Density Functional Theory Calculations of the Structures, Binding Energies, and Infrared Spectra of Methanol Clusters

Interaction between hydroxymethanesulfonic acid and several organic compounds and its atmospheric significance

The interactions of the micro-mechanism of hydroxymethanesulfonic acid (HMSA) with the typical small organic molecule in atmospheric (X = methanol, formaldehyde, formic acid, methyl formate, dimethyl ether, acetone) has been investigated by density functional theory (DFT), quantum theory of atoms in molecules (QTAIM), Generalized Kohn-Sham Enery Decomposition Analysis (GKS-EDA) and the atmospheric clusters dynamic code (ACDC). The results of DFT show that the stable six- to eight-membered ring structures are easily formed in HMSA-X clusters. According to the topological analysis results of the AIM theory and the IRI method, a strong hydrogen bonding interaction is present in the complex. GKS-EDA results show that electrostatic energy is the main contributor to the interaction energy as it accounts for 51 %-55 % of the total attraction energy. The evaporation rates of HMSA-HMSA and HMSA-HCOOH clusters were much lower than those of the other HMSA complexes. In addition, the Gibbs energy of formation (ΔG) of HMSA-X dimers is investigated under atmosphere temperature T = 217-298 K and p = 0.19-1.0 atm, the ΔG decreased with decreasing of the atmosphere temperature and increased with the decrease of atmospheric pressure, indicating that the low temperature and high pressure may significantly facilitate to the formation of dimers.

Ionizing radiation induces cross-linking of two noncovalently bound collagen mimetic peptide triple helices in the absence of a molecular environment

Cross-linking is a fundamental molecular process that is highly important for many applications, in particular, to tune the properties of collagen-based biomaterials. Chemical reagents, the action of enzymes or physical factors such as heat or radiation can facilitate collagen cross-linking. Ionizing radiation has the advantages of being fast, efficient and free from potentially toxic reagents. Collagen cross-linking by ionizing radiation is thought to occur via a water-mediated pathway. In the past, synthesized collagen mimetic peptides have proven to be of great value for understanding the influence of the amino acid sequence on the stability of tertiary (fibrous) as well as secondary (triple helical) structures of collagen. Cross-linking of synthetic collagen mimetic peptides is often used for modifying the properties of biomaterials. In this work, for the first time, we apply radiation-induced cross-linking to synthetic collagen mimetic peptides and present an experimental and theoretical study of peptide hexamers consisting of two noncovalently bound triple helices in the absence of a molecular environment, i.e. in the gas phase. Our results show that X-ray photoabsorption of the hydroxylated hexamer leads to ionization and cross-linking of the two triple helices: thus, we found evidence that cross-linking can be achieved by ionizing radiation, without the presence of any reagent or water. We propose a cross-linking mechanism involving the creation of two radicals on hydroxyproline side-chains and their recombination, ultimately leading to covalent bond formation between the triple helices.

Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning

We propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in ab initio methods to train a deep-learning machine learning (ML) model using SchNet.

Effect of confinement on the dynamics of 1-propanol and other monohydroxy alcohols

We report the effect of confinement on the dynamics of three monohydroxy alcohols (1-propanol, 2-ethyl-1-hexanol, and 4-methyl-3-heptanol) differing in their chemical structure and, consequently, in the dielectric strength of the "Debye" process. Density functional theory calculations in bulk 1-propanol identified both linear and ring-like associations composed of up to five repeat units. The simulation results revealed that the ring structures, with a low dipole moment (∼2 D), are energetically preferred over the linear assemblies with a dipole moment of 2.18 D per repeat unit. Under confinement in nanoporous alumina (in templates with pore diameters ranging from 400 to 20 nm), all dynamic processes were found to speed up irrespective of the molecular architecture. The characteristic freezing temperatures of the α and the Debye-like processes followed the pore size dependence: T_a,D=T_a,D ^bulk-A/d^1/2, where d is the pore diameter. The characteristic "freezing" temperatures for the Debye-like (the slow process for confined 1-propanol is non-Debye) and the α-processes decrease, respectively, by 6.5 and 13 K in confined 1-propanol, by 9.5 and 19 K in confined 2-ethyl-1-hexanol, and by 9 and 23 K in confined 4-methyl-3-heptanol within the same 25 nm pores. In 2-ethyl-1-hexanol, confinement reduced the number of linearly associated repeats from approximately heptamers in the bulk to dimers within 25 pores. In addition, the slower process in bulk 2-ethyl-1-hexanol and 4-methyl-3-heptanol, where the signal is dominated by ring-like supramolecular assemblies, is clearly non-Debye. The results suggest that the effect of confinement is dominant in the latter assemblies.

Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids

Hydrogen-bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc.); hence, the lifetime of these structures is an important microscopic parameter, which can be calculated via computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short-timescale regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and be weakly dependent on criteria such as the bonding distance and angle, much similar to non-hydrogen-bonding simple liquids, while the long-timescale regime is known to have some power law dependence. Unexpectedly, all the hydrogen-bonding liquids studied herein, namely water and alcohols, display three highly hierarchical specific lifetimes, in the sub-picosecond range 0-0.5 ps. The dominant lifetime depends very strongly on the bonding-distance criterion and is related to hydrogen-bonded pairs. This mode is absent in non-H-bonding simple liquids. The secondary and tertiary mean lifetimes are related to clusters and are nearly independent of the bonding criterion. Of these two lifetimes, only the first one can be related to that of simple liquids, which poses the question of the nature of the third lifetime. The study of alcohols reveals that this third lifetime is related to the topology of the H-bonded clusters and that its distribution may also be affected by the alkyl tail surrounding the "bath". This study shows that hydrogen-bonding liquids have a universal hierarchy of hydrogen-bonding lifetimes with a timescale regularity across very different types, and which depend on the topology of the cluster structures.

Temperature-dependent oxidation of BSCAPE molecule in methanol medium

Temperature-dependent solvation free energy and oxidation by free energy of ionization of 2-Phenylethyl (2E)-3-(1-benzenesulfonyl-4,5-dihydroxyphenyl) acrylate (BSCAPE) in methanol medium are the concerns of the present work. This molecule is a relevant phenolic acid enclosing multiple bioactivities. The explicit, implicit and discrete-continuum models of solvation were used. The methanol molecules were coordinated to this acid to form cluster complexes. The dual method M06-2X/6-31++G(d,p)//B3LYP/6-31G(d) was employed along with basis set superposition error correction. The results show that, the free energy of coordination and solvation are distant. Both quantities increase with temperature. From discrete-continuum treatment, there is non-spontaneity of solvation process, while coordination yielded spontaneity and non-spontaneity at cold and hot room temperatures, respectively. The ionization potential in gas phase, decreases with temperature. All the solvation models yielded lower ionization potential than that of gas phase. Thus, it follows that, the increase of temperature and methanol medium favours the oxidation of BSCAPE. Consequently, this favours its metabolism processes.

Infrared spectra of PEHA molecule and its resistance to oxidation in water and methanol media at 298.15 K: solvent cluster size dependency

The present work investigates the infrared spectra and solvation free energies (SE) of PEHA ((E)-2-(Pyridin-2-yl) ethyl 3-(3,4-dihydroxyphenyl) acrylate) and their impact on the oxidation. The latter was examined through the ionization potential parameter (IP). These investigations were carried out by the DFT method at B3LYP/6-31G(d) for optimization and frequency calculations and corrected for BSSE. X3LYP/6-311++G(2d,2p) was employed for single-point energy calculations. Water and methanol cluster sizes were used for solvation through the explicit solvent model. Thus, the infrared spectra show that the overview frequencies of PEHA compare well with the experimental results. The intense infrared absorptions of complexes are due to the stretching of O-H bonds of solvent clusters in the range 2600-3850 cm^-1. The binding energy per solvent molecule of complexes was calculated and shows that water and methanol clusters mimic the liquid state as from 5 to 10 solvent molecules. The SE of PEHA increases with the increase of the cluster size of water and methanol in the direction of the limit. The latter was censured by the solvation done using the combined explicit-implicit solvent model. As for IP parameter, the results are largely above the IP limit and lower than the IP from gas phase. Thus, water and methanol media have an effect of lowering the IP of PEHA compound. Consequently, both media favour the oxidation of PEHA molecule, which facilitates its metabolism in human organism.

Internal electric fields in methanol [MeOH]2-6 clusters

Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding pattern in water and methanol are due to the presence of the methyl group in methanol. The presence of the methyl group leads to formation of C-HO hydrogen bonds apart from the usual O-HO hydrogen bonds. The electric fields evaluated along the hydrogen bonded donor OH and CH groups reveal that the C-HO hydrogen bonds can significantly influence the structure and energetics (by about 20%) of methanol clusters. A linear Stark effect was observed on the hydrogen bonded OH groups in methanol clusters with a Stark tuning rate of 3.1 cm^-1 (MV cm^-1)^-1 as an average behaviour. Furthermore, the Stark tuning of the OH oscillators in methanol depends on their hydrogen bonding environment wherein molecules with the DAA motif show higher rates than the rest. The present work suggests that the OH group of methanol has higher sensitivity as a vibrational probe relative to the OH group of water.

Exploration of the potential energy surfaces of small ethanol clusters

The potential energy surfaces of small ethanol clusters, from dimer to pentamer, have been thoroughly explored using two different levels of theory. There is a clear relative energy gap between cyclic, linear and branched cyclic structures.

FTIR studies, DFT calculations and time domain reflectometry studies on tetrahydrofuran - methanol binary solutions

FTIR signature of neat tetrahydrofuran (THF), methanol (MeOH) and their binary solutions at various molefractions (0.8:0.2 (THF:MeOH), 0.6:0.4, 0.4:0.6 and 0.2:0.8) have been recorded. Density Functional Theory (DFT) calculations have also been carried out on THF, MeOH multimers and possible THF-MeOH complex molecules. The results of FTIR studies and DFT calculations confirm the formation of 1:3 (THF:MeOH) and 1:4 complex structures with (MeOH)O - H⋯O(THF), (MeOH methyl)C - H⋯O(THF) and (THF methylene)C - H⋯O(MeOH) H-bond interactions. (MeOH)O - H⋯O(MeOH) homointeractions among the MeOH trimers and tetramers are stronger than the THF-MeOH heterointeractions in complexes. But, the stability of 1:4 complexes is more than that of the trimers and tetramers as inferred from the interaction energy values obtained by DFT calculations. Time Domain Reflectometry (TDR) study has also been carried out on the THF-MeOH binary solutions in the frequency range 10 MHz-30 GHz at 298 K. The results of dielectric studies have been correlated with that of FTIR studies and DFT calculations.

Competition between hydrogen bonds and van der Waals forces in intermolecular structure formation of protonated branched-chain alcohol clusters

To investigate the influence of bulky alkyl groups on hydrogen-bonded (H-bonded) network structures of alcohols, infrared (IR) spectra of protonated clusters of 2-propanol (2-PrOH) and tert-butyl alcohol (t-BuOH) were observed in the OH and CH stretch regions. In addition, by varying the tag species, the temperature dependence profile of the isomer population of H+(t-BuOH)n was revealed. An extensive search for stable isomers was performed using dispersion-corrected density functional theory methods, and temperature-dependent IR spectral simulations were done on the basis of the harmonic superposition approximation. The computational results qualitatively agreed with the observed size and temperature dependence of the H-bonded network structures of these protonated bulky alcohol clusters. However, the difficulty in the quantitative evaluation of dispersion was also demonstrated. It was shown that H+(2-PrOH)n (n = 4-7) have essentially the same network structures as the protonated normal alcohol clusters studied so far. On the other hand, H+(t-BuOH)n (n = 4-8) showed a clear preference for the smaller-membered ring structures, that is very different from the preference of the protonated normal alcohol clusters. The origin of the different structure preferences was discussed in terms of the steric effect and dispersion.

Accurate Quantification of N-Glycolylneuraminic Acid in Therapeutic Proteins Using Supramolecular Mass Spectrometry

Practical applications of innovative host-guest systems are challenging because of unexpected guest competitors and/or subtle environmental differences. Herein, a supramolecular mass spectrometry (MS)-based method using a synthetic host, cucurbit[7]uril (CB[7]), was developed for identifying and quantifying N-glycolylneuraminic acid (Neu5Gc) in therapeutic glycoproteins, which critically reduces drug efficacy. The development of a reliable derivatization-free analytical method for Neu5Gc is highly challenging because of the interference by the abundant N-acetylneuraminic acid (Neu5Ac). CB[7] recognized the subtle structural differences between Neu5Gc and Neu5Ac. Distinct host-guest interactions between CB[7] and the two sialic acids produced a highly linear relationship between the complexation and concentration proportions of the two sialic acids in MS. Furthermore, the developed method had sub-picomolar quantification limits and a wide range of applicability for diverse glycoproteins, demonstrating the potential utility of this method as a reliable assay of Neu5Gc in therapeutic glycoproteins.

Solvation energies of the proton in methanol revisited and temperature effects

Various functionals assessing solvation free energies and enthalpies of the proton in methanol.

Hydrogen bond docking site competition in methyl esters

The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm^-1)>TFE-MF (93cm^-1)>TFE-MTFA (44cm^-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol^-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF₃ substitution on MTFA, while the replacement of an H atom with a CH₃ group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

Contribution of methane sulfonic acid to new particle formation in the atmosphere

Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants. Topological analysis employing quantum theory of atoms in molecules shows that the charge density of the SOH⋯O hydrogen bonds of the MSA complexes falls in the range of hydrogen bonding criteria, but the Laplacian at bond critical points exceeds the range, which is due to the strong hydrogen bonding interactions. In all the studied complexes, the electrostatic interactions are found to be the main attractive force by localized molecular orbital energy decomposition analysis. All these indicate the environmental fate of MSA could play the role of nucleation centers in new particle formation. The effect of the atmospheric heights (0-12 km) was also considered. The Gibbs free energy of formation decreases with the increase of the atmospheric height owing to the decrease of the atmospheric temperature and pressure. The calculated Gibbs free energies of formation within the atmospheric temperature and pressure range could help to understand the atmospheric pollution.

Infrared absorption of methanol-water clusters (CH3OH)n(H2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique

We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as M_nW, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters M_nW as protonated forms M_n-1WH⁺. The variations in intensities of M_n-1WH⁺ were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm^-1. IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H₂O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm^-1, whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm^-1. For M₂W, the free OH band of H₂O was observed at 3721 cm^-1, whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm^-1, corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M₃W, the free OH shifted to 3715 cm^-1, and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm^-1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M₄W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M₅ of which the cyclic form dominates.

Hydrogen bonding in cyclic complexes of carboxylic acid–sulfuric acid and their atmospheric implications

Carboxylic acids form cyclic ring structures with sulfuric acid and they could potentially be important in new particle formation.

Structural properties of methanol–water binary mixtures within the quantum cluster equilibrium model

The Quantum Cluster Equilibrium (QCE) method computes cluster distributions and thermodynamic properties of binary methanol–water mixtures in agreement with experiments.

Mass-selected IR-VUV (118 nm) spectroscopic studies of radicals, aliphatic molecules, and their clusters

Mass-selected IR plus UV/VUV spectroscopy and mass spectrometry have been coupled into a powerful technique to investigate chemical, physical, structural, and electronic properties of radicals, molecules, and clusters. Advantages of the use of vacuum ultraviolet (VUV) radiation to create ions for mass spectrometry are its application to nearly all compounds with ionization potentials below the energy of a single VUV photon, its circumventing the requirement of UV chromophore group, its inability to ionize background gases, and its greatly reduced fragmenting capabilities. In this review, mass-selected IR plus VUV (118 nm) spectroscopy is introduced first in a general manner. Selected application examples of this spectroscopy are presented, which include the detections and structural analysis of radicals, molecules, and molecular clusters in a supersonic jet.

Solvation Energies of the Proton in Methanol

pKa's, proton affinities, and proton dissociation free energies characterize numerous properties of drugs and the antioxidant activity of some chemical compounds. Even with a higher computational level of theory, the uncertainty in the proton solvation free energy limits the accuracy of these parameters. We investigated the thermochemistry of the solvation of the proton in methanol within the cluster-continuum model. The scheme used involves up to nine explicit methanol molecules, using the IEF-PCM and the strategy based on thermodynamic cycles. All computations were performed at B3LYP/6-31++G(dp) and M062X/6-31++G(dp) levels of theory. It comes out from our calculations that the functional M062X is better than B3LYP, on the evaluation of gas phase clustering energies of protonated methanol clusters, per methanol stabilization of neutral methanol clusters and solvation energies of the proton in methanol. The solvation free energy and enthalpy of the proton in methanol were obtained after converging the partial solvation free energy of the proton in methanol and the clustering free energy of protonated methanol clusters, as the cluster size increases. Finally, the recommended values for the solvation free energy and enthalpy of the proton in methanol are -257 and -252 kcal/mol, respectively.

Dynamics and mechanism of structural diffusion in linear hydrogen bond

Dynamics and mechanism of proton transfer in a protonated hydrogen bond (H-bond) chain were studied, using the CH(3)OH(2)(+)(CH(3)OH)(n) complexes, n = 1-4, as model systems. The present investigations used B3LYP/TZVP calculations and Born-Oppenheimer MD (BOMD) simulations at 350 K to obtain characteristic H-bond structures, energetic and IR spectra of the transferring protons in the gas phase and continuum liquid. The static and dynamic results were compared with the H(3)O(+)(H(2)O)(n) and CH(3)OH(2)(+)(H(2)O)(n) complexes, n = 1-4. It was found that the H-bond chains with n = 1 and 3 represent the most active intermediate states and the CH(3)OH(2)(+)(CH(3)OH)(n) complexes possess the lowest threshold frequency of proton transfer. The IR spectra obtained from BOMD simulations revealed that the thermal energy fluctuation and dynamics help promote proton transfer in the shared-proton structure with n = 3 by lowering the vibrational energy for the interconversion between the oscillatory shuttling and structural diffusion motions, leading to a higher population of the structural diffusion motion than in the shared-proton structure with n = 1. Additional explanation on the previously proposed mechanisms was introduced, with the emphases on the energetic of the transferring proton, the fluctuation of the number of the CH(3)OH molecules in the H-bond chain, and the quasi-dynamic equilibriums between the shared-proton structure (n = 3) and the close-contact structures (n ≥ 4). The latter prohibits proton transfer reaction in the H-bond chain from being concerted, since the rate of the structural diffusion depends upon the lifetime of the shared-proton intermediate state.

THE COOPERATIVITY BETWEEN HYDROGEN AND HALOGEN BONDS

The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y ( X: C2H2, H2O, NH3, HCI, HCN, HF; Y: HF, BrF, Br2 is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X -ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y -ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.