Single Water Molecule Research Articles

Releasing Preferentially Sequestered Na+ from Its Confinement by Beauvericin: A Single Water Molecule is the Accomplice.

Beauvericin (Bv) is a natural ionophore capable of transporting ions across biological membranes. Mass spectrometry and infrared spectroscopy show that Bv specifically captures sodium ions with a unique 6-fold coordination in its cavity, which illustrates how ions are carried through the membrane. But with no reports on how ions are released from Bv at the interface, a complete picture of the ion transport process has yet to be established. In this study, conformational changes of Bv complexes with alkali metal ions upon hydration were investigated using infrared spectroscopy and computational calculations. The addition of a single water molecule to Na+Bv pries the ion away from the 6-fold cavity to the amide face of the ionophore, evidence of the first step of ion release. In contrast, there is little impact on the other M+Bv complexes, with the ion bound to the three carbonyl groups on the amide face. Analysis of the carbonyl C═O and water OH stretching modes reveals the competition between ion-ionophore, ion-water, and water-ionophore interactions and demonstrates how water actively participates in ion transport by initiating ion release from the ionophore.

Accurate nuclear quantum statistics on machine-learned classical effective potentials.

The contribution of nuclear quantum effects (NQEs) to the properties of various hydrogen-bound systems, including biomolecules, is increasingly recognized. Despite the development of many acceleration techniques, the computational overhead of incorporating NQEs in complex systems is sizable, particularly at low temperatures. In this work, we leverage deep learning and multiscale coarse-graining techniques to mitigate the computational burden of path integral molecular dynamics (PIMD). In particular, we employ a machine-learned potential to accurately represent corrections to classical potentials, thereby significantly reducing the computational cost of simulating NQEs. We validate our approach using four distinct systems: Morse potential, Zundel cation, single water molecule, and bulk water. Our framework allows us to accurately compute position-dependent static properties, as demonstrated by the excellent agreement obtained between the machine-learned potential and computationally intensive PIMD calculations, even in the presence of strong NQEs. This approach opens the way to the development of transferable machine-learned potentials capable of accurately reproducing NQEs in a wide range of molecular systems.

Reconstruction of calcite (10.4) manifests itself in the tip-assisted diffusion of water

Calcite (calcium carbonate) is the most abundant carbonate in the Earth's crust. Due to its omnipresence it plays a prominent role in fields such as geochemistry, biomineralization and industrial processes. Moreover, the interaction of water with the most stable cleavage plane, calcite (10.4), has been studied intensively, elucidating atomic-scale details of water binding and structure formation on this surface. Interestingly, calcite (10.4) reconstructs under ultrahigh vacuum conditions, exhibiting a (2 × 1) surface unit cell. Although first indications of this reconstruction have been presented more than 20 years ago, a clear confirmation of the existence has been provided only very recently. Here, we study the tip-assisted diffusion of water molecules on calcite (10.4) under ultrahigh vacuum conditions. By recording images series using dynamic atomic force microscopy we follow the movement of water molecules on the surface kept at 140 K. Analyzing the change in consecutive images allows for elucidating details of the molecular movement on the surface. Most notably, the analysis reveals that water molecules occupy one type of adsorption position exclusively, while the other type is not adopted. Our analysis thus demonstrates that the (2 × 1) reconstruction manifests itself in the movement of single water molecules on this surface.

Insights into the catalytic effect of atmospheric organic trace species on the hydration of Criegee intermediates

The bimolecular reactions between Criegee intermediates (CIs) and atmospheric trace species have been extensively investigated, with a particular focus on the reaction with water, while the catalytic role of atmospheric organic compounds in hydration reactions was often neglected. In this study, we employed quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations to investigate the catalytic effects of atmospheric organic amines, organic acids, and alcohols on the hydration reactions of CIs in the gas phase and at the gas-liquid interface. The catalytic reactions were found to follow a cyclic catalytic structure and a stepwise reaction mechanism. Gas-phase studies revealed that organic acids exhibited stronger catalytic effects compared to amines and alcohols, and the catalytic efficiency of amines and alcohols was similar to those of single water molecule. In addition, the catalytic reaction barriers of organic acids and alcohols were positively correlated with their gas-phase acidity (R2 = 0.94 to 0.97). A negative correlation was observed between the catalytic reaction barrier of amines and their gas-phase basicity (R2 = 0.84 to 0.90) and proton affinity (R2 = 0.84 to 0.92). At the gas-liquid interface, organic acids promoted the formation of hydroxyethyl hydroperoxide (HEHP, CH3CH(OH)(OOH)), organic acid ions, and H3O+, whereas the catalytic hydration of CIs by organic amines resulted in the formation of CH3CH(OH)OO and amine ions. Both HEHP and CH3CH(OH)OO can be further decomposed to form OH and HO2, or participate in new particles formation as precursors. This study complements the research gap on the reaction of CIs with water, providing valuable insights into the atmospheric sources of HEHP and HOx as well as the formation of secondary organic aerosols (SOAs).

Experimentally Delineating the Catalytic Effect of a Single Water Molecule in the Photochemical Rearrangement of the Phenylperoxy Radical to the Oxepin-2(5H)-one-5-yl Radical.

Catalysis plays a pivotal role in both chemistry and biology, primarily attributed to its ability to stabilize transition states and lower activation free energies, thereby accelerating reaction rates. While computational studies have contributed valuable mechanistic insights, there remains a scarcity of experimental investigations into transition states. In this work, we embark on an experimental exploration of the catalytic energy lowering associated with transition states in the photorearrangement of the phenylperoxy radical-water complex to the oxepin-2(5H)-one-5-yl radical. Employing matrix isolation spectroscopy, density functional theory, and post-HF computations, we scrutinize the (photo)catalytic impact of a single water molecule on the rearrangement. Our computations indicate that the barrier heights for the water-assisted unimolecular isomerization steps are approximately 2-3 kcal mol-1 lower compared to the uncatalyzed steps. This decrease directly coincides with the energy difference in the required wavelength during the transformation (Δλ = λ546nm - λ579nm ≡ 52.4-49.4 = 3.0 kcal mol-1), allowing us to elucidate the differential transition state energy in the photochemical rearrangement of the phenylperoxy radical catalyzed by a single water molecule. Our work highlights the important role of water catalysis and has, among others, implications for understanding the mechanism of organic reactions under atmospheric conditions.

Hydration mechanism of molybdenite affected by surface oxidation: New insights from DFT and MD simulations

The oxidation and hydration of molybdenite surfaces cannot be avoided during the crushing and flotation processes in industry, which adversely affects its clean separation and extraction. In this study, the hydration mechanism under the influence of molybdenite surface oxidation was investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The results showed that the adsorption energy of a single water molecule on the molybdenite (0 0 1) surface changed from −0.33 kcal/mol to −2.07 kcal/mol after oxidation. Dissociated O acted as a bridging link on the molybdenite (0 0 1) surface, inducing hybridization of the Hw 1 s orbitals with the Os 2p orbitals, thereby enhancing the adsorption of water molecules. The adsorption energy of a single water molecule on the molybdenite (1 1 0) surface changed from −33.97 kcal/mol to −3.37 kcal/mol after oxidation. The dissociated O hindered the hybridization of the Mo 4d and Ow 2p orbitals, thus preventing the adsorption of water molecules on the (1 1 0) surface. After oxidation, the interfacial interaction between the molybdenite (0 0 1) surface and water molecules was enhanced, while the interfacial interaction between the molybdenite (1 1 0) surface and water molecules was weakened. The water molecules near the surface of molybdenite are adsorbed through hydrogen bonding and gradually form a hydrated film consisting of three layers of water molecules with a thickness of 8–9 Å as the water coverage increases.

Mixing water, sugar, and lipid: Conformations of isolated and micro-hydrated glycolipids in the gas phase.

Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.

The multi-scale polarizable pseudo-particle solvent coarse-grained approach: From NaCl salt solutions to polyelectrolyte hydration.

We discuss key parameters that affect the reliability of hybrid simulations in the aqueous phase based on an efficient multi-scale coarse-grained polarizable pseudo-particle approach, denoted as pppl, to model the solvent water, whereas solutes are modeled using an all atom polarizable force field. Among those parameters, the extension of the solvent domain (SD) at the solute vicinity (domain in which each solvent particle corresponds to a single water molecule) and the magnitude of solute/solvent short range polarization damping effects are shown to be pivotal to model NaCl salty aqueous solutions and the hydration of charged systems, such as the hydrophobic polyelectrolyte polymer that we have recently investigated [Masella et al., J. Chem. Phys. 155, 114903 (2021)]. Strong short range damping is pivotal to simulate aqueous salt NaCl solutions at moderate concentration (up to 1.0M). The SDextension (as well as short range damping) has a weak effect on the polymer conformation; however, it plays a pivotal role in computing accurate polymer/solvent interaction energies. As the pppl approach is up to two orders of magnitude computationally more efficient than all atom polarizable force field methods, our results show it to be an efficient alternative route to investigate the equilibrium properties of complex charged molecular systems in extended chemical environments.

Controlled dissolution of a single ion from a salt interface

Interactions between monatomic ions and water molecules are fundamental to understanding the hydration of complex polyatomic ions and ionic process. Among the simplest and well-established ion-related reactions is dissolution of salt in water, which is an endothermic process requiring an increase in entropy. Extensive efforts have been made to date; however, most studies at single-ion level have been limited to theoretical approaches. Here, we demonstrate the salt dissolution process by manipulating a single water molecule at an under-coordinated site of a sodium chloride film. Manipulation of molecule in a controlled manner enables us to understand ion–water interaction as well as dynamics of water molecules at NaCl interfaces, which are responsible for the selective dissolution of anions. The water dipole polarizes the anion in the NaCl ionic crystal, resulting in strong anion–water interaction and weakening of the ionic bonds. Our results provide insights into a simple but important elementary step of the single-ion chemistry, which may be useful in ion-related sciences and technologies.

Shapeshifting Nucleophile Singly Hydrated Hydroperoxide Anion Leads to the Occurrence of the Thermodynamically Unfavored SN2 Product.

Single water molecules alone may introduce unusual features into the kinetics and dynamics of chemical reactions. The singly hydrated hydroperoxide anion, HOO-(H2O), was found to be a shapeshifting nucleophile, which can be transformed to HO- solvated by hydrogen peroxide HO-(HOOH). Herein, we performed direct dynamics simulations of its reaction with methyl iodide to investigate the effect of individual water molecules. In addition to the normal SN2 product CH3OOH, the thermodynamically unfavored proton transfer-induced HO--SN2 path (produces CH3OH) was also observed, contributing ∼4%. The simulated branching ratio of the HO--SN2 path exceeded the statistical estimation (0.6%) based on the free energy barrier difference. The occurrence of the HO--SN2 path was attributed to the shallow entrance channel well before a submerged saddle point, thus providing a region for extensive proton exchange and ultimately leading to the formation of CH3OH. In comparison, changing the leaving group from Cl to I increased the overall reaction rate as well as the proportion of the HO--SN2 path because the CH3I system has a smaller internal barrier. This work elucidates the importance of the dynamic effect introduced by a single solvent molecule to alter the product channel and kinetics of typical ion-molecule SN2 reactions.

(+)-Cedrol hemihydrate: a natural product derived from drying eastern red cedar (Juniperus virginiana) wood.

Cedrol-like compounds are of pharmacological interest due to their diverse range of medicinal effects and are used globally in traditional medicines and cosmetics. Many cedrol tautomers are known from molecular studies but few have been studied in crystalline form by X-ray diffraction. Acicular white crystals collected from the wood of eastern red cedar (Juniperus virginiana) are determined to be (+)-cedrol hemihydrate, namely, (1S,2R,5S,7R,8R)-2,6,6,8-tetramethyltricyclo[5.3.1.01,5]undecan-8-ol hemihydrate, C15H26O·0.5H2O, a novel packing of two unique cedrol molecules (Z' = 2) with a single water molecule [space group P212121; a = 6.1956 (1), b = 14.5363 (1), and c = 30.9294 (4) Å]. The hydrogen bonding forms a one-dimensional spiral chain running along the a axis, following the chirality of the cedrol molecule, through hydrogen-bonding interactions with a right-handed helical configuration in graph-set notation Δ-C33(6) > a > c > b. The crystal packing and symmetry are different from crystalline isocedrol due to the different hydrogen-bonding geometry.

The reaction mechanism of SO3 with the multifunctional compound ethanolamine and its atmospheric implications.

SO3 is an important reactive species in sulfur cycle and sulfuric acid formation processes and its reactions with some functional group substances, such as H2O, NH3, CH3OH, and organic and inorganic acids, have been extensively studied. However, its loss mechanism with multifunctional species is still lacking in detail. Herein, the reaction mechanism between SO3 and monoethanolamide (MEA) was investigated in the gas phase and on water droplets. The quantum chemical calculations indicate that the gas-phase reactions of SO3 with the OH and NH2 moieties of MEA hardly occur as their reaction energy barriers are up to 21.9-29.4 kcal mol-1. When a single water molecule is added into the SO3 + MEA reaction, it not only decreases the reaction barrier by at least 15.0 kcal mol-1 and thus enhances the rate obviously, but can also lead to the main product changing from HOCH2CH2NHSO3H to NH2CH2CH2OSO3H. The Born Oppenheimer molecular dynamics simulations on a water droplet show that the routes of the NH2CH2CH2OSO3-⋯H3O+ ion pair, HSO4- and HOCH2CH2NH3+ ions and zwitterionic formations of HOCH2CH2NH2+-SO3- and SO3--OCH2CH2NH3+ occur through a loop-structure route or chain reaction process, and can be finished within several picoseconds. Interestingly, the nucleation simulations show that the products of HOCH2CH2NHSO3H and NH2CH2CH2OSO3H have a potential ability to participate in the formation of new particles as they can form larger clusters with H2SO4, NH3 and H2O molecules within 20 ns. Thus, the present study will not only give new insight into the reaction between SO3 and multifunctional compounds, but also provide a new potential formation mechanism for particles resulting from the loss of SO3.

M(II) effect on encapsulation of guests into a series of M3L2 chiral cages: enantio-recognition.

Self-assembly of M(ClO4)2 (M2+ = Ni2+, Cu2+, and Zn2+) with (1S,1'S,1''S,2R,2'R,2''R)-(benzenetricarbonyltris(azanediyl))tris(2,3-dihydro-1H-indene-2,1-diyl) trinicotinate (s,r-L) and the corresponding enantiomer (r,s-L) as a pair of chiral tridentate donors gives rise to the chiral cage pairs [M3(s,r- and r,s-L)2](ClO4)6. For the two pairs of [(Me2CO)(H2O)@M3(r,-s and s,r-L)2](ClO4)6 (M2+ = Ni2+ and Zn2+), the inner cavity is occupied by both an acetone and a single water molecule, whereas for the copper(II) pair of [Me2CO@Cu3(r,s- and s,r-L)2](ClO4)6 under the same conditions, the cavity is filled by only one acetone molecule. Thus, the encapsulation of guest molecules into the cages during self-assembly shows significant metal(II) ion effects. These chiral cages are effective for the enantio-recognition of chiral (S)-2-butanol and (R)-2-butanol via the shifts of the electrochemical oxidation potentials obtained by the linear sweep voltammetry (LSV) technique, density functional theory (DFT) calculations, and the chiral 2-butanol adsorption in the single-crystal-to-single-crystal (SCSC) mode.

Water is a radiation protection agent for ionised pyrrole.

Radiation-induced damage of biological matter is an ubiquitous problem in nature. The influence of the hydration environment is widely discussed, but its exact role remains elusive. Utilising well defined solvated-molecule aggregates, we experimentally observed a hydrogen-bonded water molecule acting as a radiation protection agent for ionised pyrrole, a prototypical aromatic biomolecule. Pure samples of pyrrole and pyrrole(H2O) were outer-valence ionised and the subsequent damage and relaxation processes were studied. Bare pyrrole ions fragmented through the breaking of C-C or N-C covalent bonds. However, for pyrrole(H2O)+, we observed a strong protection of the pyrrole ring through the dissociative release of neutral water or by transferring an electron or proton across the hydrogen bond. Overall, a single water molecule strongly reduces the fragmentation probability and thus the persistent radiation damage of singly-ionised pyrrole.

Vibrational circular dichroism spectra of proline in water at different pH values.

Recording VCD spectra of aqueous solution poses a particular challenge as water is a strong infrared absorber. Likewise, the computational analysis of VCD spectra by means of DFT-based spectral calculations requires the consideration of explicit solvent molecules, thus posing an even greater challenge. Several studies suggested that by modeling the solvent environment with a few water molecules in a micro-solvation approach would be sufficient to describe experimental spectra. For example, using proline at different pH values, we herein show that a change in the relative spatial orientation of a single water molecule in five-fold solvated structures strongly affects the computed VCD spectral signatures and that Boltzmann-weighted spectra do not correctly reproduce the experiment. We thus explored an approach based on molecular dynamics and subsequent DFT-calculations, in which we considered 30 water molecules (about 1.5 solvation shells). Once again, it was found that the Boltzmann-weighted spectra obtained on the basis of several hundred structures did not correctly reproduce experimental signatures, and a simple averaging scheme resulted in well-matching spectra with comparable bandwidths. The rationale behind the procedure was that sampling the configurational space of the solvent molecules is as equally important as the conformational sampling of the solute. For conformationally more flexible molecules, it is assumed that a much larger set of structures will have to be computed in order to properly sample the conformational space of both solute and solvent.

Proton exchange of carbonic acid and methylamine complex accelerated by a single-water molecule via intermolecular hydrogen bonding: A theoretical investigation

A theoretical investigation of the microsolvation effect on proton exchange (PE) between carbonic acid and methylamine (CA-MTA) has been explored by quantum dynamics simulations. The structural, energy, and dynamic properties of the CA-MTA complex with and without an explicit water molecule are elucidated at the molecular level. The reactions from this study have been clarified into different types: single-step PE (SSPE) and stepwise PE (SWPE). Without the water molecule, the SSPE mechanism is hardly found but observable with a low probability of 0.2. In particular, the water molecule interacting through intermolecular hydrogen-bonded network between CA and MTA in CA-MTA-Win could affect PE by showing both SSPE and SWPE mechanisms. In addition, the existing water molecule plays the significant role in shortening intermolecular hydrogen bonding interactions within the complex resulting in increasing the probability of PE up to 0.92 especially in CA-MTA-Wout. Hence, one water molecule could be used to provide reliable results to represent the significant activity that occurs for the proton exchangeability of the CA and MTA complex.

An implicit electrolyte model for plane wave density functional theory exhibiting nonlinear response and a nonlocal cavity definition.

We have developed and implemented an implicit electrolyte model in the Vienna Ab initio Simulation Package (VASP) that includes nonlinear dielectric and ionic responses as well as a nonlocal definition of the cavities defining the spatial regions where these responses can occur. The implementation into the existing VASPsol code is numerically efficient and exhibits robust convergence, requiring computational effort only slightly higher than the original linear polarizable continuum model. The nonlinear + nonlocal model is able to reproduce the characteristic "double hump" shape observed experimentally for the differential capacitance of an electrified metal interface while preventing "leakage" of the electrolyte into regions of space too small to contain a single water molecule or solvated ion. The model also gives a reasonable prediction of molecular solvation free energies as well as the self-ionization free energy of water and the absolute electron chemical potential of the standard hydrogen electrode. All of this, combined with the additional ability to run constant potential density functional theory calculations, should enable the routine computation of activation barriers for electrocatalytic processes.

Strong H-bonding from Zeolite Bro̷nsted Acid Site to Water: Origin of the Broad IR Doublet.

Hydrogen bonding between water molecules and zeolite Bro̷nsted acid sites (BAS) has received much attention due to the significant influence of water on the adsorption and catalytic properties of these widely used porous materials. When a single water molecule is adsorbed at the BAS, the zeolite O-H stretch vibration decreases in frequency and splits into two extraordinarily broad bands peaked near 2500 and 2900 cm-1 in the infrared (IR) spectrum. This broad doublet feature is the predominant IR signature used to identify and interpret water-BAS H-bonding at low hydration levels, but the origin of the band splitting is not well understood. In this study, we used broadband two-dimensional infrared (2D IR) spectroscopy to investigate zeolite HZSM-5 prepared with a single water molecule per BAS. We find that the 2D IR spectrum is not explained by the most common interpretation of Fermi resonance coupling between the stretch and the bend of the BAS OH group, which predicts intense excited-state transitions that are absent from the experimental results. We present an alternative model of a double-well proton stretch potential, where the band splitting is caused by excited-state tunneling through the proton-transfer barrier. This one-dimensional model reproduces the basic experimental pattern of transition frequencies and amplitudes, suggesting that the doublet bands may originate from a highly anharmonic potential in which the excited state proton wave functions are delocalized over the H-bond between zeolite BAS and adsorbed H2O. Additional details about molecular orientation and coordination of the adsorbed water molecule are also resolved in the 2D IR spectroscopy.

Unravelling the structural features of monosaccharide glyceraldehyde upon mono-hydration by quantum chemistry and rotational spectroscopy.

Water is a fundamental molecule for life, and investigating its interaction with monosaccharides is of great interest in order to understand its influence on their conformational behavior. In this study, we report on the conformational landscape of monosaccharide glyceraldehyde, the simplest aldose sugar, in the presence of a single water molecule in the gas phase. This investigation was performed using a combination of Fourier transform microwave spectroscopy and theoretical calculations. Out of the nine calculated conformers, only the lowest energy conformer was experimentally observed and characterized. Interestingly, the presence of water was found to induce structural features in the lowest energy conformer of the glyceraldehyde monomer, with water positioned between the alcohol groups. To analyze this interaction further, non-covalent interaction plots were employed to map the intermolecular interactions in the observed species. Additionally, natural bond orbital analysis was conducted to study the effects of charge transfer in the monohydrate system. Furthermore, topological analysis based on Bader's Atoms in Molecules theory was performed to gain insights into the observed complex. The results of all three analyses consistently showed the formation of relatively strong hydrogen bonds between water and glyceraldehyde, leading to the formation of a seven-member ring network.

Can a single ammonia and water molecule enhance the formation of methanimine under tropospheric conditions?: kinetics of •CH2NH2 + O2 (+NH3/H2O).

The aminomethyl (•CH2NH2) radical is generated from the photo-oxidation of methylamine in the troposphere and is an important precursor for new particle formation. The effect of ammonia and water on the gas-phase formation of methanimine (CH2NH) from the •CH2NH2 + O2 reaction is not known. Therefore, in this study, the potential energy surfaces for •CH2NH2 + O2 (+NH3/H2O) were constructed using ab initio//DFT, i.e., coupled-cluster theory (CCSD(T))//hybrid-density functional theory, i.e., M06-2X with the 6-311++G (3df, 3pd) basis set. The Rice-Ramsperger-Kassel-Marcus (RRKM)/master equation (ME) simulation with Eckart's asymmetric tunneling was used to calculate the rate coefficients and branching fractions relevant to the troposphere. The results show 40% formation of CH2NH at the low-pressure (<1 bar) and 100% formation of CH2NH2OO• at the high-pressure limit (HPL) condition. When an ammonia molecule is introduced into the reaction, there is a slight increase in the formation of CH2NH; however, when a water molecule is introduced into the reaction, the increase in the formation of CH2NH was from 40% to ∼80%. The calculated rate coefficient for •CH2NH2 + O2 (+NH3) [1.9 × 10-23cm3 molecule-1 s-1] and for CH2NH2 + O2 (+H2O) [3.3 × 10-17cm3 molecule-1 s-1] is at least twelve and six order magnitudes smaller than those for free •CH2NH2 + O2 (2 × 10-11cm3 molecule-1 s-1 at 298K) reactions, respectively. Our result is consistent with that of previous experimental and theoretical analysis and in good agreement with its isoelectronic analogous reaction. The work also provides a clear understanding of the formation of tropospheric carcinogenic compounds, i.e., hydrogen cyanide (HCN).