Dynamic mechanical properties of poly-α-olefins containing ring structures in side chains

Dynamic loss modulus curves have been determined over a temperature range beginning at liquid nitrogen temperature for poly-α-olefin polymers containing various ring structures, i.e., phenyl, cyclohexyl, cyclopentyl, and naphthyl, in the side chain. Glass transition and appropriate secondary relaxation temperatures were observed for each polymer. Separation of each pendant ring structure from the main backbone chain by successive additions of methylene units results in lower glass-transition temperatures. Comparison of polymers with similar side chains and different ring structures shows that the respective glass-transition temperatures decrease in the order naphthyl > cyclohexyl > phenyl > cyclopentyl. Secondary relaxation peaks were obtained at about ?150°C for polymers containing the cyclohexyl and cyclopentyl rings. A similar peak was observed for the polymer possessing a phenyl ring separated from the main chain backbone by two methylene units. The comparable polymer containing the naphthyl ring structure exhibited a broad secondary relaxation peak centered at ?20°C. The polymers possessing cyclohexyl rings separated from the main chain backbone by one or two methylene units had an additional low temperature peak at ?80°C. The molecular mechanism associated with this relaxation may be related to intramolecular transformations of the cyclohexyl ring between its “chair–chair” conformations.     

AB initio calculations on the equilibruim geometry and rotation barriers in biphenyl

The geometry of the biphenyl molecule has been studied with the MO LCAO method using a gausian basis set of “double zeta” quality. For various values of the twist angle between the phenyl ring planes the positions of the hydrogen atoms in the 2-position and the distance between the two rings have been simultaneously optimized. The lowest energy has been obtained for a non-planar conformation having a twist angle of 32°. The rotation barriers are 1.2 and 4.5 kcal/mol for the planar perpendicular cases, respectively.     

Ab initioSTO-3G optimization of planar,perpendicular, and twisted molecular structures of biphenyl

The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO -3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C₂ symmetry axis along the CC interring bond. The minimum torsional angle obtained was ? = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for ? = 0° and ? = 90°, respectively.     

Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers

Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers—r(AAA) and r(AAG)—obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.     

A cis‐stilbene derivative

The title compound, 4′‐methoxy‐α,2,3′,4‐tetra­nitro­stilbene, C₁₅H₁₀N₄O₉, crystallizes in the centrosymmetric space group P2₁/c with one mol­ecule in the asymmetric unit. The phenyl rings are inclined to one another and form a dihedral angle of 57.4 (1)°. The size of this angle is a result of intermolecular C—H⃛O interactions involving the phenyl H atoms. The torsion angle between the phenyl rings, −7.5 (3)°, indicates a cis geometry between them. The methoxy group is almost coplanar with the phenyl ring, and the nitro groups are twisted with respect to the phenyl rings because of the short H⃛O contacts. The crystal packing is stabilized by C—H⃛O hydrogen bonds, and the intermolecular hydrogen bonds form a C(12) graph‐set chain running along the [010] direction.     

Multirotations of (Anilinium)([18]Crown‐6) Supramolecular Cation Structure in Magnetic Salt of [Ni(dmit)2]−

A solid‐state dynamic supramolecular structure consisting of (anilinium)([18]crown‐6) was arranged as the cation in a salt of [Ni(dmit)₂]^? (dmit=2‐thioxo‐1,3‐dithiole‐4,5‐dithiolate). With the ammonium moiety of anilinium located within the cavity of [18]crown‐6, a hydrogen‐bonded supramolecular structure is formed, with an orthogonal arrangement between the π plane of anilinium and the mean O6 plane of [18]crown‐6. In this supramolecular cation, both anilinium and [18]crown‐6 act as dynamic units with different rotational modes in the solid state. The uniform stacks of cations form an antiparallel arrangement, thus producing a layer structure. Sufficient space for the 180° flip‐flop motion of the phenyl ring and the rotation of [18]crown‐6 was observed in the cation layer. Thermally activated 180° flip‐flop motions, with a frequency of 6 MHz at room temperature and an activation energy of 31 kJ mol^?1, were confirmed by temperature‐dependent ²H NMR spectra of ([D₅]anilinium)‐([18]crown‐6)[Ni(dmit)₂]. A double‐minimum potential for the molecular rotation of anilinium, with a barrier of approximately 40 kJ mol^?1, was indicated by ab initio calculations. The wide‐line ¹H NMR spectra indicated a thermally activated rotation of [18]crown‐6 at temperatures above 250 K. Therefore, multiple molecular motions of the 180° flip‐flop motion of the phenyl ring and the rotation of [18]crown‐6 occur simultaneously in the solid state. The temperature‐dependent dielectric constants revealed that the molecular motion of [18]crown‐6, other than the flip‐flop motion, dominates the dielectric response in the measured temperature and frequency range.     

The molecular structure of cis- and trans-bicyclo [4.2.0]-octane in the gas phase as studied by electron diffraction and molecular mechanics

The molecular structure of Cis- and trans-bicyclo[4.2.0]octane in the gas phase was studied. Molecular mechanics calculations applying Boyd's force Held were used for constraining differences between structural parameters during least squares analysis and for calculating vibrational amplitudes. The cyclohexane ring was found to have a distorted chair conformation, the ring in the cis isomer being flattened along the junction and more twisted in the other part. For the trans compound the reverse is true. The following structural parameters were obtained (r_a-structure):cis: r(C-C)_av. = 1.535 Å. Cyclohexane ring: average bond angle 112.9°; average torsional angle 48°. Cyclobutane ring: average bond angle 88.9°; puckering 157°. The dihedral angle between the bisecting planes of the C(2)-C(1)-C(6)-C(5) and C(8)-C(1)-C(6)-C(7) torsional angles, is 119° - the “connection angle” of the two rings.trans: r(C-C)_av.= 1.532 Å. Cyclohexane ring: average bond angle 110.4° ; average torsional angle 57°. Cyclobutane ring: average bond angle 87.3°; puckering 145°. The “connection angle” is 180° (C₂ symmetry).Comparison is made with structures of related compounds.     

5‐Amino‐4‐(4‐diethyl­amino­phenyl)‐2‐(4‐hydroxy­phenyl)‐7‐(pyrrolidin‐1‐yl)‐1,6‐naphthyridine‐8‐carbo­nitrile

In the title compound, C₂₉H₃₀N₆O, the naphthyridine moiety is planar with a dihedral angle between the fused rings of 1.9 (1)°. The phenol ring is nearly coplanar, while the diethyl­amino­phenyl substituent is orthogonal to the central naphthyridine ring and the pyrrolidine ring makes an angle of 11.2 (1)° with it. The O atom of the hydroxy substituent is coplanar with the phenyl ring to which it is attached. The molecular structure is stabilized by a C—H?N‐type intramolecular hydrogen bond and the packing is stabilized by intermolecular C—H?π, O—H?N and N—H?O hydrogen bonds.     

An unconventional ligand-binding mechanism of substrate-binding proteins: MD simulation and Markov state model analysis of BtuF

In conventional “Venus Flytrap” mechanism, substrate-binding proteins (SBPs) interconvert between the open and closed conformations. Upon ligand binding, SBPs form a tightly closed conformation with the ligand bound at the interface of two domains. This mechanism was later challenged by many type III SBPs, such as the vitamin B₁₂-binding protein BtuF, in which the apo- and holo-state proteins adopt very similar conformations. Here, we combined molecular dynamics simulation and Markov state model analysis to study the conformational dynamics of apo- and B₁₂-bound BtuF. The results indicate that the crystal structures represent the only stable conformation of BtuF. Meanwhile, both apo- and holo-BtuF undergo large-scale interdomain motions with little energy cost. B₁₂ binding casts little restraints on the interdomain motions, suggesting that ligand binding affinity is enhanced by the remaining conformational entropy of holo-BtuF. These results reveal a new paradigm of ligand recognition mechanism of SBPs. © 2019 Wiley Periodicals, Inc.     

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.     

Do­decyl 2‐nitro­phenyl disulphide

Do­decyl 2‐nitro­phenyl disulphide, C₁₈H₂₉NO₂S₂, contains an intramolecular S?O contact of 2.623 (3) Å. The angle between the planes of the NO₂ group and the attached phenyl ring is 4.2 (3)°. The thermal vibrations of the atoms increase along the paraffinic chain. The nitro­so O atom not involved in the S?O intramolecular contact also has high thermal motion. Attempts to create disordered models to allow for the thermal motions were unsuccessful.     

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.     

The Structure of Cellulose by Conformational Analysis. 1. Cellobiose and Methyl-β-cellobioside

Conformational analysis studies on the tertiary structure of cellobiose and methyl-β-cellobioside were carried out by using calculations of van der Waals, H-bond, electrostatic, and torsional energy interactions between the atoms and groups of the molecules. Energy maps as functions of the rotational anglesΨo and Φ° of the glucosidic bond were obtained in increments of 20° and refined in increments of 1°. Two “primary” and one “secondary” conformations of minimum energy were obtained for both cellobiose and methyl-β-cellobioside, some of which are equivalent to results obtained by x-ray diffraction. The H-bond forces are shown to be, together with the van der Waals forces, the predominant factors in the fixation of the conformations of minimum energy. The position and energy contributions of the H-bonds patterns for the favored conformations are identified.     

Molecular dynamics simulations of a poly(p-phenylene) oligomer

We have studied the conformation and coefficient of thermal expansion in the poly(p-phenylene) oligomer p-sexiphenyl (C₃₆H₂₆) by molecular dynamics simulations. Studies of the backbone phenyl–phenyl torsion angle in a simulated p-sexiphenyl crystal at room temperature indicate the presence of torsional librations of approximately ±20°. Further analysis of the phenyl–phenyl backbone torsion angle in less closely packed regions of the simulated crystal (crystal ends) indicate the presence of 180° phenyl ring flips, in agreement with solid-state deuterium NMR data on poly(p-phenylene oligomers). The linear coefficient of thermal expansion was also calculated and found to be negative, in qualitative agreement with experimental data on rigid-rod compounds. © 1993 John Wiley & Sons, Inc.     

Two isomeric 2‐[4‐chloro‐2‐fluoro‐5‐(prop‐2‐ynyloxy)phenyl]hexahydro­isoindole‐1,3‐dione compounds

The molecular structures of 2‐[4‐chloro‐2‐fluoro‐5‐(prop‐2‐ynyloxy)phenyl]‐1,3,4,5,6,7‐hexahydro­isoindole‐1,3‐dione, C₁₇H₁₃ClFNO₃, (I), and the isomeric compound 2‐[4‐chloro‐2‐fluoro‐5‐(prop‐2‐ynyloxy)phenyl]‐cis‐1,3,3a,4,7,7a‐hexahydro­isoindole‐1,3‐dione, (II), are, as anticipated, significantly different in their conformations and in the distances between the farthest two atoms. The six‐membered ring of the 1,3,4,5,6,7‐hexahydro­isoindole‐1,3‐dione moiety in (I) adopts a half‐chair conformation. The dihedral angle between the five‐membered dione ring of (I) and the benzene ring is 50.96 (7)°. The six‐membered ring of the cis‐1,3,3a,4,7,7a‐hexahydro­isoindole‐1,3‐dione moiety in (II) adopts a boat conformation. The dihedral angle in (II) between the five‐membered dione ring and the benzene ring is 61.03 (13)°. In the crystal structures, the molecules are linked by C—H⋯O hydrogen bonds and weak π–π interactions. Compound (I) is a much more potent herbicide than (II). The Cl⋯H distances between the farthest two atoms in (I) and (II) are 11.37 and 9.97 Å, respectively.     

4‐[N,N‐Bis(2‐hydroxy­imino‐2‐phenyl­ethyl)­amino]‐1,5‐di­methyl‐2‐phenyl‐2,3‐di­hydro‐1H‐pyrazol‐3‐one monohydrate

The title compound, C₂₇H₂₇N₅O₃·H₂O, is built up from pyrazolinone, phenyl and aceto­phenone oxime moieties. The 2‐­phenyl substituent is nearly perpendicular to the pyrazo­linone ring, with a dihedral angle of 87.66 (1)°. The aceto­phenone oxime moieties are twisted out of the pyrazolinone‐ring plane by 47.04 (1)°. The mol­ecules in the crystal pack in an antiparallel fashion and are held together by hydrogen‐bonded water mol­ecules and intermolecular O—H⋯O and O—H⋯N hydrogen bonds.     

Energetics of phase transformations in polyethylene

The molecular mechanisms involved in the orthorhombic-to-monoclinic phase transformation in polyethylene were investigated by the computer simulation of a structure–energy map based on empirically justified intermolecular potential functions. Stable packing structures for the orthorhombic and monoclinic form were isolated as relative minima, cohesive energies were determined from the energy minima, specific chain motions involved in the transformation were identified by the minimum energy path connecting the packing minima, and the activation energy for the transformation was determined from the energy barrier along the minimum energy transformation path. The packing structure parameters predicted from the energy map were in excellent agreement with unit cell dimensions observed near 0°K. The activation energy predicted for the transformation is relatively low (～0.5 kcal/mole of ethylene at 0°K and 0.25 kcal/mole of ethylene near the melting point, 411°K). Monoclinic packing was predicted to be slightly more stable than orthorhombic. Since this result is inconsistent with a large body of observations, we propose that the intramolecular energy of chain folds plays a dominant role in establishing chain-packing geometry. The inclusion of fold-transition energetics could give rise to transformation mechanisms which differ in details from those proposed in this work.     

2‐Nitroso‐1,3‐diphenyl‐1,2,3,4‐tetrahydrobenzo[b][1,6]naphthyridine

The title compound, C₂₄H₁₉N₃O, crystallizes in the centrosymmetric space group P2₁/a with one mol­ecule in the asymmetric unit. The tetra­hydro­pyridine ring has a boat conformation. The dihedral angle between the fused pyridine rings is 16.2 (1)°. The equatorial and axial orientations of the two phenyl groups with respect to the tetra­hydro­pyridine ring are confirmed. The nitroso group is coplanar with the attached C—N—C group. The interplanar angle formed between the fused tetra­hydro­pyridine and benzene planes is 13.4 (1)°. The crystal packing is stabilized by an intermolecular C—H⃛O hydrogen bond, which forms a C(9) graph‐set chain running along the [001] direction.     

Hydro­gen bonds and C—H⋯O interactions in 2,2′‐dimethoxybiphenyl‐5,5′‐dimethanol at 150 K

The title compound, C₁₆H₁₈O₄, crystallized in the centrosymmetric space group P2₁/c with one mol­ecule in the asymmetric unit. The two hydroxyl‐H atoms are ordered, and are involved in intermolecular hydrogen bonds with O_donor?O_acceptor distances of 2.761 (1) and 2.699 (1) Å, and O—H?O angles of 157 (2) and 168 (2)°. Seven leading intermolecular C—H?O interactions have H?O distances ranging from 2.41 to 2.76 Å and C—H?O angles ranging from 125 to 170°. The hydrogen bonds and C—H?O interactions form chain and ring patterns, resulting in a richly three‐dimensional network. The bi­phenyl twist angle is 67.2 (1)°.     

Surface reorientation of hydrogels based on methacrylate copolymers

Surface molecular structures of two statistical copolymers, poly(2-hydroxyethyl methacrylate-co-butyl methacrylate) (HEMA-co-BMA) and poly[2-(2-ethoxyethoxy)ethyl methacrylate-co-butyl methacrylate] (EOEOEMA-co-BMA), were studied by X-ray photoelectron spectroscopy (XPS). Besides the classical “dry” XPS technique, where the polymer samples were air-dried, also “deep-freezing” technique was used, where the samples were investigated in deep-frozen hydrated state. The differences in results obtained by the two techniques are discussed from the point of view of the polymer surface chain reorientation in response to various environment. The reverse polymer chain reorientation from the hydrated towards dry state was also followed.