Polystyrene models. III. modeling backbone/side-group interactions by an ab initio study of 2,4-diphenylpentane

The Structure and the energy of the stable conformations of the two possible stereochemical configurations of 2,4-diphenylpentane are obtained using the ab initio molecular orbital theory. The objective was to mimic the possible structures and determine the corresponding energies of the dyads of syndiotactic and isotactic polystyrene and, consequently, to study the interactions between the phenyl groups. The results of complete geometry optimization showed significant changes in geometrical parameters compared with those expected from the ideal hydrocarbon structure. The steric strain is most pronounced in some of the gauche conformations where large (approximately 40°) distortions of the backbone torsional angles and/or simultaneous phenyl group rotations in the range of 30°–40° away from its global minimum position may occur. In addition to the discussion of the geometrical parameters, the corresponding dipole moments are also calculated and differences related to the various structures and discussed. © 1993 John Wiley & Sons. Inc.     

Conformational properties of α- and β-azabicyclane opiates. The effect of conformation on pharmacological activity

Conformational energy calculations using the MM 2 (molecular mechanics II) program are reported for diastereoisomeric α- and β-azabicyclanes (3-methyl-9-methoxy-9-phenyl-3-azabicyclo [3.3.1] nonanes) which are prototypical phenyl-axial and phenyl-equatorial opiates. After energy minimization, both compounds are found to prefer a chair–chair conformation of the piperidine and cyclohexane rings with two mirror image orientations of the phenyl and methoxyl groups. The calculations also indicate that the equilibrium conformations of the phenyl and methoxyl groups are very similar in the two diastereoisomers. A morphine-like conformation of the phenyl group was found to be very unfavorable because of a high barrier to rotation of the phenyl group. This does not have an apparent effect on opiate agonist properties, but does result in a significant weakening of the antagonist activity of the N-allyl derivative of α-azabicyclane. This is discussed in terms of a model for phenyl-axial and phenyl-equatorial opiate substrates which accounts for both similarities and differences in their structure–activity relationships. A detailed comparison is also made between the computed structures and those observed by x-ray crystallography with excellent agreement between the two.     

1H n.m.r. spectra of N-phenylmaleimide in isotropic and nematic phases

¹H n.m.r. spectra of N-phenylmaleimide have been investigated in isotropic as well as nematic phases; the chemical shifts, the direct dipolar and the indirect spin–spin coupling constants have been determined. The direct dipolar coupling constants are consistent with rapidly interconverting energetically equivalent twisted conformations of C₂ symmetry. Under the assumption that only two such conformers are predominantly present, the angle between the phenyl and the maleimide planes is determined as 52.9±0.9°.     

Preparation of phenyl‐modified natural rubber in latex stage

Phenyl‐modified natural rubber was prepared in latex stage by bromination of deproteinized natural rubber followed by Suzuki‐Miyaura cross‐coupling reaction. First, the bromination of natural rubber was carried out using N‐bromosuccinimide in latex stage. The bromine atom content increased as amount of N‐bromosuccinimide increased. Second, the allylic bromine atom was replaced with a phenyl group using phenyl boronic acid in the presence of a palladium catalyst, according to the Suzuki‐Miyaura cross‐coupling reaction in latex stage. The resulting products were characterized by nuclear magnetic resonance (NMR) spectroscopy. Signal at 7.13 ppm was assigned to the phenyl group of the product, while signals at 3.98, 4.14, and 4.44 ppm were assigned to the remaining allylic brominated cis‐1,4‐isoprene units. The estimated phenyl group content and the conversion of the Suzuki‐Miyaura cross‐coupling reaction were 1.32 and 23.7 mol%, respectively. Glass transition temperature (T_g) of deproteinized natural rubber increased from ?62°C to ?46.7°C, when the phenyl group was introduced into the rubber.     

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.     

Orthorhombic polymorphs of two trans‐4‐aminoazoxybenzenes

The two isomeric compounds 4‐amino‐ONN‐azoxy­benzene [or 1‐(4‐amino­phenyl)‐2‐phenyl­diazene 2‐oxide], i.e. the α isomer, and 4‐amino‐NNO‐azoxy­benzene [or 2‐(4‐amino­phenyl)‐1‐phenyl­diazene 2‐oxide], i.e. the β isomer, both C₁₂H₁₁N₃O, crystallized from a polar solvent in orthorhombic space groups, and their crystal and molecular structures have been determined using X‐ray diffraction. There are no significant differences in the bond lengths and valence angles in the two isomers, in comparison with their monoclinic polymorphs. However, the conformations of the mol­ecules are different due to rotation along the Ar—N bonds. In the α isomer, the benzene rings are twisted by 31.5 (2) and 14.4 (2)° towards the plane of the azoxy group; the torsion angles along the Ar—N bond in the β isomer are 24.3 (3) and 23.5 (3)°. Quantum‐mechanical calculations indicate that planar conformations are energetically favourable for both isomers. The N—H?O hydrogen bonds observed in both networks may be responsible for the deformation of these flexible mol­ecules.     

Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers

The conformational behavior of cellobiose (D -glc-ß(1→4)-D -glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ?, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long-lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the ⁴C₁ conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.     

Static atomistic modelling of the structure and ring dynamics of bulk amorphous polystyrene

A detailed static atomistic model of dense, glassy polystyrene is simulated using a well established technique that previously proved successful for simple vinyl polymers. Initial chain conformations that are generated using a Monte Carlo technique including periodic continuation conditions are “relaxed” by potential energy minimization. In total 24 microstructures at densities of 1,07 g/cm³ were obtained with a cube-edge length of 18,65 Å. Detailed analysis of the minimized structures indicates that intermolecular packing influences create a large variety of chain conformations different from the purely intramolecular ground states. The systems are amorphous, exhibiting random coil behavior. The described structures have been used for a quasistatic simulation of localized motions. These motions include stepwise rotation and oscillation of the phenyl groups. The frequency distribution for the simulated ring motions covers many orders of magnitude. It is very rare that an energy barrier with a reorientation angle indicating a ring “flip” is overcome. Motions with small reorientation of the phenyl rings, and therefore not leading to a ring “flip”, dominate with an average reorientation angle of 16° (±12°). The intermolecular effects of the analyzed processes were found very important and far-reaching, widely influencing the cooperative motions of molecular groups.     

Conformational preferences of 2-methoxypyridine from 1H and 13C NMR and from STO-3G molecular orbital calculations

Observable coupling over five formal bonds between the methoxy group protons and the ortho ring proton in 2-methoxypyridine, coupliugs between the methoxy group carbon and ring protons, and methoxy carbon spin-lattice relaxation times are all consistent with a preference for the planar cis conformer, in which conjugation is favoured and repulsions between the methyl group and the ortho hydrogen are reduced. Small-amplitude torsioas about the C-2–O bond may carry the methoxy group away from this orientation, but more distant conformations can probably be excluded. Methyl group rotation is less hindered in the cis than in the trans conformer. Molecular orbital calculations at the STO-3G level, with complete geometry optimization, support the conduskus drawn from experimental evidence.     

Phase transitions in the crystals of L- and DL-cysteine on cooling: intermolecular hydrogen bonds distortions and the side-chain motions of thiol-groups. 1. L-cysteine

The role of the distortion of the hydrogen bond network and of the motions of the -CH 2SH side chains in the phase transition in the orthorhombic L-cysteine ( (+)NH 3-CH(CH 2SH)-COO (-)) on cooling and the reverse transformation on heating is discussed. The extended character of the phase transition, which was recently discovered by adiabatic calorimetry [ J. Phys. Chem. B 2007, 111, 9186 ], and its very high sensitivity to the thermal prehistory of the sample could be interpreted based on the changes in the polarized Raman spectra measured for the single-crystals in several orientations in the temperature range 3-300 K and precise diffraction data on the changes in intramolecular conformations and intermolecular hydrogen bonding. In the low-temperature phase the SH...S hydrogen bonds dominate as compared to the weaker SH...O contacts, and at ambient temperature the situation is inverse. The transition from one phase to another goes via a series of states differing in conformations of the cysteine zwitterions and the intermolecular contacts of the thiol-group. Motions of different molecular fragments (NH 3 (+), CH 2, CH, SH) are activated at different temperatures. Structural strain on cooling involves several dynamic processes, such as a rigid rotation of the molecule in the lattice, a rigid rotation of the NH 3 group with respect to NH 3-CH bond, and the rotation of the thiol side chain resulting in the switching of S-H hydrogen bonding from one type to another. Different NH...O hydrogen bonds forming the framework in the L-cysteine crystal structure are distorted to a different extent, and this provokes the rotation of the -CH 2SH side chains within the cavities of this framework resulting in a change in the coordination from SH...O to SH...S at low temperatures. The results are interesting for understanding the polymorphism of molecular crystals and the factors determining their dynamics and structural instability, and also for biophysical chemistry, since the properties of the hydrogen bonded thiole-groups in biomolecules can be mimicked using L-cysteine in the crystalline state, variations in temperature and pressure serving as powerful tools, to modify the intramolecular conformations and the intermolecular hydrogen bonding.     

Hydration of Sugars in the Gas Phase: Regioselectivity and Conformational Choice in N‐Acetyl Glucosamine and Glucose

The influence of an acetamido group in directing the preferred choice of hydration sites in glucosamine and a consequent extension of the working rules governing regioselective hydration and conformational choice, have been revealed through comparisons between the conformations and structures of “free” and multiply hydrated phenyl N‐acetyl‐β‐D ‐glucosamine (βpGlcNAc) and phenyl β‐D ‐glucopyranoside (βpGlc), isolated in the gas phase at low temperatures. The structures have been assigned through infrared ion depletion spectroscopy conducted in a supersonic jet expansion, coupled with computational methods. The acetamido motif provides a hydration focus that overwhelms the directing role of the hydroxymethyl group; in multiply hydrated βpGlcNAc the water molecules are all located around the acetamido motif, on the “axial” faces of the pyranose ring rather than around its edge, despite the equatorial disposition of all the hydrophilic groups in the ring. The striking and unprecedented role of the C‐2 acetamido group in controlling hydration structures may, in part, explain the differing and widespread roles of GlcNAc, and perhaps GalNAc, in nature.     

Stereodynamics of triethylamine: Molecular mechanics calculations on the direct rotational racemization of the C3-symmetric conformers

The direct interconversion of the two C₃-symmetric enantiomeric conformations of triethylamine, via C? N bond rotation, has been studied by molecular mechanics (MM 2) calculations. The MM 2 calculations have been used to characterize the minima (equilibrium geometries) and first-order saddle points (transition states) for this process. For one interconversion, there are five saddle points and six minima. The highest energy saddle point results from the uncoupled rotation of one ethyl group to eclipse the lone pair. Two of the barriers result from coupled rotation of two ethyl groups in close passage.     

Energy transfer in the nanostar: the role of coulombic coupling and dynamics

We present a theoretical investigation of energy transfer in the phenylene ethynelene dendrimer known as the nanostar. Data from extensive molecular dynamics simulations are used to model the dynamical effects caused by torsional motion of the phenyl groups. We compare rate constants for energy transfer between the two-ring chromophore and the three-ring chromophore obtained via the F?rster model, the ideal dipole approximation (IDA), and the transition density cube (TDC) method, which has as its limit an exact representation of the Coulombic coupling. We find that the rate constants obtained with the TDC are extremely sensitive to the phenyl group rotation, whereas the constants computed with the F?rster model and the IDA are not. The implications of these results for the interpretation of recent pump-probe experiments on the nanostar are discussed in detail. Finally, we predict the temperature dependence of the rate constant for energy transfer.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

Steric interactions in 2-substituted imidazoles. The molecular structure of 1-methyl-2-phenylimidazole and 1-methyl-4-phenylimidazole

The crystal and molecular structures are reported for two isomeric imidazoles: 1-methyl-2-phenylimida-zole ( 1 ) and 1-methyl-4-phenylimidazole ( 2 ). In molecule 2 the phenyl ring is rotated by 7.3° from the het-erocyclic plane due to steric interactions. The steric congestion is much more severe in 1 , with the adjacent methyl and phenyl substituents mininizing nonbonded interactions via a 32.3° rotation of the phenyl ring and a 0.159 Å displacement of the methyl carbon from the heterocyclic plane.     

The equilibrium structure of ferrocene.

The molecular structures of ferrocene in the eclipsed (equilibrium) and staggered (saddle‐point) conformations have been determined by full geometry optimizations at the levels of second‐order Møller–Plesset (MP2) theory, coupled‐cluster singles‐and‐doubles (CCSD) theory, and CCSD theory with a perturbative triples correction [CCSD(T)] in a TZV2P+f basis set. Existing experimental results are reviewed. The agreement between the CCSD(T) results and experiment is in all cases excellent; the calculated structure parameters and the barrier to internal rotation of the ligand rings differ from the most accurate experimental values by less than two estimated standard deviations. The CCSD(T) calculations for single‐configuration‐dominated transition metal complexes such as ferrocene thus appear to have an accuracy comparable to that observed for molecules containing only first‐ and second‐row atoms, and to be of a quality similar to that obtained experimentally. A comparison with previous DFT results indicates that the B3LYP model gives overall the best DFT results, with a deviation of around 2 pm for the metal–carbon distance and smaller errors for the cyclopentadienyl rings.     

The Mechanism of NO Bond Cleavage in Rhodium‐Catalyzed CH Bond Functionalization of Quinoline N‐oxides with Alkynes: A Computational Study

Metal‐catalyzed C?H activation not only offers important strategies to construct new bonds, it also allows the merge of important research areas. When quinoline N‐oxide is used as an arene source in C?H activation studies, the N?O bond can act as a directing group as well as an O‐atom donor. The newly reported density functional theory method, M11L, has been used to elucidate the mechanistic details of the coupling between quinoline N?O bond and alkynes, which results in C?H activation and O‐atom transfer. The computational results indicated that the most favorable pathway involves an electrophilic deprotonation, an insertion of an acetylene group into a Rh?C bond, a reductive elimination to form an oxazinoquinolinium‐coordinated Rh^I intermediate, an oxidative addition to break the N?O bond, and a protonation reaction to regenerate the active catalyst. The regioselectivity of the reaction has also been studied by using prop‐1‐yn‐1‐ylbenzene as a model unsymmetrical substrate. Theoretical calculations suggested that 1‐phenyl‐2‐quinolinylpropanone would be the major product because of better conjugation between the phenyl group and enolate moiety in the corresponding transition state of the regioselectivity‐determining step. These calculated data are consistent with the experimental observations.     

Crystal Structures of Analogs of threo-Methylphenidate

The crystal structures of the chloride salts of five analogs of threo-methylphenidate have been obtained. Four of these have different substituents on the phenyl ring while the fifth is the ethyl ester of methylphenidate. All five structures have similar three-dimensional conformations and these are compared with the global minimum obtained by MM2-87 calculations. There is good agreement between the crystal structures and the computed global minimum with the major difference being the presence of a chloride counterion in the crystal structures that prevents the carbonyl oxygen from approaching the equatorial ammonium hydrogen as closely as in the computed global minimum.     

Oxidation with a “Stopover” – Stable Zwitterions as Intermediates in the Oxidation of α-Tocopherol (Vitamin E) Model Compounds to their Corresponding ortho-Quinone Methides

As a prominent member of the vitamin E group, α-tocopherol is an important lipophilic antioxidant. It has a special oxidation chemistry that involves phenoxyl radicals, quinones and quinone methides. During the oxidation to the ortho-quinone methide, an intermediary zwitterion is formed. This aromatic intermediate turns into the quinone methide by simply rotating the initially oxidized, exocyclic methyl group into the molecule's plane. This initial zwitterionic intermediate and the quinone methide are not resonance structures but individual species, whose distinct electronic structures are separated by a mere 90° bond rotation. In this work, we hindered this crucial rotation, by substituting the affected methyl group with alkyl or phenyl groups. The alkyl groups slowed down the conversion to the quinone methide by 18-times, while the phenyl substituents, which additionally stabilize the zwitterion electronically, completely halted the conversion to the quinone methide at −78 °C, allowing for the first time the direct observation of a tocopherol-derived zwitterion. Employing a ¹³C-labeled model, the individual steps of the oxidation sequence could be observed directly by NMR, and the activation energy for the rotation could be estimated to be approximately 2.8 kcal/mol. Reaction rates were solvent dependent, with polar solvents exerting a stabilizing effect on the zwitterion. The observed effects confirmed the central relevance of the rotation step in the change from the aromatic to the quinoid state and allowed a more detailed examination of the oxidation behavior of tocopherol. The concept that a simple bond rotation can be used to switch between an aromatic and an anti-aromatic structure could find its use in molecular switches or molecular engines, driven by the specific absorption of external energy.     

Structures and NMR Parameters of 1,2-Diphenylcyclobutanes

A new reaction scheme for obtaining cis and trans 1,2-diphenylcyclobutane is described. Using ¹H-NMR at 600 MHz, full spectral assignment was made for both isomers, obtaining all J coupling constants and chemical shifts. NMR results on cis and trans 1,2-diphenylcyclobutane are compared with the vicinal coupling constants obtained by the Barfield–Smith equations from the literature internal and dihedral angles of cyclobutane. In the trans isomer, in agreement with previous results on halo-cyclobutanes, the conformation with the phenyls in the pseudo-di-equatorial position is strongly preferred. On the contrary, the cis isomer fluctuates between the two equivalent conformations: phenyl pseudo-axial and pseudo-equatorial.