Interactions Of Substituents Research Articles

Two-Dimensional Hydrogen Bond Networks Supported by CH/π Interaction Leading to a Molecular Packing Appropriate for Topochemical Polymerization of 1,3-Diene Monomers

Strong and weak hydrogen bonds, as intermolecular interactions, are used for the construction of designer crystals with organic small molecules as the building blocks. We report here crystal engineering for the synthetic plan of the topochemical polymerization using the ammonium derivatives of 1,3-diene mono- and dicarboxylic acids on the basis of intermolecular interactions such as NH/O and CH/π interactions. The isomerism of hydrogen bond network structures obstructs the prediction of crystal structure and reactivity, although topochemical polymerization requires that monomer molecules stack in a column with a stacking distance of 5 A in the crystals. The structures of hydrogen bond networks are roughly classified into a two-dimensional type appropriate for topochemical polymerization, and the others consisting of two-dimensional sheets or one-dimensional ladders not for polymerization. We conclude that the CH/π interaction of naphthylmethyl and benzyl substituents promises to give polymerizable lamella...

A 50% n-octylmethyl, 50% diphenyl-polysiloxane as stationary phase with unique selectivity for gas chromatography.

An n-octylmethyl, diphenyl-polysiloxane called SOP-50-Octyl was prepared by a condensation reaction of bis(dimethylamino) n-octylmethylsilane with diphenylsilanediol. The resulting copolymer was a gum with high molecular weight and was obtained with a yield of 80%. 1H and 29Si NMR spectroscopy revealed that the copolymer was a 52% octylmethyl, 48% diphenyl-polysiloxane with random microstructure. Small cyclic impurities could be almost quantitatively removed via a purification step. SOP-50-Octyl was used as stationary phase for the preparation of wall coated open tubular fused silica capillary columns for gas-liquid chromatography. The capillary columns exhibited high separation efficiency and high inertness. The stationary phase offered a unique selectivity due to its unique composition. The Rohrschneider-McReynolds constants indicated a low overall polarity in spite of the high phenyl content, as the polarity was distinctly decreased by the octyl substituent. Furthermore, the octyl substituent was responsible for a high column bleed, reducing the maximum allowable operating temperature to 280 degrees C. The elution temperatures of apolar compounds were increased due to increased interaction of the octyl substituent with the analytes. Some applications with volatile and semi-volatile organic compounds illustrate that SOP-50-Octyl is an excellent choice for confirmational analyses.

A structural study of 1,8-bis(dimethyl phosphonito) naphthalene and related crowded chalcogeno derivatives

1,8-Bis(dimethylphosphonito) naphthalene Nap[P(OMe)2]2 (Nap = naphthalene-1,8-diyl) and a complete series of its mono- and di-oxidized phosphonato counterparts Nap[P(E)(OMe)2]2 (E = O, S, Se, lone pair and all their permutations) were prepared and fully characterized by X-ray crystallography and multinuclear NMR, IR, Raman and MS. Molecular distortion due to non-bonded substituent interactions was studied as a function of the bulk of the phosphorus substituents. The least and most strained molecules in the series are Nap[P(OMe)2]2 and Nap[P(Se)(OMe)2]2 with non-bonding P⋯P distances of 2.91 and 3.79 A respectively.

The High Resolution Structures of Free and Inhibitor-bound Trypanosoma rangeli Sialidase and its Comparison with T. cruziTrans-sialidase

The structure of the recombinant Trypanosoma rangeli sialidase (TrSA) has been determined at 1.6Å resolution, and the structures of its complexes with the transition state analog inhibitor 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (DANA), Neu-5-Ac-thio-α(2,3)-galactoside (NATG) and N-acetylneuraminic acid (NANA) have been determined at 1.64Å, 2.1Å and 2.85Å, respectively. The 3D structure of TrSA is essentially identical to that of the natural enzyme, except for the absence of covalently attached sugar at five distinct N-glycosylation sites. The protein exhibits a topologically rigid active site architecture that is unaffected by ligand binding. The overall binding of DANA to the active site cleft is similar to that observed for other viral and bacterial sialidases, dominated by the interactions of the inhibitor carboxylate with the conserved arginine triad. However, the interactions of the other pyranoside ring substituents (hydroxyl, N-acetyl and glycerol moieties) differ between trypanosomal, bacterial and viral sialidases, providing a structural basis for specific inhibitor design. Sialic acid is found to bind the enzyme with the sugar ring in a distorted (half-chair or boat) conformation and the 2-OH hydroxyl group at hydrogen bonding distance of the carboxylate of Asp60, substantiating a direct catalytic role for this residue. A detailed comparison of TrSA with the closely related structure of T.cruzitrans-sialidase (TcTS) reveals a highly conserved catalytic center, where subtle structural differences account for strikingly different enzymatic activities and inhibition properties. The structure of TrSA in complex with NATG shows the active site cleft occupied by a smaller compound which could be identified as DANA, probably the product of a hydrolytic side reaction. Indeed, TrSA (but not TcTS) was found to cleave O and S-linked sialylated substrates, further stressing the functional differences between trypanosomal sialidases and trans-sialidases.

Substituent interactions in trans-2-substituted methoxycyclohexanes: an explanation to the conformational behaviour in a chemometric and theoretical view

Principal component analysis of theoretical data [B3LYP/6-311+g(d,p)] may predict the main interactions governing the conformational equilibrium of a series of trans-2-substituted methoxycyclohexanes. The classical syn-1,3-diaxial repulsion, as well as the ‘ gauche effect’ for some substituents, explain the preference towards the eq– eq conformation, although dipolar and steric repulsions between the eq– eq substituents is also an important intramolecular interaction present in these systems favouring the ax– ax form. The intramolecular interactions were supported by theoretical variables, such as nuclear repulsion energy, hardness, charges and bond order (obtained from the density matrix of the theoretical calculations), which led to the conformers separation into ax– ax and eq– eq classes.

Analysis of quinazoline and pyrido[2,3-d]pyrimidine N9-C10 reversed-bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductase.

Structural studies of two ternary complexes of Pneumocystis carinii dihydrofolate reductase (pcDHFR) with the cofactor NADP(+) and potent antifolates, the N9-C10 reversed-bridge inhibitor 2,4-diamino-6-[N-(2',5'-dimethoxybenzyl)-N-methylamino]quinazoline (1) and its 3',5'-dimethoxypyrido[2,3-d]pyrimidine analog (2), were carried out. Data for the monoclinic crystals were refined to 1.90 A resolution for the complex with (1) (R = 0.178) and to 2.1 A resolution for the complex with (2) (R = 0.193). The effect of the N9-C10 reversed-bridge geometry is to distort the bridge from coplanarity with the pyrido[2,3-d]pyrimidine or quinazoline ring system and to twist the C10 methylene conformation toward a gauche conformation. This change also influences the conformation of the methoxybenzyl ring, moving it away from a trans position. This change places the 5'-methoxy group deeper within the hydrophobic pocket made by Ile65, Pro66 and Phe69 of the pcDHFR active site. These results also revealed the first observation of an unusual conformation for the reversed-bridge geometry (C5-C6-N9-C10 torsion angle) in antifolate (2). The electron density is consistent with the presence of two models (conformers 2-1 and 2-2) that result from inversion of the geometry at N9. The four examples of N9-C10 reversed-bridge antifolates cluster in two conformations, with the structure of quinazoline (1) similar to that previously reported for its 2',5'-dimethoxypyrido[2,3-d]pyrimidine analog (3). The two conformers of (2) differ from these and each other by a twisted-bridge geometry that results in the dimethoxybenzyl ring occupying the same conformational space. Conformer 2-2 also has the N9-C10 reversed bridge perpendicular to the pyrido[2,3-d]pyrimidine plane, in contrast to the gauche-trans conformation normally observed. As a result of these changes, the N9 methyl probes conformational space in the active site not normally occupied by antifolate structures. The N9 methyl of conformer 2-2 makes close contacts to the conserved Leu25 as well as the hydroxyl O atoms of the nicotinamide ribose and Ser64, whereas the other three reversed-bridge conformers make weak hydrophobic contacts with Ile123, Thr61 and Ile65. These antifolates are ten times more selective for pcDHFR than the C9-N10 bridge parent trimetrexate. However, pyrido[2,3-d]pyrimidines (2) and (3) are three times more selective for pcDHFR than quinazoline (1) is for rat liver DHFR. These data suggest that the loss of hydrogen-bonding interactions with N8 is more important to potency than the interactions of the methoxybenzyl substituents.

Space‐demanding intramolecular isomerizations in the solid state

AbstractThe thermal isomerizations of meso‐ and rac‐3,4‐dibromo‐1,6‐diphenyl‐1,6‐bis(p‐tolyl)‐1,2,4,5‐hexatetraene (1) to give stereospecifically the 3,4‐bis(phenyl‐p‐tolylmethylene)‐1,2‐dibromocyclobutenes 3 and 5 + 6 were studied in the solid state using atomic force microscopy (AFM) and interpreted on the basis of known crystal structural data. These isomerizations run to completion in the bulk and include highly space‐demanding internal rotations around the central bond. Far‐reaching anisotropic molecular movements are detected on the major faces that align the surface features along cleavage planes in the initial phase rebuilding stage. Only one of three identified cleavage planes of meso‐1 is successful, owing to closer interactions of the bromine substituents in the non‐used cleavage planes. Thus, very fine details can be correlated and predicted for the occurrence of internal rotations and molecular movements in the crystal lattice. The second stage in these intramolecular isomerizations, the phase transformation, produces very high features up to 100 nm and still parallel to the preferred cleavage plane of meso‐1 but in the µm range without relation to the initial crystal structure in the case of rac‐1. Copyright © 2002 John Wiley & Sons, Ltd.

Soluble polydiacetylenes: molecular properties and solid state organization

The solution properties of a novel soluble polydiacetylene, poly[1,6-bis(3,6-dihexadecyl- N-carbazolyl)-2,4-hexadiyne] (polyDCHD-HS), have been investigated by use of spectroscopic (UV–VIS absorption, fluorescence and FT-Raman) and light scattering techniques in benzene and toluene. The unique spectroscopic and molecular properties of these solutions are reported and discussed in relation to the particular interactions of the polymer substituents with aromatic solvents. The introduction of the long alkyl-substituents on the carbazolyl side groups not only improves the processability relative to the parent unsubstituted polymer but also suppresses the chromic effects observed in other soluble polydiacetylenes. The side groups are also responsible for the peculiar supramolecular organization observed in the powder phase of the red form.

Supramolecular assistance to regioselectivity in the reactions of chlorocyclophosphazenes with sodium oxyanions: macrocyclic effect and anion dependence.

Comparative studies of the naphtholysis of crown-bearing tetrachlorocyclotriphosphazene 2 and its acyclic analogue, nongem-diethoxytetrachlorocyclotriphosphazene 5 (which was synthesized and isolated in the pure cis form for the purpose of this study), reveal a significant macrocyclic effect of the substituent on both the kinetics and regiochemistry of chlorine substitution in the N(3)P(3) ring. Whereas substitution of 5 with sodium naphthoxide provided moderate yields of the respective sterically and electronically favored nongem-naphthoxydiethoxy derivative as the major product, isolated as the mixture of cis and trans isomers 8 + 9, the corresponding reaction of crown substrate 2 resulted in highly regioselective formation of the gem-to-macrocycle substituted mononaphthoxy PNP-crown derivative 11a. The importance of the PNP-crown related effects for the regio- and stereocontrol of the substitution of chlorine atoms in the N(3)P(3) ring is discussed in terms of supramolecular sodium cation-assisted interactions between the ring oxy substituent(s) and incoming oxyanions. To approach the problem of the anion-dependence of the regioselectivity, a comparison has been drawn between the reactions of the PNP-crown substrate 2 with sodium arylates derived from beta-naphthol (10a) and phenol (10b), carried out with equimolar or 100% excess sodium oxyanion with respect to 2, and the corresponding reactions of 2 with sodium monoenolates derived from the beta-dicarbonyl compounds: acetylacetone (10c) and ethyl acetylacetate (10d). The effectiveness of supramolecularly assisted transition state stabilization is found to be dependent not only on the dimensional complementarity between the cation and the macrocycle but also on the properties of the four interacting ionic centers according to the HSAB principle and on the nature of the electronic interaction of the PNP-crown substituent with the N(3)P(3) ring, the latter determining the extent of regiocontrol to either one or two macrocyclic chloride functions. The increase of the extent of regioselectivity of gem-substitution at the PNP-macrocycle when passing from arylate to beta-dicarbonyl enolate oxy anions is related to the observed trends in the (31)P NMR chemical shifts and refers to the electronic structure of the oxy substituent.

17O NMR studies on (E)‐3‐arylidenechromanone and ‐flavanone derivatives

Abstract17O NMR data for some 3‐arylidenechromanones and ‐flavanones are discussed in terms of mesomeric and steric substituent interactions. The transmission of long‐range substituent effects was studied. 17O NMR chemical shifts were correlated with Hammett σp+ values for 4′‐substituted derivatives. Copyright © 2001 John Wiley & Sons, Ltd.

Differentiation of positional isomers of nitro meso-tetraphenylporphyrins by tandem mass spectrometry

We studied by tandem mass spectrometry two isomers of nitro meso-tetraphenylporphyrin, one with a nitro group in the para position of a phenyl ring and the other with the same group in a β-pyrrolic position, and their copper complexes. Collisional activation of the molecular ions of both free-base porphyrins and of their copper complexes produces an array of product ions that permit ready differentiation of the two positional isomers. The diagnostic ions, when the nitro group is in a β-pyrrolic position, may be produced through intramolecular and double cyclization processes, triggered by the interaction of the nitro substituent with the neighboring meso-phenyl ring. These diagnostic ions do not form when the nitro group is in the para position. The gas-phase processes have precedents in solution chemistry.

Manganeseporphyrin catalyzed cyclohexene epoxidation by iodosylbenzene: The remarkable effect of the meso-phenyl orthoOH substituent

Catalytic cyclohexene epoxidation with iodosylbenzene by the following Mn-porphyrins bearing ortho substituents on a meso group: MnTTP, MnM 2-OHPTTP(5-(2-hydroxyphenyl)-10,15,20-tritolylporphyrin) and MnM 2-BrPTTP(5-(2-(3-bromo-1-propoxy)phenyl)-10,15,20-tritolylporphyrin), has been studied. The effect of dioxygen and imidazole axial ligand on the yields of epoxide and allylic oxidation products, i.e. alcohol and ketone, was investigated. It was observed that the product selectivity is strongly dependent on the distribution of the Im/MnP species (M, MIm and MIm 2 obtained by spectrophotometric titrations). For MnTPP at Im/MnP=1 the best epoxide yield associated with the maximum MIm concentration was observed. The presence of the OH substituent produced a remarkable effect on the reactivity and catalytic properties of the porphyrin system, i.e. drastic reduction in allylic oxidation, slight increase on the epoxide yield, a decrease on the formation of the MnP/Im complexes and change of the reactivity of the Mn center with PhIO. These results are discussed in terms of a possible electronic interaction of the oxygen ortho substituent and the porphyrin ring.

Molecular structure and electric properties of N-methyl-N-nitroaniline and its derivatives

A comparative study of the molecular structure of N-methyl-N-nitroaniline and its derivatives is carried out employing the Kerr effect and dipole moments methods in combination with the crystallographic analysis. The obtained experimental structural data agree with the quantum-chemical calculations by the B3LYP/6-31G∗ and MP2/3-21G∗ methods. The measurement and calculation results are used to draw conclusions about the mutual interaction and role of various substituents to the N-methyl-N-nitroaniline molecule.

New, optically active phosphine oxazoline (JM-Phos) ligands: syntheses and applications in allylation reactions.

Three different syntheses of the phosphine oxazoline systems 1 are presented. Two of these approaches are divergent routes designed to involve an advanced intermediate that can be transformed into several different end-products. The third is a shorter route specifically designed to facilitate preparations of these systems on a larger scale using minimal functional group protection. Overall, eight different phosphine oxazolines were prepared. These were screened in several palladium-mediated allylation reactions. They proved to be most useful for asymmetric alkylation of 3-acetoxy-1,3-diphenylpropene and less suitable/effective for the more challenging substrates (a pentenyl derivative and a cyclohexenyl system). X-ray crystallographic analysis of the complex [(eta 3-PhCHCHCHPh)Pd(1a)][PF6] led to the conclusion that the origins of asymmetric induction in these systems might be indirectly attributed to interaction of the oxazoline-phenyl substituent with the palladium and with an allyl-phenyl substituent. Finally, data is presented for allylation of a silylenolate of an N-acyl oxazolidinone; excellent enantioselectivities and yields were obtained.

Computational study of the electronic structure of substituted phenylcarbene in the gas phase

Gas-phase calculations for ortho-, meta-, and para-substituted phenylcarbenes demonstrate that aromatic ring substituents can have a large effect on the singlet-triplet splitting in these molecules. For example, p-aminophenylcarbene is predicted to have a singlet-triplet splitting (DeltaE(ST)) of 0.7 kcal/mol, which is 4.7 kcal/mol smaller than that of the parent phenylcarbene. However, when the mesomeric effect of pi-donation is removed, as in the meta-substituted molecules, this affect is greatly attenuated. m-Amino substitution lowers the DeltaE(ST) to 5.2 kcal/mol, a change of only 0.2 kcal/mol from the parent phenylcarbene. The sensitivity of phenylcarbene to substitution is judged by the slope of the line correlating the singlet-triplet gaps to linear free energy (LFE) parameters. In this study, the best linear correlation for DeltaE(ST) in the para-substituted phenycarbenes is observed when plotted against sigma(p)(+). The resultant slope (rho) is 5.0. The origin of this effect is preferential interaction of aryl substituents with the singlet rather than the triplet species as demonstrated by electron density analyses.

Formation, structure and conformational dynamics of highly substituted diphenylcarbonates

The symmetrical carbonates 5-8 were prepared from ethyl 4-hydroxybenzoates with aryl-, 4-(arylethynyl)-phenyl-, arylethynyl- or arylbutadiynyl-substituents in the 3- and 5-positions, by reaction with triphosgene. The choice of base (pyridine, DMAP, NaH) had a strong influence on the conversion: For the synthesis of the carbonates 5 and 6, it was sufficient to use pyridine as the base. However, for the synthesis of the carbonates 7 and 8, NaH had to be used instead. Single-crystal X-ray structure analysis of these carbonates revealed that the substituents point towards the corners of a distorted tetrahedron with the carbonate group sitting in the middle of the tetrahedron and the two angular phenolic building blocks intersecting with an angle of 51-71 degrees. In solution at room temperature, all four substituents are magnetically equivalent as a consequence of conformational flexibility. The two enantiomeric conformers of carbonate 5a interconvert rapidly, probably via a perfect trans conformation with the plane of the Aralpha perpendicular to the carbonate plane. In the case of carbonates 6-8 this process is inhibited by unfavourable interaction of the long substituents at the benzoate moiety. The dynamic process, which has an energy barrier of 8-10 kcalmol(-1), is described in a simplified manner as a continuous rotation of the angular building blocks around the carbonate unit with the C(aryl)-O bonds as the axes of rotation.

Substituent Effects on the Benzene Ring. Determination of the Intramolecular Interactions of Substituents in tert-Alkyl-Substituted Catechols from Thermochemical Measurements

Chemical equilibria of reactions of transalkylation among tert-butylphenols and tert-butylcatechols in the liquid phase were investigated in the temperature range 373−483 K. The molar enthalpies of fusion of the catechol, 4-tert-butylcatechol, and 3,5-di-tert-butylcatechol were measured by DSC. The standard (p° = 0.1 MPa) molar enthalpies of formation Δf (cr) at the temperature T = 298.15 K were measured by means of combustion calorimetry for 4-tert-butylcatechol and 3,5-di-tert-butylcatechol. The standard molar enthalpies of sublimation of these compounds, and also the enthalpy of vaporization of 3-tert-butylcatechol, were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. The measured reaction enthalpies were utilized for reconciliation of calorimetrically derived standard molar enthalpies of formation of tert-butyl-substituted phenols and catechols, as a stringent test of thermodynamic consistency of results derived from the diverse techniques employed ...

Epitaxial Adsorption of Monodendron-Jacketed Linear Polymers on Highly Oriented Pyrolytic Graphite

Linear polymers with monodendron side groups adsorb on highly oriented pyrolytic graphite (HOPG) in a remarkably regular pattern. The wormlike molecules have been depicted individually by scanning force microscopy with their long axis aligned according to the 3-fold symmetry of HOPG. The positional and orientational order of the adsorbed molecules is explained by the specific interaction of the alkyl substituents of the monodendrons with the HOPG surface. Direct evidence of the epitaxial adsorption was found by scanning tunneling microscopy of monolayers of the monomeric dendrons on HOPG. Ordering depended on the number of the alkoxy substitutes on the monodendrons. If the substitution of the monodendrons by the alkoxy groups was too dense, regular adsorption of the alkyl tails was impeded.

Structure correlation study of four-coordinate copper(I) and (II) complexes

The geometries of four-coordinate CuI and CuII complexes in the Cambridge Structural Database (CSD) have been analysed systematically and compared using symmetry-deformation coordinates and principal component analysis. The observed stereochemistries have been rationalized in terms of the d-electron configurations, interligand repulsion and pi-bonding effects. The results confirm that the majority of four-coordinate copper(I) complexes in the CSD adopt tetrahedral geometries and deviations from tetrahedral symmetry are caused by the presence of chelating ligands or by the incorporation of copper centres into dimeric or polymeric structures. Four-coordinate copper(II) complexes generally adopt geometries close to square planar; this is particularly evident for bis(chelate) complexes where pi-bonding is important. Distortions towards tetrahedral geometries are attributable to steric interactions of bulky substituents in the bidentate ligands.

Structural analysis of transition metal beta-X substituent interactions. Toward the use of soft computing methods for catalyst modeling

Fuzzy logic and neural network techniques are used to classify intramolecular interactions between transition metals (M) and beta-X substituents in the following structural motif (LnMC(alpha)(A1)(A2)-C(beta)(B1)(B2)X). These interactions are relevant to the direct polymerization of functionalized olefins by Ziegler-Natta (ZN) catalysis. The efficiency and effectiveness of different soft computing techniques are compared. These methods give not only encouraging results with respect to general data mining issues but also insight into the factors that effect interactions between transition metals and beta-X substituents.