The Grotthuss mechanism explains the anomalously high proton mobility in water as a sequence of proton transfers along a hydrogen-bonded (H-bonded) network. However, the vibrational spectroscopic ...signatures of this process are masked by the diffuse nature of the key bands in bulk water. Here we report how the much simpler vibrational spectra of cold, composition-selected heavy water clusters, D⁺(D₂O)n, can be exploited to capture clear markers that encode the collective reaction coordinate along the proton-transfer event. By complexing the solvated hydronium "Eigen" cluster D₃O⁺(D₂O)₃ with increasingly strong H-bond acceptor molecules (D₂, N₂, CO, and D₂O), we are able to track the frequency of every O-D stretch vibration in the complex as the transferring hydron is incrementally pulled from the central hydronium to a neighboring water molecule.
We review the role that gas-phase, size-selected protonated water clusters, H+(H2O) n , have played in unraveling the microscopic mechanics responsible for the spectroscopic behavior of the excess ...proton in bulk water. Because the larger (n ≥ 10) assemblies are formed with three-dimensional cage morphologies that more closely mimic the bulk environment, we report the spectra of cryogenically cooled (10 K) clusters over the size range 2 ≤ n ≤ 28, over which the structures evolve from two-dimensional arrangements to cages at around n = 10. The clusters that feature a complete second solvation shell around a surface-embedded hydronium ion yield spectral signatures of the proton defect similar to those observed in dilute acids. The origins of the large observed shifts in the proton vibrational signature upon cluster growth were explored with two types of theoretical analyses. First, we calculate the cubic and semidiagonal quartic force constants and use these in vibrational perturbation theory calculations to establish the couplings responsible for the large anharmonic red shifts. We then investigate how the extended electronic wave functions that are responsible for the shapes of the potential surfaces depend on the nature of the H-bonded networks surrounding the charge defect. These considerations indicate that, in addition to the sizable anharmonic couplings, the position of the OH stretch most associated with the excess proton can be traced to large increases in the electric fields exerted on the embedded hydronium ion upon formation of the first and second solvation shells. The correlation between the underlying local structure and the observed spectral features is quantified using a model based on Badger’s rule as well as via the examination of the electric fields obtained from electronic structure calculations.
The effects of atmospheric aerosols on our climate are one of the biggest uncertainties in global climate models. Calculating the pathway for the formation of pre-nucleation clusters that become ...aerosols is challenging, requiring a comprehensive analysis of configurational space and highly accurate Gibbs free energy calculations. We identified a large set of minimum energy configurations of (H2SO4)3 using a sampling technique based on a genetic algorithm and a stepwise density functional theory (DFT) approach and computed the thermodynamics of formation of these configurations with more accurate wavefunction-based electronic energies computed on the DFT geometries. The DLPNO-CCSD(T) methods always return more positive energies compared to the DFT energies. Within the DLPNO-CCSD(T) methods, extrapolating to the complete basis set limit gives more positive free energies compared to explicitly correlated single-point energies. The CBS extrapolation was shown to be robust as both the 4-5 inverse polynomial and Riemann zeta function schemes were within chemical accuracy of one another.
We present a computational investigation of the sulfuric acid, glycine, serine, ammonia, and water system to understand if this system can form prenucleation clusters, which are precursors to larger ...aerosols in the atmosphere. We have performed a comprehensive configurational search of all possible clusters in this system, starting with the four different monomers and zero to five waters. Accurate Gibbs free energies of formation have been calculated with the DLPNO-CCSD(T)/complete basis set (CBS) method on ωb97xd/6-31++G** geometries. For the dry dimers of sulfuric acid, the weakest base, serine, is found to form the most stable complex, which is a consequence of the strong di-ionic complex formed between the bisulfate ion and the protonated serine cation. For the dry dimers without sulfuric acid, the glycine–serine complex is more stable than the glycine–ammonia or serine–ammonia complexes, stemming from the detailed structure and not related to base strength. For the larger complexes, sulfuric acid deprotonates and the proton is shifted to glycine, serine, or ammonia. The two amino acids and ammonia are almost interchangeable and there is no easy way to predict which molecule will be protonated without the calculated results. Assuming reasonable starting concentrations and a closed system of sulfuric acid, glycine, serine, ammonia, and five waters, we predict the concentrations of all possible complexes at two temperatures spanning the troposphere. The most negative ΔG° values are a function of the detailed molecular interactions of these clusters. These details are more important than the base strength of ammonia, glycine, and serine.
The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei ...(CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H2O) n and Ser(H2O) n , where n = 1–5. We predict that serine–water clusters have higher concentrations at n = 1 and 5, while glycine–water clusters have higher concentrations at n = 2–4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.
The emergence of life on the prebiotic Earth must have involved the formation of polypeptides, yet the polymerization of amino acids is thermodynamically unfavorable under biologically relevant ...aqueous conditions because amino acids are zwitterions in solution and because of the production of a water molecule through a condensation reaction. Many mechanisms for overcoming this thermodynamic unfavorability have been proposed, but the role of gas phase water clusters has not been investigated. We present the thermodynamics of the water-mediated gas phase dimerization reaction of glycine as a model for the atmospheric polymerization of amino acids prior to the emergence of biological machinery. We hypothesize that atmospheric aerosols may have played a major role in the prebiotic formation of peptide bonds by providing the thermodynamic driving force to facilitate increasingly stable linear oligopeptides. In addition, we hypothesize that small aerosols orient amino acids on their surfaces, thus providing the correct molecular orientations to funnel the reaction pathways of peptides through transition states that lead eventually to polypeptide products. Using density functional theory and a thorough configurational sampling technique, we show that the thermodynamic spontaneity of the linear dimerization of glycine in the gas phase can be driven by the addition of individual water molecules.
The dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has ...been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known as cis and trans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas‐phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of the cis transition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm‐based configurational sampling, density functional theory geometries, and domain‐based local pair natural orbital coupled‐cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concerted cis mechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.
The formation of oligopeptides and polypeptides started before the machinery of biology through natural catalysis of peptide bond formation. The ability of gaseous water molecules to catalyze this reaction is explored using quantum chemistry. The Gibbs free energy barrier for glycine dimerization is lowered by the addition of individual water molecules that stabilize the transition state, thereby catalyzing peptide bond formation.
We explored the hypothesis that on the nanoscale level, acids and bases might exhibit different behavior than in bulk solution. Our study system consisted of sulfuric acid, formic acid, ammonia, and ...water. We calculated highly accurate Domain-based Local pair-Natural Orbital- Coupled-Cluster/Complete Basis Set (DLPNO-CCSD(T)/CBS) energies on DFT geometries and used the resulting Gibbs free energies for cluster formation to compute the overall equilibrium constants for every possible cluster. The equilibrium constants combined with the initial monomer concentrations were used to predict the formation of clusters at the top and the bottom of the troposphere. Our results show that formic acid is as effective as ammonia at forming clusters with sulfuric acid and water. The structure of formic acid is uniquely suited to form hydrogen bonds with sulfuric acid. Additionally, it can partner with water to form bridges from one side of sulfuric acid to the other, hence demonstrating that hydrogen bonding topology is more important than acid/base strength in these atmospheric prenucleation clusters.
Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy‐metal transport in the troposphere. The chemical and physical complexity of ...atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.
Over the last decade, quantum chemical calculations have become a powerful tool to study atmospheric processes, providing important insight into complex reactions involving atmospheric particulate matter. This work reviews recent progress in quantum chemical applications that have advanced our understanding of aerosol processes, bringing new knowledge of particle formation and the chemistry taking place on aerosols. Quantum chemical studies of atmospheric particulate matter provide key insights into aerosol reactions and their effects on climate, health, and the overall Earth system.
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