Single Water Molecule Research Articles

Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach

The structural stability and transport properties of the cyclic peptide nanotube (CPN) 8 × [Cys–Gly–Met–Gly]2 in different phospholipid bilayers such as POPA (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid), POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) and POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine) with water have been investigated using molecular dynamics (MD) simulation. The hydrogen bonds and non-bonded interaction energies were calculated to study the stability in different bilayers. One µs MD simulation in POPA lipid membrane reveals the stability of the cyclic peptide nanotube, and the simulations at various temperatures manifest the higher stability of 8 × [Cys–Gly–Met–Gly]2. We demonstrated that the presence of sulphur-containing amino acids in CPN enhances the stability through disulphide bonds between the adjacent rings. Further, the water permeation coefficient of the CPN is calculated and compared with human aquaporin-2 (AQP2) channel protein. It is found that the coefficients are highly comparable to the AQP2 channel though the mechanism of water transport is not similar to AQP 2; the flow of water in the CPN is taking place as a two-line 1–2–1–2 file fashion. In addition to that, the transport behavior of Na+ and K+ ions, single water molecule, urea and anti-cancer drug fluorouracil were investigated using pulling simulation and potential of mean force calculation. The above transport behavior shows that Na+ is trapped in CPN for a longer time than other molecules. Also, the interactions of the ions and molecules in Cα and mid-Cα plane were studied to understand the transport behavior of the CPN.AbbreviationsAQP2Aquaporin-2CPNCyclic peptide nanotubeMDMolecular dynamicsPOPA1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acidPOPE1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolaminePOPG1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerolPOPS1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserineCommunicated by Ramaswamy H. Sarma

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR

Covalent modification of outer membrane lipids of Gram-negative bacteria can impact the ability of the bacterium to develop resistance to antibiotics as well as modulating the immune response of the host. The enzyme LpxR from Salmonella typhimurium is known to deacylate lipopolysaccharide molecules of the outer membrane, however the mechanism of action is unknown. Here we employ molecular dynamics and Monte Carlo simulations to study the conformational dynamics and substrate binding of LpxR in representative outer membrane models and also detergent micelles. We examine the roles of conserved residues and provide an understanding of how LpxR binds its substrate. Our simulations predict that the catalytic H122 must be Nɛ-protonated for a single water molecule to occupy the space between it and the scissile bond, with a free binding energy of −8.5 kcal mol−1. Furthermore, simulations of the protein within a micelle enable us to predict the structure of the putative ‘closed’ protein. Our results highlight the need for including dynamics, a representative environment and the consideration of multiple tautomeric and rotameric states of key residues in mechanistic studies; static structures alone do not tell the full story.

Mechanism research on surface hydration of kaolinite, insights from DFT and MD simulations

The surface hydration is one of the main reasons for the difficulty of coal slurry water sedimentation and dewatering, the Density functional theory (DFT) and Molecular dynamics (MD) simulations on the surface hydration of kaolinite were investigated in this study. The results indicate that the adsorption of single water molecule on kaolinite (0 0 1) surface and (001¯) surface mainly by forming hydrogen bonds, and the adsorption energies of single water molecule on different initial positions of kaolinite (0 0 1) surface are −72.12 to −19.23 kJ/moL, less than that of kaolinite (001¯) surface with −19.23 to −5.77 kJ/moL, which mean that the water molecule preferentially adsorption on kaolinite (0 0 1) surface. The binding force between kaolinite surfaces and water molecules decreased with the increase of water coverage rate (or the number of water molecules), the hydrogen-bond interaction on kaolinite/water interface gradually weakened, and the water molecules on hydrophilic kaolinite surfaces can be gradually formed 3 layers of water molecules. The hydrated film of kaolinite surface is mainly composed of about 3 layers of water molecules, and its thickness is about 8–10 Å. The hydration mechanism of kaolinite surface is mainly that the water molecules at kaolinite interface are adsorbed on surface with hydrogen bonds, and a hydrated film composed of multiple water molecules is gradually formed on kaolinite surface with the increase of water coverage rate.

Enhancement of electron accepting ability of para-benzoquinone by a single water molecule.

Electron acceptors built upon the para-benzoquinone (pBQ) electrophore are ubiquitous in nature. Here, we present a frequency-resolved photoelectron spectroscopic study of the cold pBQ radical anion, pBQ-, solvated by a single water molecule, as commonly encountered in nature. Our results show that the electron accepting ability is enhanced by the single water molecule and by elevated temperatures.

Influence of the microsolvation on hemibonded and protonated hydrogen sulfide: infrared spectroscopy of [(H2S)n(X)1]+ and H+(H2S)n(X)1 (n = 1 and 2, X = water, methanol, and ethanol).

Changes of the excess charge accommodation motif in hemibonded and protonated hydrogen sulfide by microsolvation are studied by infrared spectroscopy of [(H2S)n(X)1]+ and H+(H2S)n(X)1 (n = 1 and 2, X = water, methanol, and ethanol) clusters. While the hemibond in the (H2S)2+ ion core is stable to the microhydration by a single water molecule, the hemibond is broken by the proton transfer with the microsolvation by a single methanol or ethanol molecule. Hetero hemibond formation between hydrogen sulfide and these solvent molecules is not observed. On the other hand, the excess proton in H+(H2S)n can be easily transferred to the solvent molecule, even though the proton affinity of the solvent molecule is lower than that of hydrogen sulfide. Implications of these results to the charge accommodation by sulfur under the biological conditions are discussed.

Reaction mechanism between small-sized Ce clusters and water molecules II: an ab initio investigation on Cen (n = 1-3) + mH2O (m = 2-6).

Possible reactions between the products of the three independent reactions involving a small Ce cluster and a single water molecule, Cen + H2O (n = 1-3), and an additional H2O molecule are systematically investigated. The ground-state isomers of the final products and the reaction pathways involving multiple water molecules are predicted. We find that under either ambient or UV-irradiation conditions, all the reactions can entail low energy barriers. In addition, the final products of the reaction between Cen and more than two H2O molecules are also predicted through an extensive structural search. The calculated reaction energies suggest that although small-sized Ce clusters can react with more than two water molecules, the reactions with one or two water molecules are dominant. The electronic structures of all the ground-state isomers and the corresponding oxidation states of Ce atoms in these isomers are computed and determined via the natural bond orbital (NBO) method. The results indicate that a single Ce atom and a Ce2 cluster can react with a maximum of four and six water molecules, respectively, while a Ce3 cluster can react with more than six water molecules. This comprehensive study offers an improved understanding of the mechanism underlying the reactions between a single Ce atom or a small Ce cluster and two or more H2O molecules. Knowledge obtained from this study can be helpful for the development of high-performance Ce-doped or Ce-based catalysts.

Reaction mechanism between small-sized Ce clusters and water molecules: an ab initio investigation on Cen + H2O.

Reactions of small-sized cerium clusters Cen (n = 1-3) with a single water molecule are systematically investigated theoretically. The ground state structures of the Cen/H2O complex and the reaction pathways between Cen + H2O are predicted. Our results show the size-dependent reactivity of small-sized Ce clusters. The calculated reaction energies and reaction barriers indicate that the reactivity between Cen and water becomes higher with increasing cluster size. The predicted reaction pathways show that the single Ce atom and the Ce2 and Ce3 clusters can all easily react with H2O and dissociate the water molecule. Under UV-irradiation, the reaction of a Ce atom with a single H2O molecule may even release an H2 molecule. The reaction of either Ce2 or Ce3 with a single H2O molecule can fully dissociate the H2O into H and O atoms while it is bonded with the Ce cluster. The electronic configuration and oxidation states of the Ce atoms in the products and the higher occupied molecular orbitals are analyzed by using the natural bond orbital (NBO) analysis method, from which the high reactivity between the reaction products of Cen + H2O and an additional H2O molecule is predicted. Our results offer deeper molecular insights into the chemical reactivity of Ce, which could be helpful for developing more efficient Ce-doped or Ce-based catalysts.

Switching of the reaction enthalpy from exothermic to endothermic for decomposition of H2CO3 under confinement.

Various size fullerenes (C60, C70 and C84) have been used as a means of confinement to study the decomposition reaction of carbonic acid alone as well as in the presence of a single water molecule in a confined environment. Quantum chemical calculations reveal that as the effect of confinement increases by reducing the size of the fullerene cage, the bare reaction switches from exothermic to endothermic gradually. As a result, the equilibrium of the reaction shifts toward the reactant side, which suggests that the decomposition of carbonic acid becomes thermodynamically disfavored under confinement. In the presence of a single water molecule inside the C84 fullerene cage, the barrier height of unimolecular decomposition is found to be decreased by ∼2.1 kcal mol-1 as compared to the gas phase reaction. Besides the effect of confinement, we have also studied the pressure dependency of and the effect of an external electric field on the title reaction. By parameterizing the behavior of the system inside the fullerene in terms of pressure, we have shown that the fullerene cage can act as a high pressure container for this reaction. Our investigations also reveal that, similar to confinement, an external electric field could also switch the reaction from exothermic to endothermic in nature.

Soliton-like propagation of dipole reorientation in confined single-file water chains

Water molecules confined in a narrow nanotube channel orient themselves into a uniformly ordered single-file chain. Here, we report by means of comprehensive molecular dynamics simulations and soliton-model-based theoretical analysis that the reorientation (i.e., rotation) of a single water molecule in this dipole chain, triggered for example by an external charge, can induce successive reorientation of the rest of the water molecules, which propagates in a soliton-like manner. The resulting local potential energy peak separating the reoriented and the pending reorientation subsections moves with an unweakened peak intensity at a constant velocity in the ambient environment, and particularly, can penetrate or make a turn through a crossed nanotube junction. The propagation velocity depends on the strength of the external charge, in agreement with our sine-Gordon soliton-based theoretical analysis. We further show that this unidirectional propagation originates from the partially inhibited fluctuation in dipole orientation of reoriented water with respect to that of original ones. These findings may be helpful in the development of high-efficiency information transmitting, processing and storage devices and the understanding of functioning of biological water channels.

Influence of water on the CH3O˙ + O2 → CH2O + HO2˙ reaction

Electronic structure calculations employing density functional theory have been used to study the effect of a single water molecule on the CH3O˙ + O2 → CH2O + HO2˙ reaction. The investigation suggests that in the presence of water the reaction barrier reduces from 3.01 kcal mol-1 to -1.86 kcal mol-1. Consequently, when we consider the bimolecular rate constants for the water catalyzed channel, they were found to be 104 to 105 times higher than that of the uncatalyzed reaction. Interestingly, the Arrhenius plot indicates a negative temperature dependency of the catalyzed channel (anti-Arrhenius behavior); as a result of this the domination of the catalyzed channel over the bare reaction increases with the lowering of the temperature. But the effective bimolecular rate constant values for the catalyzed channel were found to be approximately four orders of magnitude lower than that of the uncatalyzed one, which implies that the contribution of the catalyzed channels to the overall rate of the reaction is very small.

Can microsolvation effects be estimated from vacuum computations? A case-study of alcohol decomposition at the H2O/Pt(111) interface.

Converting biomass into sustainable chemicals and energy feed-stocks requires innovative heterogeneous catalysts, which are able to efficiently work under aqueous conditions. Computational chemistry is a key asset in the design of these novel catalysts, but it has to face two challenges: the large reaction networks and the potential role of hydration. They can be addressed using scaling relations such as Brønsted-Evans-Polanyi (BEP) and solvation models, respectively. In this study, we show that typical reaction and activation energies of alcohol decomposition on Pt(111) are not strongly modified by the inclusion of the water solvent as a continuum model. In contrast, adding a single water molecule strongly favours O-H and C-OH scission and it prevents C-O and to a lesser extent C-C scissions. The resulting BEP relationships partially reflect these changes induced by the solvent. Predicting Pt-catalysed alcohol decomposition in water should thus account for the influence of the solvent on thermodynamics and kinetics. In addition, we found that the reaction energies obtained in the presence of an explicit water molecule scale with the ones obtained in a vacuum. Hence, we reveal that vacuum computations in combination with corrections based on our linear regressions are able to capture the important H-bonding effect.

Elucidating the mechanism and kinetics of the water-assisted reaction of nitrous acid with hydroxyl radical.

The effect of a single water molecule on the atmospheric reaction between nitrous acid (HONO) and the hydroxyl radical (OH) has been investigated in this work. The CCSD(T)/aug-cc-pVTZ//UωB97X-D/aug-cc-pVTZ level of theory was used to obtain all stationary points on the energy surface and to determine the rate constants. Due to the two HONO configurations (cis- and trans-) existing in the atmosphere, the water-free HONO + OH reaction has two major elementary channels, both based on the HONO hydrogen abstraction by the hydroxyl radical. The products, NO2 + H2O, are formed with substantial energy gain, but separated by relatively low energy barriers. In the presence of water, the reaction becomes more complex, proceeding through twelve different channels, each starting with the formation of a binary complex between water and one reactant followed by its interaction with the third species. The products are similar to those of the water-free reaction. At 298 K, the rate constants of water-free cis-HONO + OH and trans-HONO + OH reactions are 1.34 × 10-12 and 1.00 × 10-15 cm3 molecule-1 s-1, respectively. The calculated rate constants for H2O-complexed HONO or OH increase by one to two orders of magnitude, but weighted by their relative abundances, the H2O-complexed fractions of the reactants in the atmosphere are so small that the effect of H2O on the overall reaction rate is minor.

Effect of microsolvation on the non-radiative decay of the eumelanin monomer.

Eumelanin is a polymeric structure made of di-hydroxyindole (DHI) as the basic motif. In order to understand the photoprotection process in eumelanin, it is imperative to understand the photoprocesses in its monomers. These photoprocesses are affected by the presence of neighboring molecules, such as water molecules, in the biological environment. Therefore, we elucidate the effect of microsolvation on the photoprocesses of DHI. As seen from previous studies on DHI, there are quite a few deactivation channels for the molecule subsequent to its excitation within the UV-visible range. In the presence of microsolvation, we notice that these deactivation channels change in their energetics. However, there is always the presence of ultrafast deactivation channels and in some cases the deactivation is expected to be faster in the presence of a single water molecule as compared to the gas phase.

Communication: Water activation and splitting by single metal-atom anions.

We report experimental and computational results pertaining to the activation and splitting of single water molecules by single atomic platinum anions. The anion photoelectron spectra of [Pt(H2O)]-, formed under different conditions, exhibit spectral features that are due to the anion-molecule complex, Pt-(H2O), and to the reaction intermediates, HPtOH- and H2PtO-, in which one and two O-H bonds have been broken, respectively. Additionally, the observations of PtO- and H2 + in mass spectra strongly imply that water splitting via the reaction Pt- + H2O → PtO- + H2 has occurred. Extending these studies to nickel and palladium shows that they too are able to activate single water molecules, as evidenced by the formation of the reaction intermediates, HNiOH- and HPdOH-. Computations at the coupled cluster singles and doubles with perturbatively connected triples level of theory provide structures and vertical detachment energies (VDEs) for both HMOH- and H2MO- intermediates. The calculated and measured VDE values are in good agreement and thus support their identification.

The adsorption of a single water molecule on low-index C3S surfaces: A DFT approach

The adsorption of water molecules on tricalcium silicate (C3S), which influences the initial hydration of C3S, is still unclear at the atomistic level. In the present paper, density functional theory is employed to depict the adsorption of a single water molecule on seven low-index M3-C3S surfaces. The calculations show that both molecular and dissociative adsorption can occur on the C3S surfaces and that the latter mode is preferential. All of the ionic O atoms on the C3S surfaces can adsorb the H atoms from dissociated water molecules, while only two-coordinated covalent O atoms on the surfaces can form OH chemical bonds. The electronic structures of the ionic and two-coordinated covalent O atoms in the first atomic layer of the C3S surfaces show similar charge density localization of the valence band maximum (VBM), which can describe the variations in the reactivity of the ionic O atoms in the bulk or exposed on the surface slab. The partial density of states (PDOS) analysis shows that the formation of new CaO bonds is mainly due to the overlap of O-2s and Ca-3p orbitals and O-2p and Ca-3d orbitals. Furthermore, the position of the OH group generated from the dissociated water molecule is found to significantly affect the adsorption energy. The general order of the adsorption energy in terms of the position of the OH group is Ehollow > Ebridge > Etop. The findings in this study provide additional support for the fundamental understanding of C3S hydration.

Criegee Intermediate Reaction with Alcohol Is Enhanced by a Single Water Molecule.

The role of water in gas-phase reactions has gained considerable interest. Here we report a direct kinetic measurement of the reaction of syn-CH3CHOO (a Criegee intermediate or carbonyl oxide) with methanol at various relative humidity (RH = 0-80%) under near-ambient conditions (298 K, 250-755 Torr). The data indicate that a single water molecule expedites the reaction by up to a factor of three. The rate coefficient of the corresponding reaction, syn-CH3CHOO + CH3OH + H2O → products, has been determined to be (1.95 ± 0.11) × 10-32 cm6 s-1 at 298 K, with no observable pressure dependence for 250-755 Torr. Quantum chemistry calculation shows that the dominating pathway involves a hydrogen-bonded ring structure, in which methanol is donating a hydrogen atom to water, water is donating a hydrogen atom to the terminal oxygen atom of the Criegee intermediate, and, on the product side, H2O is reformed and acts as a catalyst.

Atmospheric Decomposition of Trifluoromethanol Catalyzed by Formic Acid.

Quantum chemistry calculations are used to investigate the energetics and kinetics of CF3OH decomposition catalyzed by a single formic acid (FA) molecule acting alone and in conjunction with a single water (H2O) molecule to form the products carbonyl fluoride (CF2O) and hydrofluoric acid (HF). While the uncatalyzed reaction has a barrier of ∼44.7 kcal/mol, the presence of a FA molecule reduces the barrier to 6.4 kcal/mol, while the presence of both a FA and H2O molecule acting in unison decreases the barrier to -1.6 kcal/mol measured relative to the separated reactants. For comparison, we have also examined the decomposition of CF3OH catalyzed by HO2 and HO2 + H2O, which have been suggested in the literature to be an important atmospheric catalyst for CF3OH decomposition. In addition, we have also examined the loss of CF3OH via its bimolecular reaction with OH radicals. The rate constants for these various reactions were calculated using canonical variational transition state theory coupled with small curvature tunneling corrections over the temperature range between 200 and 300 K. Our results show that the rates for the CF3OH + FA and CF3OH + FA + H2O reactions are ∼104 times faster compared, respectively, to the corresponding reactions involving CF3OH + HO2 and CF3OH + HO2 + H2O at 300 K. Further, we find that, although the CF3OH + FA reaction has a higher barrier compared to CF3OH + FA + H2O, measured relative to the separated reagents, its effective first order rate for CF3OH decomposition is significantly faster for temperatures above 240 K compared to that of CF3OH + FA + H2O. This trend arises from the higher unimolecular reaction barrier for the reactant complex associated with the CF3OH + H2O + FA reaction compared to that for CF3OH + FA, as well as the lower concentration of reactant dimer complexes for CF3OH + H2O + FA compared to the concentration of the monomer FA reactant in the CF3OH + FA reaction. Finally, our calculations show that the rate for CF3OH decomposition catalyzed by FA is ∼104 times faster relative to the loss of CF3OH via its bimolecular reaction with OH radicals over the 200-300 K temperature range. Thus, the present study suggests that, among the various known loss mechanisms, a unimolecular reaction catalyzed by FA is likely the dominant gas phase decomposition pathway for CF3OH in the troposphere.

Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule.

In this work, we have developed an anisotropic polarizable model for the AMOEBA force field that is derived from electrostatic fitting on a gas phase water molecule as the primary approach to improve the many-body polarization model. We validate our approach using small to large water cluster benchmark data sets and ambient liquid water properties and through comparisons to a variational energy decomposition analysis breakdown of molecular interactions for water and water-ion trimer systems. We find that the accounting of anisotropy polarization for a single water molecule demonstrably improves the description of the many-body polarization energy in all cases. This study provides a proof of principle for extending our protocol for developing a general purpose anisotropic polarizable force field for other biological and material functional groups to better describe complex and asymmetric environments for which accurate polarization models are most needed.

Fully Coupled Quantum Treatment of Nanoconfined Systems: A Water Molecule inside a Fullerene C60.

We implemented a systematic procedure for treating the quantal rotations by including all translational and vibrational degrees of freedom for any triatomic bent molecule in any embedded or confined environment, within the MCTDH framework. Fully coupled quantum treatments were employed to investigate unconventional properties in nanoconfined molecular systems. In this way, we facilitate a complete theoretical analysis of the underlying dynamics that enables us to compute the energy levels and the nuclear spin isomers of a single water molecule trapped in a C60 fullerene cage. The key point lies in the full 9D description of both nuclear and electronic degrees of freedom, as well as a reliable representation of the guest-host interaction. The presence of occluded impurities or inhomogeneities due to noncovalent interactions in the interfullerene environment could modify aspects of the potential, causing significant coupling between otherwise uncoupled modes. Using specific n-mode model potentials, we obtained splitting patterns that confirm the effects of symmetry breaking observed by experiments in the ground ortho-H2O state. Further, our investigation reveals that the first rotationally excited states of the encapsulated ortho- and para-H2O have also raised their 3-fold degeneracy. In view of the complexity of the problem, our results highlight the importance of accurate and computational demanding approaches for building up predictive models for such nanoconfined molecules.

The adsorption behavior of a single and multi‐water molecules on tricalcium silicate (111) surface from DFT calculations

AbstractThe interaction between water and tricalcium silicate (C3S) is important for the portland cement hydration, but the description at the atomistic level is still unclear. In this work, we investigate a single and multi‐water molecules adsorption behavior on tricalcium silicate (111) surface using DFT approach. For a single water molecule, both molecular and dissociative adsorption of a single water molecule can occur on the calcium silicate (111) surface and the dissociative state is preferred. The dissociative adsorption of water can only occur on the ionic O atoms while molecular adsorption can be found on the Ca atoms. The higher reactivity of ionic O atoms can be explained by the significant contribution of the Oi‐2p orbital in the valence band maximum of the surface slab. The surface reconstruction leading by dissociative adsorption is more significant than that of molecular adsorption. For two or three water molecules adsorbing on one surface unit cell, full dissociative adsorption is the most energetic mode. For 4‐15 water molecules, a mixed adsorption mode is found to be favorable. As the water coverage increase, the stepwise adsorption of water decreases due to the interaction between adsorbed water molecules.