Quantum cluster equilibrium theory applied to liquid ammonia.

Through this paper, the authors propose using the quantum cluster equilibrium (QCE) theory to reinvestigate ammonia clusters in the liquid phase. The ammonia clusters from size monomer to hexadecamer were considered to simulate the liquid ammonia in this approach. The clusterset used to model the liquid ammonia is an ensemble of different structures of ammonia clusters. After studious research of the representative configurations of ammonia clusters through the cluster research program ABCluster, the configurations have been optimized at the MN15/6-31++G(d,p) level of theory. These optimizations lead to geometries and frequencies as inputs for the Peacemaker code. The QCE study of this molecular system permits us to get the liquid phase populations in a temperature range of 190-260 K, covering the temperatures from the melting point to the boiling point. The results show that the population of liquid ammonia comprises mainly the ammonia hexadecamer followed by pentadecamer, tetradecamer, and tridecamer. We noted that the small-sized ammonia clusters do not contribute to the population of liquid ammonia. In addition, the thermodynamic properties, such as heat of vaporization, heat capacity, entropy, enthalpy, and free energies, obtained by the QCE theory have been compared to the experiment given some relatively good agreements in the gas phase and show considerable discrepancies in liquid phase except the density. Finally, based on the predicted population, we calculated the infrared spectrum of liquid ammonia at 215 K temperature. It comes out that the calculated infrared spectrum qualitatively agrees with the experiment.

Structures, binding energies, temperature effects, infrared spectroscopy of [Mg(NH3 )n = 1-10 ]+ clusters from DFT and MP2 investigations.

The possible isomers of [Mg(NH3 )n = 1 - 10 ]+ clusters have been investigated using both M06-2X/6-31++G(d,p) and MP2/6-31++G(d,p) levels of theory. The isomeric distribution for each n size has been studied as a function of temperatures ranging from 25 to 400 K. To the best of our knowledge, for clusters size n > 6, this is the first theoretical study available in the literature. From the calculated values in the considered clusters and using a fitting procedure, we have evaluated the binding energies (-14.0 kcal/mol), clustering energies (-10.1 kcal/mol), clustering free energies (-2.8 kcal/mol), and clustering enthalpies (-10.3 kcal/mol). On the basis of our structural and infrared (IR) spectroscopy outcomes, we find that the first solvation shell can hold up to six ammonia molecules. © 2019 Wiley Periodicals, Inc.

Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method.

Solvent effects on the structural and vibrational features of l-glycylvaline (L-GV) and l-glycylvalylglycine (L-GVG) in zwitterionic forms have been performed by means of DFT method. Relaxed potential energy surface scans (RPES) performed at B3LYP/6-31++G(d) level were used to map the reaction coordinate surfaces and to identify the geometries corresponding to the minima energy. Explicit solvation model, where L-GV and L-GVG are respectively surrounded by 9 and 11 water molecules interacting with H-donor and H-acceptor sites, as well as the different hybrid solvation models of solvation (explicit/COSMO, explicit/PCM and explicit/CPCM) allowed to analyze the hydration effects. Those number of water molecules are sufficient to fully hydrate carboxyl(CtOO-), amine (NtH3+) and amide (NH, C=O) groups. Harmonic vibrational modes calculated after geometry optimization on each solvated complex are performed at B3LYP/6-31++g(d) and PBE0/6-31++g(d) methods and a post-processing treatment enable us to assign the vibrational modes of LGV and L-GVG. The frequencies of the assigned modes obtained using B3LYP in explicit/COSMO are in good agreement with available IR and Raman values than those found in both explicit/PCM and explicit/CPCM which proved to be very close.

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.

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.

TDDFT prediction of UV-vis absorption and emission spectra of tocopherols in different media.

We use the TDDFT/PBE0/6-31+G* method to determine the electronic absorption and emission energies, in different media, of the four forms of tocopherol, which differ by the number and the position of methyl groups on the chromanol. Geometries of the ground state S0 and the first singlet excited state S1 were optimized in the gas phase, and various solvents. The solvent effect is evaluated using an implicit solvation model (IEF-PCM). Our results are compared to the experimental ones obtained for the vitamin E content in several vegetable oils. For all forms of tocopherols, the HOMO-LUMO first vertical excitation is a π-π* transition. Gas phase and non-polar solvents (benzene and toluene) give higher absorption wavelengths than polar solvents (acetone, ethanol, methanol, DMSO, and water); this can be interpreted by a coplanarity between the O-H group and the chroman, allowing a better electronic resonance of the oxygen lone pairs and the aromatic ring, and therefore giving an important absorption wavelength, whereas the polar solvents give high emission wavelengths comparatively to gas phase and non-polar solvents. Fluorescence spectra permit the determination, the separation, and the identification of the four forms of tocopherols by a large difference in emission wavelength values. Graphical Abstract Scheme from process methodological to obtain the absorption and emission spectra for tocopherols.

Revision of the thermodynamics of the proton in gas phase.

Proton transfer is ubiquitous in various physical/chemical processes, and the accurate determination of the thermodynamic parameters of the proton in the gas phase is useful for understanding and describing such reactions. However, the thermodynamic parameters of such a proton are usually determined by assuming the proton as a classical particle whatever the temperature. The reason for such an assumption is that the entropy of the quantum proton is not always soluble analytically at all temperatures. Thereby, we addressed this matter using a robust and reliable self-consistent iterative procedure based on the Fermi-Dirac formalism. As a result, the free proton gas can be assumed to be classical for temperatures higher than 200 K. However, it is worth mentioning that quantum effects on the gas phase proton motion are really significant at low temperatures (T ≤ 120 K). Although the proton behaves as a classical particle at high temperatures, we strongly recommend the use of quantum results at all temperatures, for the integrated heat capacity and the Gibbs free energy change. Therefore, on the basis of the thermochemical convention that ignores the proton spin, we recommend the following revised values for the integrated heat capacity and the Gibbs free energy change of the proton in gas phase and, at the standard pressure (1 bar): ΔH0→T = 6.1398 kJ mol(-1) and ΔG0→T = -26.3424 kJ mol(-1). Finally, it is important noting that the little change of the pressure from 1 bar to 1 atm affects notably the entropy and the Gibbs free energy change of the proton.

Visible photodissociation spectra of the 1- and 2-methylnaphthalene cations: laser spectroscopy and theoretical simulations.

The electronic absorption spectra of the two methyl derivatives of the naphthalene cation were measured using an argon tagging technique. In both cases, a band system was observed in the visible range and assigned to the D2 ← D0 electronic transition. The 1-methylnaphthalene(+) absorption bands revealed a red shift of 808 cm(-1), relative to those of the naphthalene cation (14,906 cm(-1)), whereas for 2-methylnaphthalene(+) a blue shift of 226 cm(-1) appeared. A short vibrational progression, similar to the naphthalene cation, was also observed for both isomers and found to involve similar aromatic ring skeleton vibrations. Moreover, insights into the internal rotation motion of the methyl group were inferred, although the spectral resolution was not sufficient to fully resolve the substructure. These measurements were supported by detailed quantum chemical calculations. They allowed exploration of the potential energy curves along this internal coordinate, along with a complete simulation of the harmonic Franck-Condon factors using the cumulant Gaussian fluctuations formalism extended to include the internal rotation.

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.

Effects of hydrogen dissociation on the infrared emission spectra of naphthalene: theoretical modeling.

The IR emission spectroscopy of naphthalene and its singly- and doubly-dehydrogenated radicals has been modeled using kinetic Monte Carlo simulations, taking into account the various relaxation pathways of radiative emission and hydrogen loss. Our modeling relies on quantum chemistry ingredients that were obtained from dedicated calculations based on density functional theory, including explicitly anharmonicity contributions. Our results show that the fragmentation products significantly contribute to the overall IR emission spectrum, especially to the intensity ratios between bands. Owing to the likely presence of polycyclic aromatic hydrocarbons in the interstellar medium, these findings are particularly relevant in the astrophysical context.

Solvation Energies of the Proton in Methanol.

pKa's, proton affinities, and proton dissociation free energies characterize numerous properties of drugs and the antioxidant activity of some chemical compounds. Even with a higher computational level of theory, the uncertainty in the proton solvation free energy limits the accuracy of these parameters. We investigated the thermochemistry of the solvation of the proton in methanol within the cluster-continuum model. The scheme used involves up to nine explicit methanol molecules, using the IEF-PCM and the strategy based on thermodynamic cycles. All computations were performed at B3LYP/6-31++G(dp) and M062X/6-31++G(dp) levels of theory. It comes out from our calculations that the functional M062X is better than B3LYP, on the evaluation of gas phase clustering energies of protonated methanol clusters, per methanol stabilization of neutral methanol clusters and solvation energies of the proton in methanol. The solvation free energy and enthalpy of the proton in methanol were obtained after converging the partial solvation free energy of the proton in methanol and the clustering free energy of protonated methanol clusters, as the cluster size increases. Finally, the recommended values for the solvation free energy and enthalpy of the proton in methanol are -257 and -252 kcal/mol, respectively.

Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: a DFT study.

The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level. Our results indicate that only K(+) and Mg(2+) prefer to be located in the bisector plane of the PO(2)(-) angle, whereas Li(+) and Na(+) deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS(-) bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g(-)g(-) conformer (with respect to the torsion angles defined around the P-O ester bonds) is not always the energetically most favorable. For instance, the g(-)t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.