Stability and Structure of Potentially Atmospherically Relevant Glycine Ammonium Bisulfate Clusters.

New particle formation (NPF) is the process by which trace atmospheric acids and bases cluster and grow into particles that ultimately impact climate. Sulfuric acid concentration drives NPF, but nitrogen-containing bases promote the formation of more stable clusters via salt bridge formation. Recent computational efforts have suggested that amino acids can enhance NPF, predicting that they can stabilize new particles via multiple protonation sites, but there has yet to be experimental validation of these predictions. We used mass spectrometry and infrared spectroscopy to study the structure and stability of cationic clusters composed of glycine, sulfuric acid, and ammonia. When collisionally activated, clusters were significantly more likely to eliminate ammonia or sulfuric acid than glycine, while quantum chemical calculations predicted lower binding free energies for ammonia but similar binding free energies for glycine and sulfuric acid. These calculations predicted several low-energy structures, so we compared experimental and computed vibrational spectra to attempt to validate the computationally predicted minimum energy structure. Unambiguous identification of the experimental structure by comparison to these calculations was made difficult by the complexity of the experimental spectra and the fact that the identity of the computed lowest-energy structure depended strongly on temperature. If their vapors are present, amino acids are likely to be enriched in new particles by displacing more weakly bound ammonia, similar to the behavior of other atmospheric amines. The carboxylic acid groups were found to preferentially interact with other carboxylic acids, suggesting incipient organic/inorganic phase separation even at these small sizes.

Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water.

Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.

The driving effects of common atmospheric molecules for formation of prenucleation clusters: the case of sulfuric acid, formic acid, nitric acid, ammonia, and dimethyl amine.

How secondary aerosols form is critical as aerosols' impact on Earth's climate is one of the main sources of uncertainty for understanding global warming. The beginning stages for formation of prenucleation complexes, that lead to larger aerosols, are difficult to decipher experimentally. We present a computational chemistry study of the interactions between three different acid molecules and two different bases. By combining a comprehensive search routine covering many thousands of configurations at the semiempirical level with high level quantum chemical calculations of approximately 1000 clusters for every possible combination of clusters containing a sulfuric acid molecule, a formic acid molecule, a nitric acid molecule, an ammonia molecule, a dimethylamine molecule, and 0-5 water molecules, we have completed an exhaustive search of the DLPNO-CCSD(T)/CBS//ωB97X-D/6-31++G** Gibbs free energy surface for this system. We find that the detailed geometries of each minimum free energy cluster are often more important than traditional acid or base strength. Addition of a water molecule to a dry cluster can enhance stabilization, and we find that the (SA)(NA)(A)(DMA)(W) cluster has special stability. Equilibrium calculations of SA, FA, NA, A, DMA, and water using our quantum chemical ΔG° values for cluster formation and realistic estimates of the concentrations of these monomers in the atmosphere reveals that nitric acid can drive early stages of particle formation just as efficiently as sulfuric acid. Our results lead us to believe that particle formation in the atmosphere results from the combination of many different molecules that are able to form highly stable complexes with acid molecules such as SA, NA, and FA.

Probing the Free Energy of Small Water Clusters: Revisiting Classical Nucleation Theory.

By addressing the defects in classical nucleation theory (CNT), we develop an approach for extracting the free energy of small water clusters from nucleation rate experiments without any assumptions about the form of the cluster free energy. For temperatures higher than ∼250 K, the extracted free energies from experimental data points indicate that their ratio to the free energies predicted by CNT exhibits nonmonotonic behavior as the cluster size changes. We show that this ratio increases from almost zero for monomers and passes through (at least) one maximum before approaching one for large clusters. For temperatures lower than ∼250 K, the behavior of the ratio between extracted energies and CNT's prediction changes; it increases with cluster size, but it remains below one for almost all of the experimental data points. We also applied a state-of-the-art quantum mechanics model to calculate free energies of water clusters (2-14 molecules); the results support the observed change in behavior based on temperature, albeit for temperatures above and below ∼298 K. We compared two different model chemistries, DLPNO-CCSD(T)/CBS//ωB97xD/6-31++G** and G3, against each other and the experimental value for formation of the water dimer.

Amino Acids Compete with Ammonia in Sulfuric Acid-Based Atmospheric Aerosol Prenucleation: The Case of Glycine and Serine.

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.

Photochemistry and Photophysics of Charge-Transfer Excited States in Emissive d10/d0 Heterobimetallic Titanocene Tweezer Complexes.

Transition-metal complexes that undergo ligand-to-metal charge transfer (LMCT) to d0 metals are of interest as possible photocatalysts due to the lack of deactivating d-d states. Herein, the synthesis and characterization of nine titanocene complexes of the formula Cp2Ti(C2Ar)2·MX (where Ar = phenyl, dimethylaniline, or triphenylamine; and MX = CuCl, CuBr, or AgCl) are presented. Solid-state structural characterization demonstrates that MX coordinates to the alkyne tweezers and CuX coordination has a greater structural impact than AgCl. All complexes, including the parent complexes without coordinated MX, are brightly emissive at 77 K (emission max between 575 and 767 nm), with the coordination of MX redshifting the emission in all cases except for the coordination of AgCl into Cp2Ti(C2Ph)2. TDDFT investigations suggest that emission is dominated by arylalkynyl-to-titanium 3LMCT in all cases except Cp2Ti(C2Ph)2·CuBr, which is dominated by CuBr-to-Ti charge transfer. In room-temperature fluid solution, only Cp2Ti(C2Ph)2 and Cp2Ti(C2Ph)2·AgCl are emissive, albeit with photoluminescent quantum yields ≤2 × 10-4. The parent complexes photodecompose in room-temperature solution with quantum yields, Φrxn, between 0.25 and 0.99. The coordination of MX decreases Φrxn by two to three orders of magnitude. There is a clear trend that Φrxn increases as the emission energy increases. This trend is consistent with a competition between energy-gap-law controlled nonradiative decay and thermally activated intersystem crossing between the 3LMCT state and the singlet transition state for decomposition.

Hydrogen-Bond Topology Is More Important Than Acid/Base Strength in Atmospheric Prenucleation Clusters.

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.

Ligand-to-Metal Charge-Transfer Photophysics and Photochemistry of Emissive d0 Titanocenes: A Spectroscopic and Computational Investigation.

Complexes with ligand-to-metal charge-transfer (LMCT) excited states involving d0 metals represent a new design for photocatalysts. Herein, the photochemistry and photophysics of d0 titanocenes of the type Cp2Ti(C2R)2, where C2R = ethynylphenyl (C2Ph), 4-ethynyldimethylaniline (C2DMA), or 4-ethynyltriphenylamine (C2TPA), have been investigated. Cp2Ti(C2Ph)2 and Cp2Ti(C2DMA)2 have also been characterized by single-crystal X-ray diffraction. The two aryl rings in Cp2Ti(C2DMA)2 are nearly face-to-face in the solid state, whereas they are mutually perpendicular for Cp2Ti(C2Ph)2. All three complexes are brightly emissive at 77 K but photodecompose at room temperature when irradiated into their lowest-energy absorption band. The emission wavelengths and photodecomposition quantum yields are as follows: Cp2Ti(C2Ph)2, 575 nm and 0.65; Cp2Ti(C2TPA)2, 642 nm and 0.42; Cp2Ti(C2DMA)2, 672 nm and 0.25. Extensive benchmarking of the density functional theory (DFT) model against the structural data and of the time-dependent DFT (TDDFT) model against the absorption and emission data was performed using combinations of 13 different functionals and 4 basis sets. The model that predicted the absorption and emission data with the greatest fidelity utilized MN15/LANL2DZ for both the DFT optimization and the TDDFT. Computational analysis shows that absorption involves a transition to a 1LMCT state. Whereas the spectroscopic data for Cp2Ti(C2TPA)2 and Cp2Ti(C2DMA)2 are well modeled using the optimized structure of these complexes, Cp2Ti(C2Ph)2 required averaging of the spectra from multiple rotamers involving rotation of the Ph rings. Consistent with this finding, an energy scan of all rotamers showed a very flat energetic surface, with less than 1.3 kcal/mol separating the minimum and maximum. The computational data suggest that emission occurs from a 3LMCT state. Optimization of the 3LMCT state demonstrates compression of the C-Ti-C bond angle, consistent with the known products of photodecomposition.

Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere.

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 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.

Calculating Reliable Gibbs Free Energies for Formation of Gas-Phase Clusters that Are Critical for Atmospheric Chemistry: (H2SO4)3.

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.

Insights into the charge-transfer character of electronic transitions in RCp2Ti(C2Fc)2 complexes using solvatochromism, resonance Raman spectroscopy, and TDDFT.

A series of complexes with low-energy FeII to TiIV metal-to-metal charge-transfer (MMCT) transitions, Cp2Ti(C2Fc)2, Cp*2Ti(C2Fc)2, and MeOOCCp2Ti(C2Fc)2, was investigated using solvatochromism and resonance Raman spectroscopy (RRS) augmented with time-dependent density functional theory (TDDFT) calculations in order to interrogate the nature of the CT transitions. Computational models were benchmarked against the experimental UV-Vis spectra and B3LYP/6-31G(d) was found to most faithfully represent the spectra. The energy of the MMCT transition was measured in 15 different solvents and a multivariate fit to the Catalán solvent parameters - solvent polarizability (SP), solvent dipolarity (SdP), solvent basicity (SB), and solvent acidity (SA) - was performed. The effect of SP indicates a greater degree of electron delocalization in the excited state (ES) than the ground state (GS). The small negative solvatochromism with respect to SdP indicates a smaller dipole moment in the ES than the GS. The effect of SB is consistent with charge-transfer to Ti. Upon excitation into the MMCT absorption band, the RRS data show enhancement of the alkyne stretching modes and of the out-of-plane bending modes of the cyclopentadienyl ring connected to Fe and the alkyne bridge. This is consistent with changes in the oxidation states of Ti and Fe, respectively. The higher-energy transitions (350-450 nm) show enhancement of vibrational modes consistent with ethnylcyclopentadienyl to Ti ligand-to-metal charge transfer (LMCT). The RRS data is consistent with the TDDFT predicted character of these transitions. TDDFT suggests that the lowest-energy transition in Cp2Ti(C2Fc)2CuI, where CuI is coordinated between the alkynes, retains its FeII to TiIV MMCT character, in agreement with the RRS data, but that the lowest-energy transitions have significant CuI to Ti character. For Cp2Ti(C2Fc)2CuI, excitation into the low-energy MMCT absorption band results in selective enhancement of the symmetric alkynyl stretching mode.

Water-Mediated Peptide Bond Formation in the Gas Phase: A Model Prebiotic Reaction.

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.

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 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.