Formamide dimers: a computational and matrix isolation study

The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.     

Vibrational spectrum of m-benzyne: a matrix isolation and computational study

m-Benzyne (2) was generated in low-temperature matrices and IR spectroscopically characterized from four different precursors. To assign the IR absorptions, the perdeuterated derivative 2-d(4) was also investigated. By comparison with CCSD(T) calculations all vibrations between 200 and 2500 cm(-)(1) with a predicted relative intensity >2% could be assigned. All experimental and theoretical results are in accordance with a biradicaloid structure for 2, while there is no evidence for a bicyclic closed-shell structure. While benzyne 2 is stable under the conditions of matrix isolation at low temperature, flash vacuum pyrolysis at high temperatures or UV irradiation results in the rearrangement to cis-enediyne. A mechanism involving ring opening accompanied by hydrogen migration is proposed.     

The phenoxyl radical-water complex--a matrix isolation and computational study

The phenoxyl radical 1 was generated in high yields by flash vacuum pyrolysis of allyl phenyl ether 2 with subsequent trapping of the products in argon at 3 K. In water-doped argon matrices, an OH···O complex between 1 and water is formed that could be characterized by IR spectroscopy. Several isotopomers of the complex were generated, and the IR spectra compared to results of density functional theory calculations. Other dimers between 1 and water were not found under these conditions. QM/MM calculations in simulated argon matrices reveal that an OH···π complex is unstable even at a time scale of picoseconds. This finding has implications on the related interaction between the tyrosyl radical and the water in biological systems.     

H-bonded clusters in the trimethylamine/water system: a matrix isolation and computational study

The environmentally important interaction products of trimethylamine (TMA) and water molecules have been observed by Matrix Isolation Fourier Transform Infrared Spectroscopy (MIS-FTIR). Infrared spectra of solid argon matrix layers, in which both TMA and H(2)O molecules were entrapped as impurities, were analyzed for bands in the ν(O-H) region, not seen in matrix layers containing either of the parent molecules alone. Results were interpreted on the basis of the emergence of several spectral band pairs and their red shifts from the position of the matrix isolated H(2)O monomers as compared to semiempirically scaled frequencies from the B3LYP/aug-cc-pVTZ calculations and empirical correlations with a large body of data on H-bonded complexes. Bands were assigned to a complex cluster of two TMA molecules flanking a closed ring of four H-bonded H(2)O molecules. The formation of this cluster is argued to be formed in the vapor phase (as opposed to being a result of diffusion of the trapped species) and is related to its large stabilization energy (enthalpy) because of strong cooperative effects in its H-bond system.     

A computational modeling study of the low-temperature pyrolysis of n-alkanes; mechanisms of propane,n-butane,and n-pentane pyrolyses

The mechanisms of the pyrolyses of the n-alkanes C₃H₈, n-C₄H₁₀, and n-C₅H₁₂ at temperatures between 390 and 560°C have been studied by the construction and evaluation of sets of several hundred reactions. Rate parameter values were assigned using literature data and calculated estimates. Time-dependent numerical solutions were computed for the experimental conditions of several rate and product studies reported in the literature. The comparisons of these a priori computations with experiment show excellent agreement for propane and agreement for butane and pentane within the estimated error limits of the assigned rate parameters. These results demonstrate that the general “state of knowledge” of the mechanism of alkane pyrolysis, namely, the reactions and their rate parameters, is such that reasonable a priori predictions of experimental results can be made. Discussions of the major stepwise processes in the pyrolyses are presented, and the importance of allyl radicals in termination is demonstrated.     

Molecular energetics of cytosine revisited: a joint computational and experimental study

A static bomb calorimeter has been used to measure the standard molar energy of combustion, in oxygen, at T = 298.15 K, of a commercial sample of cytosine. From this energy, the standard (p degrees = 0.1 MPa) molar enthalpy of formation in the crystalline state was derived as -(221.9 +/- 1.7) kJ.mol(-1). This value confirms one experimental value already published in the literature but differs from another literature value by 13.5 kJ.mol(-1). Using the present standard molar enthalpy of formation in the condensed phase and the enthalpy of sublimation due to Burkinshaw and Mortimer [J. Chem. Soc., Dalton Trans. 1984, 75], (155.0 +/- 3.0) kJ.mol(-1), results in a value for the gas-phase standard molar enthalpy of formation for cytosine of -66.9 kJ.mol(-1). A similar value, -65.1 kJ.mol(-1), has been estimated after G3MP2B3 calculations combined with the reaction of atomization on three different tautomers of cytosine. In agreement with experimental evidence, the hydroxy-amino tautomer is the most stable form of cytosine in the gas phase. The enthalpies of formation of the other two tautomers were also estimated as -60.7 kJ.mol(-1) and -57.2 kJ.mol(-1) for the oxo-amino and oxo-imino tautomers, respectively. The same composite approach was also used to compute other thermochemical data, which is difficult to be measured experimentally, such as C-H, N-H, and O-H bond dissociation enthalpies, gas-phase acidities, and ionization enthalpies.     

N-Hydroxyurea dimers: A matrix isolation and theoretical study

The dimerization of N-hydroxyurea (NH₂CONHOH) has been investigated by FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-311++G(2d,2p) calculations. The analysis of NH₂CONHOH/Ar matrix spectra and comparison with theoretical ones reveal the formation of two types of dimers with a strong OH⋯O hydrogen bond. There is an additional weak interaction between the oxygen atom of the OH group of the proton donor molecule and the NH or NH₂ group of the proton acceptor in both dimers, respectively. The identified structures correspond to local minima on the PES. The formation of the less stable structures not the most stable ones indicates that the creation of N-hydroxyurea dimers is related to the dipole-dipole interaction at the initial stage of the dimerization process, which favours generation of polar dimers.     

CH stretching vibration of N-methylformamide as a sensitive probe of its complexation: infrared matrix isolation and computational study

The complexes between trans-N-methylformamide (t-NMF) and Ar, N(2), CO, H(2)O have been studied by infrared matrix isolation spectroscopy and/or ab initio calculations. The infrared spectra of NMF/Ne, NMF/Ar and NMF/N(2)(CO,H(2)O)/Ar matrices have been measured and the effect of the complexation on the perturbation of t-NMF frequencies was analyzed. The geometries of the complexes formed between t-NMF and Ar, N(2), CO and H(2)O were optimized in two steps at the MP2/6-311++G(2d,2p) level of theory. The four structures, found for every system at this level, were reoptimized on the CP-corrected potential energy surface; both normal and CP corrected harmonic frequencies and intensities were calculated. For every optimized structure the interaction energy was partitioned according to the SAPT scheme and the topological distribution of the charge density (AIM theory) was performed. The analysis of the experimental and theoretical results indicates that the t-NMF-N(2) and CO complexes present in the matrices are stabilized by very weak N-H···N and N-H···C hydrogen bonds in which the N-H group of t-NMF serves as a proton donor. In turn, the t-NMF-H(2)O complex present in the matrix is stabilized by O-H···O(C) hydrogen bonding in which the carbonyl group of t-NMF acts as a proton acceptor. Both, the theoretical and experimental results indicate that involvement of the NH group of t-NMF in formation of very weak hydrogen bonds with the N(2) or CO molecules leads to a clearly noticeable red shift of the CH stretching wavenumber whereas engagement of the CO group as a proton acceptor triggers a blue shift of this wavenumber.     

Aggregation of acetic and propionic acid in argon matrices--a matrix isolation and computational study

Monomeric acetic acid MA and propionic acid MP were isolated in argon matrices at 10K by using a pulse deposition technique. The dimerization of the monomers was induced by warming the matrices from 10 to 40 K. Under these conditions the diffusion of small trapped molecules is rapid and the dimerization could be monitored directly by IR spectroscopy. Both carboxylic acids form the symmetrical dimers B with two strong C=O...HO hydrogen bridges as the thermodynamically most stable dimers. With acetic acid a less stable dimer AA could be obtained if high concentrations of acetic acid in argon were used during the deposition of the matrix. On annealing this dimer rearranges to the more stable BA. In contrast, propionic acid does not form a corresponding less stable dimer under any experimental condition. These observations are rationalized on the basis of DFT and ab initio calculations.     

The Walden cycle revisited: a computational study of competitive ring closure to alpha- and beta-lactones

The text-book Walden cycle which interconverts the stereochemical configurations of chlorosuccinic and malic acids involves a beta-lactone intermediate in preference to an alpha-lactone intermediate because the O(nuc) C Cl angle in the transition structure for the former (174 degrees) is more favourable than that for the latter (139 degrees), as determined by PCM(epsilon = 78.4)/B3LYP/6-31+G* calculations; the smaller ring-strain energy of the beta-lactone contributes little to the reactivity difference.     

Conformers and photochemistry of propyl nitrites: a matrix isolation study

The infrared spectra of both constitutional isomers (n and i) of propyl nitrite have been recorded in an Ar matrix. Conformational analysis and assignments of the vibrational transitions have been carried out on the basis of quantum chemical calculations. Assignment of spectral lines to different conformers was also aided experimentally, by utilizing the different rate of photodecomposition of the conformers, as well as by employing conformational cooling using a supersonic jet as the inlet source for matrix deposition. The rate of photodecomposition is primarily determined by the steric alignment of the nitrite group, whereas jet cooling affects mainly the conformation of the alkyl tail. On the basis of these experimental observations and computational predictions two to three conformers of isopropyl nitrite and eight conformers of n-propyl nitrite were identified. After broadband ultraviolet-visible (UV-vis) photolysis of isopropyl nitrite in the matrix, HNO, acetone, HNO.acetone complex, acetaldehyde, and nitrosomethane were identified as the main products. Furthermore, in a small amount, NO and possibly the isopropoxy radical were also present in the matrix. Photolysis of n-propyl nitrite yielded HNO, propanal, and their 1:1 complex as the main products together with a small amount of NO and cis-1-nitrosopropanol.     

The primary fragmentation step of isoxazole upon electron impact. A correlation with photochemistry

Three isomeric compounds, I, II and III, were prepared and their mass spectra recorded. Comparisons of the spectra showed that the fragmentation of I proceeds only by way of II, and that II itself is transformed in part to III upon electron impact. It is suggested that selective ionization of each one of the two isolated functional groups in II may afford two isomeric radical ions, IIa and IIb. A possible interrelation to the photochemistry of these compounds is also discussed.     

The role of microstructure in the pyrolysis of polypropylene. A preliminary study on the syndiotactic stereoisomer

The pyrolysis of two syndiotactic polypropylene samples with different molar mass and microstructure has been studied by means of TGA. The volatiles evolved have been analysed as a whole by mass spectrometry. The relative content of the different low mass alkenes, alkanes and dienes provides a fingerprint which has been used to asses the similarity of the mechanism. The changes in the apparent E_a with conversion have been shown by means of the Friedman’s method.The results show that, even though the chemical pattern is identical in both samples, important differences in the E_a trends are found. Such disparity in the energy requirements for the pyrolysis to take place can be reasonably attributed to the different microstructure of the samples.     

Matrix isolation and computational study of the photochemistry of p-azidoaniline

The photochemistry of p-azidoaniline was studied in argon matrices in the absence and presence of oxygen. With the help of quantum chemical calculations we were able to characterize the triplet p-aminophenylnitrene as well as the cis- and trans-p-aminophenylnitroso oxides. It was found that the latter two isomers can be interconverted by selective irradiation and that they are ultimately converted into p-nitroaniline. Although restricted wavefunctions of the nitroso oxides are unstable, CASSCF calculations turned up no evidence for the claimed diradical character of these compounds. Also we found no evidence for dioxaziridines as intermediates of the conversion of the nitroso oxides to p-nitroaniline.     

A matrix isolation i.r. study on molecular complexes of hexamethylbenzene and tetracyanoethylene

The i.r. spectra of Ar and N₂ matrices containing trapped hexamethylbenzene (HMB), tetracyanoethylene (TCNE) and their complex species are presented. The formation of complex species (essentially the 1:1 complex) is indicated by the arising of new bands at 1295 cm⁻¹ (the A_1g CCH₃ stretching of HMB) and at 1546 cm⁻¹ (the CC stretching of TCNE). However, the comparison with the spectra of the crystalline 1:1 and 2:1 complexes (HMB:TCNE), indicates that the contribution of vibronic mechanisms to band intensities is greatly reduced by the isolation of complex units in the matrix.     

Isomerical and structural determination of N-hydroxyurea: a matrix isolation and theoretical study

The structure, isomerization pathways and vibrational spectra of the important N-hydroxyurea (HU) molecule were studied by matrix isolation FT-IR spectroscopy and molecular orbital calculations undertaken at the MP2/6-311++G(2d,2p) level of theory. In agreement with theoretical predictions, 1Ea represents the most stable keto isomer in the gas-phase, being the dominant species trapped in argon matrices, while the 1Za isomer also contributes to the spectrum of isolated HU molecules. According to the calculated abundance values at the temperature of evaporation of the compound (393 K), the 1Ea and 1Za isomers together with a small contribution of 1Eb are expected to appear in the experimental spectra. Since the barrier for interconversion 1Ea? 1Eb is only ～2 kJ mol(-1), these two isomers are in equilibrium in the matrices and, at low temperature, the population of the less stable 1Eb form is too small to be observed. Full assignment of the observed spectra of N-hydroxyurea and its deuterium analogue was undertaken on the basis of comparison with theoretical data.     

Conformations of trimethyl phosphite: a matrix isolation infrared and ab initio study

The conformations of trimethyl phosphite (TMPhite) were studied using matrix isolation infrared spectroscopy. TMPhite was trapped in a nitrogen matrix using an effusive source maintained at two different temperatures (298 and 410 K) and a supersonic jet source. The experimental studies were supported by ab initio computations performed at the B3LYP/6-31++G** level. Computations identified four minima for TMPhite, corresponding to conformers with C(1)(TG(±)G(±)), C(s)(TG(+)G(-)), C(1)(G(±)TT), and C(3)(G(±)G(±)G(±)) structures, given in order of increasing energy. Computations of the transition state structures connecting the C(s)(TG(+)G(-)) and C(1)(G(±)TT) conformers to the global minimum C(1)(TG(±)G(±)) structure were also carried out. The barriers for the interconversion of C(s)(TG(+)G(-)) and C(1)(G(±)TT) to the ground state C(1)(TG(±)G(±)) conformer were 0.2 and 0.6 kcal/mol, respectively. Comparison of conformational preferences of TMPhite with the related carbon compound, trimethoxymethane, and the organic phosphate, trimethyl phosphate, was also made using natural bond orbital analysis.     

Matrix isolation and computational study of the photochemistry of 1,3,2,4-benzodithiadiazine

Photolysis of 1,3,2,4-benzodithiadiazine (1) at ambient temperature yields stable 1,2,3-benzodithiazolyl radicals. In order to reveal the mechanism of this unusual transformation, the photochemistry of 1 was studied in argon matrices using IR and UV-vis spectroscopy. A series of intermediates, including four- and five-membered heterocyclic and o-quinoid acyclic species, were characterized spectroscopically with the help of quantum chemical calculations. With selective irradiation, these intermediates can be mutually interconverted as well as converted back to the starting compound 1.