HCN Dimer Research Articles

Vacuum Ultraviolet Single Photon Ionization and Decomposition of 2-Aminopropionitrile in Astrophysical Objects

The molecule 2-aminopropionitrile (2-APN; H3CCH(NH2)CN) is a chiral precursor of the amino acid alanine and could play an important role in the emergence of the homochirality of life. To date, 2-APN has not yet been detected in the interstellar medium. To address the question of its absence, possibly through destruction by vacuum ultraviolet radiation in astrophysical media, we studied its photoionization and dissociative photoionization in the 9–14 eV (89–137 nm) energy range using photoelectron–photoion coincidence spectroscopy with velocity map imaging. Density functional theory calculations were performed at the PBE0/aug-cc-pVTZ level to determine structures for the various cationic fragments identified experimentally. Their appearance energies were calculated. The adiabatic ionization energy (AIE) of 2-APN is AIE = (9.85±0.01) eV and the appearance energy (AE) of the major fragment ion N≡CC(H)NH2 + is AE = (10.57±0.01) eV. Both ions, 2-APN+ and N≡CC(H)NH2 +, make up more than 90% of the formed ions. N≡CC(H)NH2 +, an isomer of the protonated HCN dimer, is also formed with high yield in the dissociative photoionization of aminoacetonitrile (NH2CH2CN), another α-aminonitrile observed in Sgr B2(N). Photoion yield spectra have been calibrated to absolute ionization cross sections. From these, we derive photoionization rates in several typical radiation fields relevant to different astrophysical objects. The rates show that, under almost all explored radiation fields, dissociative ionization is the dominant pathway for photoionization, leading to the loss of a methyl group (CH3) to form the planar thermodynamically stable amino cyano methylidynium ion N≡CC(H)NH2 +. The observed absence of 2-APN in Sgr B2 could thus be due to dominant dissociative photoionization.

Abundant Z-cyanomethanimine in the interstellar medium: paving the way to the synthesis of adenine

ABSTRACT We report the first detection in the interstellar medium (ISM) of the Z-isomer of cyanomethanimine (HNCHCN), an HCN dimer proposed as precursor of adenine. We identified six transitions of Z-cyanomethanimine, along with five transitions of E-cyanomethanimine, using IRAM 30m observations towards the Galactic Centre quiescent molecular cloud G + 0.693. The Z-isomer has a column density of (2.0 ± 0.6) × 1014 cm−2 and an abundance of 1.5 × 10−9. The relative abundance ratio between the isomers is [Z/E]∼6. This value cannot be explained by the two chemical formation routes previously proposed (gas phase and grain surface), which predicts abundances ratios between 0.9 and 1.5. The observed [Z/E] ratio is in good agreement with thermodynamic equilibrium at the gas kinetic temperature (130−210 K). Since isomerization is not possible in the ISM, the two species may be formed at high temperature. New chemical models, including surface chemistry on dust grains and gas-phase reactions, should be explored to explain our findings. Whatever the formation mechanism, the high abundance of Z-HNCHCN shows that precursors of adenine are efficiently formed in the ISM.

Fundamental Vibrational Analyses of the HCN Monomer, Dimer and Associated Isotopologues.

In this work we provide high level ab initio treatments of the structures, vibrational frequencies, and electronic energies of the HCN monomer and dimer systems along with several isotopologues. The plethora of information related to this system within the literature is summarized and serves as a basis for comparison with the results of this paper. The geometry of the dimer and monomer are reported at the all electroncoupled-cluster singles, doubles, and perturbative triples level of theory [AE-CCSD(T)] with the correlation consistent quadruple-zeta quality basis sets with extra core functions (cc-pCVQZ) from Dunning. The theoretical geometries and electronic structures are further analyzed through the use of the Natural Bond Orbital (NBO) method and Natural Resonance Theory (NRT). At the AE-CCSD(T)/cc-pCVQZ level of theory, the full cubic with semi-diagonal quartic force field for nine dimer and four monomer isotopologues (the parent isotopologue along with 15 N, 13 C, and D derivatives) were obtained to treat the anharmonicity of the vibrations via second order vibrational perturbation theory (VPT2). Lastly, the enthalpy change associated with the formation of the dimer from two monomer units was determined using the focal point analysis. Computations including coupled-cluster through perturbative quadruples as well as basis sets up to six-zeta quality, including core functions (cc-pCVXZ, X=D,T,Q,5,6) were used to extrapolate to the AE-CCSDT(Q)/CBS energy associated with this hydrogen-bond forming process. After appending anharmonic zero-point vibrational, relativistic, and diagonal Born-Oppenheimer corrections, we report a value of -3.93 kcal mol-1 for the enthalpy of formation. To our knowledge, each set of results (geometries, vibrational frequencies, and energetics) reported in this study represents the highest-level and most reliable theoretical predictions reported for this system.

Prebiotic Chemistry of HCN Tetramerization by Automated Reaction Search.

HCN oligomerization is considered to be one of the important pathways in chemical evolution. Nucleobases, aminoacids, and many other complex organic molecules can evolve through this pathway. We report an explorative study based on an automated reaction search method that avoids the cognitive bias present when searching chemical reaction space. We discuss the chemical space of the HCN dimer in detail, and the important trimers and tetramers are discussed briefly. A component-wise molecular-fingerprint-based methodology is proposed to identify molecular similarity. We present four different thermal routes to cis/trans-2,3-diaminomaleonitrile and 4-amino-1H-imidazole-5-carbonitrile, which are important intermediates in prebiotic chemistry.

CN radical hydrogenation from solid H2 reactions, an alternative way of HCN formation in the interstellar medium

Context. Molecular hydrogen (H2) is the most abundant molecule of the interstellar medium (ISM) in gas phase and it has been assumed to exist in solid state or as coating on grains. Aims. Our goal is to show that solid H2 can act as a hydrogenation agent, reacting with CN radicals to form HCN. Methods. In a H2 matrix, we studied the hydrogenation of the CN radical generated from the vacuum ultraviolet photolysis (VUV-photolysis) of C2N2 at 3.8 K. We modified the wavelengths and the host gas in order to be sure that CN radicals can abstract H from H2 molecules. Results. HCN monomers, dimers, and oligomers have been characterised by Fourier transform infrared spectroscopy (FTIR). H2CN as well as CN radicals have also been clearly observed during the photolysis performed at 3.8 K. Conclusions. H2 is a hydrogenation reagent towards CN radicals producing HCN. This type of reaction should be taken into account for the reactivity at low temperature in contaminated H2 ice macro-particles (CHIMPs), H2 flakes or in the first sublayers of grains where solid H2 has accumulated.

Understanding the most favourable dimer of HCN for the oligomerization process in the gas phase of interstellar clouds

The dimerization reaction for the formation of HCN dimer from two molecules HCN in the gas phase, has been studied theoretically using density functional theory (DFT) method at the B3LYP hybrid together with 6-311g(d, p) basis set level. The mechanisms considered for the isomerization pathway from HCN isomer shows that the iminoacetonitrile is the most stable dimer (−6kcal/mol) and is passing through the smallest barrier energy to be 41kcal/mol. Consequently, this dimer is energetically and kinetically most favourable, under isolated conditions, for the prebiotic syntheses of amino acid and nucleobase or adenine product by oligomerization process under interstellar conditions.

Hydrogen-bonded glycine–HCN complexes in gas phase: structure, energetics, electric properties and cooperativity

Twelve hydrogen-bonded complexes of glycine and hydrogen cyanide have been studied using high-level quantum-chemical calculations in gas phase. In particular, six 1:1 glycine–HCN dimers and six 1:2 glycine–HCN trimers have been considered. Besides the characteristics of the hydrogen bonds and their effect on molecular structure and energetics, several molecular electric properties have been calculated utilising two different models: MP2/6-31++G(d,p) and DFT-B3LYP/6-31++G(d,p). Although the structural parameters calculated by the two models are similar, equilibrium electronic energies of the clusters show model dependence. The lowest energy dimer is same in both the models which is ca. 3.0 kcal/mol more stable than the highest energy dimer. However, the lowest energy trimer is different in two methods. The energetic difference of stability between the highest and lowest trimer is 4.2 kcal/mol (4.4 kcal/mol) at an MP2 (B3LYP) level of calculation. The bond angles of glycine, in particular, are quite sensitive to the hydrogen-bond formation. Four out of six trimers are found to be strongly cooperative in both the models. Significant changes of dipole moments and polarisabilities of isolated glycine and hydrogen cyanide are observed due to the formation of hydrogen bonding. The Rayleigh scattering intensities of all clusters are much larger than those of their constituent monomers.

Mechanisms of Prebiotic Adenine Synthesis from HCN by Oligomerization in the Gas Phase

We explored the potential energy surfaces for adenine synthesis by oligomerizations of HCN or HNC from CBS-QB3 calculations. The pathways have been obtained for the formation of the covalently bound HCN dimer, trimer, tetramer, and pentamer (adenine) by sequential additions of HCN or HNC. The activation energies of the individual oligomerization stages are a few hundred kilojoules per mole, which prevent efficient adenine synthesis in interstellar space or in the atmosphere of Titan. On the other hand, when the oligomerizations start from HCNH(+), the activation energies of sequential HCN or HNC additions are significantly reduced. Kinetic analyses results suggest that adenine synthesis by proton-catalyzed oligomerizations cannot occur efficiently in interstellar space or in the atmosphere of Titan, even though some oligomerization stages can occur under the latter condition.

DETECTION OF E-CYANOMETHANIMINE TOWARD SAGITTARIUS B2(N) IN THE GREEN BANK TELESCOPE PRIMOS SURVEY

The detection E-cyanomethanimine (E-HNCHCN) towards Sagittarius B2(N) is made by comparing the publicly available Green Bank Telescope (GBT) PRIMOS survey spectra (Hollis et al.) to laboratory rotational spectra from a reaction product screening experiment. The experiment uses broadband molecular rotational spectroscopy to monitor the reaction products produced in an electric discharge source using a gas mixture of NH3 and CH3CN. Several transition frequency coincidences between the reaction product screening spectra and previously unassigned interstellar rotational transitions in the PRIMOS survey have been assigned to E cyanomethanimine. A total of 8 molecular rotational transitions of this molecule between 9 and 50 GHz are observed with the GBT. E-cyanomethanimine, often called the HCN dimer, is an important molecule in prebiotic chemistry because it is a chemical intermediate in proposed synthetic routes of adenine, one of the two purine nucleobases found in DNA and RNA. New analyses of the rotational spectra of both E-cyanomethanimine and Z-cyanomethanimine that incorporate previous mm-wave measurements are also reported.

Dimerization of HCN in the gas phase: A theoretical mechanistic study

Potential energy surfaces for the formation of covalently bound HCN dimers from two molecules of HCN or HNC were determined from CBS-QB3/APNO calculations. Several novel pathways, with and without the aid of protons, were found for the formation of iminoacetonitrile (HNCHCN), an intermediate in adenine synthesis from HCN by oligomerization. Covalent C–C or C–N bonds between the two monomers were formed after rearrangement of bimolecular complex intermediates. Energetic and kinetic analyses suggest that the proton-catalyzed dimerizations substantially lower reaction barriers but cannot occur efficiently under interstellar conditions.

Cooperative and diminutive hydrogen bonding in Y⋯HCN⋯HCN and NCH⋯Y⋯HCN trimers (Y=BF,CO,N2)

A computational study of the cooperative effect of hydrogen bonding in Y...HCN...HCN and its diminutive effect in NCH...Y...HCN (Y=BF,CO,N2) linear complexes relative to the Y...HCN dimer was undertaken at the MP2/6-311++G(2d,2p) level of theory. It was found that the additional hydrogen bond in Y...HCN...HCN leads to an enhanced Y...HCN dissociation energy, extended H-C bond length, and larger redshift of the H-C stretch relative to Y...HCN, while opposite features are observed in NCH...Y...HCN. The cooperativity is diminished as the hardness of the Y atom directly bonded to the HCN molecule increases. A particularly interesting result is that the small bond contraction and blueshift associated with the H-C bond in BF...HCN is converted to a small bond extension and redshift on the formation of the BF...HCN...HCN trimer.

Two-Body Dissociative Charge Exchange Dynamics of sym-Triazine

Translational spectroscopy coupled with coincidence detection techniques has been used to investigate the two-body dissociation of sym-triazine to HCN + (HCN)2 upon electronic excitation from charge exchange between the sym-triazine cation and cesium. This dissociation mechanism was determined to occur after excitation of sym-triazine into the 3s Rydberg electronic manifold, and the observed dynamics suggest that the mechanism competes with a stepwise three-body dissociation mechanism to three HCN products that occurs from this same electronic excitation. On the basis of reported stabilization energies of several isomers of the HCN dimer, possible structures of the metastable (HCN)2 species are discussed in light of the current measurements.

The covalently bound HC [tbnd]N dimer ions HC [dbnd]N−N [dbnd]CH [rad]+ and HC [dbnd]N−C( [dbnd]N)H [rad]+ are stable species in the gas-phase, but the neutral counterparts are not

Tandem mass spectrometry based experiments and computational chemistry (CBS-QB3/APNO methods) indicate that ionized s-tetrazine eliminates N 2 to yield the elusive linear HC N dimer ion HC N–N CH + ( 1). The ion is stable in the rarefied gas-phase but, as it is generated with considerable internal energy, it readily interconverts with HC N–C( N)H + ( 2), via a 1,2-HCN shift. This more stable HCN dimer ion was generated independently by loss of HCN from ionized s-triazine. Whereas the HN C dimer ion HN C C NH + has a (kinetically) stable neutral counterpart, theory and experiment (neutralization–reionization mass spectrometry) agree that the HC N dimer ions 1 and 2 do not.

Observation and assignment of the hot band ν2 + ν91 − ν91in (HCN)2

The high-resolution infrared absorption spectrum for (HCN)2 in the spectral region 3100–3300 cm−1 is recorded in a static multipass cell at 240 K under equilibrium conditions. The spectrum shows extensive rovibrational structures which are due to the bound C–H stretching vibration band ν2 of (HCN)2 and several hot bands associated to ν2. We manage to assign 63 new rovibrational transitions [P(97) to R(98)] associated with the ν2 band leading to an extended analysis of the ν2 band. This enables the assignment of 60 rovibrational transitions associated with the hot band ν2 + ν91 − ν91 in (HCN)2 together with the first rovibrational analysis of this hot band. The determined positive value of the anharmonicity constant X2,9 of 0.2569(13) cm−1 indicates that the intermolecular low-frequency bending vibration ν91 increases in frequency upon simultaneous excitation of the ν2 mode. This result confirms that the HCN dimer is stiffer and more tightly bound upon vibrational excitation of the bound C–H stretching mode.

Energetics and cooperativity in three-center hydrogen bonding interactions. I. Diacetamide-X dimers (X=HCN, CH3OH)

High level ab initio calculations are carried out on diacetamide–X (DA–X) dimers, X=HCN, CH3OH. The dimers are used as model systems to investigate the energetics and cooperative phenomomena in intermolecular three-center hydrogen-bond (H-bond) interactions relative to two-center H-bond interactions. The trans–trans conformer of diacetamide is chosen as a suitable model for intermolecular three-center H bonding where one H atom is interacting with two acceptor atoms. The proton–acceptor atoms are rigidly held in the same molecule. For both model systems, it is found that the calculated interaction energy per H bond is appreciably smaller in the three-center than in the two-center H-bond dimers, suggesting possibly a general characteristic of intermolecular three-center H bonds, namely, a negative cooperativity. More importantly, it is found that frequency shifts, intensity factors, bond lengths, and H1 nuclear magnetic resonance chemical shifts all support the energetic calculations in that the intermolecular three-center H-bond dimers exhibit marked negative cooperative effects. Despite the negative cooperativity, the three-center DA–HCN dimer is actually energetically favorable over the two-center counterpart, whereas the three-center DA–CH3OH dimer is energetically unfavorable over the two-center counterpart.

The production of HCN dimer and more complex oligomers in dense interstellar clouds

Using quantum chemical and kinetic techniques, we show that the reaction between two HCN molecules under interstellar conditions cannot lead efficiently to a dimer of this species (H2 C2 N2 ), whatever its structure. If the dimerization reaction does not occur efficiently, then it is impossible to synthesize detectable abundances of the pre-biotic HCN oligomer adenine (H5 C5 N5 ) in the interstellar medium via successive neutral-neutral reactions between HCN and its dimer, trimer, and tetramer.

Intermolecular potential energy surfaces and spectra of Ne–HCN complex from ab initio calculations

Ab initio calculations of five two-dimensional intermolecular potential energy surfaces of the Ne–HCN dimer have been performed using the symmetry-adapted perturbation theory and the supermolecular method at different levels of electron correlation. A basis set of spdf-symmetry orbitals (including midbond functions) was used. HCN was assumed linear with interatomic distances fixed at their vibrationally averaged 〈r−2〉−1/2 values. Fits to all calculated potential energy surfaces were obtained in the form of angular expansions incorporating the ab initio asymptotic coefficients. It has been found that high-order correlation effects are very important for Ne–HCN and contribute about 20% to the well depth. All of the five surfaces feature a global minimum at the linear Ne–HCN geometry and a narrow and relatively flat valley surrounding HCN. Rovibrational calculations on the surfaces yielded rotational spectra and a rotational constant whose relative differences from their experimental counterparts range from 2% to 12% depending on the method used to obtain the surface. This large sensitivity of spectral quantities to relatively modest differences between the potentials is related to the unusual shape of the potential well.

Strongly Bonded Bimolecular Complexes between HCN and HNC

The equilibrium structures, vibrational properties, and interaction energies for four bimolecular complexes of HCN and HNC (HCN···HCN, HNC···HNC, HCN···HNC, and HNC···HCN) were studied with ab initio methods. Different electron correlation levels and basis sets up to CCSD(T)/6-311++G(2d,2p) were used in the geometry optimizations and interaction energy calculations, and the vibrational frequencies were calculated at the MP2 and MP3 levels of theory. To study the nature of the intermolecular interactions, an energy decomposition analysis was carried out. For the HNC···HCN complex, which possesses a hydrogen bridge between two carbons, the counterpoise-corrected interaction energy and its decomposition has been calculated as a function of the intermolecular distance. The effect of subunit deformation on the interaction energy has also been considered. The results indicate that the HNC dimer has considerably stronger intermolecular interaction than the HCN dimer, and the HNC···HCN complex is bonded as strongly as the HCN dimer. The comparison of the various properties of the complexes and the energy decomposition analysis in particular indicate that carbon can act as both a hydrogen acceptor and donor, and the resulting hydrogen bonds in these complexes are relatively strong.

Solvent mediated vibrational relaxation: Superfluid helium droplet spectroscopy of HCN dimer

Rotationally resolved infrared spectra are reported for the HCN dimer, grown and solvated in liquid helium droplets. This is the first study for which two different vibrational modes within the same liquid helium solvated molecule have been observed, namely those associated with the “free” and the “hydrogen-bonded” C–H stretching vibrations. Comparing the line broadening in these two bands, we conclude that the helium solvent plays an important role in the vibrational relaxation dynamics of the dimer. The rotational constants obtained from these spectra indicate that the dimer rotates more slowly in the liquid than in the gas phase.

Electron and anion mobility in low density hydrogen cyanide gas. I. Dipole-bound electron ground states

We measured the mobility of excess electrons in the polar hydrogen cyanide gas (D=2.985 D) at low densities as a function of density and temperature by the so-called pulsed Townsend method. Experiments were performed at 294 and 333 K in the gas number density range 1.23×1017⩽n⩽3.61×1018 cm−3. We found a strong density dependence of the “zero-field” density-normalized mobility (μn). Only about 10% of the observed density variation can be qualitatively explained by coherent and incoherent multiple scattering effects. With increasing gas density an increasing number of linear HCN dimers is formed which due to the high dipole moment (D=6.552 D) represent much stronger electron scatterers than the HCN monomers. It was found that the dimers may be only in part responsible for the observed density effect. Therefore, we consider a transport process where short-lived dipole-bound electron ground states (lifetime ⩾12 ps) as quasilocalized states are involved. For comparison the electron mobility in saturated 2-aminoethanol vapor with a dipole moment of similar size (D=3.05 D) does not show any anomalous density behavior in the temperature range 298⩽T⩽435 K. In contrast to this the electron mobility in saturated but also in nonsaturated CH3CN gas (D=3.925 D) shows a density behavior similar to that in HCN.