Quantum Tunneling Facilitates Water Motion across the Surface of Phenanthrene.

Quantum tunneling is a fundamental phenomenon that plays a pivotal role in the motion and interaction of atoms and molecules. In particular, its influence in the interaction between water molecules and carbon surfaces can have significant implications for a multitude of fields ranging from atmospheric chemistry to separation technologies. Here, we unveil at the molecular level the complex motion dynamics of a single water molecule on the planar surface of the polycyclic aromatic hydrocarbon phenanthrene, which was used as a small-scale carbon surface-like model. In this system, the water molecule interacts with the substrate through weak O-H···π hydrogen bonds, in which phenanthrene acts as the hydrogen-bond acceptor via the high electron density of its aromatic cloud. The rotational spectrum, which was recorded using chirped-pulse Fourier transform microwave spectroscopy, exhibits characteristic line splittings as dynamical features. The nature of the internal dynamics was elucidated in great detail with the investigation of the isotope-substitution effect on the line splittings in the rotational spectra of the H218O, D2O, and HDO isotopologues of the phenanthrene-H2O complex. The spectral analysis revealed a complex internal dynamic showing a concerted tunneling motion of water involving its internal rotation and its translation between the two equivalent peripheral rings of phenanthrene. This high-resolution spectroscopy study presents the observation of a tunneling motion exhibited by the water monomer when interacting with a planar carbon surface with an unprecedented level of detail. This can serve as a small-scale analogue for water motions on large aromatic surfaces, i.e., large polycyclic aromatic hydrocarbons and graphene.

Rotational dive into the water clusters on a simple sugar substrate.

Most biomolecular activity takes place in aqueous environments, and it is strongly influenced by the surrounding water molecules. The hydrogen bond networks that these water molecules form are likewise influenced by their interactions with the solutes, and thus, it is crucial to understand this reciprocal process. Glycoaldehyde (Gly), often considered the smallest sugar, represents a good template to explore the steps of solvation and determine how the organic molecule shapes the structure and hydrogen bond network of the solvating water cluster. Here, we report a broadband rotational spectroscopy study on the stepwise hydration of Gly with up to six water molecules. We reveal the preferred hydrogen bond networks formed when water molecules start to form three-dimensional (3D) topologies around an organic molecule. We observe that water self-aggregation prevails even in these early stages of microsolvation. These hydrogen bond networks manifest themselves through the insertion of the small sugar monomer in the pure water cluster in a way in which the oxygen atom framework and hydrogen bond network resemble those of the smallest three-dimensional pure water clusters. Of particular interest is the identification, in both the pentahydrate and hexahydrate, of the previously observed prismatic pure water heptamer motif. Our results show that some specific hydrogen bond networks are preferred and survive the solvation of a small organic molecule, mimicking those of pure water clusters. A many-body decomposition analysis of the interaction energy is also performed to rationalize the strength of a particular hydrogen bond, and it successfully confirms the experimental findings.

The Role of Non-Covalent Interactions on Cluster Formation: Pentamer, Hexamers and Heptamer of Difluoromethane.

The role of non-covalent interactions (NCIs) has broadened with the inclusion of new types of interactions and a plethora of weak donor/acceptor partners. This work illustrates the potential of chirped-pulse Fourier transform microwave technique, which has revolutionized the field of rotational spectroscopy. In particular, it has been exploited to reveal the role of NCIs' in the molecular self-aggregation of difluoromethane where a pentamer, two hexamers and a heptamer were detected. The development of a new automated assignment program and a sophisticated computational screening protocol was essential for identifying the homoclusters in conditions of spectral congestion. The major role of dispersion forces leads to less directional interactions and more distorted structures than those found in polar clusters, although a detailed analysis demonstrates that the dominant interaction energy is the pairwise interaction. The tetramer cluster is identified as a structural unit in larger clusters, representing the maximum expression of bond between dimers.

How does the composition of a PAH influence its microsolvation? A rotational spectroscopy study of the phenanthrene-water and phenanthridine-water clusters.

We report on the noncovalent intermolecular interactions established between the polycyclic aromatic hydrocarbons phenanthrene and phenanthridine with water. Such noncovalent interactions involving extended aromatic systems and water molecules are ubiquitous in a variety of chemical and biological systems. Our study provides spectroscopic results on simple model systems to understand the impact that an extended aromatic surface and the presence of a heteroatom have on the nature of the noncovalent interactions established with the solvent. Microhydrated phenanthrene and phenanthridine clusters with up to three water molecules have been observed and unambiguously characterised by means of broadband rotational spectroscopy and quantum chemical calculations. The presence of a nitrogen atom in the backbone of phenanthridine remarkably affects the geometries of the water clusters and the interaction networks at play, with O-HN and C-HO interactions becoming preferred in the phenanthridine-water clusters over the O-Hπ interactions seen in the phenanthrene-water clusters. The presence of this heteroatom induces nuclear quadrupole coupling, which was used to understand the cooperativity effects found with increasing cluster size. Our results provide important insight to draw a more complete picture of the noncovalent interactions involving solvent molecules and aromatic systems larger than benzene, and they can be significant to enhance our understanding of the aromatic-polar interactions at play in a myriad of chemical and biological contexts.

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry.

The computational study of the formation and growth of atmospheric aerosols requires an accurate Gibbs free energy surface, which can be obtained from gas phase electronic structure and vibrational frequency calculations. These quantities are valid for those atmospheric clusters whose geometries correspond to a minimum on their potential energy surfaces. The Gibbs free energy of the minimum energy structure can be used to predict atmospheric concentrations of the cluster under a variety of conditions such as temperature and pressure. We present a computationally inexpensive procedure built on a genetic algorithm-based configurational sampling followed by a series of increasingly accurate screening calculations. The procedure starts by generating and evolving the geometries of a large set of configurations using semi-empirical models then refines the resulting unique structures at a series of high-level ab initio levels of theory. Finally, thermodynamic corrections are computed for the resulting set of minimum-energy structures and used to compute the Gibbs free energies of formation, equilibrium constants, and atmospheric concentrations. We present the application of this procedure to the study of hydrated glycine clusters under ambient conditions.

Water Triggers Hydrogen-Bond-Network Reshaping in the Glycoaldehyde Dimer.

Carbohydrates are ubiquitous biomolecules in nature. The vast majority of their biomolecular activity takes place in aqueous environments. Molecular reactivity and functionality are, therefore, often strongly influenced by not only interactions with equivalent counterparts, but also with the surrounding water molecules. Glycoaldehyde (Gly) represents a prototypical system to identify the relevant interactions and the balance that governs them. Here we present a broadband rotational-spectroscopy study on the stepwise hydration of the Gly dimer with up to three water molecules. We reveal the preferred hydrogen-bond networks formed when water molecules sequentially bond to the sugar dimer. We observe that the dimer structure and the hydrogen-bond networks at play remarkably change upon the addition of just a single water molecule to the dimer. Further addition of water molecules does not significantly alter the observed hydrogen-bond topologies.

Water induces the same crown shapes as Li+ or Na+ in 15-crown-5 ether: a broadband rotational study.

15-Crown-5 ether (15C5) and its complexes with water have been studied using broadband Fourier transform microwave spectroscopy in a supersonic jet. A new conformer of 15C5 has been observed and established as the new global minimum out of a total of nine isolated structures. In addition, two 15C5-H2O and two 15C5-(H2O)2 clusters have been observed. The cluster structures have been unambiguously identified through the observation of water 18O isotopologue spectra. In all the clusters, at least one water molecule, located close to the axis of the 15C5 ring, interacts through two simultaneous hydrogen bonds to the endocyclic oxygen atoms. This interaction reshapes the 15C5 ring to reduce its rich conformational landscape to only two open structures, related to those found in complexes with Li+ or Na+ ions. In the most abundant 15C5-(H2O)2 form, the two water molecules repeat the same interaction scheme while binding to opposite sides of the ring. In the second most abundant dihydrated form the two water molecules lie on the same side of the ring. This finding is exceptionally rare because water-water interactions typically prevail over the formation of additional solute-water contacts, and it showcases the particular binding features of crown ethers.

Exploring the Rich Potential Energy Surface of (H2O)11 and Its Physical Implications.

The rich potential energy surface of the water undecamer (H2O)11 was explored with a basin hopping algorithm using a TIP4P potential and other methods followed by extensive ab initio MP2 minimizations and CCSD(T) corrections. This protocol yielded 17, 66, and 125 distinct isomers within 0.5, 1.0, and 2.0 kcal mol-1 of the complete basis set CCSD(T) global minimum, respectively. These isomers were categorized into 15 different families based on their oxygen framework and hydrogen bonding topology. Determination of the global minimum proved challenging because of the presence of many nearly isoenergetic isomers. The predicted global minimum varied among ab initio methods, density functionals, and model potentials, and it was sensitive to the choice of energy extrapolation schemes, higher-order CCSD(T) corrections, and inclusion of zero-point vibrational energy. The presence of a large number of nearly degenerate structures and the isomerization between them has manifested itself in the anomalous broadening of the heat capacity curve of the undecamer in simulations around the melting region.

Effect of Mixing Ammonia and Alkylamines on Sulfate Aerosol Formation.

Sulfate aerosols' cooling effect on the global climate has spurred research to understand their mechanisms of formation. Both theoretical and laboratory studies have shown that the formation of sulfate aerosols is enhanced by the presence of a base like ammonia. Stronger alkylamine bases such as monomethylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) further increase aerosol formation rates by many orders of magnitude relative to that of ammonia. However, recent lab measurements have found that the presence of ammonia and alkylamines together increases nucleation rates by another 1-2 orders of magnitude relative to the stronger alkylamines alone. This work explores that observation by studying the thermodynamic stability of clusters containing up to two sulfuric acids and two bases of the same or different type. Initial configurational sampling is performed using genetic algorithm (GA) interfaced to semiempirical methods to find a large number of low-energy configurations. These structures are then subject to quantum mechanical calculations using PW91, M06-2X, and ωB97X-D functionals and MP2 with large basis sets. The thermodynamics of formation is reviewed to determine if it rationalizes why mixed base systems yield higher rates of aerosol formation than single base ones. The gas phase basicity of the bases in a cluster is the main determinant of binding strength in smaller clusters such as those in the current study while aqueous phase basicity is more important for larger particles. Besides thermodynamic considerations, the differences in aerosol formation mechanisms as a function of size and between the gas and particle phases are discussed.

Capturing the Elusive Water Trimer from the Stepwise Growth of Water on the Surface of the Polycyclic Aromatic Hydrocarbon Acenaphthene.

Polycyclic aromatic hydrocarbons (PAHs) are key players in reaction chemistry. While it is postulated that they serve as a basis for ice grains, there has been no direct detection of PAHs in astronomical environments. We aim to investigate the hydration of PAHs to set a foundation for the future exploration of potential ice formation pathways. We report results from chirped pulse Fourier transform microwave spectroscopy and quantum-chemical calculations for the PAH acenaphthene and acenaphthene complexed with up to four water molecules. The acenaphthene-(H2O)3 complex is of particular interest as the elusive cyclic water trimer was observed. It appears in a slightly distorted configuration when compared with the pure water trimer. This is explained by hydrogen-bond net cooperativity effects. Binding energies for the complexes are presented. Our results provide insight into the onset of complex aggregation that could be occurring in extraterrestrial environments as part of ice grain formation.

Corannulene and its complex with water: a tiny cup of water.

We report the results of a broadband rotational spectroscopic study of corannulene, C20H10, all of its singly substituted 13C isotopologues, and a complex of corannulene with one molecule of water. Corannulene is a polycyclic aromatic hydrocarbon (PAH) with a curved structure that results in a large dipole moment. Observation of 13C isotopic species in natural abundance allowed us to precisely determine the molecular structure of corannulene. The differences between the experimental C-C bond lengths correlate to the double-bond character predicted using Kekule's resonance structures. In the case of C20H10-H2O, the water molecule is found to reside inside the bowl-like structure of corannulene. Our experimental and theoretical results indicate that the water molecule rotates freely around its C2 axis and that dispersion interactions are the dominant contribution to the binding.

ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm.

When assessing the similarity between two isomers whose atoms are ordered identically, one typically translates and rotates their Cartesian coordinates for best alignment and computes the pairwise root-mean-square distance (RMSD). However, if the atoms are ordered differently or the molecular axes are switched, it is necessary to find the best ordering of the atoms and check for optimal axes before calculating a meaningful pairwise RMSD. The factorial scaling of finding the best ordering by looking at all permutations is too expensive for any system with more than ten atoms. We report use of the Kuhn-Munkres matching algorithm to reduce the cost of finding the best ordering from factorial to polynomial scaling. That allows the application of this scheme to any arbitrary system efficiently. Its performance is demonstrated for a range of molecular clusters as well as rigid systems. The largely standalone tool is freely available for download and distribution under the GNU General Public License v3.0 (GNU_GPL_v3) agreement. An online implementation is also provided via a web server ( http://www.arbalign.org ) for convenient use.

Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism.

The nature of the intermolecular forces between water molecules is the same in small hydrogen-bonded clusters as in the bulk. The rotational spectra of the clusters therefore give insight into the intermolecular forces present in liquid water and ice. The water hexamer is the smallest water cluster to support low-energy structures with branched three-dimensional hydrogen-bond networks, rather than cyclic two-dimensional topologies. Here we report measurements of splitting patterns in rotational transitions of the water hexamer prism, and we used quantum simulations to show that they result from geared and antigeared rotations of a pair of water molecules. Unlike previously reported tunneling motions in water clusters, the geared motion involves the concerted breaking of two hydrogen bonds. Similar types of motion may be feasible in interfacial and confined water.

Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters.

MP2 describes hydrogen-bonded systems well, yet a higher-order electron correlation correction in the form of a CCSD(T) calculation is usually necessary to achieve benchmark quality energies. We evaluated the importance and reliability of small basis set CCSD(T) corrections to MP2 (δ(MP2)(CCSD(T))) both on the binding (ΔE) and relative (ΔΔE) energies for a large number of systems including four water dimer stationary points and 57 other clusters up to undecamers, (H2O)11. By comparing the MP2 energies with CCSD(T) and the explicitly correlated MP2-F12 energies with variants of CCSD(T)-F12 using different basis sets, we were able to establish that the correction to the binding energy (ΔE) is sensitive to basis set size, especially for small double-ζ basis sets. On the other hand, the basis set sensitivity of the correction to the relative energy (ΔΔE) within each cluster size is very small. While the δ(MP2)(CCSD(T)) correction to the binding energy might vary in magnitude with basis set size, its effect on relative energy (and hence the stability of isomers) is remarkably consistent. Therefore, we recommend the inclusion of this correction to obtain the relative stability of closely spaced isomers using a double-ζ basis set with polarization and diffuse functions such as aug-cc-pVDZ.

Hydrogen bond cooperativity and the three-dimensional structures of water nonamers and decamers.

Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor OO distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three-body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical OO distances are in good agreement. The cooperativity effects revealed by the hydrogen bond OO distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules.

Hydration of the sulfuric acid-methylamine complex and implications for aerosol formation.

The binary H2SO4-H2O nucleation is one of the most important pathways by which aerosols form in the atmosphere, and the presence of ternary species like amines increases aerosol formation rates. In this study, we focus on the hydration of a ternary system of sulfuric acid (H2SO4), methylamine (NH2CH3), and up to six waters to evaluate its implications for aerosol formation. By combining molecular dynamics (MD) sampling with high-level ab initio calculations, we determine the thermodynamics of forming H2SO4(NH2CH3)(H2O)n, where n = 0-6. Because it is a strong acid-base system, H2SO4-NH2CH3 quickly forms a tightly bound HSO4(-)-NH3CH3(+) complex that condenses water more readily than H2SO4 alone. The electronic binding energy of H2SO4-NH2CH3 is -21.8 kcal mol(-1) compared with -16.8 kcal mol(-1) for H2SO4-NH3 and -12.8 kcal mol(-1) for H2SO4-H2O. Adding one to two water molecules to the H2SO4-NH2CH3 complex is more favorable than adding to H2SO4 alone, yet there is no systematic difference for n ≥ 3. However, the average number of water molecules around H2SO4-NH2CH3 is consistently higher than that of H2SO4, and it is fairly independent of temperature and relative humidity.

Structural analysis of α-fetoprotein (AFP)-like peptides with anti-breast-cancer properties.

The abundance of α-fetoprotein (AFP), a natural protein produced by the fetal yolk sac during pregnancy, correlates with lower incidence of estrogen receptor positive (ER+) breast cancer. The pharmacophore region of AFP has been narrowed down to a four amino acid (AA) region in the third domain of the 591 AA peptide. Our computational study focuses on a 4-mer segment consisting of the amino acids threonine-proline-valine-asparagine (TPVN). We have run replica exchange molecular dynamics (REMD) simulations and used 120 configurational snapshots from the total trajectory as starting configurations for quantum chemical calculations. We optimized structures using semiempirical (PM3, PM6, PM6-D2, PM6-H2, PM6-DH+, PM6-DH2) and density functional methods (TPSS, PBE0, M06-2X). By comparing the accuracy of these methods against RI-MP2 benchmarks, we devised a protocol for calculating the lowest energy conformers of these peptides accurately and efficiently. This protocol screens out high-energy conformers using lower levels of theory and outlines a general method for predicting small peptide structures.

Computational study of the hydration of sulfuric acid dimers: implications for acid dissociation and aerosol formation.

We have investigated the thermodynamics of sulfuric acid dimer hydration using ab initio quantum mechanical methods. For (H(2)SO(4))(2)(H(2)O)(n) where n = 0-6, we employed high-level ab initio calculations to locate the most stable minima for each cluster size. The results presented herein yield a detailed understanding of the first deprotonation of sulfuric acid as a function of temperature for a system consisting of two sulfuric acid molecules and up to six waters. At 0 K, a cluster of two sulfuric acid molecules and one water remains undissociated. Addition of a second water begins the deprotonation of the first sulfuric acid leading to the di-ionic species (the bisulfate anion HSO(4)(-), the hydronium cation H(3)O(+), an undissociated sulfuric acid molecule, and a water). Upon the addition of a third water molecule, the second sulfuric acid molecule begins to dissociate. For the (H(2)SO(4))(2)(H(2)O)(3) cluster, the di-ionic cluster is a few kcal mol(-1) more stable than the neutral cluster, which is just slightly more stable than the tetra-ionic cluster (two bisulfate anions, two hydronium cations, and one water). With four water molecules, the tetra-ionic cluster, (HSO(4)(-))(2)(H(3)O(+))(2)(H(2)O)(2), becomes as favorable as the di-ionic cluster H(2)SO(4)(HSO(4)(-))(H(3)O(+))(H(2)O)(3) at 0 K. Increasing the temperature favors the undissociated clusters, and at room temperature we predict that the di-ionic species is slightly more favorable than the neutral cluster once three waters have been added to the cluster. The tetra-ionic species competes with the di-ionic species once five waters have been added to the cluster. The thermodynamics of stepwise hydration of sulfuric acid dimer is similar to that of the monomer; it is favorable up to n = 4-5 at 298 K. A much more thermodynamically favorable pathway forming sulfuric acid dimer hydrates is through the combination of sulfuric acid monomer hydrates, but the low concentration of sulfuric acid relative to water vapor at ambient conditions limits that process.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Hydration of the bisulfate ion: atmospheric implications.

Using molecular dynamics configurational sampling combined with ab initio energy calculations, we determined the low energy isomers of the bisulfate hydrates. We calculated the CCSD(T) complete basis set (CBS) binding electronic and Gibbs free energies for 53 low energy isomers of HSO(4)(-)(H(2)O)(n=1-6) and derived the thermodynamics of adding waters sequentially to the bisulfate ion and its hydrates. Comparing the HSO(4)(-)/H(2)O system to the neutral H(2)SO(4)/H(2)O cluster, water binds more strongly to the anion than it does to the neutral molecules. The difference in the binding thermodynamics of HSO(4)(-)/H(2)O and H(2)SO(4)/H(2)O systems decreases with increasing number of waters. The thermodynamics for the formation of HSO(4)(-)(H(2)O)(n=1-5) is favorable at 298.15 K, and that of HSO(4)(-)(H(2)O)(n=1-6) is favorable for T < 273.15 K. The HSO(4)(-) ion is almost always hydrated at temperatures and relative humidity values encountered in the troposphere. Because the bisulfate ion binds more strongly to sulfuric acid than it does to water, it is expected to play a role in ion-induced nucleation by forming a strong complex with sulfuric acid and water, thus facilitating the formation of a critical nucleus.