Models of Adjacent Re‐Entry Folds in the β Form of Syndiotactic Polystyrene. Conformational and Packing Analysis by Molecular Mechanics

The adjacent re‐entry folds of chains of syndiotactic polystyrene crystallized in the β form have been investigated by molecular mechanics. Various models of fold of chains along bilayers have been found. The results are in agreement with the literature experimental data indicating that the fold surface is irregular. Both the conformational and the packing energy of folded chains have been minimized by various techniques using several set of potential functions. A theoretical prediction of the work of fold is given.     

Chain Conformations in the Crystalline Field of Syndiotactic Vinyl Polymers Deriving from 1,3‐Diene Monomers. Analysis by Molecular Mechanics

Summary: Conformational energy calculations on the chain conformation in the crystalline field have been performed for various syndiotactic vinyl polymers deriving from 1,3‐diene monomers. Energy maps as a function of the independent torsion angles have evidenced for all the polymers minima corresponding to highly extended and to helical chains. Energy minimizations as a function of all the internal parameters for the s(2/1)2 and t cm symmetries have allowed the evaluation of the energy differences between chains having the two symmetries and the prediction of the values of the conformational parameters for each polymer. The results have been compared with the experimental data reported in the literature for some of the studied polymers.

Conformational energy map of sPBD12.     

Influence of the Temperature on the Crystal Structure of Poly(p‐phenylene sulfide): A Study by X‐Ray Measurements and Molecular Mechanics

The crystal structure of poly(p‐phenylene sulfide) (PPS) has been investigated by X‐ray analysis on fiber samples and by molecular mechanics calculations over a wide range of temperatures, from 0 K to 548 K, showing that all the structural parameters remain substantially constant. The thermal expansion coefficients of the a and b axes have been evaluated. Structural parameters experimentally obtained at the various temperatures have been used in calculations by molecular mechanics. The crystal structures calculated by various methods and using several potential functions are in very good agreement. New parameters are proposed for the nonbonded terms of the potential functions.     

Energetics of Stretching of Conformational Defects in Extended Poly(methylene) Chains

The deformation energetics of highly extended poly(methylene) segments with conformational defects of the kink and jog types, is investigated by molecular mechanics calculations. The deformation potential displays abrupt discontinuities as a result of sudden gauche‐to‐trans conformational transitions accompanied by a release of the elastic energy stored in all valence parameters. By stretching, the chain defects are sequentially annihilated, with the weakest elements interconverting first. Due to sudden drops in force the calculated force–length curves F(R) display a sawtooth‐like profile. The force jumps define a maximum load F_c that defect chains can bear prior to conformational “yielding”. The F_c in the range about 0.7–1.1 nN is found in highly extended multikink chains. The results suggest that the sawtooth‐like profile can be a common feature of mechanochemistry of bridging polymers with the restricted number of available conformations. A similar pattern of F(R) curves were previously observed at stretching and sequential unfolding of compact structural domains in biomacromolecules. Further, the calculations predict a distinct reduction of the longitudinal Young's modulus E with increasing concentration of kinks in molecules.     

Chain Folding in Poly(p‐phenylene sulfide): A Study of the Packing of the Adjacent Re‐Entry Folds by Molecular Mechanics

Models of tight isolated folds between adjacent chains of poly(p‐phenylene sulfide) have been found for folds in the (020), (200) and (110) planes and optimized by molecular mechanics. Minimizations of the conformational energy of the folded chains have given low energy values, mainly for the (110) fold planes. Minimizations of the packing energy of the folded chains in the crystal for each of the three fold planes have given a low energy value only for the folds in the (110) planes. The energy required to fold the chains evaluated by our calculations has been compared with the work of fold derived by experimental measurements and reported in the literature. A possible model of the crystal growth direction as bilayers along b is also suggested.     

On the Crystal Structure of Isotactic cis‐1,4‐Poly(1,3‐pentadiene)

Summary: A comparison between the crystal structure of isotactic cis‐1,4‐poly(1,3‐pentadiene) previously predicted by molecular mechanics calculations and that successively determined by other authors by experimental data is reported. The agreement between the two structures is very good as far as the space group, the unit cell parameters and the conformation of the polymer chain are concerned. The mode of packing of the chains proposed in the experimental crystal structure is very similar to that found as relative minimum in the previous energy calculations. The coexistence, in different amounts, of these two modes of packing is suggested by the analysis of the simulated X‐ray spectra and by the results of new energy calculations.

A mode of packing of chains of isotactic cis‐1,4‐poly(1,3‐pentadiene).     

Determination of the electron density in methyl (±)‐(1S,2S,3R)‐2‐methyl‐1,3‐diphenylcyclopropanecarboxylate using refinements with X‐ray scattering factors from wavefunction calculations of the whole molecule

The molecule of the title compound, C₁₈H₁₈O₂, is a substituted cyclopropane ring. The electron density in this molecule has been determined by refining single‐crystal X‐ray data using scattering factors derived from quantum mechanical calculations. Topological analysis of the electron densities in the three cyclopropane C—C bonds was carried out. The results show the effects of this substitution on these C—C bonds.     

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phenylamide) Dimethyl ( tetra-methylcyclopenta-dienyl ) Silane Titanium Dichloride

Crystal and molecular structure of (2,6-dipropylphenylamide) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained from a mixture of ether/hexane as orthorhombic, with a = 12.658 (3) (A), b = 16.62 (3)(A), c = 11.760 (2)(A), V = 2474.2 (9)(A) 3, Z = 4, space group Pnma, R = 0.0399. Componud I compose of the π-bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.     

Two polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone with flexible dibenzylamino groups

We obtained two conformational polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone, C₃₄H₃₀Cl₂N₂O₂. Both polymorphs have an inversion centre at the centre of the hydroquinone ring (Z′ = ), and there are no significant differences between their bond lengths and angles. The most significant structural difference in the molecular conformations was found in the rotation of the phenyl rings of the two crystallographically independent benzyl groups. The crystal structures of the polymorphs were distinguishable with respect to the arrangement of the hydroquinone rings and the packing motif of the phenyl rings that form part of the benzyl groups. The phenyl groups of one polymorph are arranged in a face‐to‐edge motif between adjacent molecules, with intermolecular C—H…π interactions, whereas the phenyl rings in the other polymorph form a lamellar stacking pattern with no significant intermolecular interactions. We suggest that this partial conformational difference in the molecular structures leads to the significant structural differences observed in their molecular arrangements.     

Naphthyl Groups in Chiral Recognition: Structures of Salts and Esters of 2‐Methoxy‐2‐naphthylpropanoic Acids

The crystal structures of salt 8 , which was prepared from (R)‐2‐methoxy‐2‐(2‐naphthyl)propanoic acid ((R)‐MβNP acid, (R)‐ 2 ) and (R)‐1‐phenylethylamine ((R)‐PEA, (R)‐ 6 ), and salt 9 , which was prepared from (R)‐2‐methoxy‐2‐(1‐naphthyl)propanoic acid ((R)‐MαNP acid, (R)‐ 1 ) and (R)‐1‐(p‐tolyl)ethylamine ((R)‐TEA, (R)‐ 7 ), were determined by X‐ray crystallography. The MβNP and MαNP anions formed ion‐pairs with the PEA and TEA cations, respectively, through a methoxy‐group‐assisted salt bridge and aromatic CH???π interactions. The networks of salt bridges formed 2₁ columns in both salts. Finally, (S)‐(2E,6E)‐(1‐²H₁)farnesol ((S)‐ 13 ) was prepared from the reaction of (2E,6E)‐farnesal ( 11 ) with deuterated (R)‐BINAL‐H (i.e., (R)‐BINAL‐D). The enantiomeric excess of compound (S)‐ 13 was determined by NMR analysis of (S)‐MαNP ester 14 . The solution‐state structures of MαNP esters that were prepared from primary alcohols were also elucidated.     

Molecular modeling for Cu(II)‐aminopolycarboxylate complexes: Structures,conformational energies,and ligand binding affinities

A ligand field molecular mechanics (LFMM) force field (FF) has been developed for d⁹ copper(II) complexes of aminopolycarboxylate ligands. Training data were derived from density functional theory (DFT) geometry optimizations of 14 complexes comprising potentially hexadentate N₂O₄, tetrasubstituted ethylenediamine (ed), and propylenediamine cores with various combinations of acetate and propionate side arms. The FF was validated against 13 experimental structures from X‐ray crystallography including hexadentate N₂O₄ donors where the nitrogens donors are forced to be cis and bis‐tridentate ONO ligands which generate complexes with trans nitrogen donors. Stochastic conformational searches for [Cu{ed(acetate)_n (propionate)_4‐n}]^2?, n = 0–4, were carried out and the lowest conformers for each system reoptimized with DFT. In each case, both DFT and LFMM predict the same lowest‐energy conformer and the structures and energies of the higher‐energy conformers are also in satisfactory agreement. The relative interaction energies for n = 0, 2, and 4 computed by molecular mechanics correlate with the experimental log β binding affinities. Adding in the predicted log β values for n = 1 and 3 suggest for this set of complexes a monotonic decrease in log β as the number of propionate arms increases. © 2013 Wiley Periodicals, Inc.     

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phcnylamidc) Dimethyl (tetra-methylecyclopenta- dienyl)Silane Titanium Dichloride

ExperimentalSynthesisofitToI.sg(4mmol.)TiCI,.THFin25mLTHFwasaddedI.sg(4mmol.)dilithium(2,6-propylphenylamide)dimethyl(tetra-methylcyclopentadienyl)silaneandthemixturewasallowedtostirforIhour,then0.639AgCI(4mmol.)wasadded.After4hoursstirring,thesolventwasmovedandtheresiduewasextractedwithdiethylether.Theetherextractwasfilteredandevaporatedtodrynesstogive0.409yellowcrystallinesolid,yield41%.'H-NMR(C,D,)f0.48(6H),l.I2(6H),l.49(6H),l.98(6H).2.18(6H),and3.04(2H).Asuitablesinglecrystalwa…     

Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′‐Phosphate in Ornithine 4,5‐Aminomutase

A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5′‐phosphate (PLP)‐dependent D ‐ornithine 4,5‐aminomutase (OAM)‐catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff‐base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial “strain” energy on the orientation of the cyclic intermediate to control its trajectory. In addition the “strain” energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP‐dependent reactions.     

Structure and Photochemical Properties of r‐1, c‐2, t‐3, t‐4‐l, 3‐Bis [2‐ (5‐R‐benzoxazolyl) ] −2,4‐di (4‐R' ‐phenyl) cyclobutane

r‐1, c‐2, t‐3, t‐4‐1,3‐Bis[2‐(5‐R‐benzoxazolyl)]‐2,4‐di(4‐R'‐phenyl)cyclobutane (IIa: R=R' = H; IIb: R=Me, R'= H; IIc: R = Me, R' = OMe) was synthesized with high stereo‐selectivity by the photodimerization of trans‐l‐[2‐(5‐R‐benzoxazolyl)]‐2‐(4‐R'‐phenyl) ethene (Ia: R=R' = H; Ib: R = Me, R' = H; Ic: R = Me, R' = OMe) in sulfuric acid. The structures of IIa–IIc were identified by elemental analysis, IR, UV, ¹H NMR, ¹³C NMR and MS. The molecular and crystal structure of IIc has been determined by X‐ray diffraction method. The crystal of IIc (C₃₄H₃₀N₂O₄. 0.5C₂OH) is monoclinic, space group P2₁/n with cell dimensions of a = 1.5416(3), b =0.5625(1), c = 1.7875(4) nm, β = 91.56 (3)°, V= 1.550(1) nm³, Z = 2. The structure shows that the molecule of IIc is centrosymmetric, which indicates that the dimerization process is a head‐to‐tail fashion. The selectivity of the photodimerization of Ia–Ic has been enhanced by using acidic solvent and the reaction speed would be decreased when electron donating group was introduced in the 4‐position of the phenyl group. That the photodimerization is not affected by the presence of oxygen as well as its high stereo‐selectivity demonstrated that the reaction proceeded through an excited singlet state. It was also found that under irradiation of short wavelength UV, these dimers underwent photolysis completely to reproduce its trans‐monomers, and then the new formed species changed into their cis‐isomers through trans‐cis isomerization.     

Concomitant polymorphs of 1,3‐bis(3‐fluorophenyl)urea

Hydrogen bonding between urea functionalities is a common structural motif employed in crystal‐engineering studies. Crystallization of 1,3‐bis(3‐fluorophenyl)urea, C₁₃H₁₀F₂N₂O, from many solvents yielded concomitant mixtures of at least two polymorphs. In the monoclinic form, one‐dimensional chains of hydrogen‐bonded urea molecules align in an antiparallel orientation, as is typical of many diphenylureas. In the orthorhombic form, one‐dimensional chains of hydrogen‐bonded urea molecules have a parallel orientation rarely observed in symmetrically substituted diphenylureas.     

2,2′‐[(Disulfanediyl)bis{5‐[(1E)‐(2‐hydroxybenzylidene)amino]‐1,3‐thiazole‐4,2‐diyl}]diphenol: synthesis,crystal structure and calculation of molecular hyperpolarizability

The title Schiff base compound {systematic name: 2‐[5‐[(E )‐(2‐hydroxybenzylidene)amino]‐4‐(2‐{5‐[(E )‐(2‐hydroxybenzylidene)amino]‐2‐(2‐hydroxyphenyl)‐1,3‐thiazol‐4‐yl}disulfanyl)‐1,3‐thiazol‐2‐yl]phenol}, C₃₂H₂₂N₄O₄S₄, incorporating a disulfanediyl (dithio) linkage, was obtained from the condensation reaction between two equivalents of salicylaldehyde and one equivalent of dithiooxamide in dimethylformamide, and was characterized by elemental analysis, IR spectroscopic analysis and single‐crystal X‐ray diffraction. A one‐dimensional chain is formed along the b axis via double intermolecular C—H…S hydrogen bonds. The HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies and some related molecular parameters were calculated at the B3LYP/6‐311G(d,p) level of theory. The molecular hyperpolarizability was also calculated.     

4‐Styrylquinolines from cyclocondensation reactions between (2‐aminophenyl)chalcones and 1,3‐diketones: crystal structures and regiochemistry

Structures are reported for two matched sets of substituted 4‐styrylquinolines which were prepared by the formation of the heterocyclic ring in cyclocondensation reactions between 1‐(2‐aminophenyl)‐3‐arylprop‐2‐en‐1‐ones with 1,3‐dicarbonyl compounds. (E)‐3‐Acetyl‐4‐[2‐(4‐methoxyphenyl)ethenyl]‐2‐methylquinoline, C₂₁H₁₉NO₂, (I), (E)‐3‐acetyl‐4‐[2‐(4‐bromophenyl)ethenyl]‐2‐methylquinoline, C₂₀H₁₆BrNO, (II), and (E)‐3‐acetyl‐2‐methyl‐4‐{2‐[4‐(trifluoromethyl)phenyl]ethenyl}quinoline, C₂₁H₁₆F₃NO, (III), are isomorphous and in each structure the molecules are linked by a single C—H…O hydrogen bond to form C(6) chains. In (I), but not in (II) or (III), this is augmented by a C—H…π(arene) hydrogen bond to form a chain of rings; hence, (I)–(III) are not strictly isostructural. By contrast with (I)–(III), no two of ethyl (E)‐4‐[2‐(4‐methoxyphenyl)ethenyl]‐2‐methylquinoline‐3‐carboxylate, C₂₂H₂₁NO₃, (IV), ethyl (E)‐4‐[2‐(4‐bromophenyl)ethenyl]‐2‐methylquinoline‐3‐carboxylate, C₂₁H₁₈BrNO₂, (V), and ethyl (E)‐2‐methyl‐4‐{2‐[4‐(trifluoromethyl)phenyl]ethenyl}quinoline‐3‐carboxylate, C₂₂H₁₈F₃NO₂, (VI), are isomorphous. The molecules of (IV) are linked by a single C—H…O hydrogen bond to form C(13) chains, but cyclic centrosymmetric dimers are formed in both (V) and (VI). The dimer in (V) contains a C—H…π(pyridyl) hydrogen bond, while that in (VI) contains two independent C—H…O hydrogen bonds. Comparisons are made with some related structures, and both the regiochemistry and the mechanism of the heterocyclic ring formation are discussed.     

Two polymorphs of N‐(2‐methoxyphenyl)‐4‐oxo‐4H‐chromone‐3‐carboxamide

The title compound, C₁₇H₁₃NO₄, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space group P2₁/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three‐dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings.     

Molecular dynamics study of the stereostructure of 1,4‐linked poly(cyclohexa‐1,3‐diene) obtained with π‐allylnickel‐based catalysts

Temperature‐constant and pressure‐constant molecular dynamics simulations of crystalline 1,4‐linked poly(cyclohexa‐1,3‐diene) (CHD) were performed using the COMPASS force field. Powder X‐ray diffraction spectra calculated from the simulated atomic coordinates were compared with the measured spectrum of the crystal of 1,4‐linked poly(CHD), obtained using a bis(allylnickel bromide) (ANiBr)/methylaluminoxane (MAO) catalyst. As a result of the comparison, the geometrical isomerism of the 1,4‐linked poly(CHD) obtained with the ANiBr/MAO catalyst was found to be cis syndiotactic. © 2001 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 39: 973–978, 2001