Effect Of Microhydration Research Articles

Effect of a single water molecule on the conformational preferences of a capped Pro–Gly dipeptide in the gas phase

Herein, we have investigated the effect of microhydration on the secondary structure of a capped dipeptide Boc-DPro-Gly-NHBn-OMe (Boc = tert-butyloxycarbonyl, Bn = Benzyl), i.e., Pro–Gly (PG) with a single H2O molecule using gas-phase laser spectroscopy combined with quantum chemistry calculations. Observation of a single conformer of the monohydrated peptide has been confirmed from IR-UV hole-burning spectroscopy. Both gas-phase experimental and theoretical IR spectroscopy results confirm that the H2O molecule is inserted selectively into the relatively weak C7 hydrogen bond (γ-turn) between the Pro C=O and NHBn N–H groups of the peptide, while the other C7 hydrogen bond (γ-turn) between the Gly N–H and Boc C=O groups remains unaffected. Hence, the single H2O molecule in the PG⋯(H2O)1 complex significantly distorts the peptide backbone without appreciable modification of the overall secondary structural motif (γ–γ) of the isolated PG monomer. The nature and strength of the intra- and inter-molecular hydrogen bonds present in the assigned conformer of the PG⋯(H2O)1 complex has also been examined by natural bond orbital and non-covalent interaction analyses. The present investigation on the monohydrated peptide demonstrates that several H2O molecules may be required for switching the secondary structure of PG from the double γ-turn to a β-turn that is favorable in the condensed phase.

Effect of Microhydration in Tuning the Photophysical Behavior of a Luminescent DNA Probe Revealed by Non‐Adiabatic Dynamics

AbstractWe report non‐adiabatic dynamics, performed in the surface hopping formalism, of 2‐thienyl‐3‐hydroxychromone, an environment‐dependent luminescent organic DNA probe. In particular we have shown that the first shell solvent water molecules undergo a rather complex reorganization upon light excitation. This involves also the triggering of a water‐mediated proton transfer process which leads to the formation of the tautomeric structure. The presence of this solvent‐mediated transfer mechanism globally diminishes the intersystem crossing efficiency, and hence the population of the triplet state manifold, as compared to the non‐solvated systems. Our results also point out the non‐innocent role of solvent networks in tuning complex photophysical processes, while opening competitive relaxation channels.

Charge-Shifted Weak Noncovalent Interactions in the Atmospherically Important OCS Microhydrates.

Stratospheric aerosol, mainly comprising microhydrated carbonyl sulfide (OCS), is among the primary drivers of climate change. In this study, we investigate the effect of microhydration on the structure, energetics, and vibrational properties of the neutral OCS molecule using ab initio calculation, molecular electrostatic potential (MESP), topological analyses of electron density, and natural bond orbital (NBO) analyses. The complexation energy increases with the cluster size, and the first solvation shell of OCS consists of four water molecules that interact with the OCS moiety preferentially through SOCS···OW, OOCS···OW, and COCS···OW type of weak noncovalent interaction instead of the typical OOCS···H-OW and SOCS···H-OW H-bonds. These noncovalent interactions originate due to the electron shift from the water oxygen lone pair to the antibonding orbital of C═S [BD*(C═S)], sometimes via BD*(C═O), which substantially perturbs the bending mode of surrounding water molecules. The present study thus unravels the underlying relationship between the OCS atmospheric hydrolysis and the charge-shifted noncovalent interactions.

Effects of Microhydration on the Mechanisms of Hydrolysis and Cl- Substitution in Reactions of N2 O5 and Seawater.

The reaction of N2 O5 at atmospheric interfaces has recently received considerable attention due to its importance in atmospheric chemistry. N2 O5 reacts preferentially with Cl- to form ClNO2 /NO3 - (Cl- substitution), but can also react with H2 O to form 2HNO3 (hydrolysis). In this paper, we explore these competing reactions in a theoretical study of the clusters N2 O5 /Cl- /nH2 O (n=2-5), resulting in the identification of three reaction motifs. First, we uncovered an SN 2-type Cl- substitution reaction of N2 O5 that occurs very quickly due to low barriers to reaction. Second, we found a low-lying pathway to hydrolysis via a ClNO2 intermediate (two-step hydrolysis). Finally, we found a direct hydrolysis pathway where H2 O attacks N2 O5 (one-step hydrolysis). We find that Cl- substitution is the fastest reaction in every cluster. Between one-step and two-step hydrolysis, we find that one-step hydrolysis barriers are lower, making two-step hydrolysis (via ClNO2 intermediate) likely only when concentrations of Cl- are high.

Low-Energy Electron Induced Reactions in Metronidazole at Different Solvation Conditions.

Metronidazole belongs to the class of nitroimidazole molecules and has been considered as a potential radiosensitizer for radiation therapy. During the irradiation of biological tissue, secondary electrons are released that may interact with molecules of the surrounding environment. Here, we present a study of electron attachment to metronidazole that aims to investigate possible reactions in the molecule upon anion formation. Another purpose is to elucidate the effect of microhydration on electron-induced reactions in metronidazole. We use two crossed electron/molecular beam devices with the mass-spectrometric analysis of formed anions. The experiments are supported by quantum chemical calculations on thermodynamic properties such as electron affinities and thresholds of anion formation. For the single molecule, as well as the microhydrated condition, we observe the parent radical anion as the most abundant product anion upon electron attachment. A variety of fragment anions are observed for the isolated molecule, with NO2− as the most abundant fragment species. NO2− and all other fragment anions except weakly abundant OH− are quenched upon microhydration. The relative abundances suggest the parent radical anion of metronidazole as a biologically relevant species after the physicochemical stage of radiation damage. We also conclude from the present results that metronidazole is highly susceptible to low-energy electrons.

Effect of Microhydration on the Temporary Anion States of Pyrene.

The influence of incremental hydration (≤4) on the electronic resonances of the pyrene anion is studied using two-dimensional photoelectron spectroscopy. The photoexcitation energies of the resonances do not change; therefore, from the anion’s perspective, the resonances remain the same, but from the neutral’s perspective of the electron–molecule reaction, the resonances decrease in energy by the binding energy of the water molecules. The autodetachment of the resonances shows that hydration has very little effect, showing that even the dynamics of most of the resonances are not impacted by hydration. Two specific resonances do show changes that are explained by the closing of specific autodetachment channels. The lowest-energy resonance leads to efficient electron capture as observed through thermionic emission and evaporation of water molecules (dissociative electron attachment). The implications of low-energy electron capture in dense molecular interstellar clouds are discussed.

Understanding the Interplay between the Nonvalence and Valence States of the Uracil Anion upon Monohydration.

In this work we present an ab initio investigation into the effect of monohydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the nonvalence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H2O)1 cluster. The results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of microhydration on the electronic structure and electron capture dynamics of nucleobases.

Infrared Spectrum of the Adamantane+ -Water Cation: Hydration-Induced C-H Bond Activation and Free Internal Water Rotation.

Diamondoid cations are reactive intermediates in their functionalization reactions in polar solution. Hydration is predicted to strongly activate their C−H bonds in initial proton abstraction reactions. To study the effects of microhydration on the properties of diamondoid cations, we characterize herein the prototypical monohydrated adamantane cation (C10H16 +–H2O, Ad+–W) in its ground electronic state by infrared photodissociation spectroscopy in the CH and OH stretch ranges and dispersion‐corrected density functional theory (DFT) calculations. The water (W) ligand binds to the acidic CH group of Jahn–Teller distorted Ad+ via a strong CH⋅⋅⋅O ionic H‐bond supported by charge–dipole forces. Although W further enhances the acidity of this CH group along with a proton shift toward the solvent, the proton remains with Ad+ in the monohydrate. We infer essentially free internal W rotation from rotational fine structure of the ν3 band of W, resulting from weak angular anisotropy of the Ad+–W potential.

Infrared Spectrum of the Adamantane+–Water Cation: Hydration‐Induced C−H Bond Activation and Free Internal Water Rotation

AbstractDiamondoid cations are reactive intermediates in their functionalization reactions in polar solution. Hydration is predicted to strongly activate their C−H bonds in initial proton abstraction reactions. To study the effects of microhydration on the properties of diamondoid cations, we characterize herein the prototypical monohydrated adamantane cation (C10H16+–H2O, Ad+–W) in its ground electronic state by infrared photodissociation spectroscopy in the CH and OH stretch ranges and dispersion‐corrected density functional theory (DFT) calculations. The water (W) ligand binds to the acidic CH group of Jahn–Teller distorted Ad+via a strong CH⋅⋅⋅O ionic H‐bond supported by charge–dipole forces. Although W further enhances the acidity of this CH group along with a proton shift toward the solvent, the proton remains with Ad+in the monohydrate. We infer essentially free internal W rotation from rotational fine structure of the ν3band of W, resulting from weak angular anisotropy of the Ad+–W potential.

Ab Initio Study of the Stepwise versus Concerted Fragmentation Pathways in Microhydrated Thymine Radical Cations.

Thymine radiation-induced fragmentation is characterised by ring opening and the loss of HNCO/NCO. These pathways have been investigated using DFT calculations in the presence of zero, one and two water molecules. In addition to the already characterised stepwise fragmentation mechanism, we propose a novel concerted pathway reported here for the first time. We show that both the stepwise and concerted mechanisms are competitive with activation energies of 2.05 eV and 2.00 eV, respectively, in the gas phase. The effect of microhydration on these mechanisms are examined based on the most stable conformations found by an exploration of the potential energy surface performed by using DFT-based ab initio molecular dynamics. Microhydration is also accompanied by an increase in the activation energies, with respect to gas phase, amounting to 0.47 eV-an increase that is associated to a stabilising effect of water in agreement with recent experimental studies. However, we also point out that this effect is greatly dependent on the specific water arrangement around thymine and could be limited to only 0.13 eV for some configurations.

Microhydration of Polymer Electrolyte Membranes: A Comparison of Hydrogen-Bonding Networks and Spectral Properties of Nafion and Bis[(perfluoroalkyl)sulfonyl] Imide.

The microhydration effects on two polymer electrolyte membrane materials, Nafion and bis[(perfluoroalkyl)sulfonyl] imide (PFSI), were investigated by analyzing optimized geometries and normal modes of vibration. The calculations were performed on periodic structural models with systematic increases of the number of water molecules around the polar head groups. A strong effect of microhydration on the structure of the polar head groups was observed due to a large red shift of the SO-H (Nafion) and N-H (PFSI) stretching modes of about 600-1000 cm-1. In addition, frequency calculations showed how H2O stretching vibrations contribute to the overall high frequency vibrational spectra. Both asymmetric and symmetric stretching modes of the SO2 group (νas(SO2) and νs(SO2)) were red-shifted indicating the S-O bond weakening upon microhydration. PFSI models showed spectral changes upon microhydration comparable to those observed for Nafion. However, distinct spectral features related to the differences in the polar head groups were observed. Lower N-H stretching frequency compared to the SO-H mode explained a stronger acid character of the PFSI polar headgroup and its earlier proton transfer ability (less water molecules needed for the proton release).

Time-resolved dynamics in iodide-uracil-water clusters upon excitation of the nucleobase.

The dynamics of iodide-uracil-water (I-·U·H2O) clusters following π-π* excitation of the nucleobase are probed using time-resolved photoelectron spectroscopy. Photoexcitation of this cluster at 4.77 eV results in electron transfer from the iodide moiety to the uracil, creating a valence-bound anion within the cross correlation of the pump and probe laser pulses. This species can decay by a number of channels, including autodetachment and dissociation to I- or larger anion fragments. Comparison of the energetics of the photoexcited cluster and its decay dynamics with those of the bare iodide-uracil (I-·U) complex provides a sensitive probe of the effects of microhydration on these species.

Ionization and fragmentation of uracil upon microhydration.

We study at the DFT level the ionization and the fragmentation of uracil in the presence of zero, one and two water molecules, to unravel the effect of microhydration on the reactivity of this nucleobase. We show that the microhydration lowers the adiabatic and vertical ionization potentials by 0.41 eV and 0.22 eV, respectively. Furthermore, microhydration increases the activation energies of the different dissociation channels up to 0.5 eV and restricts the formation of some fragments, in particular those corresponding to the C5-C6 fragmentation pathway. For the first time, our theoretical study shows new transition states and minima not found for the gas phase, hence indicating a change in the fragmentation mechanisms, as well as a stabilizing effect of microhydration, confirming previous experimental studies.

Role of hydrogen bonding in the conformations of lidocaine, mepivacaine and bupivacaine under aqueous solvation

We report the lowest energy conformers obtained by a conformational search for protonated lidocaine, mepivacaine and bupivacaine in the gas phase at the B3LYP/cc-pVTZ level of theory, and examine the effect of aqueous solvation on the energetics using the COSMO continuous solvent model. We also look at the effect of microhydration by crystallization water molecules on the relative energies of the conformers. We found that water molecules and chloride ion stabilize conformers by hydrogen bonding. We report a revised structure for the conformer present in solution for lidocaine hydrochloride.

Microhydration of oxalic acid leading to dissociation

ABSTRACTThe effect of microhydration on the simplest dicarboxylic acid, namely oxalic acid, leading to the dissociation of its proton, is studied using first principle-based electronic structure calculations. The geometry of the hydrated clusters of oxalic acid considering up to seven water molecules is determined at ωB97X-D/aug-cc-pVDZ level of theory. Solvent stabilisation and interaction energy parameters are calculated applying CCSD(T) level of theory. The calculated free energy of formation shows that the hydrated oxalic acid clusters are stable only at low temperature and pressure. Though the solvent stabilisation energy increases linearly with an increase in the size of the hydrated cluster, the calculated interaction energy, acidic O–H bond dipole moment and hydrogen bond energy show characteristic features of ion pair formation. The spectral manifestation of the weakening hydroxyl bond is observed as red shift in its stretching frequency. A rigid potential energy scan, altering the dissociating O–H bond length of the oxalic acid molecule, shows an energy barrier for acid to water proton transfer in all cases except hepta-hydrate of oxalic acid, where a barrier-less proton transfer occurs. The number of water molecules (n) needed for dissociation of oxalic acid molecule is consistent with the value obtained from recently reported emperical correlation between n and pKa.

Theoretical study of resonance formation in microhydrated molecules. I. Pyridine-(H2O)n, n = 1,2,3,5

We present R-matrix calculations for electron scattering from microhydrated pyridine. We studied the pyridine-H2O cluster at static-exchange (SE), SE + polarization, and close-coupling levels, and pyridine-(H2O)n n = 2, 3, and 5 at SE level only in order to investigate the effect of hydrogen bonding on the resonances of pyridine. We analyse the results in terms of direct and indirect effects. We observe that the total (direct plus indirect) effect of microhydration leads to the stabilization of all resonances studied, both shape and core-excited. The size of the shift is different for different resonances and seems to be linked to the dipole moment of the cluster.

Microhydration effects on the structures and electrophilic properties of cytidine

Adiabatic electron affinities (AEAs) for cytidine hydrates with up to four water molecules.

Microhydration effects on geometric properties and electronic absorption spectra of ortho-aminobenzoic acid

TD-DFT and a combination of polarized continuum model (PCM) and microhydration methods helped to simulate the optical electronic absorption spectrum of ortho-aminobenzoic acid (o-Abz). The microhydration method involved the use of different numbers, from 1 to 5, of first solvation layer water molecules. We examined how implicit and explicit water affected the energies of the HOMO–LUMO transition in the o-Abz/water systems. Adding until five water molecules, the theoretical spectrum becomes closer to the experimental data. Microhydration combined with the PCM method leads to agreement between the theoretical result for five water molecules and the experimentally measured absorption bands.

Dissociation, absorption and ionization of some important sulfur oxoanions (S2On2−n = 2, 3, 4, 6, 7 and 8)

In this work, a systematic theoretical study was performed on the dissociation, absorption and ionization of several important sulfur oxoanions (S2On2− (n=2, 3, 4, 6, 7 and 8)). ΔEelec (thermal corrected energy), ΔH° and ΔG° of the dissociation reactions of the oxoanions to their radical monoanions were calculated using combined computational levels of theories such as Gaussian-3 (G3) and a new version of complete basis set method (CBS-4M) in different environments including gas phase, microhydrated in gas phase and different solvents. Calculations showed S2O72− is the most stable anion against the dissociation to its radical monoanions (SO4−+SO3−). It was also found that S2O42− has more tendency to dissociate to its radical anions (SO2−+SO2−) compared to the other anions. The absorption spectra of the anions were also calculated using the time-dependent density functional theory (TD-DFT) employing M062X functional. The effect of microhydration and electrostatic field of solvent on the different aspects (intensity, energy shift and assignment) of the absorption spectra of these anions were also discussed. It was observed that both hydrogen bonding and electrostatic effect of water increases the intensity of the absorption spectrum compared to the gas phase. Effect of microhydration in shifting the spectra to the shorter wavelength is considerably higher than the effect of electrostatic field of water. Finally, several gas phase ionization energies of the anions were calculated using the symmetry-adapted cluster–configuration interaction methodology (SAC–CI) and found that the first electron detachment energies of S2O22−, S2O32− and S2O42− are negative. Natural bonding orbital (NBO) calculations were also performed to assign the electron detachment bands of the anions.

Catalysis effect of micro-hydration on the intramolecular proton transfer in cytosine

Structural and thermodynamic properties of nine isomers of cytosine were studied in gas and aqueous phases and in micro-hydrated environment employing B3LYP and MP2 methods. Also, isomerizations of cytosine were studied in gas phase and the activation energies (Ea) and Gibbs free energies (ΔG#) of the internal OH rotations and proton transfer processes were calculated. The calculated OH rotational barriers were smaller than 50kJ/mol while the activation energies of intramolecular proton transfers were in the range of 110–190kJ/mol. Effect of mono- and di-hydration of the cytosine isomers on the transition state structures and the energy barriers was investigated.