The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry.

The Molecular Education and Research Consortium in Undergraduate Computational Chemistry (MERCURY) has supported a diverse group of faculty and students for over 20 years by providing computational resources as well as networking opportunities and professional support. The consortium comprises 38 faculty (42% women) at 34 different institutions, who have trained nearly 900 undergraduate students, more than two-thirds of whom identify as women and one-quarter identify as students of color. MERCURY provides a model for the support necessary for faculty to achieve professional advancement and career satisfaction. The range of experiences and expertise of the consortium members provides excellent networking opportunities that allow MERCURY faculty to support each other's teaching, research, and service needs, including generating meaningful scientific advancements and outcomes with undergraduate researchers as well as being leaders at the departmental, institutional, and national levels. While all MERCURY faculty benefit from these supports, the disproportionate number of women in the consortium, relative to their representation in computational sciences generally, produces a sizable impact on advancing women in the computational sciences. In this report, the women of MERCURY share how the consortium has benefited their careers and the careers of their students.

Correction: New particle formation and growth from methanesulfonic acid, trimethylamine and water.

Correction for 'New particle formation and growth from methanesulfonic acid, trimethylamine and water' by Haihan Chen et al., Phys. Chem. Chem. Phys., 2015, 17, 13699-13709.

Reactions of Methanesulfonic Acid with Amines and Ammonia as a Source of New Particles in Air.

New particle formation (NPF) from gaseous precursors as a significant source of aerosol needs to be better understood to accurately predict the impacts on visibility, climate change, and human health. While ternary nucleation of sulfuric acid, amines/NH3, and water is recognized as a significant driver for NPF, increasing evidence suggests a contribution from methanesulfonic acid (MSA) and amines under certain conditions. Here we report the formation of particles 2.5-10 nm in diameter from the reactions of MSA with methylamine (MA), dimethylamine (DMA), and NH3 at reaction times of 2.3-7.8 s in a flow reactor and compare these particles with those previously reported to be formed from reaction with trimethylamine (TMA). The effects of water vapor and concentrations of gaseous precursors on the particle number concentration and particle size were studied. The presence of water significantly enhances particle formation and growth. Under similar experimental conditions, particle number concentrations decrease in the order MA ≫ TMA ≈ DMA ≫ NH3, where NH3 is 2-3 orders of magnitude less efficient than DMA. Quantum chemical calculations of likely intermediate clusters were carried out to provide insights into the role of water and the different capacities of amines/NH3 in particle formation. Both gas-phase basicity and hydrogen-bonding capacity of amines/NH3 contribute to the potential for particles to form and grow. Our results indicate that, although amines typically have concentrations 1-3 orders of magnitude lower than that of NH3 in the atmosphere, they still play an important role in driving NPF.

New particle formation and growth from methanesulfonic acid, trimethylamine and water.

New particle formation from gas-to-particle conversion represents a dominant source of atmospheric particles and affects radiative forcing, climate and human health. The species involved in new particle formation and the underlying mechanisms remain uncertain. Although sulfuric acid is commonly recognized as driving new particle formation, increasing evidence suggests the involvement of other species. Here we study particle formation and growth from methanesulfonic acid, trimethylamine and water at reaction times from 2.3 to 32 s where particles are 2-10 nm in diameter using a newly designed and tested flow system. The flow system has multiple inlets to facilitate changing the mixing sequence of gaseous precursors. The relative humidity and precursor concentrations, as well as the mixing sequence, are varied to explore their effects on particle formation and growth in order to provide insight into the important mechanistic steps. We show that water is involved in the formation of initial clusters, greatly enhancing their formation as well as growth into detectable size ranges. A kinetics box model is developed that quantitatively reproduces the experimental data under various conditions. Although the proposed scheme is not definitive, it suggests that incorporating such mechanisms into atmospheric models may be feasible in the near future.

Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on isolated defects where it involves formation of H3O(+)-acid anion contact ion pairs. This behavior is found in simulations of a model of the ice quasi-liquid layer corresponding to large defect concentrations in crystalline ice. The results are in accord with experiments. (iv) Ionization of acids on wet quartz. A monolayer of water on hydroxylated silica is ordered even at room temperature, but the surface lattice constant differs significantly from that of crystalline ice. The ionization processes of HCl and H2SO4 are of high yield and occur in a few picoseconds. The results are in accord with experimental spectroscopy. (v) Photochemical reactions on water and ice. These simulations require excited state quantum chemical methods. The electronic absorption spectrum of methyl hydroperoxide adsorbed on a large ice cluster is strongly blue-shifted relative to the isolated molecule. The measured and calculated adsorption band low-frequency tails are in agreement. A simple model of photodynamics assumes prompt electronic relaxation of the excited peroxide due to the ice surface. SEMD simulations support this, with the important finding that the photochemistry takes place mainly on the ground state. In conclusion, dynamics simulations using quantum chemical potentials are a useful tool in atmospheric chemistry of water media, capable of comparison with experiment.

Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: evidence for repulsion of surface water by NO2 gas.

The interaction of water, 1,4 dioxane, and gaseous nitrogen dioxide, has been studied as a function of distance measured through the liquid-vapour interface by Raman spectroscopy with a narrow (<0.1 mm) laser beam directed parallel to the interface. The Raman spectra show that water is present at the surface of a dioxane-water mixture when gaseous NO2 is absent, but is virtually absent from the surface of a dioxane-water mixture when gaseous NO2 is present. This is consistent with recent theoretical calculations that show NO2 to be mildly hydrophobic.

Reaction of a charge-separated ONONO2 species with water in the formation of HONO: an MP2 Molecular Dynamics study.

The reaction of (NO(+))(NO3(-)) with water is modelled in ONONO2·(H2O)4 clusters. Molecular Dynamics simulations using second-order Møller-Plesset perturbation (MP2) theory support the feasibility of the reaction of a charge-separated species to produce HONO and nitric acid.

Photooxidation of ammonia on TiO2 as a source of NO and NO2 under atmospheric conditions.

Ammonia is the most abundant reduced nitrogen species in the atmosphere and an important precursor in the industrial-scale production of nitric acid. A coated-wall flow tube coupled to a chemiluminescence NOx analyzer was used to study the kinetics of NH3 uptake and NOx formation from photochemistry initiated on irradiated (λ > 290 nm) TiO2 surfaces under atmospherically relevant conditions. The speciation of NH3 on TiO2 surfaces in the presence of surface-adsorbed water was determined using diffuse reflection infrared Fourier transform spectroscopy. The uptake kinetics exhibit an inverse dependence on NH3 concentration as expected for reactions proceeding via a Langmuir-Hinshelwood mechanism. The mechanism of NOx formation is shown to be humidity dependent: Water-catalyzed reactions promote NOx formation up to a relative humidity of 50%. Less NOx is formed above 50%, where increasing amounts of adsorbed water may hinder access to reactive sites, promote formation of unreactive NH4(+), and reduce oxidant levels due to higher OH radical recombination rates. A theoretical study of the reaction between the NH2 photoproduct and O2 in the presence of H2O supports the experimental conclusion that NOx formation is catalyzed by water. Calculations at the MP2 and CCSD(T) level on the bare NH2 + O2 reaction and the reaction of NH2 + O2 in small water clusters were carried out. Solvation of NH2OO and NHOOH intermediates likely facilitates isomerization via proton transfer along water wires, such that the steps leading ultimately to NO are exothermic. These results show that photooxidation of low levels of NH3 on TiO2 surfaces represents a source of atmospheric NOx, which is a precursor to ozone. The proposed mechanism may be broadly applicable to dissociative chemisorption of NH3 on other metal oxide surfaces encountered in rural and urban environments and employed in pollution control applications (selective catalytic oxidation/reduction) and during some industrial processes.

Nitrogen dioxide at the air-water interface: trapping, absorption, and solvation in the bulk and at the surface.

The interaction of NO(2) with water surfaces in the troposphere is of major interest in atmospheric chemistry. We examined an initial step in this process, the uptake of NO(2) by water through the use of molecular dynamics simulations. An NO(2)-H(2)O intermolecular potential was obtained by fitting to high-level ab initio calculations. We determined the binding of NO(2)-H(2)O to be about two times stronger than that previously calculated. From scattering simulations of an NO(2) molecule interacting with a water slab we observed that the majority of the scattering events resulted in outcomes in which the NO(2) molecule became trapped at the surface or in the interior of the water slab. Typical surface-trapped/adsorbed and bulk-solvated/absorbed trajectories were analyzed to obtain radial distribution functions and the orientational propensity of NO(2) with respect to the water surface. We observed an affinity of the nitrogen atom for the oxygen in water, rather than hydrogen-bonding which was rare. The water solvation shell was less tight for the bulk-absorbed NO(2) than for the surface-adsorbed NO(2). Adsorbed NO(2) demonstrated a marked orientational preference, with the oxygens pointing into the vacuum. Such behavior is expected for a mildly hydrophobic and surfactant molecule like NO(2). Estimates based on our results suggest that at high NO(2) concentrations encountered, for example, in some sampling systems, adsorption and reaction of NO(2) at the surface may contribute to the formation of gas-phase HONO.

Simplified mechanism for new particle formation from methanesulfonic acid, amines, and water via experiments and ab initio calculations.

Airborne particles affect human health and significantly influence visibility and climate. A major fraction of these particles result from the reactions of gaseous precursors to generate low-volatility products such as sulfuric acid and high-molecular weight organics that nucleate to form new particles. Ammonia and, more recently, amines, both of which are ubiquitous in the environment, have also been recognized as important contributors. However, accurately predicting new particle formation in both laboratory systems and in air has been problematic. During the oxidation of organosulfur compounds, gas-phase methanesulfonic acid is formed simultaneously with sulfuric acid, and both are found in particles in coastal regions as well as inland. We show here that: (i) Amines form particles on reaction with methanesulfonic acid, (ii) water vapor is required, and (iii) particle formation can be quantitatively reproduced by a semiempirical kinetics model supported by insights from quantum chemical calculations of likely intermediate clusters. Such an approach may be more broadly applicable in models of outdoor, indoor, and industrial settings where particles are formed, and where accurate modeling is essential for predicting their impact on health, visibility, and climate.

Analysis of the HOOO torsional potential.

Torsional levels of cis and trans HOOO and DOOO, observed previously via infrared action spectroscopy [E. L. Derro, T. D. Sechler, C. Murray, and M. I. Lester, J. Chem. Phys. 128, 244313 (2008)], have been used in conjunction with ab initio theory to obtain a torsional potential energy surface for the hydrotrioxy radical. High level electronic structure calculations based on the equation-of-motion coupled-cluster method for ionized states (EOMIP-CCSD) are utilized to produce a torsional potential. Eigenvalues of the potential are computed by diagonalizing the torsional hamiltonian in a free-rotor basis. Uniform scaling of the theoretical potential by a factor of 1.35 yields vibrational frequencies in good agreement with the experiment, and allows prediction of the barrier height to isomerization of ∼340 cm(-1) and relative stability of trans-HOOO with respect to cis-HOOO of ∼70 cm(-1). Examination of the optimized nuclear coordinates with respect to the torsional angle, suggests that the central O-O bond length is strongly coupled to the torsion and is important in determining the relative stabilities of the two conformers. The scaled potential is then used to determine the torsional contribution to the partition function for atmospheric modeling of HOOO.

Dissociation energy of the HOOO radical.

The dissociation of the hydrotrioxy (HOOO) radical to OH and O(2) has been studied theoretically using coupled-cluster methods. The calculated dissociation energy for the trans-HOOO isomer is 2.5 kcal mol(-1) including zero-point corrections. The minimum energy path to dissociation has been explored and an exit barrier has been revealed, which may help to rationalize the apparent disagreement between theory and experiment on the magnitude of the bond energy.

Vibrational overtone spectrum of matrix isolated cis, cis-HOONO.

Cis, cis-peroxynitrous acid is known to be an intermediate in atmospheric reactions between OH and NO2 as well as HOO and NO. The infrared absorption spectra of matrix-isolated cc-HOONO and cc-DOONO in argon have been observed in the range of 500-8000 cm-1. Besides the seven fundamental vibrational modes that have been assigned earlier for this molecule [Zhang et al., J. Chem. Phys. 124, 084305 (2006)], more than 50 of the overtone and combination bands have been observed for cc-HOONO and cc-DOONO. Ab initio CCSD(T)/atomic natural orbital anharmonic force field calculations were used to help guide the assignments. Based on this study of the vibrational overtone transitions of cis, cis-HOONO that go as high as 8000 cm-1 and the earlier paper on the vibrational fundamentals, we conclude that the CCSD(T)/ANO anharmonic frequencies seem to correct to +/-35 cm-1. The success of the theoretically predicted anharmonic frequencies {upsilon} in assigning overtone spectra of HOONO up to 8000 cm-1 suggests that the CCSD(T)/ANO method is producing a reliable potential energy surface for this reactive molecule.

Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.

Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA(Lys,3)UUU three modified bases are present in the anticodon stem-loop--2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine (psi) at position 39--two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human tRNA(Lys,3)UUU [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390-13395]. Molecular dynamics simulations of nine tRNA anticodon stem-loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to psi39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.

A comparison of experimental and calculated spectra of HNO3 in the near-infrared using Fourier transform infrared spectroscopy and vibrational perturbation theory.

This work combines new laboratory studies of the near-infrared vibrational spectra of HNO3 with theoretical predictions of these spectra as a means to understand the properties of this molecule at energies well above the fundamental region. Trends in overtone and combination band energy levels and intensities are compiled and examined. The theoretical calculations are in excellent agreement with the observed frequencies and intensities of the transitions in this spectral region. The calculations also serve as a valuable aid for assigning many of the transitions. This work validates the ab initio generated potential energy surface for HNO3 by comparing vibrational perturbation theory calculations to experimental spectra focused on combination band and overtone absorptions.

Infrared absorption spectra of matrix-isolated cis, cis-HOONO and its ab initio CCSD(T) anharmonic vibrational bands.

The infrared absorption spectra of matrix-isolated cis, cis-peroxynitrous acid (HOONO and DOONO) in argon have been observed. Six of the nine fundamental vibrational modes for cis, cis-HOONO have been assigned definitively, and one tentatively. Coupled-cluster, ab initio anharmonic force field calculations were used to help guide some of the assignments. The experimental matrix frequencies (cm(-1)) for cis, cis-HOONO are (a' modes) nu1 = 3303+/-1, nu2 = 1600.6+/-0.6, nu3 = 1392+/-1, nu4 = 922.8+/-0.5, nu5 = 789.7+/-0.4, nu6 = 617+/-1; and (a" mode) nu8 = 462+/-1. The fundamentals for the deuterated isotopomer, cis, cis-DOONO, are (a' modes) nu1 = 2447.2+/-0.6, nu2 = 1595.7+/-0.7, nu3 = 1089.1+/-0.4, nu4 = 888.1+/-0.4, nu5 = 786.6+/-0.5, nu6 = 613.9+/-0.9; and (a" mode) nu8 = 456.5+/-0.5.

Infrared overtone spectroscopy and unimolecular decay dynamics of peroxynitrous acid.

Peroxynitrous acid (HOONO) is generated in a pulsed supersonic expansion through recombination of photolytically generated OH and NO(2) radicals. A rotationally resolved infrared action spectrum of HOONO is obtained in the OH overtone region at 6971.351(4) cm(-1) (origin), providing definitive spectroscopic identification of the trans-perp (tp) conformer of HOONO. Analysis of the rotational band structure yields rotational constants for the near prolate asymmetric top, the ratio of the a-type to c-type components of the transition dipole moment for the hybrid band, and a homogeneous linewidth arising from intramolecular vibrational energy redistribution and/or dissociation. The quantum state distribution of the OH (nu=0,J(OH)) products from dissociation is well characterized by a microcanonical statistical distribution constrained only by the energy available to products, 1304+/-38 cm(-1). This yields a 5667+/-38 cm(-1) [16.2(1) kcal mol(-1)] binding energy for tp-HOONO. An equivalent available energy and corresponding binding energy are obtained from the highest observed OH product state. Complementary high level ab initio calculations are carried out in conjunction with second-order vibrational perturbation theory to predict the spectroscopic observables associated with the OH overtone transition of tp-HOONO including its vibrational frequency, rotational constants, and transition dipole moment. The same approach is used to compute frequencies and intensities of multiple quantum transitions that aid in the assignment of weaker features observed in the OH overtone region, in particular, a combination band of tp-HOONO involving the HOON torsional mode.

Propargyl radical: ab initio anharmonic modes and the polarized infrared absorption spectra of matrix-isolated HCCCH2.

The propargyl radical has twelve fundamental vibrational modes, gamma(vib)(HCCCH2) = 5a1 [symbol: see text] 3b1 [symbol: see text] 4b2, and nine have been detected in a cryogenic matrix. Ab initio coupled-cluster anharmonic force field calculations were used to help guide some of the assignments. The experimental HC=:C-:CH2 matrix frequencies (cm(-1)) and polarizations are a1 modes--3308.5 +/- 0.5, 3028.3 +/- 0.6, 1935.4 +/- 0.4, 1440.4 +/- 0.5, 1061.6 +/- 0.8; b1 modes--686.6 +/- 0.4, 483.6 +/- 0.5; b2 modes--1016.7 +/- 0.4, 620 +/- 2. We recommend a complete set of gas-phase vibrational frequencies for the propargyl radical, HC=:C-:CH2 2 X (2)B1. From an analysis of the vibrational spectra, the small electric dipole moment, mu(D)(HCCCH2) = 0.150 D, and the large resonance energy (HCCCH2), roughly 11 kcal mol(-1), we conclude that propargyl is a completely delocalized hydrocarbon radical and is best written as HC=:C-:CH2.