Hydrogen bonding in 2‐amino‐4,6‐dimethoxypyrimidine, 2‐benzylamino‐4,6‐bis(benzyloxy)pyrimidine and 2‐amino‐4,6‐bis(N‐pyrrolidino)pyrimidine: chains of fused rings and a centrosymmetric dimer

Molecules of 2‐amino‐4,6‐di­methoxy­pyrimidine, C₆H₉N₃O₂, (I), are linked by two N—H?N hydrogen bonds [H?N 2.23 and 2.50 Å, N?N 3.106 (2) and 3.261 (2) Å, and N—H?N 171 and 145°] into a chain of fused rings, where alternate rings are generated by centres of inversion and twofold rotation axes. Adjacent chains are linked by aromatic π–π‐stacking interactions to form a three‐dimensional framework. In 2‐­benzylamino‐4,6‐bis(benzyloxy)pyrimidine, C₂₅H₂₃N₃O₂, (II), the mol­ecules are linked into centrosymmetric R(8) dimers by paired N—H?N hydrogen bonds [H?N 2.13 Å, N?N 2.997 (2) Å and N—H?N 170°]. Molecules of 2‐amino‐4,6‐bis(N‐pyrrolidino)­pyrimidine, C₁₂H₁₉N₅, (III), are linked by two N—H?N hydrogen bonds [H?N 2.34 and 2.38 Å, N?N 3.186 (2) and 3.254 (2) Å, and N—H?N 163 and 170°] into a chain of fused rings similar to that in (I).     

Two polymorphs,with Z′ = 1 and 2, of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine in P21/c,and 2‐amino‐4‐chloro‐6‐piperidino­pyrimidine,which is isomorphous and almost isostructural with the Z′ = 2 polymorph

Crystallization of 2‐amino‐4‐chloro‐6‐morpholino­pyrimidine, C₈H₁₁ClN₄O, (I), yields two polymorphs, both with space group P2₁/c, having Z′ = 1 (from diethyl ether solution) and Z′ = 2 (from di­chloro­methane solution), denoted (Ia) and (Ib), respectively. In polymorph (Ia), the mol­ecules are linked by an N—H⋯O and an N—H⋯N hydrogen bond into sheets built from alternating R(8) and R(40) rings. In polymorph (Ib), one mol­ecule acts as a triple acceptor of hydrogen bonds and the other acts as a single acceptor; one N—H⋯O and three N—H⋯N hydrogen bonds link the mol­ecules in a complex chain containing two types of R(8) and one type of R(18) ring. 2‐Amino‐4‐chloro‐6‐piperidino­pyrimidine, C₉H₁₃ClN₄, (II), which is isomorphous with polymorph (Ib), also has Z′ = 2 in P2₁/c, and the mol­ecules are linked by three N—­H⋯N hydrogen bonds into a centrosymmetric four‐mol­ecule aggregate containing three R(8) rings.     

Kinetic study of the gas‐phase photolysis and OH radical reaction of E,Z‐ and E,E‐2,4‐Hexadienedial

Unsaturated 1,6‐dicarbonyls like 2,4‐hexadienedial are ring opening products in the OH initiated photo‐oxidation of aromatic hydrocarbons. In the present study, the photolysis of E,Z‐ and E,E‐2,4‐hexadienedial has been investigated under natural sunlight conditions in a large volume outdoor reaction chamber. In the case of the E,Z‐isomer, an extremely rapid isomerization into the E,E‐form was observed. The photoisomerization frequency, relative to that of NO₂, was found to be J(E,Z‐2,4‐hexadienedial)/J(NO₂) = (0.148 ± 0.012). A more complex photolysis behavior was observed for E,E‐2,4‐hexadienedial. Here, a fast equilibrium preceded a comparably slow photolysis. For the equilibrium reaction, relative frequencies of J(E,E‐2,4‐hexadienedial → EQUI)/J(NO₂) = (0.113 ± 0.009) and J(EQUI → E,E‐2,4‐hexadienedial)/J(NO₂) = (0.192 ± 0.016) were obtained, giving an equilibrium constant of K = (0.59 ± 0.07). For the photolysis frequencies, ratios of J(E,E‐2,4‐hexadienedial → products)/J(NO₂) = J(EQUI → products)/J(NO₂) = (1.22 ± 0.45)·10⁻² were determined. Qualitative aerosol measurements during the experiments showed that the photolysis of 2,4‐hexadienedials is a source of secondary organic aerosol. In addition to the photolysis study, OH radical reaction rate constants were determined, values of (7.4 ± 1.9)·10⁻¹¹ and (7.6 ± 0.8)·10⁻¹¹ cm³ s⁻¹ were obtained for E,Z‐ and E,E‐2,4‐hexadienedial, respectively. The results indicate that the dominant fate of E,Z‐2,4‐hexadienedial in the atmosphere will be photoisomerization, while for E,E‐2,4‐hexadienedial, both photolysis and OH radical reaction will be important sinks. © 1999 John Wiley & Sons, Inc. Int J Chem Kinet 31: 689–697, 1999     

A facile synthesis of stable phosphorus ylides derived from 3,6‐dibromocarbazole and kinetic investigation of the reactions by UV spectrophotometry technique

Stable crystalline phosphorus ylides were obtained in excellent yields from the 1:1:1 addition reaction between triphenylphosphine and dialkyl acetylenedicarboxylates, in the presence of NH‐acid, such as 3,6‐dibromocarbazole. These stable ylides exist in solution as a mixture of two geometrical isomers as a result of restricted rotation around the carbon–carbon partial double bond, resulting from the conjugation of the ylide moiety with the adjacent carbonyl group. To determine the kinetic parameters of the reactions, they were monitored by UV spectrophotometry. The second‐order fits were drawn, and the values of the second‐order rate constant (k₂) were calculated using standard equations within the program. At the temperature range studied, the dependence of the second‐order rate constant (ln k₂) on reciprocal temperature was in a good agreement with the Arrhenius equation. This provided the relevant plots to calculate the activation energy of all reactions. Furthermore, useful information was obtained from studies of the effect of solvent, structure of reactants (different alkyl groups within the dialkyl acetylenedicarboxylates), and also the concentration of reactants on the rate of reactions. The proposed mechanism was confirmed according to the obtained results and a steady‐state approximation and the first step (k₂) of reaction was recognized as a rate‐determining step on the basis of the experimental data. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:723–732, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20501     

Unequivocal total assignment of 13C and 1H NMR spectra of some pyrido[1,2‐a]pyrimidine derivatives by 2D‐NMR

We report the total assignments of the ¹³C and ¹H NMR spectra of some 4‐methyl‐2‐oxo‐(2H)‐pyrido[1,2‐a]pyrimidine and 2‐methyl‐4‐oxo‐(4H)‐pyrido[1,2‐a]pyrimidine derivatives. The products were characterized by ¹H and ¹³C NMR and reported data for similar compounds. No comparative data for the two sets of isomeric compounds with respect to ¹³C and ¹H NMR have been reported to date. We made some detailed studies of the 2D NMR spectra of these compounds and observed that assignments made for non‐protonated carbon atoms by us and those reported in the literature for similar compounds need correction. The revised assignments were made on the basis of heteronuclear single quantum correlation (HSQC) and heteronuclear multiple bond correlation (HMBC) techniques. Copyright © 2003 John Wiley & Sons, Ltd.     

Structural,theoretical and multinuclear NMR study of mercury(II) complexes of phosphorus ylides: Mono and binuclear complexes

Reaction of phosphorus ylide Ph₃PCHC(O)C₆H₄Cl (Y₁) with HgX₂ (X = Cl, Br and I) and ylide (p-tolyl)₃PCHC(O)CH₃ (Y₂) with HgI₂ in equimolar ratios using methanol as solvent leads to binuclear products. The bridge-splitting reaction of binuclear complex [(Y₁) · HgCl₂]₂ by DMSO yields a mononuclear complex containing DMSO as ligand. O-coordination of DMSO is revealed by single crystal X-ray analysis in mononuclear complex of [(Y₁) · HgCl₂ · DMSO]. C-coordination of ylides is confirmed by X-ray structure of binuclear complex [(Y₂) · HgI₂]₂. Characterization of the obtained compounds was also performed by elemental analysis, IR, ¹H, ³¹P, and ¹³C NMR. Theoretical studies on mercury(II) complexes of Y₁ show that formation of mononuclear complexes in DMSO solution in which DMSO acts as a ligand, energetically is more favorable than that of binuclear complexes.     

Experimental and theoretical study of the homogeneous,unimolecular gas‐phase elimination kinetics of 2‐furoic acid

The kinetics of the gas‐phase elimination kinetics of CO₂ from furoic acid was determined in a static system over the temperature range 415–455°C and pressure range 20–50 Torr. The products are furan and carbon dioxide. The reaction, which is carried out in vessels seasoned with allyl bromide and in the presence of the free‐radical suppressor toluene and/or propene, is homogeneous, unimolecular, and follows a first‐order rate law. The observed rate coefficient is expressed by the following Arrhenius equation: log k₁(s^?1) = (13.28 ± 0.16) ? (220.5 ± 2.1) kJ mol^?1 (2.303 RT)^?1. Theoretical studies carried out at the B3LYP/6‐31++G** computational level suggest two possible mechanisms according to the kinetics and thermodynamic parameters calculated compared with experimental values. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 298–306, 2007     

Hydrogen‐bonded supramolecular motifs in 2‐amino‐4,6‐dimethoxypyrimidinium picrate and pyrimethaminium picrate dimethyl sulfoxide solvate

In the crystal structures of 2‐amino‐4,6‐dimethoxypyrimidinium 2,4,6‐trinitrophenolate (picrate), C₆H₁₀N₃O₂⁺·C₆H₂N₃O₇⁻, (I), and 2,4‐diamino‐5‐(4‐chlorophenyl)‐6‐ethylpyrimidin‐1‐ium (pyrimethaminium or PMN) picrate dimethyl sulfoxide solvate, C₁₂H₁₄ClN₄⁺·C₆H₂N₃O₇⁻·C₂H₆OS, (II), the 2‐amino‐4,6‐dimethoxypyrimidine and PMN cations are protonated at one of the pyrimidine N atoms. The picrate anion interacts with the protonated cations through bifurcated N—H...O hydrogen bonds, forming R₂¹(6) and R₁²(6) ring motifs. In (I), Z′ = 2. In (II), two inversion‐related PMN cations are connected through a pair of N—H...N hydrogen bonds involving the 4‐amino group and the uncharged N atom of the pyrimidine ring, forming a cyclic hydrogen‐bonded R₂²(8) motif. In addition to the pairing, the O atom of the dimethyl sulfoxide solvent molecule bridges the 2‐amino and 4‐amino groups on both sides of the paired bases, resulting in a self‐complementary …DADA… array of quadruple hydrogen‐bonding patterns.     

1H NMR analysis of O‐methyl‐inositol isomers: a joint experimental and theoretical study

Density functional theory (DFT) calculations of ¹H NMR chemical shifts for l ‐quebrachitol isomers were performed using the B3LYP functional employing the 6‐31G(d,p) and 6‐311 + G(2d,p) basis sets. The effect of the solvent on the B3LYP‐calculated NMR spectrum was accounted for using the polarizable continuum model. Comparison is made with experimental ¹H NMR spectroscopic data, which shed light on the average uncertainty present in DFT calculations of chemical shifts and showed that the best match between experimental and theoretical B3LYP ¹H NMR profiles is a good strategy to assign the molecular structure present in the sample handled in the experimental measurements. Among four plausible O‐methyl‐inositol isomers, the l ‐quebrachitol 2a structure was unambiguously assigned based only on the comparative analysis of experimental and theoretical ¹H NMR chemical shift data. The B3LYP infrared (IR) spectrum was also calculated for the four isomers and compared with the experimental data, with analysis of the theoretical IR profiles corroborating assignment of the 2a structure. Therefore, it is confirmed in this study that a combined experimental/DFT spectroscopic investigation is a powerful tool in structural/conformational analysis studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Theoretical investigation of solvent effects on tautomeric equilibrium of 2‐diazo‐4,6‐dinitrophenol

The density functional theory has been used to study the tautomeric equilibrium of 2‐diazo‐4,6‐dinitrophenol(DDNP) in the gas phase and in 14 solvents at the B3LYP/6‐31G* level. The solvent effects on the tautomeric equilibria were investigated by the self‐consistent reaction field theory (SCRF) based on conductor polarized continuum model (CPCM) in apolar and polar solvents and by the hybrid continuum‐discrete model in protic solvent, respectively. Solvent effects on the computed molecular properties, such as molecular geometries, dipole moments, E_LUMO, E_HOMO, total energies for DDNP tautomers and transition state, tautomerization energies and solvation energies have been found to be evident. The tautomeric equilibrium of DDNP is solvent‐dependent to a certain extent. The tautomer I (cyclic azoxy form) is preferred in the gas phase, while in nonpolar solvents tautomer I and II (quinold form) exist in comparable amounts, and in highly polar solvents, the tautomeric equilibrium is shifted in favor of the more polar tautomer II . © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Experimental and theoretical IR,Raman, NMR spectra of 2‐, 3‐, and 4‐nitrobenzoic acids

The influence of the position of nitro group toward the carboxylic group on the vibration structure of the molecule was estimated. Optimized geometrical structures were calculated (HF, B3PW91, B3LYP). Experimental and theoretical FT‐IR, FT‐Raman, and nuclear magnetic resonance (NMR) spectra of the title compounds were recorded and analyzed. The most important vibrational bands of nitro and carboxyl groups and the benzene ring were assigned. Wavenumbers and intensities for the three acids studied were compared and discussed. Data of chemical shifts in ¹H and ¹³C NMR spectra of 2‐, 3‐, and 4‐nitrobenzoic acids were analyzed in comparison with benzoic acid molecule. The calculated parameters are compared with experimental characteristics of these molecules. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Complete NMR assignment of (+)‐10β,14‐dihydroxy‐allo‐aromadendrane

The assignment of ¹H and ¹³C NMR of the sesquiterpene (+)‐10β,14‐dihydroxy‐allo‐aromadendrane by means of two‐dimensional NMR is reported. Copyright © 2003 John Wiley & Sons, Ltd.     

Tautomeric behaviour and isotopic multiplets in the 13C NMR spectra of partially deuterated 5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones and 5‐arylazo‐2‐thioxo‐pyrimidine (1H,3H,5H)‐4,6‐diones—evidence for elucidation of tautomeric forms

NMR spectra of the synthesized azo dyes, 5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones (5a–g), 1,3‐dimethyl‐5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones (6a–g), and 5‐arylazo‐2‐thioxo‐pyrimidine (1H,3H,5H)‐4,6‐diones (7a–g) were studied in (CD₃)₂SO (three drops of CD₃OD were added into solutions of the dyes in two different concentrations). All dyes showed intramolecular hydrogen bonding. Dyes 5a–7a showed bifurcated intramolecular hydrogen bonds. Tautomeric behaviours of some of N‐methylated azo dyes (6a‐g) were studied in two different concentrations. The solvent–substrate proton exchange of dyes 5a–d, 6a and 7a–e was examined in presence of three drops of CD₃OD. The dyes which were soluble in (CD₃)₂SO containing CD₃OD showed isotopic splitting (β‐isotope effect) in the ¹³C NMR spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

2‐(2′‐Pyridyl)‐4,6‐diphenylphosphinine versus 2‐(2′‐Pyridyl)‐4,6‐diphenylpyridine: Synthesis,Characterization, and Reactivity of Cationic RhIII and IrIII Complexes Based on Aromatic Phosphorus Heterocycles

The bidentate P,N hybrid ligand 1 allows access for the first time to novel cationic phosphinine‐based Rh^III and Ir^III complexes, broadening significantly the scope of low‐coordinate aromatic phosphorus heterocycles for potential applications. The coordination chemistry of 1 towards Rh^III and Ir^III was investigated and compared with the analogous 2,2′‐bipyridine derivative, 2‐(2′‐pyridyl)‐4,6‐diphenylpyridine ( 2 ), which showed significant differences. The molecular structures of [RhCl(Cp*)( 1 )]Cl and [IrCl(Cp*)( 1 )]Cl (Cp*=pentamethylcyclopentadienyl) were determined by means of X‐ray diffraction and confirm the mononuclear nature of the λ³‐phosphinine–Rh^III and Ir^III complexes. In contrast, a different reactivity and coordination behavior was found for the nitrogen analogue 2 , especially towards Rh^III as a bimetallic ion pair [RhCl(Cp*)( 2 )]⁺[RhCl₃(Cp*)]^? is formed rather than a mononuclear coordination compound. [RhCl(Cp*)( 1 )]Cl and [IrCl(Cp*)( 1 )]Cl react with water regio‐ and diastereoselectively at the external P?C double bond, leading exclusively to the anti‐addition products [MCl(Cp*)( 1 H ? OH)]Cl as confirmed by X‐ray crystal‐structure determination.