Diatomic molecule | EPFL Graph Search

Diatomic molecules () are molecules composed of only two atoms, of the same or different chemical elements. If a diatomic molecule consists of two atoms of the same element, such as hydrogen () or oxygen (), then it is said to be homonuclear. Otherwise, if a diatomic molecule consists of two different atoms, such as carbon monoxide () or nitric oxide (), the molecule is said to be heteronuclear. The bond in a homonuclear diatomic molecule is non-polar. The only chemical elements that form stable homonuclear diatomic molecules at standard temperature and pressure (STP) (or typical laboratory conditions of 1 bar and 25 °C) are the gases hydrogen (), nitrogen (), oxygen (), fluorine (), and chlorine (). The noble gases (helium, neon, argon, krypton, xenon, and radon) are also gases at STP, but they are monatomic. The homonuclear diatomic gases and noble gases together are called "elemental gases" or "molecular gases", to distinguish them from other gases that are chemical compo

Survival of rotational alignment in H-2 scattering from Si(100)

Christopher Scott Reilly

We report a state-prepared, state-resolved study of rotational scattering of a diatomic molecule from a solid surface. Specifically, H-2 molecules with 80 meV kinetic energy are rotationally aligned in the j = 3 rotational state via stimulated Raman pumping and then scattered from a Si(100) surface at normal incidence. The rotational alignment of the scattered molecules is determined by measuring, for both the incident and scattered molecules, the ionization yield of a probe laser, tuned to selectively ionize molecules in the j = 3 rotation level, as the probe laser polarization is rotated. The measurement is performed for two initial rotational alignments: a "helicoptering " alignment with the bonds constrained to lie primarily parallel to the surface and a "cartwheeling " alignment with the bonds lying primarily normal to the surface. For both initial alignments, the modulation of the probe ionization yield with laser polarization for the scattered molecules is pronounced, although significantly weaker than the modulation measured for the incident molecules. This indicates a significant modification but not a complete elimination of the initial alignment. The modulation is found to be stronger for the scattered molecules originating in the cartwheeling alignment than for the helicoptering alignment. These results contribute toward an improved understanding of the role of rotational motion in molecule-surface dynamics.

AIP Publishing2021

Heterogeneous kinetics of some atmospherically relevant reactions

A low pressure reactor (Knudsen cell) coupled to molecular beam modulated mass spectrometry was used to study the heterogeneous kinetics of the following three systems: (1) NO2 on amorphous carbon, (2) H2O vapor on ice and (3) gaseous HCl on ice. The first system was investigated at ambient temperature while the two last ones were investigated at temperatures typical of the stratosphere, that is roughly between 160 and 220K. The solid phase samples correspond to model surfaces whose physicochemical properties come very close to the ones of atmospheric particulates. Firstly, we studied the interaction of gaseous NO2 with three different commercial samples of amorphous carbon having widely differing physicochemical properties. Using in situ laser-induced fluorescence, the only major product was unambiguously determined to be NO with the oxidation product of carbon apparently remaining on the surface. Probing the gas phase with mass spectrometry (MS), both pulsed valve dosing and steady state experiments were performed and revealed a complex reaction mechanism for both the uptake as well as product formation. The initial uptake coefficient γo for NO2 was (6.4±2.0)·10-2 and proved to be identical within experimental uncertainty for all three types of amorphous carbon. The initial NO2 uptake rate was independent of the mass of the carbon sample and scaled with its external geometrical surface. Applying a simple chemical kinetic model to both pulsed dosing and steady state experiments resulted in an effective surface for uptake on amorphous carbon ranging between a factor of 2.8 to 8.4 larger than the geometrical surface area, but inversely proportional to the measured BET surface area of the three types of amorphous carbon. This means that the amorphous carbon with the highest BET surface (FW2) had the lowest external surface for NO2 adsorption. The chemical kinetic model included competing processes between Langmuir-type adsorption and inhibition controlling the adsorption kinetics of NO2 and revealed that the NO generation rate differed greatly between the three carbon samples examined. All samples showed saturation effects of differing degree that were partially reversible through prolonged pumping at 10-4 Torr and/or heating. Virgin amorphous carbon samples did not take up H2O vapor at 20 mTorr, and no HONO and/or HNO3 was detected in simultaneous NO2/H2O exposure experiments. CO and CO2 were detected when a sample previously exposed to NO2 was heated by an incandescent lamp. Moreover, upon heating such a sample, a MS signal m/e 62 originating from NO3 and/or N2O5 was detected. In addition to the experiments conducted on the three commercial carbon samples, we carried out uptake experiments of NO2 on acetylene soot. Originating from the flame of an acetylene burner, this soot was freshly deposited on glass dishes before each experiment. The initial uptake coefficient γo for NO2 was measured to be (3.0±1.1)·10-2 is smaller by a factor of two compared to γo observed in the uptake on commercial samples whose mass was a factor of 10 higher. In addition to NO, a net formation of HONO (m/e 47) was observed. This HONO formation is strongly dependent on the instantaneous water desorption from the sample as well as on the NO2 partial pressure in the reactor. On the other hand, it is not enhanced by an external water flow which did not show any interaction with the carbon sample. Upon heating the sample using an incandescent lamp, significant amounts of water desorbed, suggesting that the water vapor had condensed into the micropores of the soot during combustion. No quantitative results are presented yet. However, as no correlation between HONO formation and NO partial pressure has been observed so far, we suggest a reaction mechanism that only involves NO2 and H2O but no NO: 2 NO2 (g) + H2O HONO + HNO3 In a second study, the kinetics of condensation and evaporation of water on ice was determined in the temperature range of 170 to 220K. The rate of evaporation Fev corresponds to the evaporation of 70±10 monolayers of H2O per second at 200K. The condensation rate constant kc has a negative activation energy of -3.l±1.5kcal/mol which is significantly larger than the one recently measured by Haynes et al. We report the first real time kinetic measurements of water condensation on ice at stratospherically relevant temperatures. At temperatures above 160K, pulsed dosing experiments show a dose dependence of the condensation rate coefficient. For example, the condensation rate coefficient increases by a factor of five with a 1000 fold increase of the H2O dose from 1·1015 to 1·1018 molecules per pulse at 180K. This pressure dependence of the condensation rate constant may be explained by an autocatalytic mechanism involving the competition of two condensation channels. These two channels feed two different surface species, one of which leads to autocatalytic condensation. This mechanism gives insight into the manner in which a gas phase molecule is stepwise incorporated into tetrahedrally coordinated bulk ice. In a third and ongoing study, the uptake kinetics of HCl on ice has been investigated by pulsed valve experiments in the temperature range of 180 to 210K and are discussed as a function of the state of the surface. In fact, some of the pulsed valve experiments present a relaxation to a steady state level. It is shown that this level originates from the evaporation of a liquid solution corresponding to a temperature specific HCl concentration. The threshold of the injected dose leading to this solution layer is estimated to be 8·1014 molecules. This threshold corresponding to a fraction of a monolayer may be explained by the formation of small domains along grain boundaries or other lattice imperfections. Within detection limit, no difference in keff has been observed for pulses on the solution or on a previously exposed sample without formation of the solution. In the case of pulses forming a solution layer, a fraction of 20±20% of the injected molecules remains permanently adsorbed on the surface. In the temperature range from 210 to 180K, the pulsed valve experiments yield values of keff roughly between 5 and 25s-1 and an activation energy of -1.6±0.7kcal/mol which are consistent with the values observed by Flueckiger in steady state experiments using the 15mm escape aperture (kuni varying from 12 to 23s-1 and an activation energy of -1.9±0.25 kcal/mol).

EPFL1996

Second harmonic scattering of water in a biological context

Tereza Schönfeldová

Water is one of the most abundant molecules in the universe. It forms a hydrogen bond network with unique structure and dynamics. Hydrogen bonding is highly relevant to many biological processes including membrane formation, protein folding, adsorption, and lubrication. However, the underlying molecular interactions within water and between water and membranes are difficult to study and hence not fully understood. In this thesis, we utilize second harmonic scattering (SHS) to investigate inhomogeneities in bulk water, probe structural changes in lipid bilayer membranes, and detect and characterize protein-membrane interactions. Firstly, we explore the structure of bulk water in comparison to a common model liquid, carbon tetrachloride. Combining SHS measurements and molecular dynamics simulations, we report on the nanoscale inhomogeneities in bulk water that occur on femtosecond timescales. We attribute the rise in the coherent second harmonic (SH) intensity to charge density fluctuations with enhanced nanoscale polarizabilities around transient voids. Even though the transient voids also exist in carbon tetrachloride, they do not show polarizability fluctuations and the SH response of carbon tetrachloride thus corresponds to that of a model isotropic liquid. Then, we study the structure of water around large unilamellar vesicles (LUVs), which serve as a model for cell membranes. We focus on the role of water during the lipid melting phase transition. Using SHS, differential scanning calorimetry, and temperature-dependent zeta-potential measurements, we investigate the structural changes of hydration shells around the vesicle membrane. We use lipids with phosphoserine, phosphocholine, and phosphate headgroups and observe different hydration behavior upon the lipid melting transition depending on the membrane composition. Next, we characterize the interface of membranes composed of lipids containing phosphocholine and phosphate headgroups in solutions with different CaCl2 concentrations. We observe that the SH intensity is decreasing with the addition of CaCl2, which we attribute to the formation of a condensed layer of Na+ counterions on the inner leaflet of the LUVs. Additionally, we extract the vesicle surface potential and second-order surface susceptibility from SHS data for membranes with different content of lipids with phosphate headgroups, and observe composition dependent behaviour which suggests structural membrane reorganization. We continue by exploring protein-membrane interactions using water as a contrast agent. We study a pore-forming toxin, perfringolysin O (PFO), known for selective insertion into cholesterol-rich membranes. Combining SHS measurements and cryo-electron microscopy, we compare the interaction between PFO and LUV membranes with a high and low cholesterol content. By obtaining a sub-picomolar insertion constant of PFO, we show that SHS can be used to determine protein-membrane binding constants in concentration ranges not accessible by conventional methods.Finally, we investigate the interaction of protein aerolysin and its mutants with lipid membranes. We observe changes in surface charge in the cap region of membrane-bound aerolysin at different pH of the surrounding solution. By combining SHS with single-channel measurements, we obtain the membrane binding constant of wild-type aerolysin and its mutants, and we dissect their pore-forming mechanism.

EPFL2022

Second harmonic scattering of water in a biological context

Tereza Schönfeldová

EPFL2022

Heterogeneous kinetics of some atmospherically relevant reactions

EPFL1996