Theoretical study of structures and properties of cyclobutadiene, cyclopentadiene and benzene and their nitrogen isoelectronic equivalents

B3LYP/aug-cc-pvDZ level of theory is applied to study the geometric structures, electronic topologies, heats of formation, hyperconjugations and steric repulsions of 27 kinds of compounds obtained by successive replacement of CH groups with nitrogen atoms in cyclobutadiene, cyclopentadiene and benzene. The results reveal that the total energy linearly decreases along with the replacement of CH groups by nitrogen atoms for the three systems. To estimate the potential of high nitrogen content high energy materials (HNC–HEMs), heats of formation are calculated by G3 method. With the increase of the number of nitrogen atoms in ring, heats of formation increase substantially. The four-membered ring system is found to have the greatest heat of formations, followed by the six-membered ring system, and then by the five-membered ring system. Especially, hexazine and tetraazacyclobutadiene have great heats of formation relative to the other compounds, which implies that they should be applicable as HNC–HEMs. In addition, our studies indicate that the relationship between the total energy or heats of formation of isomers and the position of nitrogen atoms is (ortho) meta < (ortho) para < ortho. NBO analysis shows that it is hyperconjugation, not steric repulsion that plays a key role in the relative stability of isomers.     

Comparative semiempirical and DFT study of styrylnaphthalenes and styrylquinolines and their photocyclization products

Semiempirical molecular orbital (PM3, PM6, and RM1) and density functional theory (DFT) (B3LYP/6‐31G*) studies are carried out for 1‐ and 2‐styrylnaphthalenes and their aza‐derivatives—2‐ and 4‐styrylquinolines. Relative stabilities of three isomeric forms: E‐ and Z‐isomers and the closed‐ring dihydrocyclophotoproduct (derivative of dihydrophenanthrene) are calculated. Compared to PM3, PM6 and especially RM1 understate heats of formation; in some cases, PM6 and RM1 even place Z‐isomer in energy below E‐isomer. PM3 rather close to DFT predicts heats of isomerization reaction, whereas PM6 and especially RM1 underestimate these values. Semiempirical methods in comparison with DFT markedly underestimate heats of cyclization reaction; however, reproduce trends in relative stabilities of different isomers in dependence on the structure of styrylnaphthalenes and styrylquinolines. Qualitative correlation is found between calculated relative stabilities of the closed‐ring forms (heats of cyclization reaction) and experimental data: cyclized products with low heats of cyclization are observed in steady‐state photolysis and those with high heats of cyclization are not. In the latter case, the closed‐ring compounds, if formed in the excited state, due to thermal instability decompose rapidly with ring opening in the ground state that prevents their observation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

15N and 13C NMR study of protonated monoaminopyridines in CDCl3-DMSO

The 2-, 3- and 4-amino-pyridine and their protonated forms, obtained by reaction with pyridinium chloride, were investigated by 15N NMR spectroscopy. Exhaustive evidence has been found that the protonation occurs mainly on the annular nitrogen. Protonation of 4-aminopyridine by dehydrohalogenation of 1,1,2,2-tetrachloroethane (TCE) was also studied by 13C NMR spectroscopy, which indicated that the protonation occurs via the formation of adducts.     

Electrophoretic investigation of the boron cluster anion [7-(2'-pyridyl)-nido-7,8-dicarbaundecaborate]- and its protonated zwitterionic product

ACN is a better solvent than methanol for both [NMe(4)] [7-(2'-pyridyl)-nido-7,8-C(2)B(9)H(11)] and its protonated anion. The investigated laboratory preparations of the salt and of its protonated anion are electrophoretically pure solids stable for 2 months at 4 degrees C. At a longer storage, the solid salt is more stable than the solid protonated anion. In the 40:60 v/v water-methanol solvent, decomposition products of the salt anion are detectable after one-week storage of the salt solution at 4 degrees C. The protonated anion does not decompose for almost 1 year in water-organic solutions at 4 degrees C. The exchange of the proton between the protonated anion and the solution is reversible and fast at room temperature. The pH dependence of the mobility of the [7-(2(-pyridyl)-nido-7,8-C(2)B(9)H(11)](-) anion reveals that the basicity of the nitrogen atom in the pyridine ring is not significantly affected by the bonding of the pyridyl group to the nido-7,8-C(2)B(9)H(11) cluster in position 7 and that the proton from the solution is accepted by the nitrogen atom in the 2-pyridyl ring. The UV-spectra of the salt and of its protonated anion indicate that the accepted proton is probably slightly shifted to the open face of the nido-7,8-C(2)B(9)H(11) cluster. The [1](-) is chiral.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

Non-empirical SCF MO studies on the protonation of biopolymer constituents

Proton affinities of several of the tautomeric forms of cytosine and thymine have been calculated using theab initio Hartree-Fock-Roothaan SCF method. Several of the most stable protonated forms may be obtained by direct protonation from one of the two most stable neutral forms. The calculated total energies do not exclude the possibility of the coexistence of several protonated forms in acidic solutions.     

Tautomeric conjugate acids of 2-aminopyrroles: effect of substituents, solvation and cosolute

The tautomeric preferences of the conjugated acids of 2-aminopyrrole derivatives have been examined both in the gas phase and in aqueous solution by using a combination of quantum mechanical, self-consistent reaction field and Monte Carlo–free-energy perturbation methods. The results show that the nature of substituents, the solvent and the presence of cosolute are relevant factors in modulating the relative stability between the tautomeric conjugate acids protonated at the heterocyclic ring and at the exocyclic amino nitrogen. Thus, attachment of electron-withdrawing groups to the ring, solvation in polar solvents, and the presence of negatively charged cosolutes tend to favor protonation at the exocyclic amino nitrogen. Nevertheless, none of these factors alone suffice to change the tautomeric preference for the ring-protonated forms. The results point out that the concerted occurrence of the three factors is necessary to shift the tautomeric preference towards the conjugated species protonated at the exocyclic nitrogen.Contribution to the Jacopo Tomasi Honorary Issue     

Copper(II) complexes of quinoline polyazamacrocyclic scorpiand-type ligands: X-ray, equilibrium and kinetic studies

The formation of Cu(II) complexes with two isomeric quinoline-containing scorpiand-type ligands has been studied. The ligands have a tetraazapyridinophane core appended with an ethylamino tail including 2-quinoline (L1) or 4-quinoline (L2) functionalities. Potentiometric studies indicate the formation of stable CuL(2+) species with both ligands, the L1 complex being 3-4 log units more stable than the L2 complex. The crystal structure of [Cu(L1)](ClO(4))(2)·H(2)O shows that the coordination geometry around the Cu(2+) ions is distorted octahedral with significant axial elongation; the four Cu-N distances in the equatorial plane vary from 1.976 to 2.183 ?, while the axial distances are of 2.276 and 2.309 ?. The lower stability of the CuL2(2+) complex and its capability of forming protonated and hydroxo complexes suggest a penta-dentate coordination of the ligand, in agreement with the type of substitution at the quinoline ring. Kinetic studies on complex formation can be interpreted by considering that initial coordination of L1 and L2 takes place through the nitrogen atom in the quinoline ring. This is followed by coordination of the remaining nitrogen atoms, in a process that is faster in the L1 complex probably because substitution at the quinoline ring facilitates the reorganization. Kinetic studies on complex decomposition provide clear evidence on the occurrence of the molecular motion typical of scorpiands in the case of the L2 complex, for which decomposition starts with a very fast process (sub-millisecond timescale) that involves a shift in the absorption band from 643 to 690 nm.     

Protonation Sites in Gaseous Pyrrole and Imidazole: A Neutralization–Reionization and ab initio Study

Mild gas-phase acids C₄H₉⁺ and NH₄⁺ protonate pyrrole at C-2 and C-3 but not at the nitrogen atom, as determined by deuterium labeling and neutralization–reionization mass spectrometry. Proton affinities in pyrrole are calculated by MP2/6–311G(2d, p) as 866, 845 and 786 kJ mol^-1 for protonation at C-2, C-3 and N, respectively. Vertical neutralization of protonated pyrrole generates bound radicals that in part dissociate by loss of hydrogen atoms. Unimolecular loss of hydrogen atom from C-2-and C-3-protonated pyrrole cations is preceded by proton migration in the ring. Protonation of gaseous imidazole is predicted to occur exclusively at the N-3 imine nitrogen to yield a stable aromatic cation. Proton affinities in imidazole are calculated as 941, 804, 791, 791 and 724 for the N-3, C-4, C-2, C-5 and N-1 positions, respectively. Radicals derived from protonated imidazole are only weakly bound. Vertical neutralization of N-3-protonated imidazole is accompanied by large Franck–Condon effects which deposit on average 183 kJ mol^-1 vibrational energy in the radicals formed. The radicals dissociate unimolecularly by loss of hydrogen atom, which involves both direct N-H bond cleavage and isomerization to the more stable C-2 H-isomer. Potential energy barriers to isomerizations and dissociations in protonated pyrrole and imidazole isomers and their radicals were investigated by ab initio calculations.     

MNDO calculations on borazine derivatives. The substitution of one [HNBH] fragment for one [HCCH] fragment in benzene to form the azaborines and the nature of the cyclotrimer of the 1,2-isomer

The three azaborine isomers with the formula C₄H₆BN, 1,2-, 1,4-, and 1,3-azaborine ( I , II , and III ), have been examined using MNDO (m odified n eglect of d iatomic o verlap) calculations. The most stable azaborine was I (heat of formation -8.147 kcal/mol), followed by II (+11.60 kcal/mol) and III (+16.64 kcal/mol). Qualitatively, although the π- and π*-orbitals calculated for the azaborines exhibited an ordering similar to that in benzene and borazine, the HOMO/LUMO energy differences (9.27, 9.68, and 8.44 eV, respectively) were smaller than was the difference calculated for borazine (12.81 eV), but of the same magnitude as the difference for benzene (9.76 eV). With the exception of borazine, each molecule had a π-orbital for the HOMO and a π*-orbital for the LUMO ; borazine's LUMO was a π*-orbital. The calculated shapes and atomic contributions for the π-and π*-orbitals of the azaborines were best described as “hybrids” of the π- and π*-orbitals of benzene and borazine. As was observed for the π- and π*-orbitals of borazine, the azaborines exhibited increased orbital density at the nitrogen atom in the π-bonding orbitals and at boron in the π-antibonding orbitals, as would be predicted from electronegativity considerations. Although I and II exhibited significant double- and single-bond localization, all of the ring bonds in III were delocalized. The delocalization in III was not uniform but, rather, resembled two inequivalent fused allyl systems. The cyclotrimer ( IV ) of 1,2-azaborine (heat of formation -44.07 kcal/mol), based purely on thermodynamic considerations, was predicted to form spontaneously from three monomer molecules with the concurrent loss of three molecules of dihydrogen. The cyclotrimers that could theoretically be produced from 1,2-azaborine without the loss of dihydrogen ( IVc and IVt ) were each calculated to be less stable (heats of formation +24.45, and +33.29 kcal/mol, respectively) than was the experimentally observed IV . The carbon molecules triphenylene ( TP ) and cis- and trans-4a,4b,8a,8b,12a,12b- hexahydrotriphenylene ( TPc and TPt ) (heats of formation +76.79, +101.6, and +103.1 kcal/mol, respectively) were each calculated to be less stable than were the azaborine cyclotrimer analogs, as was observed in comparisons of benzene with the azaborines and borazine.     

Studies of intramolecular hydrogen bonding in protonated and non-protonated hexahydropyridinobenzodioxins

The conformational stability of hexahydropyridobenzodioxin and related derivatives in both protonated and non-protonated forms have been investigated by means of ab initio molecular orbital methods as well as semi-empirical AM1 and PM3 methods. One of the cis conformers (cis2e) has been found to be most stable due to the formation of an intramolecular hydrogen bond, other conformers including the trans isomer cannot form this interaction but are of different stability because of the orientation of the polar oxygens and the nitrogen. The effect of the intramolecular hydrogen bonding on the stability of hexahydropyridobenzodioxin and its methylated derivatives has been examined using various basis sets levels. In protonated form, both the semi-empirical and ab initio calculations give excellent agreement in energetic order; however, different orderings of conformer stabilities are observed by different computational methods in non-protonated form. The results provide insight into the intramolecular hydrogen bonding in computational studies of biologically important molecules.     

An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple‐photon dissociation (IRMPD) spectroscopy and electronic‐structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free‐electron laser (FEL) and an electrospray‐ion‐trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6‐311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the α‐amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol^?1) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side‐chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the α‐amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol^?1 higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760–1800 cm^?1 is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.     

The kinetics of the solvolysis of propylene and cyclopropane in concentrated aqueous sulfuric acid relative energies of the 2-propyl cation and protonated cyclopropane

The rates of solvolysis of propylene and cyclopropane in 6.49M H₂SO₄ have been measured as a function of temperature. From the data, calculations of the relative heats of formation in solution of the 2-propyl cation and protonated cyclopropane have been made. The heat of formation of protonated cyclopropane has been found to be 6.4 kcal/mol greater than that of the 2-propyl cation. The implications of this result are discussed.     

Role of the pyridine nitrogen in pyridoxal 5'-phosphate catalysis: activity of three classes of PLP enzymes reconstituted with deazapyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (PLP; vitamin B(6))-catalyzed reactions have been well studied, both on enzymes and in solution, due to the variety of important reactions this cofactor catalyzes in nitrogen metabolism. Three functional groups are central to PLP catalysis: the C4' aldehyde, the O3' phenol, and the N1 pyridine nitrogen. In the literature, the pyridine nitrogen has traditionally been assumed to be protonated in enzyme active sites, with the protonated pyridine ring providing resonance stabilization of carbanionic intermediates. This assumption is certainly correct for some PLP enzymes, but the structures of other active sites are incompatible with protonation of N1, and, consequently, these enzymes are expected to use PLP in the N1-unprotonated form. For example, aspartate aminotransferase protonates the pyridine nitrogen for catalysis of transamination, while both alanine racemase and O-acetylserine sulfhydrylase are expected to maintain N1 in the unprotonated, formally neutral state for catalysis of racemization and β-elimination. Herein, kinetic results for these three enzymes reconstituted with 1-deazapyridoxal 5'-phosphate, an isosteric analogue of PLP lacking the pyridine nitrogen, are compared to those for the PLP enzyme forms. They demonstrate that the pyridine nitrogen is vital to the 1,3-prototropic shift central to transamination, but not to reactions catalyzed by alanine racemase or O-acetylserine sulfhydrylase. Not all PLP enzymes require the electrophilicity of a protonated pyridine ring to enable formation of carbanionic intermediates. It is proposed that modulation of cofactor electrophilicity plays a central role in controlling reaction specificity in PLP enzymes.     

Acylhydrazone Subunits as a Proton Cargo Delivery System in 7-Hydroxyquinoline

The reimagined concept of long-range tautomeric proton transfer using crane subunits is shown by designing and synthesising two new acylhydrazones containing a 7-hydroxyquinoline (7-OHQ) platform. The acylhydrazone subunits attached to the 7-OHQ at the 8th position act as crane arms for delivering proton cargo to the quinoline nitrogen. Light-induced tautomerization to their keto forms leads to Z/E isomerization of the C=C axle bond, followed by proton delivery to the quinoline nitrogen by the formation of covalent or hydrogen bonds. The axle‘s being either an imine or ketimine bond is the structural difference between the studied compounds. The −CH₃ group in the latter provides steric strain, resulting in different proton transport pathways. Both compounds show long thermal stability in the switched state, which creates a tuneable action of bidirectional proton cargo transport by using different wavelengths of irradiation. Upon the addition of acid, the quinoline nitrogen is protonated; this results in E/Z configuration switching of the acylhydrazone subunits. This was proven by single-crystal X-ray structure analysis and NMR spectroscopy.     

First Principles Study of Al-Li Intermetallic Compounds

The structural properties, heats of formation, elastic properties, and electronic structures of four compositions of binary Al-Li intermetallics, Al₃Li, AlLi, Al₂Li₃, and Al₄Li₉, are ana-lyzed in detail by using density functional theory. The calculated formation heats indicate a strong chemical interaction between Al and Li for all the Al-Li intermetallics. In partic-ular, in the Li-rich Al-Li compounds, the thermodynamic stability of intermetallics linearly decreases with increasing concentration of Li. According to the computational single crystal elastic constants, all the four Al-Li intermetallic compounds considered here are mechani-cally stable. The polycrystalline elastic modulus and Poisson's ratio have been deduced by using Voigt, Reuss, and Hill approximations, and the calculated ratios of bulk modulus to shear modulus indicate that the four compositions of binary Al-Li intermetallics are brittle materials. With the increase of Li concentration, the bulk modulus of Al-Li intermetallics decreases in a linear manner.     

New molecular species of potential interest to interstellar chemistry: A theoretical study of MgSiN, MgNSi and related species

An ab initio study has been performed to characterize the probable magnesium containing interstellar species MgSiN, MgNSi and their ionized, hydrogenated and protonated forms. We are able to locate four protonated and four hydrogenated magnesium species with planar geometry at MP2(Full)/cc-pVTZ level of theory. MgNSi is found to be more stable than MgSiN and their connecting transition state is also located. The ionization potential for both MgSiN and MgNSi are small, 7.91 eV and 7.01 eV, respectively. All possible protonation sites are considered for these two species but the preferred protonation sites are found to be silicon for MgNSi and nitrogen for MgSiN. Enthalpies of formation at 0 K (Δ_fH°) and bond dissociation energies (D^o(X–Y)) are computed for all the species at G3 and G3MP2 level of theory. Finally, the reaction enthalpies for ion–molecule processes are calculated and most of the processes are found to be exothermic and hence thermodynamically favorable in interstellar region.     

MINDO-SCF-MO-berechnung der cis-trans-isomerisierung von N-methyl- und N-phenylazomethin

MINDO/2-SCF-MO calculations for the ground state properties of N-methyl- and N-phenyl-azomethin have been carried out. The calculated rotation barrier for the methyl group in N-methyl-azomethin was 0·8 kcal/mol, the eclipsed conformation being most stable. The calculated rotation barrier about the CN bond in the protonated methylazomethin was 27·9 kcal/mol. MINDO/1-SCF-MO treatment for the N-inversion barrier of the unprotonated species yielded 13·00 kcal/mol. Similar MINDO/2 calculations for N-phenylazomethin yielded 4·0 kcal/mol for the rotation barrier of the phenyl ring around the CN= bond, the perpendicular conformation of the ring to the CNC plane being most stable. For the corresponding N protonated derivative the value 27·3 kcal/mol was calculated for the rotation barrier around the CN bond. MINDO/1 treatment yielded an inversion barrier of 14·0 kcal/mol for N-phenylazomethin.     

1,2,3‐Triazolo[4,5,‐e]furazano[3,4,‐b]pyrazine 6‐Oxide—A Fused Heterocycle with a Roving Hydrogen Forms a New Class of Insensitive Energetic Materials

The straightforward synthesis and energetic properties of a new class of energetic materials, 1,2,3‐triazolo‐ [4,5‐e]furazano[3,4‐b]pyrazine 6‐oxide and its energetic salts are described. They were characterized by IR and multinuclear NMR spectroscopy, elemental analysis, differential scanning calorimetry, and single‐crystal X‐ray diffraction are given. The X‐ray structures show that in the title compound, the hydrogen atom is bonded to the nitrogen in the pyrazine ring; however, in the salts, the negative charge is associated with the triazole nitrogen. Heats of formation for all compounds were calculated with the G2 method and then combined with experimentally determined densities to obtain detonation pressures (P) and velocities (D) by using EXPLO5 program. These new materials exhibit good densities and thermal stabilities, high heats of formation, acceptable detonation properties, and are insensitive to impact.     

Spiropyrans based on 5,1 0-dimethyl-4, 9-diazapyrene

The corresponding mono- and displropyrans, the cyclic forms of which are more stable than the analogous compounds of the phenanthridine series, were obtained by condensation of mono- and diquaternary salts of 5,10-dimethyl-4,9-diazapyrene with aromatic o-hydroxy aldehydes. Successive opening of the pyran rings of the dispiropyrans occurs in acetic acid solutions, whereas the monospiropyrans, after opening of the pyran ring, are protonated at the nitrogen atom in the 9 position.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 321–327, March, 1976.