Theoretical Spectroscopic Study of Two Ketones of Atmospheric Interest: Methyl Glyoxal (CH3COCHO) and Methyl Vinyl Ketone (CH3COCH═CH2).

Two ketones of atmospheric interest, methyl glyoxal and methyl vinyl ketone, are studied using explicitly correlated coupled cluster theory and core-valence correlation-consistent basis sets. The work focuses on the far-infrared region. At the employed level of theory, the rotational constants can be determined to within a few megahertz of the experimental data. Both molecules present two conformers, trans/cis and antiperiplanar (Ap)/synperiplanar (Sp), respectively. trans-Methyl glyoxal and Ap-methyl vinyl ketone are the preferred structures. cis-Methyl glyoxal is a secondary minimum of very low stability, which justifies the unavailability of experimental data in this form. In methyl vinyl ketone, the two conformers are almost isoenergetic, but the interconversion implies a relatively high torsional barrier of 1798 cm-1. A very low methyl torsional barrier was estimated for trans-methyl glyoxal (V3 = 273.6 cm-1). Barriers of 429.6 and 380.7 cm-1 were computed for Ap- and Sp-methyl vinyl ketone. Vibrational second-order perturbation theory was applied to determine the rovibrational parameters. The far-infrared region was explored using a variational procedure of reduced dimensionality. For trans-methyl glyoxal, the ground vibrational state was estimated to split by 0.067 cm-1, and the two low excited energy levels (1 0) and (0 1) were found to lie at 89.588 cm-1/88.683 cm-1 (A2/E) and 124.636 cm-1/123.785 cm-1 (A2/E). For Ap- and Sp-methyl vinyl ketone, the ground vibrational state splittings were estimated to be 0.008 and 0.017 cm-1, respectively.

Neutral and Multicharged Ions of Small Aluminum Oxides: Structures, Spectroscopy, and Energetics.

We use accurate ab initio methodologies at the Coupled Cluster level to compute the stable forms of AlxOyq+ (x = 1, 2; y = 1, 2; q = 0-3) species for which we derive an accurate set of geometrical and vibrational spectroscopic data. We also determine their adiabatic single, double, and triple ionization energies. These spectroscopic and thermodynamical data may help for identifying these species in laboratory, in astrophysical media, and in plasma and confirm previous observations of multi-charged AlxOy clusters by Atom Probe Tomography (ATP) coupled to mass spectrometry. They should help for identifying and understanding the complex chemical processes occurring during the Al2O3 growth in laboratory and in astrophysical media and those taking place at the degradation of Al-containing materials by high temperature corrosion/oxidation.

Explicitly correlated potential energy surface of the CO2-CO van der Waals dimer and applications.

The four-dimensional-potential energy surface (4D-PES) of the CO2-CO van der Waals complex is generated using the explicitly correlated coupled cluster with single, double, and perturbative triple excitation (CCSD(T)-F12) method in conjunction with the augmented correlation-consistent triple zeta (aug-cc-pVTZ) basis set. This 4D-PES is developed over the set of inter-molecular coordinates and where the CO2 and CO monomers are treated as rigid rotors. Afterwards, analytic fits of this 4D-PES are carried out. In addition to the already known C-bound and O-bound stable structures of CO2-CO, we characterise a new isomer: it has a T-shaped structure where the O atom of the CO2 moiety points into the centre of mass of CO. We also find the saddle points connecting these minimal structures. This new isomer may play a role during the intramolecular isomerization processes at low energies. Then, the 4D-PES expansion is incorporated into bound vibrational state computations of C-bound and O-bound complexes. We also computed the temperature dependence of the second virial coefficient for CO2-CO. A good agreement with experiments is found.

Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase.

The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.

Inelastic scattering dynamics of ortho and para hydronium ions, o-H3O+ and p-H3O+, with He at low temperature.

The hydronium ion, H3O+, presents a crucial key to understanding the chemistry of the interstellar clouds where it has been frequently observed. The present paper is devoted to studying the inelastic scattering of both forms of the hydronium ion, o-H3O+ and p-H3O+, by helium atoms. The interaction potential between H3O+ and He was mapped in Jacobi coordinates leading to a new three dimensional potential energy surface (3D-PES) at the CCSD(T)/aug-cc-pVQZ+BF (CCSD(T)/AVQZ+BF) level of theory. Close coupling treatment was used to obtain rotational cross-sections for both o-H3O+ and p-H3O+ involving 9 rotational states in each case. The cross-sections were computed from energy thresholds up to 500 cm-1 for o-H3O+ and up to 300 cm-1 for p-H3O+, in order to generate rotational rate coefficients for the kinetic temperature range 5-50 K for both forms. The use of the present rates are viewed to be a good tool to estimate hydronium abundance.

Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine.

Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.

Accurate theoretical characterization of dioxygen difluoride: a problem resolved.

Dioxygen difluoride is a tough molecule that has defied accurate theoretical description for many decades. In the present work we have identified the reason for this resistance: the flatness of the OO, and more important OF, stretching potential energy curves, which make it difficult to localise the global minimum. It is not related to the weak multi-reference character. Using high-level CCSD(T)-F12/VTZ-F12 ab initio theory, the global minimum has been properly located and vibrationally averaged bond lengths obtained. These vibrationally averaged parameters agree with experimental data to within 0.01 Å. Averaging was found essential to achieve this unprecedented accuracy. We have then simulated the IR and UV spectra, which compare well with experimental data and permit identification of the observed transitions.

Mobility gap and quantum transport in a functionalized graphene bilayer.

In a Bernal graphene bilayer, carbon atoms belong to two inequivalent sublattices A and B, with atoms that are coupled to the other layer by [Formula: see text] bonds belonging to sublattice A and the other atoms belonging to sublattice B. We analyze the density of states and the conductivity of Bernal graphene bilayers when atoms of sublattice A or B only are randomly functionalized. We find that for a selective functionalization on sublattice B only, a mobility gap of the order of 0.5 eV is formed close to the Dirac energy at concentration of adatoms [Formula: see text]. In addition, at some other energies conductivity presents anomalous behaviors. We show that these properties are related to the bipartite structure of the graphene layer.

Does the Residues Chirality Modify the Conformation of a Cyclo-Dipeptide? Vibrational Spectroscopy of Protonated Cyclo-diphenylalanine in the Gas Phase.

The structure of a protonated diketopiperazine dipeptide, cyclo-diphenylalanine, is studied by means of infrared multiple photon dissociation spectroscopy combined with quantum chemical calculations. Protonation exclusively occurs on the oxygen site and, in the most stable conformer, results to an intramolecular OH···π interaction, accompanied by a CH···π interaction. Higher-energy conformers with free OH and NH···π interactions are observed as well, due to kinetic trapping. Optimization of the intramolecular interactions involving the aromatic ring dictates the geometry of the benzyl substituents. Changing the chirality of one of the residues has consequences on the CH···π interaction, which is of CαH···π nature for LD, while LL shows a CßH···π interaction. Higher-energy conformers also display some differences in the nature of the intramolecular interactions.

The gas-phase structure of dimethyl peroxide.

There has been a disagreement amongst experimentalists and between experimentalists and theoreticians as to the gas-phase structure of dimethyl peroxide. We have investigated this problem with high-level CCSD(T)-F12 and MRCI procedures. There can be no doubt anymore that, at the minimum of the potential energy surface, the COOC fragment has a trans-structure. The dynamical structure of the molecule can, however, be different and be explained by the very slow torsional motion. We have analysed the dynamical structure using numerical wavefunctions of the torsional motion and a fully optimized potential curve of MP2/aug-cc-pVTZ quality. Computational and all experimental results are shown to be in complete agreement. The problem that has persisted for more than thirty years, highlighted in a recent review article by Oberhammer titled "Gas phase structures of peroxides: experiments and computational problems", has been resolved.

Solvation energies of the proton in ammonia explicitly versus temperature.

We provide in this work, the absolute solvation enthalpies and the absolute solvation free energies of the proton in ammonia explicitly versus temperature. As a result, the absolute solvation free energy of the proton remains quite constant for temperatures below 200 K. Above this temperature, it increases as a linear function of the temperature: ΔGam(H+,T)=-1265.832+0.210 T. This indicates that a temperature change of 100 K would induce a solvation free energy change of 21 kJ mol-1. Thus, ignoring this free energy change would lead to a bad description of hydrogen bonds and an unacceptable error higher than 3.7 pKa units. However, the absolute solvation enthalpy of the proton in ammonia is not significantly affected by a temperature change and, the room temperature value is -1217 kJ mol-1. The change of the solvation enthalpy is only within 3 kJ mol-1 for a temperature change up to 200 K.

Structures and spectroscopy of medium size protonated ammonia clusters at different temperatures, H+(NH3)10-16.

Structures of protonated ammonia clusters (H+(NH3)n) are very important for the determination of pKa's and solvation energies of the proton in ammonia. In this work, their structures were investigated at M06-2X/6-31++g(d,p) level of theory, for n=10-16 and for temperatures ranging from 0 to 400 K. In the cluster community, this is the first theoretical study on the protonated ammonia clusters larger than the nonamer. We noted that the population of the investigated clusters is reproduced by branched cage or cage like structures at low temperatures, while branched linear and branched cyclic or branched double cyclic isomers are the only isomers responsible for the population at higher temperatures. In these isomers, the proton is highly and entirely solvated at the center of the cluster. In addition, protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules. Moreover, infrared (IR) spectra of all isomers have been investigated and these spectra show good agreement with the experiment. This allowed us to assign experimental peaks and to provide the constitution of the populations of the various clusters.

Structures and spectroscopy of protonated ammonia clusters at different temperatures.

The accurate determination of the solvation energies of a proton in ammonia is based on the precise knowledge of the structures of neutral and protonated ammonia clusters. In this work, we have investigated all the possible and stable structures of protonated ammonia clusters H+(NH3)n=2-9, along with their isomeric distribution at a specific temperature. New significant isomers are reported here for the first time and show that the structures of protonated ammonia clusters are not only branched linear as assumed by all previous authors. Branched linear structures are the only ones responsible for the population of protonated ammonia clusters for n = 4-6 at any temperature. However, for larger cluster sizes, these types of structures compete with branched cyclic, double cyclic, branched double cyclic and triple cyclic structures depending on the temperature. In addition, we have shown that protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules. We have also carried out a study of the hydrogen bond network of protonated ammonia clusters establishing the stability rule governing the various isomers of each cluster from estimated energies of the hydrogen bond types in H+(NH3)n=2-9. With all these results, a route for the accurate determination of the solvation energies of a proton in ammonia at a given temperature could be conceivable.

Toward the laboratory identification of [O,N,S,S] isomers: Implications for biological NO chemistry.

Benchmark ab initio calculations are performed to investigate the stable isomers of [O,N,S,S]. These computations are carried out using coupled cluster (RCCSD(T)) and explicitly correlated coupled cluster methods (RCCSD(T)-F12). In addition to the already known cis isomer of SSNO, nine other stable forms are predicted. The most stable isomer is cis-OSNS. Nine structures are chain bent-bent with relatively large dipole moments which make them detectable, as cis-SSNO, by infrared, far-infrared, and microwave spectroscopies. We found also a C2v isomer (NS2O). Since these species are strongly suggested to play an important role as intermediates during the bioactive reaction products of the NO/H2S interaction, the rotational and vibrational spectroscopic parameters are presented to help aid the in vivo identification and assignment of these spectra. Results from this work show that [O,N,S,S] may play key roles during nitric oxide transport and deliver in biological media, as well as, provide an explanation for the weak characteristic of disulfide bridges within proteins.

Structures and relative stabilities of ammonia clusters at different temperatures: DFT vs. ab initio.

A hydrogen bond network in ammonia clusters plays a key role in understanding the properties of species embedded in ammonia. This network is dictated by the structures of neutral ammonia clusters. In this work, structures of neutral ammonia clusters (NH3)n(=2-10) have been studied at M06-2X/6-31++G(d,p) and MP2/6-31++g(d,p) levels of theory. The analysis of the relative stabilities of various hydrogen bond types has also been studied and vibrational spectroscopy of the ammonia pentamer and decamer is investigated. We noted that M06-2X provides lower electronic energies, greater binding energies and higher structural resolution than MP2. We also noted that at the M06-2X level of theory, the binding energy converges to the experimental vaporization enthalpy faster than that at the MP2 level of theory. As a result, it is found that the M06-2X functional could be more suitable than the MP2 ab initio method in the description of structures and energies of ammonia clusters. However, we found that the electronic energy differences obtained at both levels of computation follow a linear relation with n (number of ammonia molecules in a cluster). As far as the structures of ammonia clusters are concerned, we proposed new "significant" isomers that have not been reported previously. The most remarkable is the global minimum electronic energy structure of the ammonia hexamer, which has an inversion centre and confirms experimental observation. Moreover, we reported the relative stabilities of neutral ammonia clusters for temperatures ranging from 25 to 400 K. The stability of isomers changes with the increase of the temperature. As a result, the branched and less bonded isomers are the most favored at high temperatures and disfavored at low temperatures, while compact and symmetric isomers dominate the population of clusters at low temperatures. In fine, from this work, the global minimum energy structures of ammonia clusters are known for the first time at a given temperature (T ∼ 0-400 K) and at a reliable computational level of theory.

On the role of HNS and HSN as light-sensitive NO-donors for delivery in biological media.

Results are presented that suggest that thiazyl hydride (HSN)/thionitrosyl hydride (sulfimide, HNS) can be used as light-sensitive compounds for NO-delivery in biological media, as well as markers for the possible detection of intermediates in nitrites + H2S reactions at the cellular level. They are expected to be more efficient than the HNO/HON isovalent species and hence they should be considered instead. A set of characteristic spectroscopic features are identified that could aid in the possible detection of these species in the gas phase or in biological environments. The possibility of intramolecular dynamical processes involving excited states that are capable of interconverting HNS and its isomeric form HSN is examined.

Potential energy surface of the CO2-N2 van der Waals complex.

Four-dimensional potential energy surface (4D-PES) of the atmospherically relevant CO2-N2 van der Waals complex is generated using the explicitly correlated coupled cluster with single, double, and perturbative triple excitation (CCSD(T)-F12) method in conjunction with the augmented correlation consistent triple zeta (aug-cc-pVTZ) basis set. This 4D-PES is mapped along the intermonomer coordinates. An analytic fit of this 4D-PES is performed. Our extensive computations confirm that the most stable form corresponds to a T-shape structure where the nitrogen molecule points towards the carbon atom of CO2. In addition, we located a second isomer and two transition states in the ground state PES of CO2-N2. All of them lay below the CO2 + N2 dissociation limit. This 4D-PES is flat and strongly anisotropic along the intermonomer coordinates. This results in the possibility of the occurrence of large amplitude motions within the complex, such as the inversion of N2, as suggested in the recent spectroscopic experiments. Finally, we show that the experimentally established deviations from the C2v structure at equilibrium for the most stable isomer are due to the zero-point out-of-plane vibration correction.

Explicit correlation treatment of the potential energy surface of CO2 dimer.

We present an extensive study of the four-dimensional potential energy surface (4D-PES) of the carbon dioxide dimer, (CO2)2. This PES is developed over the set of intermolecular coordinates. The electronic computations are carried out at the explicitly correlated coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)-F12] level of theory in connection with the augmented correlation-consistent aug-cc-pVTZ basis set. An analytic representation of the 4D-PES is derived. Our extensive calculations confirm that "Slipped Parallel" is the most stable form and that the T-shaped structure corresponds to a transition state. Later on, this PES is employed for the calculations of the vibrational energy levels of the dimer. Moreover, the temperature dependence of the dimer second virial coefficient and of the first spectral moment of rototranslational collision-induced absorption spectrum is derived. For both quantities, a good agreement is found between our values and the experimental data for a wide range of temperatures. This attests to the high quality of our PES. Generally, our PES and results can be used for modeling CO2 supercritical fluidity and examination of its role in planetary atmospheres. It can be also incorporated into dynamical computations of CO2 capture and sequestration. This allows deep understanding, at the microscopic level, of these processes.

Rotationally inelastic dynamics of LiH (X(1)Σ(+), v = 0) in collisions with Ar: State-to-state inelastic rotational rate coefficients.

A theoretical study of rotational collision of LiH(X(1)Σ(+),v = 0, J) with Ar has been carried out. The ab initio potential energy surface (PES) describing the interaction between the Ar atom and the rotating LiH molecule has been calculated very accurately and already discussed in our previous work [Computational and Theoretical Chemistry 993 (2012) 20-25]. This PES is employed to evaluate the de-excitation cross sections. The ab initio PES for the LiH(X(1)Σ(+))-Ar((1)S) Van der waals system is calculated at the coupled-cluster [CCSD(T)] approximation for a LiH length fixed to an experimental value of 3.0139 bohrs. The basis set superposition error (BSSE) is corrected and the bond functions are placed at mid-distance between the center of mass of LiH and the Ar atom. The cross sections are then derived in the close coupling (CC) approach and rate coefficients are inferred by averaging these cross sections over a Maxwell-Boltzmann distribution of kinetic energies. The 11 first rotational levels of rate coefficients are evaluated for temperatures ranging from 10 to 300 K. We notice that the de-excitation rate coefficients appear large in the order 10(-10) cm(-3) s(-1) and show very low temperature dependence. The rate coefficients magnify significantly the propensity toward ∆ J = -1 transitions. These results confirm the same propensity already noted for the cross sections.

Structures of protonated methanol clusters and temperature effects.

The accurate evaluation of pKa's, or solvation energies of the proton in methanol at a given temperature is subject to the determination of the most favored structures of various isomers of protonated (H(+)(MeOH)n) and neutral ((MeOH)n) methanol clusters in the gas phase and in methanol at that temperature. Solvation energies of the proton in a given medium, at a given temperature may help in the determination of proton affinities and proton dissociation energies related to the deprotonation process in that medium and at that temperature. pKa's are related to numerous properties of drugs. In this work, we were interested in the determination of the most favored structures of various isomers of protonated methanol clusters in the gas phase and in methanol, at a given temperature. For this aim, the M062X/6-31++G(d,p) and B3LYP/6-31++G(d,p) levels of theory were used to perform geometries optimizations and frequency calculations on various isomers of (H(+)(MeOH)n) in both phases. Thermal effects were retrieved using our homemade FORTRAN code. Thus, we accessed the relative populations of various isomers of protonated methanol clusters, in both phases for temperatures ranging from 0 to 400 K. As results, in the gas phase, linear structures are entropically more favorable at high temperatures, while more compact ones are energetically more favorable at lower temperatures. The trend is somewhat different when bulk effects are taken into account. At high temperatures, the linear structure only dominates the population for n ≤ 6, while it is dominated by the cyclic structure for larger cluster sizes. At lower temperatures, compact structures still dominate the population, but with an order different from the one established in the gas phase. Hence, temperature effects dominate solvent effects in small cluster sizes (n ≤ 6), while the reverse trend is noted for larger cluster sizes.