Conformational mobility of the six-membered ring in 5-oxo-1,3-cyclohexadiene and its derivatives

Molecular mechanics and MNDO calculations showed that the six-membered ring in the molecule of 5-oxo-1,3-cyclohexadiene possesses high conformational mobility. The transition from a planar equilibrium conformation to a distorted sofa conformation in which the C(sp²)-C(=O)-C(sp³)-C(sp²) torsion angle is equal to ±30° increases the energy of the molecule by less than 1 kcal mol^–1. The influence of steric (R = Me, Et, Prⁱ, Bu^t) and electronic (R = NH₂, NO₂) effects of substituents R on the equilibrium conformation and mobility of the carbocycle has been analyzed. Both types of substituents at unsaturated C atoms do not change the equlibrium conformation or flexibility of the six-membered ring. Substituents at saturated C atoms cause the transition of the carbocycle to the distorted sofa conformation and significantly restrict its mobility. The electronic structures of 5-oxo-1,3-cyclohexadiene and its amino and nitro derivatives have been analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 849–854, May, 1995.     

(1R,2S)‐2‐[N‐Methyl‐N‐(4‐toluene­sulfonyl)amino]‐1‐phenylpropan‐1‐ol

In the title compound, C₁₇H₂₁NO₃S, the S atom is in a distorted tetrahedral geometry and the N atom exhibits sp² character. The antiperiplanar conformation is observed for the N and hydroxyl‐O atoms and the torsion angle around the N—C linkage is ?136.3 (2)°. The mol­ecules are linked by O—H?O intermolecular hydrogen bonds to form an infinite one‐dimensional chains along the c axis.     

Benzoaza-15-crown-5 ethers: synthesis,structure, and complex formation with metal and ethylammonium ions

Benzoaza-15-crown-5 ethers containing one or two nitrogen atoms in different positions of the macrocycle and bearing different substituents at these atoms were synthesized. The structures of azacrown ethers and their metal complexes were studied by X-ray diffraction. The stability constants of the complexes of azacrown ethers with Na⁺, Ca²⁺, Ba²⁺, Ag⁺, Pb²⁺, and EtNH₃ ⁺ ions were determined by ¹H NMR titration in MeCN-d₃. In free benzoazacrown ethers containing secondary nitrogen atoms bound to the benzene ring, as well as in N-acetyl derivatives, the N atoms are sp²-hybridized and have a planar geometry. The nitrogen lone pairs on the p orbitals are efficiently conjugated to the benzene ring or the carbonyl fragment of the acetyl group, which is unfavorable for the complex formation. In addition, the formation of complexes with benzoazacrown ethers containing secondary nitrogen atoms is hindered because the hydrogen atoms of the NH groups are directed to the center of the macrocyclic cavity. In benzoazacrown ethers bearing N-alkyl substituents or secondary nitrogen atoms distant from the benzene ring, the N atoms show a substantial contribution of the sp³-hybridized state and have a pronounced pyramidal configuration, which promotes the complex formation. The lead and calcium cations form the most stable complexes due to the high affinity of Pb²⁺ ions for O,N-containing ligands, a high charge density on these ions, and the better correspondence of the cavity size of the 15-membered macrocycles to the diameter of the Ca²⁺ ion. An increase in the stability of the complexes is observed mainly in going from monoazacrown ethers to diazacrown ethers containing identical substituents at the N atoms and in the following series of substituents: C(O)Me < H < Me < CH₂CO₂Et. In the case of the CH₂CO₂Et substituents, the carbonyl oxygen atom is also involved in the coordination to the cation. The characteristic features of the complexing ability of N-alkylbenzomonoaza-15-crown-5 ethers bearing the nitrogen atom conjugated to the benzene ring show that macro-cyclic ligands having this structure are promising as selective and efficient complexing agents for metal cations.     

The value of the π-bond order–bond length relationship in geometry prediction and chemical bonding interpretation

The π-bond order–bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π-bond order and overlap population results for carbon–carbon, carbon–nitrogen, and carbon–oxygen bonds obtained from ab initio STO -3G calculations using theoretically-optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order–length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp² – sp² and sp – sp hybridized C? C, C? N, and C? O bonds, and in evaluating the relative importance of hybridization, π-electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π-bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4-21G basis set are also presented.     

1‐Acetyl‐3′‐(4‐bromophenyl)‐3′‐chlorospiro[3H‐indole‐3,2′‐oxetan]‐2(1H)‐one

In the title compound, C₁₈H₁₃BrClNO₃, the heterocyclic ring of the indole is distorted from planarity towards an envelope conformation. The orientations of the indole, oxetane, chloro and bromo­phenyl substituents are conditioned by the sp³ states of the spiro‐junction and the Cl‐attached C atoms.     

Conformational preferences of 6-furfuryl amino purine and 6-benzyl amino purine

Conformational preferences of N⁶-furfurylamino purine (kinetin) and N⁶-benzyl amino purine (BAP ) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals method. The predicted most stable conformations for these molecules are quite similar. The N⁶ substituents in both these molecules are oriented toward N(1) and away from the imidazole moiety of the purine. The furfuryl ring in kinetin as well as the aromatic benzene ring in BAP are not coplanar with the purine ring. Comparison of these results with the preferred conformation of another compound N⁶-(Δ²-isopentenyl) adenine reveals striking similarity in the orientations of the N⁶ substituents in these cytokinin-active plant-growth-stimulating substances.     

Quantum semiempirical study on the reactivity of silylated diamines in the synthesis of aromatic polyamides

The reasons for the reactivity increase toward acyl chlorides caused in aromatic amines by silylation are studied by quantum semiempirical and ab initio methods. Silylated amino groups adopt an sp² planar geometry, in contrast to that observed in the unsilylated series, where a partially pyramidal structure intermediate between sp³ and sp² geometry was obtained. Silylation also causes a strong increase of electronic density on the amine nitrogen and an increase of the Highest Occupied Molecular Orbital (HOMO) energy, both effects favoring the higher reactivity of these silylated amines. In addition to that, silylation produces a decrease of the activation energy in the reaction with an acyl chloride, relative to the unsilylated amines, thus increasing reaction rate.     

Substituent effects in trans‐p,p′‐disubstituted azobenzenes: X‐ray structures at 100 K and DFT‐calculated structures

The crystal and molecular structures of two para‐substituted azobenzenes with π‐electron‐donating –NEt₂ and π‐electron‐withdrawing –COOEt groups are reported, along with the effects of the substituents on the aromaticity of the benzene ring. The deformation of the aromatic ring around the –NEt₂ group in N,N,N′,N′‐tetraethyl‐4,4′‐(diazenediyl)dianiline, C₂₀H₂₈N₄, (I), may be caused by steric hindrance and the π‐electron‐donating effects of the amine group. In this structure, one of the amine N atoms demonstrates clear sp²‐hybridization and the other is slightly shifted from the plane of the surrounding atoms. The molecule of the second azobenzene, diethyl 4,4′‐(diazenediyl)dibenzoate, C₁₈H₁₈N₂O₄, (II), lies on a crystallographic inversion centre. Its geometry is normal and comparable with homologous compounds. Density functional theory (DFT) calculations were performed to analyse the changes in the geometry of the studied compounds in the crystalline state and for the isolated molecules. The most significant changes are observed in the values of the N=N—C—C torsion angles, which for the isolated molecules are close to 0.0°. The HOMA (harmonic oscillator model of aromaticity) index, calculated for the benzene ring, demonstrates a slight decrease of the aromaticity in (I) and no substantial changes in (II).     

3‐Benzyl­oxy‐16‐[(N‐methyl‐N‐phenyl­amino)­methyl­idene]­estra‐1,3,5(10)‐trien‐17‐one

In the title compound, C₃₃H₃₅NO₂, the five‐membered ring adopts a half‐chair conformation. The N‐methyl‐N‐phenyl‐substituted keto–enamine moiety shows a comparatively long Csp²—N bond.     

Alternant boron nitride cages: A theoretical study

Heteroatomic cages (B_N/2N_N/2) with borons and nitrogens fully replacing alternant sets of carbons in cages are built graph-theoretically and investigated via the semiempirical MNDO Hamiltonian. The comparison with their parent carbon cages C_N is made in terms both of electronic and of geometric changes. Infinite classes first of octahedral symmetry and second of hexagonal-bipyramidal symmetry fullerenoid cages are considered in detail. The difference in the electronegativities for boron and nitrogen implies the opening of HOMO-LUMO gaps for alternant BN clusters. In general, the borons prefer planar geometry (sp² hybridization) while the nitrogens prefer pyramidalization (sp³ hybridization). © 1997 John Wiley & Sons, Inc.     

Synthesis of Artificial Glycoconjugate Polymers Carrying 6-O-Phosphocholine α-D-Glucopyranoside,Biologically Active Segment of Main Cell Membrane Glycolipids of Mycoplasma Fermentas

ABSTRACT

The conformation of two mannose-based amidines, the N-benzylmannoamidine and a pseudo (1→6) dimannoside, has been evaluated using semi-empirical AMI calculations and ¹H NMR studies. The most stable conformations of the mannoamidine ring correspond to the half-chair forms ³H₄ and ⁴H₃. The conformations (Z) or (E) about the exocyclic C-N bond depend on the substituents and it was shown that, in solution, the N-benzylmannoamidine was (E)-configured whilst the pseudo (1→6) dimannoside was (Z)-configured. Using the grid-search approach, the potential energy maps of both mannoamidines were calculated as a function of the torsion angles which define the orientation of the amidine substituent. Three stable conformers were identified for the N-benzylmannoamidine and seven for the pseudo (1→6) dimannoside. Inter-glycosidic NOE have provided evidence for a preferred conformation of the pseudo (1→6) dimannoside in solution. The transition state structure of the α-phenylmannose hydrolysis was optimized using the AMI method and compared to the N-benzylmannoamidine. The developing oxocarbenium ion is well matched by the mannoamidine ring but the orientation of the phenyl group in the inhibitor differs significantly from the position of the leaving group in the transition state. The use of sugar type amidines as haptens to obtain catalytic antibodies is then discussed.

     

The use of MM/QM calculations of 13C and 15N chemical shifts in the conformational analysis of alkyl substituted anilines

The calculation of the ¹³C and ¹⁵N NMR chemical shifts by a combined molecular mechanics (Pcmodel 9.1/MMFF94) and ab initio (GIAO (B3LYP/DFT, 6-31 + G(d)) procedure is used to investigate the conformations of a variety of alkyl substituted anilines. The ¹³C shifts are obtained from the GIAO isotropic shielding (Ciso) with separate references for sp³ and sp² carbons (δc = δref − Ciso). The ¹⁵N shifts are obtained similarly from the GIAO isotropic shielding (Niso) with reference to the ¹⁵N chemical shift of aniline. Comparison of the observed and calculated shifts provides information on the molecular conformations. Aniline and the 2,6-dialkylanilines exist with a rapidly inverting symmetric pyramidal nitrogen atom. The 2-alkylanilines have similar conformations with the NH₂ group tilted away from the 2-alkyl substituent. The N,N-dialkylanilines show more varied conformations. N,N-dimethylaniline has a similar structure to aniline, but N-ethyl, N-methylaniline, N,N-diethylaniline, and N,N-diisopropylaniline are conformationally mobile with two rapidly interconverting conformers. In contrast, the anilines substituted at C₂ and the nitrogen atom exist as one conformer where the steric interaction between the C₂ substituent and the N substituent determines the conformation. In 2-methyl-N-methylaniline, the nitrogen atom is pyramidal as usual with the N-methyl opposite to the 2-methyl, but in 2-methyl-N,N-dimethyl aniline, the NMe₂ group is now almost orthogonal to the phenyl plane. This is also the case with 2-methyl-N,N-diethylaniline and 2,6-diisopropyl-N,N-dimethylaniline. The comparison of the observed and calculated ¹⁵N chemical shifts confirms the above findings, in particular the pyramidal conformation of aniline and the above observations with respect to the conformations of the N,N-dialkylanilines.     

Principal component analysis of the 13C NMR spectra of enamino ketones

The ¹³C NMR spectra of eleven 3-N,N-dialkylamino-5,5-dimethylcyclohex-2-en-1-ones have been determined. The chemical shifts of the three sp² carbons and of the two methylene carbons on the cyclohexenone moiety have been subjected to factor analysis. Two factors are necessary and sufficient to account for more than 93% of the total variance. The more important axis (79%) corresponds to a factor closely related to the inductive and steric effects of the alkyl nitrogen substituents. The second parameter is more difficult to interpret and could correspond to the ‘ipso effects’ of amino groups.     

Supramolecular Ribbons. Crystal Structure and Spectroscopic Properties of 2,2′-Bipyrroyl

 A crystal structure determination of 2,2′-bipyrroyl (1; 2,2′-dipyrryl-diketone, bis (2-pyrrolyl)ethanedione) and its spectroscopic properties in solution are reported. In the crystal, 1 self-assembles via hydrogen bonding into supramolecular ribbons that extend indefinitely through the crystal lattice. The observed molecular conformation is one where each pyrrole ring and adjacent carbonyl group are co-planar (torsion angle ∼ 0.9°), with the N-H pointing in the same direction as the C=O. The two carbonyls have a transoid but not co-planar geometry with a torsion angle of ∼128°. Adjacent molecules in the crystal are linked by pairs of intermolecular hydrogen bonds, pyrrole NH to carbonyl oxygen, to form a matrix of polymeric chains that lie like neatly stacked, parallel streams of ribbons. Molecular mechanics calculations on the monomer indicate an intra-molecularly hydrogen bonded planar conformation (sp, ap, sp) at the global energy minimum. In CHCl₃, 1 is monomeric according to vapor pressure osmometry (MW _obs=179±10 vsċMW _calc=188). In THF, the measured molecular weight is 340±15, which corresponds best to one molecule of 1 solvated by two THF molecules (MW=322 for C₁₀H₈N₂O₄ċ2 C₄H₈O) rather than to a dimer.     

Supramolecular Ribbons. Crystal Structure and Spectroscopic Properties of 2,2′-Bipyrroyl

Summary.  A crystal structure determination of 2,2′-bipyrroyl (1; 2,2′-dipyrryl-diketone, bis (2-pyrrolyl)ethanedione) and its spectroscopic properties in solution are reported. In the crystal, 1 self-assembles via hydrogen bonding into supramolecular ribbons that extend indefinitely through the crystal lattice. The observed molecular conformation is one where each pyrrole ring and adjacent carbonyl group are co-planar (torsion angle ∼ 0.9°), with the N-H pointing in the same direction as the C=O. The two carbonyls have a transoid but not co-planar geometry with a torsion angle of ∼128°. Adjacent molecules in the crystal are linked by pairs of intermolecular hydrogen bonds, pyrrole NH to carbonyl oxygen, to form a matrix of polymeric chains that lie like neatly stacked, parallel streams of ribbons. Molecular mechanics calculations on the monomer indicate an intra-molecularly hydrogen bonded planar conformation (sp, ap, sp) at the global energy minimum. In CHCl₃, 1 is monomeric according to vapor pressure osmometry (MW _obs=179±10 vsċMW _calc=188). In THF, the measured molecular weight is 340±15, which corresponds best to one molecule of 1 solvated by two THF molecules (MW=322 for C₁₀H₈N₂O₄ċ2 C₄H₈O) rather than to a dimer. Received October 21, 1999. Accepted November 2, 1999     

Constrained‐Geometry Bisphosphazides Derived from 1,8‐Diazidonaphthalene: Synthesis,Spectroscopic Characteristics,Structural Features,and Theoretical Investigations

Investigations on the Staudinger reaction between 1,8‐diazidonaphthalene and phosphorous(III) building blocks, a key step in the synthesis of superbasic bisphosphazene proton sponges, yielded a set of bisphosphazides with a constrained geometry 1,8‐disubstituted naphthalene backbone. This compound class has attracted our interest not only due to their surprisingly high stability, but in particular because of their theoretically predicted basicity in the range of their bisphosphazene analogues that can be referred to the constrained geometry interaction of two highly basic nitrogen atoms. Eleven new bisphosphazides bearing simple P‐amino groups as well as P‐guanidino substituents, azaphosphatrane moieties, P₂ building blocks, or chiral P‐amino substituents derived from L ‐proline are presented. They were studied concerning their spectroscopic properties and partly also their chromophoric and structural features. In the case of the pyrrolidino‐substituted TPPN(2N₂) (TPPN=1,8‐bis(trispyrrolidinophosphazenyl)naphthalene), the stepwise nitrogen elimination is investigated theoretically and experimentally, which led to the isolation and structural characterization of TPPN(1N₂) bearing a phosphazide and a phosphazene functionality in one molecule. Attempts to protonate the obtained bisphosphazides and to prove the computationally predicted pK_BH⁺ values through NMR titration reactions resulted in their decay, which again was rationalized by theoretical calculations. Altogether we present the so far most extensive spectroscopic, structural and theoretical investigation of constrained geometry bisphosphazides and their Brønsted and Lewis basic properties.     

The effect of substituents on the conformational mobility of the heterocycle in 1,4-dihydropyrimidine and its derivatives

The equilibrium geometry of 1,4-dihydropyrimidine, 4,7-dihydro-1,2,4-triazolo[1,5-a]pyrimidine, and their alkyl (Me, Et, Prⁱ, Bu^t) and phenyl derivatives has been calculated by molecular mechanics method. The equilibrium conformation of unsubstituted molecules is planar, but it is easily transformed to the boat conformation with a small change in the conformational energy. The effect of substituents on the geometry and conformational mobility of the dihydropyrimidine ring has been studied.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1394–1397, August, 1994.     

Gas‐phase functionalized carbon‐carbon coupling reactions catalyzed by Ni (II) complexes

Gas‐phase C―C coupling reactions mediated by Ni (II) complexes were studied using a linear quadrupole ion trap mass spectrometer. Ternary nickel cationic carboxylate complexes, [(phen)Ni (OOCR¹)]⁺ (where phen = 1,10‐phenanthroline), were formed by electrospray ionization. Upon collision‐induced dissociation (CID), they extrude CO₂ forming the organometallic cation [(phen)Ni(R¹)]⁺, which undergoes gas‐phase ion‐molecule reactions (IMR) with acetate esters CH₃COOR² to yield the acetate complex [(phen)Ni (OOCCH₃)]⁺ and a C―C coupling product R¹‐R². These Ni(II)/phenanthroline‐mediated coupling reactions can be performed with a variety of carbon substituents R¹ and R² (sp³, sp², or aromatic), some of them functionalized. Reaction rates do not seem to be strongly dependent on the nature of the substituents, as sp³‐sp³ or sp²‐sp² coupling reactions proceed rapidly. Experimental results are supported by density functional theory calculations, which provide insights into the energetics associated with the C―C bond coupling step.     

Synthesis, spectroscopic characterization, crystal structures, theoretical studies, and antibacterial evaluation of two novel N-phosphinyl ureas

Abstract  

Two novel N-phosphinyl ureas containing different substituents were synthesized and characterized by ¹H, ¹³C, and ³¹P NMR, IR, UV, mass spectroscopy, and elemental analysis. The crystal structures of these compounds were determined by X-ray crystallography. The structure of one compound exhibits the presence of two independent forms of the molecule with equal occupancy in the lattice and theoretical data reveal the same stabilization energies for these conformers. The title molecules have anti conformation with respect to the C=O and P=O bonds, whereas the other compound shows syn configuration. Quantum chemical calculations were applied to clarify this conformational behavior. Furthermore, the molecular geometry and vibrational frequencies of the new derivatives in the ground state were calculated by using the Hartree–Fock (HF) and density functional method (B3LYP) with 6-31+G** and 6-311+G** basis sets and compared with experimental values. The new derivatives were additionally tested in view of their antibacterial properties.     

An axial tert‐butyl group in strained cyclohexene: X‐ray analysis and theoretical calculations of 2‐(2‐tert‐butylcyclohex‐3‐enyl)propan‐2‐ol

The structure of the title compound, C₁₃H₂₄O, (I), shows a sofa conformation of the ring with two pseudo‐axial substituents. The dihedral angle between these substituents is 131.56 (12)°. Calculations using the B3LYP/6‐31G* level of theory show two minima, one corresponding to the crystal structure and the other to a boat conformation of the ring with two equatorial substituents. The energy of this latter conformation is 17.4 kcal mol⁻¹ higher than that of (I). The molecule forms an infinite co‐operative hydrogen‐bonded chain running in the b direction.