopt half‐chair conformations, and intramolecular O—H...Br [in (I)] and O—H...O_nitro [in (II)] hydrogen bonds affect the dispositions of the hydroxy groups. Classical intermolecular O—H...O hydrogen bonds are found in both molecules but play quite dissimilar roles in the crystal structures. In (I), O—H...O hydrogen bonds form zigzag C(9) chains of molecules along the a axis. Because of the tetragonal symmetry, similar chains also form along b. In (II), however, similar contacts involving an O atom of the nitro group form inversion dimers and generate R₂²(12) rings. These also result in a close intermolecular O...O contact of 2.686 (4) Å. For (I), four additional C—H...O hydrogen bonds combine with π–π stacking interactions between the benzene rings to build an extensive three‐dimensional network with molecules stacked along the c axis. The packing in (II) is much simpler and centres on the inversion dimers formed through O—H...O contacts. These dimers are stacked through additional C—H...O hydrogen bonds, and further weak C—H...O interactions generate a three‐dimensional network of dimer stacks.     

N,N′‐Diethyl‐4‐nitrobenzene‐1,3‐diamine, 2,6‐bis(ethylamino)‐3‐nitrobenzonitrile and bis(4‐ethylamino‐3‐nitrophenyl) sulfone

N,N′‐Diethyl‐4‐nitrobenzene‐1,3‐diamine, C₁₀H₁₅N₃O₂, (I), crystallizes with two independent molecules in the asymmetric unit, both of which are nearly planar. The molecules differ in the conformation of the ethylamine group trans to the nitro group. Both molecules contain intramolecular N—H...O hydrogen bonds between the adjacent amine and nitro groups and are linked into one‐dimensional chains by intermolecular N—H...O hydrogen bonds. The chains are organized in layers parallel to (101) with separations of ca 3.4 Å between adjacent sheets. The packing is quite different from what was observed in isomeric 1,3‐bis(ethylamino)‐2‐nitrobenzene. 2,6‐Bis(ethylamino)‐3‐nitrobenzonitrile, C₁₁H₁₄N₄O₂, (II), differs from (I) only in the presence of the nitrile functionality between the two ethylamine groups. Compound (II) crystallizes with one unique molecule in the asymmetric unit. In contrast with (I), one of the ethylamine groups, which is disordered over two sites with occupancies of 0.75 and 0.25, is positioned so that the methyl group is directed out of the plane of the ring by approximately 85°. This ethylamine group forms an intramolecular N—H...O hydrogen bond with the adjacent nitro group. The packing in (II) is very different from that in (I). Molecules of (II) are linked by both intermolecular amine–nitro N—H...O and amine–nitrile N—H...N hydrogen bonds into a two‐dimensional network in the (10) plane. Alternating molecules are approximately orthogonal to one another, indicating that π–π interactions are not a significant factor in the packing. Bis(4‐ethylamino‐3‐nitrophenyl) sulfone, C₁₆H₁₈N₄O₆S, (III), contains the same ortho nitro/ethylamine pairing as in (I), with the position para to the nitro group occupied by the sulfone instead of a second ethylamine group. Each 4‐ethylamino‐3‐nitrobenzene moiety is nearly planar and contains the typical intramolecular N—H...O hydrogen bond. Due to the tetrahedral geometry about the S atom, the molecules of (III) adopt an overall V shape. There are no intermolecular amine–nitro hydrogen bonds. Rather, each amine H atom has a long (H...O ca 2.8 Å) interaction with one of the sulfone O atoms. Molecules of (III) are thus linked by amine–sulfone N—H...O hydrogen bonds into zigzag double chains running along [001]. Taken together, these structures demonstrate that small changes in the functionalization of ethylamine–nitroarenes cause significant differences in the intermolecular interactions and packing.     

An algorithm for packing regular multistrand polypeptide structures by energy minimization

An algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum-energy regular structures of three-stranded (L -Ala)₈, three-stranded (L -Val)₆, five-stranded (L -Ile)₆, and the regular and truncated three-stranded (Gly-L -Pro-L -Pro)₄ triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.     

The electronic structure of bicyclo [2.2.1] heptane and of bicyclo [2.2.2] octane

An ab initia SCF-LCAO-MO study of bicyclo [2.2.1] heptane(I) and of bicyclo [2.2.2] octane(II) has been performed. The electronic structure and the nature of the molecular orbitals and of the bonds have been analyzed. Interactions between fragment orbitals may be recognized. The bridgehead C-H bonds interact dominantly “through-space” in I and “through-bond” in II. Some relations between electronic structure and molecular properties are discussed.     

Ab Initio prediction of possible crystal structures for general organic molecules

The performance of a new crystal packing procedure for the ab initio prediction of possible molecular crystal structures is presented. The method is based upon only molecular information, i.e., no unit cell parameters are assumed to be known. The search for the global crystal energy minimum and all local minima inside an energy window is derived from Monte Carlo simulated annealing methods and has been applied to various organic molecules containing heteroatoms and polar groups. A systematic evaluation of the search method and of the quality of the potential energy function has been established. It is demonstrated that the packing of general organic molecules is possible even with standard force fields like CHARMM provided that the charges defining the electrostatic interactions are based upon physical models rather than transferable empirical parameters. Concepts of crystal packing that were based till now upon assumptions and speculations could be proved or disproved by solving directly the extended global optimization problem related to crystal packing. Crystal structures of molecules as complex as those treated in this article have not been, till now, predicted by a computational approach. In one case, a disagreement between the predicted and experimental structure was evident and, based upon the computations, we suspect that the published structure is the wrong one. © 1992 by John Wiley & Sons, Inc.     

Stereochemical aspects of crystalline synthetic macromolecules

The most relevant conformational aspects of different skeletal sequences of macromolecules in the crystalline state are discussed. The general importance of the minimum intramolecular energy rule is stressed. Because of the higher energy barriers separating the rotational isomers, sequences of C atoms show a much greater tendency to regular (i.e. “staggered”) conformations than those involving CH₂O or CH₂N bonds. This is reflected in the surprisingly large variety of conformational polymorphs observed especially in polyoxides and in polyformals.     

Calculation of the structure and evaluation of the reactivity of N-methyl-N-(β-d-xylopyranosyl)-N-nitrosourea under acid-base catalysis conditions

An investigation of N-methyl-N-(-D-xyloxyl)urea (I) and its nitroso derivative (II) has been carried out in the MINDO/3 approximation by the MO-LCAO method. It has been shown that the very significant difference between the energies of molecule I in the free state and in a crystal is due to the potential energy of the crystal field and intermolecular hydrogen bonds. An analysis of the distribution of the charges on the atoms showed that the most probable site for protonation and nucleophilic attack in I and II is the carbonyl group. A picture of the changes in the electronic structure and properties of the reaction centers in I and II under model acid-base catalysis conditions has been obtained.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 21, No. 5, pp. 596–599, September–October, 1985.     

Thermal decomposition of metal complexes: II. Mixed complexes of iron(II) iodide with 1,10-phenanthroline,and 4,7-disubstituted-1,10-phenanthrolines

The thermal behavior of the Fe(II) iodide mixed complexes with 1,10-phenanthroline and 4,7-disubstituted phenanthrolines in nitrogen atmosphere is investigated.In order to determine to what extent small changes in ligand field symmetries influence the “activation energy” E_a, this energy is determined. The results are discussed in relation to the changes of the σ and π bonds.