Zoubeida Dhaouadi

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.

Solvation Energies of the Proton in Methanol

pKas, 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.

Structures of protonated methanol clusters and temperature effects

The accurate evaluation of pKas, 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. pKas 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.

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.

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 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 pKas 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.

Active learning in physics a way for rational thinking, a way for development

Science Development leads to new concepts, new tools and new techniques. It leads to a society development with new Truth. This Truth is shared by the Society which development is built on Knowledge, on rationality thinking and scientific behavior. This takes its origin in the experimental approach introduced by Ibn Al Haythem in optics at the Xth century. By the end of the last millennium, this approach-known as Active Learning in Physics- has been adopted in most developed countries in physics education programs. Active Learning in Optics and Photonics- ALOP- is extended actually to some developing countries through a UNESCO program. A French edition of ALOP takes place through many workshops over Morocco and Tunisia. It aims to build Truth on evidence and not on intuition or personal authority.

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.

Using mobile camera for a better exploitation and understanding of interference and diffraction experiments

To deduce the wave nature of light, explain its behavior when it interacts with material obstacles (diffraction) or its behavior when light from two coherent sources interfere with each other (interference), we need to explain what are waves and what are their properties (wavelength, frequency, mathematical relationship between wavelength and frequency, superposition principle, …). Two principal approaches are generally used to introduce waves: 1/ An experimental approach (the example commonly used approach): to observe the water waves pattern obtained when drops of water (with an eye dropper, two eye droppers, or equivalent) fall -at a steady rate- on a calm pool of water surface. 2/ A theoretical approach: Wave coming from one source is represented by a sinusoidal function; Superposition of waves coming from two coherent sources is done by a sum of two sinusoidal functions with constant phase difference. In Tunisia, different workshops on “wave nature of light based on interference and diffraction” using Active Learning process have been organized for about 150 secondary school teachers in 2009. These workshops are based on UNESCO Active Learning in Optics and Photonics (ALOP) project. This paper will show how taking water wave’s pattern using some participant’s mobile camera helps to make some misconceptions resolved and includes at the same time other more complex phenomena.

Hands-on experimental and computer laboratory in optics: the Young double slit experiment

Teaching optics to small groups of students allows them to share ideas and leads to discussions, which will enable them to understand concepts better. This is a form of peer teaching/evaluation. This group dynamic favors creativity and inhibits obstacles to learning and understanding due to shyness, and other psychological factors. In addition, this paradigm allows the learner to be an active participant in the learning process rather than a passive recipient of knowledge as in the traditional lecture based teaching methodology. The project proposed here is based on both experimental and numerical approaches. Groups of students will be using simple and inexpensive equipment in a hands-on way. Additionally using numerical tools with open source environments such as the Python programming language allows one to perform numerical experiments. These two approaches are perfectly complementary; indeed the experiments favor observations and measurements and on the other hand numerical modeling favors abstraction and familiarization of mathematical formalisms of the optical phenomena. We propose a pedagogical methodology “Active Learning in Simulating Optics” (ALSO), where the active learning method is used not only for hands on experimentation while numerical modeling facilitates development of computer codes wherein students can design their own experiments. Mixing these two approaches, experimentation and simulation, is also very well adapted in working within projects for the elaboration of a new tools for teaching. This ALSO methodology will be presented along with results from workshops utilizing this technique.