Ab initio studies of structural features not easily amenable to experiment. 25. Conformational analysis of methyl propanoate and comparison with the methyl ester of glycine

The molecular geometries of three conformations of methyl propanoate (MEP) (C? C? C?O torsions of 0°, 120°, and 180°) and the potential-energy surfaces of MEP (C? C? C?O torsions) and of the methyl ester of glycine (MEG) (N? C? C?O torsions) have been determined by ab initio gradient calculations at the 4-21G level. MEP has conformational energy minima at 0° and 120° of the C? C? C?O torsion, while the 60–90° range and 180° are energy maxima. For MEG there are two minima (at 0° and 180°) and one barrier to N? C? C?O rotation in the 60–90° range. The N? C? C?O barrier height is about twice as high (4 kcal/mol) as the C? C? C?O barrier. The 180° N? C? C?O minimum is characteristically wide and flat allowing for considerable flexibility of the N? C? C?O torsion in the 150–210° range. This flexibility could be of potential importance for polypeptide systems, since the N? C? C?O angles of helical forms are usually found in this region. The molecular structures of the methyl ester group CH₃OC(?O)CHRR′ in several systems are compared and found to be rather constant when R ? H and R′ ? H, CH₃, CH₃CH₂; or when R ? NH₂ and R′ ? H, CH₃, or CH(CH₃)₂.     

An empirical potential for the O-H ⋯ O hydrogen bond: Part 2. Comparison with observed hydrogen bond geometries

The room temperature distribution of O-H ? O hydrogen bond geometries has been predicted by a Monte Carlo calculation, with an empirical potential energy function for the hydrogen bond. The results are compared with a recent survey of hydrogen bonds in carbohydrate crystal structures. The calculated and observed distributions of the O-H ? O angle have mean values of 165.5° and 167.1° respectively. Both the theoretical and experimental results suggest that short O ? H hydrogen bonds tend to be more linear than long O ? H bonds. The distribution of hydrogen bonding within the lone pair plane of the acceptor oxygen atom is predicted to be broader than the distribution perpendicular to this plane, in agreement with the experimental data. The empirical hydrogen bond function, in conjunction with the molecular mechanics program MMI, has also been used to predict the geometries of inter-residue hydrogen bonds in five disaccharides. The O ? H distances and O-H ? O angles are reproduced with r.m.s. deviations of 0.06 Å and 9° respectively.     

PM3 semiempirical study and its comparison with X-ray crystal structure of 2-methyl-4-(4-methoxyphenylazo)phenol

The crystal and molecular structure of 2-methyl-4-(4-methoxyphenylazo)phenol have been determined by X-ray single crystal diffraction technique. The compound crystallizes in the monoclinic space group P2₁/c with a=9.7763(8) Å, b=11.3966(8) Å, c=11.9531(8) Å and β=108.752(6)°. In addition to the molecular geometry from X-ray experiment, its optimized molecular structure has been obtained with the aid of PM3 semiempirical quantum mechanical method, and then the corresponding geometric parameters were compared with those of X-ray crystallography. To determine conformational flexibility and crystal packing effects on the molecules, molecular energy profile of the title compound was obtained with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Crystal structure of the title compound is a fibroid structure constructed by C–H···O and O–H···N type intermolecular hydrogen bonds. The most favorable conformer of the title compound has been determined by the crystal packing effects and there is no steric hindrance during rotation around the selected torsion angles.     

Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields

Ab initio self-consistent field (SCF) Hartree-Fock calculations of sulfates R? O? SO₃(?1) (R = Me, Et, i-Pr) and sulfamates R? NHSO₃(?1) (R = H, Me, Et, i-Pr) were performed at the 4-31G(*S*N) //3-21G(*S*N) basis set levels, where asterisks indicate d functions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6-31G*//6-31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the C? O bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single O? S bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn-periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the C? N bond and 3.3 kcal/mol around the N? S bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the N? S bond of only 1.7 kcal/mol. These and other data were used to parameterize the well-known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6-31G*//6-31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β-D -glucose-6-sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.     

4‐Fluoro‐2‐(phospho­no­methyl)­benzene­sulfonic acid monohydrate

The title compound, C₇H₈FO₆PS·H₂O, contains both phospho­nic and sulfonic acid functionalities. An extensive network of O—H?O hydrogen bonds is present in the crystal structure. The three acidic protons are associated with the phospho­nate group. Two protons experience typical hydrogen‐bond contacts with the sulfonate‐O atoms, while the third has a longer covalent bond of 1.05 (3) Å to the phospho­nate‐O atom and a short hydrogen‐bond contact of 1.38 (3) Å to the water O atom (all O—H?O angles are in the range 162–175°). The sulfonate group is positioned so that one S—O bond is nearly coplanar with the phenyl ring [torsion angle O—S—C—C ?8.6 (2)°]. The phospho­nate group is oriented approximately perpendicular to the ring [torsion angle P—C—C—C 99.2 (2)°] with one P—O bond anti to the benzyl C—C bond. The mol­ecules pack in layers in the b–c plane with the water mol­ecules in between adjacent pairs of inverted layers.     

Molecular modeling studies of novel heteroarotinoids

The molecular structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles ?₁ and ?₂ in closest agreement with the crystal structure, and all three computational methods yield values of ?₁ and ?₂ within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus ?₁ and ?₂ indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

trans‐4‐Bromo‐ONN‐azoxy­benzene at 100 K

The crystal structure of the α isomer of trans‐4‐bromo­azoxy­benzene [systematic name: trans‐1‐(bromophenyl)‐2‐phenyl­diazene 2‐oxide], C₁₂H₉BrN₂O, has been determined by X‐ray dif­frac­tion. The geometries of the two mol­ecules in the asymmetric unit are slightly different and are within ∼0.02 Å for bond lengths, ∼2° for angles and ∼3° for torsion angles. The azoxy bridges in both mol­ecules have the typical geometry observed for trans‐azoxy­benzenes. The crystal network contains two types of planar mol­ecules arranged in columns. The torsion angles along the Ar—N bonds are only 7 (2)°, on either side of the azoxy group.     

THE CRYSTAL AND MOLECULAR STRUCTURE OF THE POTENTIAL ANTIBACTERIAL AGENT 2-PYRIDYL-PHENYL SULPHONE

Abstract

Crystals of 2-pyridyl-phenyl sulphone are monoclinic, space group P2₁/c, with eight molecules in the unit cell of dimensions a = 11.781, b = 5.903, c = 29.748 Å and B = 94.13°. The dihedral angles between the best planes of the two aromatic rings are significantly different in two crystallographically independent molecules (88.4° and 71.9° for molecule A and molecule B, respectively), as well as those between the CSC plane and the pyridine ring (59.4° and 67.4°) and between the CSC plane and the phenyl ring (51.7° and 81.8°). The average bond distances of interest include C?S 1.77(1) and S?O 1.44(1) Å; among the bond angles there are CSO = 108.1(7), CSC = 105.0(6) and OSO = 118.7(6)°. The packing of the molecule in the crystal is determined by the van der Waals interactions and by two intermolecular H?O contacts of 2.43 and 2.49 Å. The observed conformation in the solid state agrees well with results of previous investigations, in the solution state, by means of dipole moment method and theoretical M.O. calculations, for the analogous di-2-pyridyl sulphone.     

2,4‐Bis(α,α‐di­methyl­benzyl)­phenol

The structure of the title compound, 2,4‐bis(1‐methyl‐1‐phenylethyl)phenol, C₂₄H₂₆O, was found to have a torsion angle of 129.95 (13)° for the C—C bond that connects the benzyl carbon to the phenol ring ortho to the OH group. A value of ～50° was expected from molecular mechanics calculations. Intermolecular interactions, in particular O—H?O and edge–face π bonding, may contribute to this discrepancy. Intramolecular O—H?π bonding is also observed.     

Crystal structure of polyisobutylene

The crystal structure of polyisobutylene was determined by x-ray analysis. The orthorhombic cell, with a = 6.88 Å, b = 11.91 Å, c (fiber axis) = 18.60 Å (space group: P2₁2₁2₁ ? D), contains two molecular chains each consisting of eight monomeric units in the fiber identity period. The chain conformation is essentially an (8/3) helix, but deviates appreciably from the exact (8/3) helix symmetry. The symmetry of the molecular chain is only a twofold screw axis in exact sense, and a crystallographic asymmetric unit consists of four monomeric units. The torsional angles are where M denotes the methyl group. The averaged skeletal C? CH₂? C and C? CM₂? C bond angles are 128° and 110°, respectively. The large C? CH₂? C bond angles may be due to steric respulsion between the adjacent methyl groups, giving intramolecular distances larger than 3.09 Å.     

Methoxy[meso‐5,10,15,20‐tetrakis(2,6‐difluorophenyl)porphyrinato]­iron(III), [Fe(TDFPP)(OCH3)]

The crystal structure of the title compound, [Fe(C₄₄H₂₀F₈N₄)(CH₃O)], has been determined. The Fe atom lies 0.485 (1) Å out of the plane of the four N atoms to which it is coordinated and from the inversion centre at the origin of the unit cell. The methoxy group is axially coordinated to the Fe atom with O—Fe—N angles of 106.3 (2) and 102.4 (2)°, a C—O—Fe angle of 128.3 (5)° and an Fe—O distance of 1.788 (5) Å. Di­fluoro­phenyl rings are tilted from the porphyrin (por) plane with torsion angles of ?68.1 (6) and 77.7 (5)° across the two C_por—­C—C—C_ar systems.     

Crystal structure of poly(m-phenylene isophthalamide)

The crystal structure of poly(m-phenyulene isophthalamide) was determined by x-ray analysis. The triclinic cell, with a = 5.27 Å, b = 5.25 Å, c (fiber axis) = 11.3 Å, α = 111.5°, β = 111.4° and γ = 88.0° and space group P1, contains one monomeric unit. The crystal density is 1.47 g/cc. The molecules in the crystal are contracted by 1 Å per monomeric unit from the fully extended conformation, and the planes of the benzene rings and adjacent amide groups make angles of about 30°. The crystal is composed of molecular chains connected by N? H···O hydrogen bonds along the a and b axes forming a “jungle gym” network structure. The low tensile modulus of this polymer as compared with that of poly(p-phenylene terephthalamide) is attributed to the contracted molecular conformation.     

Least-squares refinement of molecular structure of polyoxymethylene

Least-squares refinement of the molecular structure of polyoxymethylene was carried out by using intensity data measured with an automatic four-circle diffractometer. The discrepancy factor was improved to 4.1% by using the anisotropic temperature factor. Physically significant values were obtained for the bond length, bond angles, and internal rotation angle: C? O = 1.429 ± 0.008 Å, ∠COC = 112.9 ± 0.6°, ∠OCO = 110.4 ± 0.8°, and τ(C? O) = 77.0 ± 0.3°. Samples for x-ray diffraction measurements were prepared by solid state polymerization of a tetroxocane single crystal.     

Methyl 2‐O‐β‐d‐glucopyranosyl‐α‐l‐rhamnopyranoside

The overall conformation of the title compound, C₁₃H₂₄O₁₀, is described by the glycosidic torsion angles ?_H (H1_g—C1_g—O2_r—C2_r) and ψ_H (C1_g—O2_r—C2_r—H2_r), which have values of 13.6 and 16.1°, respectively. The former is significantly different from the value predicted by consideration of the exo‐anomeric effect (?_H～ 60°) and from that in solution (?_H～ 50°), as determined previously by NMR spectroscopy. An intramolecular O3_r—H?O2_g hydrogen bond may help to stabilize the conformation in the solid state. The orientation of the hydroxy­methyl group of the glucose residue is gauche–gauche, with a torsion angle ω (O5_g—C5_g—C6_g—O6_g) of ?70.4 (4)°. Both pyranose rings are in their expected chair conformations, i.e.⁴C₁ for d ‐glucose and ¹C₄ for l ‐rhamnose.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

(n‐Nitrophenyl)acetonitrile,with n = 2, 3 and 4

The molecular structures of the three title nitro‐substituted phenyl­aceto­nitriles, C₈H₆N₂O₂, at 123 K show that the mol­ecules are linked together very differently. In the 2‐ and 4‐nitro compounds, there are both O?H and N_cyano?H interactions, whereas the crystal lattice of the 3‐nitro compound is essentially built up by O?H interactions. The O atoms seem to prefer the aromatic H atoms, while the cyano N atoms prefer the methyl­ene H atoms. The phenyl–nitro torsion angles are ?19.83 (13), ?5.69 (12) and ?2.88 (12)°, while the phenyl–cyano­methyl torsion angles are ?62.27 (12), ?147.99 (9) and ?16.75 (14)° in the 2‐, 3‐ and 4‐NO₂‐substituted compounds, respectively.     

Methyl 4‐O‐β‐d‐galacto­pyran­osyl α‐d‐gluco­pyran­oside (methyl α‐lactoside)

Methyl α‐lactoside, C₁₃H₂₄O₁₁, (I), is described by glycosidic torsion angles ϕ (O5_gal—C1_gal—O1_gal—C4_glc) and ψ (C1_gal—O1_gal—C4_glc—C5_glc), which have values of −93.52 (13) and −144.83 (11)°, respectively, where the ring atom numbering conforms to the convention in which C1 is the anomeric C atom and C6 is the exocyclic hydroxy­methyl (–CH₂OH) C atom in both residues. The linkage geometry is similar to that observed in methyl β‐lactoside methanol solvate, (II), in which ϕ is −88.4 (4)° and ψ is −161.3 (4)°. As in (II), an inter­molecular O3_glc—H⋯O5_gal hydrogen bond is observed in (I). The hydroxy­methyl group conformation in both residues is gauche–trans, with torsion angles ω_gal (O5_gal—C5_gal—C6_gal—O6_gal) and ω_glc (O5_glc—C5_glc—C6_glc—O6_glc) of 69.15 (13) and 72.55 (14)°, respectively. The latter torsion angle differs substantially from that found for (II) [−54.6 (2)°; gauche–gauche]. Cocrystallization of methanol, which is hydrogen bonded to O6_glc in the crystal structure of (II), presumably affects the hydroxy­methyl conformation in the Glc residue in (II).     

Methyl 4‐O‐β‐l‐fucopyranosyl α‐­d‐­glucopyranoside hemihydrate

The crystal structure of methyl 4‐O‐β‐l ‐fuco­pyran­osyl α‐d ‐gluco­pyran­oside hemihydrate C₁₃H₂₄O₁₀·0.5H₂O is organized in sheets with antiparallel strands, where hydro­phobic interaction accounts for partial stabilization. Infinite hydrogen‐bonding networks are observed within each layer as well as between layers; some of these hydrogen bonds are mediated by water mol­ecules. The conformation of the disaccharide is described by the glycosidic torsion angles: ?_H = ?6.1° and ψ_H = 34.3°. The global energy minimum conformation as calculated by molecular mechanics in vacuo has ?_H = ?58° and ψ_H = ?20°. Thus, quite substantial changes are observed between the in vacuo structure and the crystal structure with its infinite hydrogen‐bonding networks.     

Crystal Structure Analysis of a trans,trans-Cyclodeca-1, 6-diene Derivative

An X-ray crystal structure analysis of the higher melting diastereoisomer of 2,7-dibromo-3,8-dimethoxy-trans,trans-cyclodeca-1,6-diene (Monoclinic; a = 5.76, b = 10.43, c = 11.32 Å, β = 94.04°; space group P2₁/n; Z = 2) has confirmed the NMR. assignment of the molecular conformation and the trans configuration of the methoxy groups. The trans,trans-cyclodeca-1,6-diene ring adopts a centrosymmetric crown conformation with a C? C?C? C torsion angle of 162°.