Gas Phase Values Research Articles

Vacuum-UV spectroscopy of interstellar ice analogs

The VUV absorption cross sections of most molecular solids present in interstellar ice mantles with the exception of H2O, NH3, and CO2 have not been reported yet. Models of ice photoprocessing depend on the VUV absorption cross section of the ice to estimate the penetration depth and radiation dose, and in the past, gas phase cross section values were used as an approximation. We aim to estimate the VUV absorption cross section of molecular ice components. Pure ices composed of CO, H2O, CH3OH, NH3, or H2S were deposited at 8 K. The column density of the ice samples was measured in situ by infrared spectroscopy in transmittance. VUV spectra of the ice samples were collected in the 120-160 nm (10.33-7.74 eV) range using a commercial microwave-discharged hydrogen flow lamp. We provide VUV absorption cross sections of the reported molecular ices. Our results agree with those previously reported for H2O and NH3 ices. Vacuum-UV absorption cross section of CH3OH, CO, and H2S in solid phase are reported for the first time. H2S presents the highest absorption in the 120-160 nm range. Our method allows fast and readily available VUV spectroscopy of ices without the need to use a synchrotron beamline. We found that the ice absorption cross sections can be very different from the gas-phase values, and therefore, our data will significantly improve models that simulate the VUV photoprocessing and photodesorption of ice mantles. Photodesorption rates of pure ices, expressed in molecules per absorbed photon, can be derived from our data.

Polarizable Six-Point Water Models from Computational and Empirical Optimization

Tröster et al. (J. Phys. Chem B 2013, 117, 9486-9500) recently suggested a mixed computational and empirical approach to the optimization of polarizable molecular mechanics (PMM) water models. In the empirical part the parameters of Buckingham potentials are optimized by PMM molecular dynamics (MD) simulations. The computational part applies hybrid calculations, which combine the quantum mechanical description of a H2O molecule by density functional theory (DFT) with a PMM model of its liquid phase environment generated by MD. While the static dipole moments and polarizabilities of the PMM water models are fixed at the experimental gas phase values, the DFT/PMM calculations are employed to optimize the remaining electrostatic properties. These properties cover the width of a Gaussian inducible dipole positioned at the oxygen and the locations of massless negative charge points within the molecule (the positive charges are attached to the hydrogens). The authors considered the cases of one and two negative charges rendering the PMM four- and five-point models TL4P and TL5P. Here we extend their approach to three negative charges, thus suggesting the PMM six-point model TL6P. As compared to the predecessors and to other PMM models, which also exhibit partial charges at fixed positions, TL6P turned out to predict all studied properties of liquid water at p0 = 1 bar and T0 = 300 K with a remarkable accuracy. These properties cover, for instance, the diffusion constant, viscosity, isobaric heat capacity, isothermal compressibility, dielectric constant, density, and the isobaric thermal expansion coefficient. This success concurrently provides a microscopic physical explanation of corresponding shortcomings of previous models. It uniquely assigns the failures of previous models to substantial inaccuracies in the description of the higher electrostatic multipole moments of liquid phase water molecules. Resulting favorable properties concerning the transferability to other temperatures and conditions like the melting of ice are also discussed.

Solvation of Hydrogen Sulfide in Liquid Water and at the Water–Vapor Interface Using a Polarizable Force Field

Molecular dynamics (MD) simulations using the Drude polarizable force field are used to study the solution and interfacial properties of hydrogen sulfide (H2S) in water. Pairwise H2O-H2S Lennard-Jones interactions were optimized to the experimental H2S gas solubility at 298 K. These parameters yield hydration free energies and diffusion coefficients for H2S that are in good agreement with the experiment over 273-323 K and 298-368 K, respectively. H2S is sparingly soluble in water, with a ΔG(hydr)° of -0.5 kcal mol(-1). The free energy perturbation (FEP) calculations and analysis of the radial distribution functions show that H2S has limited hydrogen bonding and electrostatic interactions with the water solvent and generally behaves like a hydrophobic solute. These features were confirmed by ab initio MD simulations. Umbrella sampling simulations were used to calculate the free energy profile of the transition of H2S across the water-vapor interface, which showed that H2S has a sizable surface excess, with a ΔG(surf) of 1.3 kcal mol(-1). This high surface excess is consistent with our calculations of the surface tension, which decreases to 20 dyn cm(-1) under high densities of H2S (g). The dipole moment of H2S increases from its gas phase value of 0.98 to 1.25 D in bulk water as it moves across the interface. Adsorbed H2S tends to be oriented perpendicular to the interface, with the sulfur atom pointing toward the vapor phase.

Vibrational Shifts of HXeCl in Matrix Environments

The hybrid quantum-classical simulations are performed to investigate the unusual vibrational spectral shifts of a noble-gas hydride HXeCl in matrix environments (in Ne, Ar, Kr, and Xe matrixes). The high-level ab initio calculations at the CCSD(T) level are employed to construct interaction potential energy surfaces between HXeCl and noble-gas atoms (Ne, Ar, Kr, and Xe). The configurations of noble-gas atoms are sampled by the Monte Carlo simulations and the vibrational levels of HXeCl in the presence of the surrounding noble-gas atoms are solved by the DVR approach. It is found that the H-Xe stretching frequencies are blue-shifted from the isolated gas-phase value in all matrix environments and that the relative blue shifts are in good agreement with the experimental results (Ne < Xe < Kr), demonstrating that the explicit treatment of matrix environments around HXeCl is essential to reproduce the observed unusual vibrational shifts.

Hydrogen adsorption on PdGa(100), (111) and ([formula omitted]) surfaces: A DFT study

Hydrogen adsorption on PdGa intermetallic compound is analyzed using density functional theory (DFT) calculations. Changes in the electronic structure of PdGa(100), (111) and (1¯1¯1¯) surfaces and H bonding after adsorption are addressed. H interacts with Pd atoms with a tilted geometry on (100) and (111) surfaces. On the (1¯1¯1¯) surface two possible forms for H adsorption are detected: one is observed atop perpendicular to the surface and the other one is subsuperficial, both with similar adsorption energies. The Ga–H interaction is energetically less stable and is only present on the (100) plane. Pd–Pd bond strength decreases up to 53.8% as the new Pd–H bond is formed. The Pd–H bond length differs less than 1%, compared to the gas phase value for the (100), (111) and atop (1¯1¯1¯). However in the (1¯1¯1¯) subsurface-H bond length is about 2.17 Å. The effect of H is limited to its first Pd neighbor. Analysis of orbital interaction reveals that the Pd–H bond mainly involves s–s and s–p orbitals with lower participation of Pd 4d orbitals. The computed H vibration frequencies after adsorption show values of 1786, 1289 and 633.5 cm−1 that correspond to top, bridge and hollow sites respectively.

Understanding the Membrane Permeability of Hydrogen Sulfide through Molecular Dynamics Simulations using a Polarizable Force Field

Hydrogen sulfide (H2S) is an acutely toxic gas, with a threshold toxicity of 200 ppm. It is also a gasotransmitter, acting through the S-sulfhydration of cysteine side chains [1]. Despite being chemically analogous to water, H2S can permeate biological membranes without a facilitator [1]. To examine this process, we used molecular dynamics simulations to calculate the potential of mean force (PMF) of H2S crossing a model lipid bilayer. As H2S is a highly polarizable molecule, we used the Drude polarizable force field for H2S developed in our group [2], in conjunction with a polarizable model for DPPC lipid bilayers [3]. Our computed PMFs show that H2S is sparingly soluble in bulk water and partitions readily into the interior of the membrane. Free energies are lowest when H2S is in the tail region of the lipids and the barriers corresponding to H2S crossing the water/lipid interface are small. This is in contrast the high free energies that occur when water molecules enter the membrane interior. Induced polarization plays a secondary role in H2S permeation, with H2S being most strongly polarized in the bulk solvent and near the lipid head groups, but having a dipole moment near the gas phase value of 0.98 D in the membrane interior. Despite a significant dipole moment and large polarizability, H2S is solvated and permeates membranes like a hydrophobic solute.[1] Gadalla, Snyder, J. Neurochem. 2010, 113, 14.[2] Mathai et al. PNAS 2009, 106, 16633.[3] Riahi, Rowley, J. Phys. Chem. B 2013, 117, 5222.[4] Chowdhary et al. J. Phys. Chem. B, 2013, 117, 9142.

Distinction of Nuclear Spin States with the Scanning Tunneling Microscope

We demonstrate rotational excitation spectroscopy with the scanning tunneling microscope for physisorbed H(2) and its isotopes HD and D(2). The observed excitation energies are very close to the gas phase values and show the expected scaling with the moment of inertia. Since these energies are characteristic for the molecular nuclear spin states we are able to identify the para and ortho species of hydrogen and deuterium, respectively. We thereby demonstrate nuclear spin sensitivity with unprecedented spatial resolution.

High-resolution infrared spectroscopy of atomic bromine in solid parahydrogen and orthodeuterium

This work extends our earlier investigation of the near-infrared absorption spectroscopy of atomic bromine (Br) trapped in solid parahydrogen (pH2) and orthodeuterium (oD2) [S. C. Kettwich, L. O. Paulson, P. L. Raston, and D. T. Anderson, J. Phys. Chem. A 112, 11153 (2008)]. We report new spectroscopic observations on a series of double transitions involving excitation of the weak Br-atom spin-orbit (SO) transition ((2)P(1/2) ← (2)P(3/2)) in concert with phonon, rotational, vibrational, and rovibrational excitation of the solid molecular hydrogen host. Further, we utilize the rapid vapor deposition technique to produce pH2 crystals with a non-equilibrium mixture of face centered cubic (fcc) and hexagonal closed packed (hcp) crystal domains in the freshly deposited solid. Gentle annealing (T = 4.3 K) of the pH2 sample irreversibly converts the higher energy fcc crystal domains to the slightly more stable hcp structure. We follow the extent of this conversion process using the intensity of the U1(0) transition of solid pH2 and correlate crystal structure changes with changes in the integrated intensity of Br-atom absorption features. Annealing the pH2 solid causes the integrated intensity of the zero-phonon Br SO transition to increase approximately 45% to a value that is 8 times larger than the gas phase value. We show that the magnitude of the increase is strongly correlated to the fraction of hcp crystal domains within the solid. Theoretical calculations presented in Paper II show that these intensity differences are caused by the different symmetries of single substitution sites for these two crystal structures. For fully annealed Br-atom doped pH2 solids, where the crystal structure is nearly pure hcp, the Br-atom SO transition sharpens considerably and shows evidence for resolved hyperfine structure.

Infrared Spectra in the 3 μm Region of Ethane and Ethane Clusters in Helium Droplets

Ethane and ethane clusters (N ≈ 10(2)-10(4)) were studied inside helium droplets with infrared laser spectroscopy. The spectra were measured in the 2880-3000 cm(-1) range, which covers the ν5, ν(8+11), and ν7 vibrational bands of ethane. Partially resolved rotational fine structure in the spectrum of the monomer reveals solvent-induced band origin blue shifts that are each approximately 1 cm(-1). The effective B(He) and A(He) rotational constants were found to be reduced by 52% and 16% in comparison to their gas phase values, respectively. Spectra of the clusters show the same three bands shifted toward low frequency by approximately 10 cm(-1) because of intermolecular interactions in the clusters. The spectra of the ethane clusters are dominated by the ν7 band, whereas the relative intensities of the ν5 and ν(8+11) bands are about a factor of 5 weaker than for single molecules or for solid ethane, the spectrum of which is also reported here.

Rovibrational spectroscopy of formaldehyde in helium nanodroplets

Formaldehyde has been characterized in superfluid helium nanodroplets in the region of the symmetric (ν1) and antisymmetric (ν5) stretching bands. The band origins are blue shifted, consistent with a decrease in the dipole moment and polarizability in going from the ground to excited vibrational states, and the lines within each band are homogeneously broadened, with vibrational lifetimes of 26 and 6.2ps for assigned transitions in the v1 and v5 bands, respectively. The A, B, and C constants are renormalized to 79%, 65%, and 49% of their gas phase values, corresponding to moments of inertia of helium, IHe, of 0.488, 6.88, and 15.3amuÅ2, about the inertial a-, b-, and c-axes, respectively. While partial breakdown of the adiabatic approximation is expected for rotations about the b- and c-axes, the small value of IHe about the a-axis is indicative of near complete breakdown. The larger value of IHe about the c-axis in comparison to the b-axis is attributed to the greater anisotropy of the interaction potential in the plane of H2CO [M.D. Wheeler, A.M. Ellis, Chem. Phys. Lett. 374 (2003) 392].

A theoretical study of the limits of the acidity of carbon acids in phase transfer catalysis in water and in liquid ammonia

Abstract The acidities of a large number of carbon acids have been theoretically calculated for the gas-phase and for DMSO solution. The gas-phase values, both ΔH and ΔG, are very well correlated with the available experimental data. From the calculated ΔG values in DMSO and the pKas in the same solvent, a homogeneous set of pK a (DMSO) values was devised that was used to generate pK a (water). These last pK as were used to establish the limits of the acidity of carbon acids for reactions under PTC conditions both alkylations and H/D exchange. A step further led to the pK as in liquid ammonia and from them to the virtual use of PTC using liquid ammonia instead of water.

Polarizable Water Models from Mixed Computational and Empirical Optimization

Here we suggest a mixed computational and empirical approach serving to optimize the parameters of complex and polarizable molecular mechanics (PMM) models for complicated liquids. The computational part of the parameter optimization relies on hybrid calculations combining density functional theory (DFT) for a solute molecule with a PMM treatment of its solvent environment at well-defined thermodynamic conditions. As an application we have developed PMM models for water featuring ν = 3, 4, and 5 points of force action, a Gaussian inducible dipole and a Buckingham potential at the oxygen, the experimental liquid phase geometry, the experimental gas phase polarizability α(exp)(g) = 1.47 ų, and, for ν = 4 and 5, the gas phase value μ(exp)(g) = 1.855 D for the static dipole moment. The widths of the Gaussian dipoles and, for ν = 4 and 5, also the electrostatic geometries of these so-called TLνP models are derived from self-consistent DFT/PMM calculations, and the parameters of the Buckingham potentials (and the static TL3P dipole moment) are estimated from molecular dynamics (MD) simulations. The high quality of the resulting models is demonstrated for the observables targeted during optimization (potential energy per molecule, pressure, radial distribution functions) and a series of predicted properties (quadrupole moments, density at constant pressure, dielectric constant, diffusivity, viscosity, compressibility, heat capacity) at certain standard conditions. Remaining deficiencies and possible ways for their removal are discussed.

Correlation among the Gas-Phase, Solution, and Solid-Phase Geometrical and NMR Parameters of Dative Bonds in the Pentacoordinate Silicon Compounds. 1-Substituted Silatranes

Silatranes XSi(OCH2CH2)3N exhibit a good linear relationship between their experimental and calculated (IGLO and GIAO) values of the NMR chemical shifts of (15)N, δN, and the lengths of dative bonds Si←N, dSiN, determined in the gas phase (ED, CCSD), solutions (COSMO PBE0, B3PW91), and crystals (X-ray). An aggregate of the obtained data provides strong evidence that the gas-phase value of dSiN in MeSi(OCH2CH2)3N should be greater by ∼0.05 Å than that determined in the electron diffraction (ED) experiment (2.45 Å). Given this condition, a long-standing contradiction between the data of the structural (X-ray, ED) and NMR (15)N experiments for the molecules of 1-methyl- and 1-fluorosilatrane regarding the sensitivity of their coordination contact Si←N to the medium effect is resolved.

Dynamics of acetone photooxidation on TiO2(110): State-resolved measurements of methyl photoproducts

State-resolved laser techniques were used to study the internal state distributions of gas phase methyl radicals which are produced during the photooxidation of acetone on TiO2(110). This approach was used as a means of understanding the nature of the bimodal kinetic energy distributions for these radicals. Specifically, we investigated the population of the ν2 "umbrella mode" which has been shown to be important in similar photodissociation reactions where methyl radicals are liberated. We observed that for methyl radicals undergoing prompt dissociation (EK = 0.15 eV), the vibrational population in the umbrella mode is quite cold and can be characterized by a Tvib = 151 ± 15 K. Methyl radicals in this channel were also characterized by a rotational energy distribution of Trot = 325 ± 25 K which is comparable to the gas phase value obtained by acetone photolysis. State-resolved energy distributions also show that methyl radicals which are vibrationally excited have an overall kinetic energy distribution which is ~35 meV less than those which are in their vibrational ground state. This value is comparable to, but not exactly in agreement with, the known vibrational spacing of the ν2 mode and suggests that vibrationally excited methyl radicals have less energy available for translation.

Matrix Isolation Spectroscopy and Nuclear Spin Conversion of NH3 and ND3 in Solid Parahydrogen

We present matrix isolation infrared absorption spectra of NH3 and ND3 trapped in solid parahydrogen (pH2) at temperatures around 1.8 K. We used the relatively slow nuclear spin conversion (NSC) of NH3 and ND3 in freshly deposited pH2 samples as a tool to assign the sparse vibration-inversion-rotation (VIR) spectra of NH3 in the regions of the ν2, ν4, 2ν4, ν1, and ν3 bands and ND3 in the regions of the ν2, ν4, ν1, and ν3 fundamentals. Partial assignments are also presented for various combination bands of NH3. Detailed analysis of the ν2 bands of NH3 and ND3 indicates that both isotopomers are nearly free rotors; that the vibrational energy is blue-shifted by 1-2%; and that the rotational constants and inversion tunneling splitting are 91-94% and 67-75%, respectively, of the gas-phase values. The line shapes of the VIR absorptions are narrow (0.2-0.4 cm(-1)) for upper states that cannot rotationally relax and broad (>1 cm(-1)) for upper states that can rotationally relax. We report and assign a number of NH3-induced infrared absorption features of the pH2 host near 4150 cm(-1), along with a cooperative transition that involves simultaneous vibrational excitation of a pH2 molecule and rotation-inversion excitation of NH3. The NSCs of NH3 and ND3 were found to follow first-order kinetics with rate constants at 1.8 K of k = 1.88(16) × 10(-3) s(-1) and k = 1.08(8) × 10(-3) s(-1), respectively. These measured rate constants are compared to previous measurements for NH3 in an Ar matrix and with the rate constants measured for other dopant molecules isolated in solid pH2.

Ab initio study of CO adsorption on PdGa(1 1 0)

CO adsorption is analyzed using Density Functional Theory (DFT) calculations. Changes in the electronic structure of PdGa(110) surface and CO bond after adsorption are addressed. CO is located only on Pd atop geometry with a tilted configuration (9.13° from the perpendicular to the surface) and no interaction with Ga is detected. The Pd–Pd bond strength decreases 54.2% as the new Pd–CO bond is formed. The C–O bond length change less than 1%, compared to the gas phase value, while its bond overlap population decrease 46.2%. The effect of CO is limited to its first Pd neighbor. Analysis of orbital interaction reveals the Pd–CO bond mainly involves s–s and s–p orbitals with less participation of Pd 4d orbitals. The computed CO vibration frequencies after adsorption shows a red shift from vacuum to ward 2013.85cm−1, which agrees with previous experimental data on PdGa intermetallic.

Anomalous Λ-Doubling in the Infrared Spectrum of the Hydroxyl Radical in Helium Nanodroplets

The X(2)Π3/2 hydroxyl (OH) radical has been isolated in superfluid (4)He nanodroplets and probed with infrared laser depletion spectroscopy. From an analysis of the Stark spectrum of the Q(3/2) transition, the Λ-doublet splittings are determined to be 0.198(3) and 0.369(2) cm(-1) in the ground and first excited vibrational states, respectively. These splittings are 3.6 and 7.2 times larger than their respective gas phase values. A factor of 1.6 increase in the Q(1/2) Λ-doublet splitting was previously reported for the He solvated X(2)Π1/2 NO radical [von Haeften, K.; Metzelthin, A.; Rudolph, S.; Staemmler, V.; Havenith, M. Phys. Rev. Lett. 2005, 95, 215301]. A simple model is presented that reproduces the observed Λ-doublet splittings in He-solvated OH and NO. The model assumes a realistic parity dependence of the rotor's effective moment of inertia and predicts a factor of 3.6 increase in the OH ground state (J = 3/2) Λ-doubling when the B0(e) and B0(f) rotational constants differ by less than one percent.

Entropies of Adsorbed Molecules Exceed Expectations

Unexpectedly large entropies of adsorbed molecules, predicted from their gas-phase values, lead to better models of the rates of surface reactions.

Basicity of neutral organic superbases with vinamidine structure in gas phase and acetonitrile: a density functional theory study

The gas-phase proton affinities (PAs) for a set of molecules with vinamidine structure are considered and their basicities in acetonitrile. It is shown that introducing double bonds to the imidazoline rings at the proton attachment site resulted in decrease in PA of the parent vinamidine. The increase in PA can be obtained by inducing modifications to the imidazoline ring at the junction of two diazepinylium rings. Placing methyl and dimethylamino substituents on the perimeter of the molecule further increased their gas-phase PAs. Studied vinamidine molecules are superbases, which possess PA values in the range between 261.0 and 284.2 kcal mol–1 in the gas phase and pKa values of 24.6–31.9 units in acetonitrile. Dismembering proton attachment site by opening the two diazepinylium and imidazoline rings resulted in the largest drop in PA values, indicating its importance in constraining the positions of imino nitrogen atoms in the neutral form of the molecule. Vinamidine molecules studied here present important pieces of the ladder of highly basic organic compounds for they possess accessible vinamidine molecular framework. Copyright © 2012 John Wiley & Sons, Ltd.

Electron spin resonance investigation of H2+, HD+, and D2+ isolated in neon matrices at 2 K

Various isotopologues of nature's simplest molecule, namely H(2)(+), HD(+), and D(2)(+), have been isolated in neon matrices at 2 K for the first time and studied by electron spin resonance (ESR). Over many years, hundreds of matrix isolation experiments employing a variety of deposition conditions and ion generation methods have been tried to trap the H(2)(+) cation radical in our laboratory. The molecule has been well characterized in the gas phase and by theoretical methods. The observed magnetic parameters for H(2)(+) in neon at 2 K are: g(∥) ≈ g(⊥) = 2.0022(1); A(iso)(H) = 881(7) MHz; and A(dip)(H) = 33(3) MHz. Reasonable agreement with gas phase values of the isotropic hyperfine interaction (A(iso)) is observed; however, the neon matrix dipolar hyperfine interaction (A(dip)) is noticeably below the gas phase value. The smaller matrix value of A(dip) is attributable to motional averaging of the H(2)(+) radical in the neon matrix trapping site--an occurrence that would prevent the full extent of the hyperfine anisotropy from being measured for a powder pattern type ESR sample.