Lateral diffusion of ions near membrane surface.

Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na+ and K+ permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl-, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1-4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15-25 times slower than in the bulk, and 4-5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns.

External electric field to control the Diels-Alder reactions of endohedral fullerene.

The present work investigates the role of External Electric Field (EEF) on a Diels-Alder reaction of endohedral fullerene by means of chemical kinetics and quantum chemical calculations. The investigation suggests that by combining two strategies, first encapsulating the cation inside the fullerene followed by applying EEF, one can easily manipulate the energy barrier of the Diels-Alder reaction. To illustrate this general strategy, we have chosen the reaction of fullerene (C60) and 1,3 cyclohexadiene, which is associated with a high energy barrier height of ∼11.2 kcal mol-1. Our calculation reveals that this reaction can be turned into a barrierless reaction by applying the EEF oriented along a suitable direction, and at the same time by changing the direction of EEF, the EEF can also act as an inhibitor.

Nitrous acid (HONO) as a sink of the simplest Criegee intermediate in the atmosphere.

In the present work, we have investigated the reaction of nitrous acid with the simplest Criegee intermediate using chemical kinetics and quantum chemical calculations. It was found that reactions can occur through four different paths. Among them, one path involves hydrogen atom transfer and leads to the formation of hydroperoxymethyl nitrite, while two paths involve cycloaddition leading to the formation of ozonide and formic acid and the remaining path involves oxygen atom transfer leading to the formation of HNO3 as a final product. Although there are various oxidation reactions of HONO present in the literature, which produce nitrogen dioxide as a final product, the possibility of in situ generation of HNO3 and formic acid from HONO is reported for the first time. Nevertheless, the hydrogen atom transfer path, which leads to the formation of hydroperoxymethyl nitrite as a final product, was found to be the fastest, and hence dominating the Criegee reaction with HONO. By comparing the title reaction with other dominant Criegee reactions, it was found that although it will be more effective than Criegee oxidation by Cl˙ or ClO˙ and can compete with Criegee oxidation by OH˙ under special circumstances, it is negligible compared to the reaction of the Criegee intermediate with a water molecule.

Effect of microsolvation on the mode specificity of the OH˙(H2O) + HCl reaction.

The present study investigates the mode specificity in the microsolvated OH˙(H2O) + HCl reaction using on-the-fly direct dynamics simulation. To the best of our knowledge, this is the first study which aims to gain insights into the effect of microsolvation on the mode selectivity. Our investigation reveals that, similar to the gas phase OH˙ + HCl reaction, the microsolvated reaction is also predominantly affected by the vibrational excitation of the HCl mode, whereas the OH vibrational mode behaves as a spectator. Interestingly, in contrast to the behavior of the bare reaction, the integral cross section at the ground state of the microsolvated reaction decreases with an increase in translational energy. However, for the vibrational excited states, the reactivity of the microsolvated reaction is found to be higher than that of the bare reaction within the selected range of translational energies.

Oxidation of HOSO˙ by Cl˙: a new source of SO2 in the atmosphere?

In the present work, we have studied the formation of SO2 in the atmosphere from the oxidation of HOSO˙ by Cl˙ at the CCSD(T)/aug-cc-pV(+d)TZ//MP2/aug-cc-pV(+d)TZ level of theory. The present work reveals that the title reaction is a barrierless reaction that proceeds through a stable intermediate sulfurochloridous acid having a stabilization energy of ∼-56.5 kcal mol-1. The rate constant values within the temperature range of 213-400 K indicate that the rate of HOSO˙ + Cl˙ = SO2 + HCl reaction does not change much with the change in temperature. Besides, the reaction was also found to be insensitive towards pressure change. Interestingly, the relative rate of HOSO˙ + Cl˙ reaction with respect to HOSO˙ + OH˙ reaction indicates that HOSO˙ + Cl˙ is always much slower than HOSO˙ + OH˙ reaction, within the temperature range of 213-400 K.

Effect of water on the oxidation of CO by a Criegee intermediate.

The present work employs the CCSD(T)/CBS//M06-2X/aug-cc-pVTZ level of theory to investigate the effect of a water monomer and dimer on the oxidation of carbon-monoxide by a Criegee intermediate (CH2OO). The present work suggests that in the presence of a water monomer the energy barrier of the title reaction reduced to ∼3.4 kcal mol-1 from the corresponding uncatalyzed barrier (∼12.4 kcal mol-1), whereas, in the presence of a water dimer it became as low as ∼-3.2 kcal mol-1. It has also been found that, in the presence of catalysts, additional channels become available from which the title reaction can proceed. The estimated values of rate constants suggest that within the temperature range of 210-320 K, the effective bimolecular rate constant for the water monomer catalyzed channel is 10 to 100 times lower than the bimolecular rate constant of the uncatalyzed channel, whereas in the case of the water dimer it is ∼5-10 times higher than that of the uncatalyzed channel.

Kinetic instability of sulfurous acid in the presence of ammonia and formic acid.

In the present work, we have studied the effect of ammonia and formic acid on the kinetic stability of sulfurous acid using high level ab initio calculations. Our investigation reveals that the decomposition reaction of sulfurous acid becomes barrierless in the presence of both ammonia and formic acid. The half-life of the isolated sulfurous acid is estimated to be ∼20 days at room temperature, which becomes only ∼4.0 × 10-3 s and ∼7.08 × 102 s in the presence of ammonia and formic acid, respectively. These results indicate that, in the presence of ammonia, the stability of sulfurous acid reduces substantially at room temperature. The temperature dependency of the rate constant values indicates that, in the presence of ammonia and formic acid, the reaction has a negative activation energy, while the uncatalyzed and water catalyzed channels have a positive activation energy. We have also studied the pressure dependency of the catalyzed reaction, which suggests that the ammonia catalyzed channel is most sensitive towards the pressure change, as the values of the bimolecular rate constant (kbi) for this channel were found to be increased by an order of magnitude on going from 0.1 to 10 atm of pressure. Whereas, for the FA and WM catalyzed channels the changes in kbi with pressure were negligible.

OH• + HCl Reaction at the Surface of a Water Droplet: An Ab Initio Molecular Dynamical Study.

The Born-Oppenheimer molecular dynamics (BOMD) simulation has been performed to investigate the dynamics of the OH• + HCl reaction at the surface of a water droplet. The investigation suggests that the reaction occurred at the surface of the water droplet becomes almost 10 times faster than the corresponding gas-phase reaction. Besides, we have also performed the quantum mechanics/molecular mechanics calculation to calculate the unimolecular energy barrier of the reaction. The results indicate that the barrier height gets decreased by ∼0.3 kcal mol-1 at the surface of the water droplet, which also justifies the rate enhancement suggested by the BOMD simulation. The BOMD simulation also indicates that, at equilibrium, the product Cl• forms four hydrogen bonds with four interfacial water molecules, which stabilize the Cl• and resist it to escape from the surface.

Effect of ammonia and formic acid on the CH3O˙ + O2 reaction: a quantum chemical investigation.

In the present work, the catalytic effect of ammonia and formic acid on the CH3O˙ + O2 reaction has been investigated employing the MN15L density functional. The investigations suggest that, in the presence of ammonia, the reaction can proceed through two different pathways, namely a single hydrogen atom transfer and a double hydrogen atom transfer path, but due to the high energy barrier associated with the double hydrogen atom transfer channel, it prefers the single hydrogen atom transfer channel. On the other hand, in the case of formic acid, only the single hydrogen atom transfer path is found to be feasible. Interestingly, it has been found that, in the presence of ammonia and formic acid, the reaction becomes a barrierless reaction. The calculated rate constant values at various temperatures indicate an anti-Arrhenius behavior for both the ammonia and formic acid catalyzed channels.

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.

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.

Revisiting the reaction energetics of the CH3O˙ + O2 (3Σ-) reaction: the crucial role of post-CCSD(T) corrections.

The CH3O˙ + O2 reaction has been studied by means of high level ab initio calculations to predict the reaction energy and barrier height with chemical accuracy. We have employed post-CCSD(T) corrections in terms of partial quadratic excitations at the coupled cluster level, along with relativistic, core, spin-orbit and diagonal Born-Oppenheimer corrections, to estimate the barrier height and energetics for the title reaction. After including all the corrections, the reaction energy and barrier height were found to be -26.86 and 2.59 kcal mol-1, respectively, which is in good agreement with the corresponding experimentally derived values. Using this information, we have also calculated the rate constants for the title reaction employing transition state theory (TST) in conjunction with zero curvature tunneling (ZCT) within a temperature range of 250 to 900 K.

Impact of Post-CCSD(T) Corrections on Reaction Energetics and Rate Constants of the OH• + HCl Reaction.

High level ab initio calculations have been performed to predict the reaction energy and barrier height for the OH• + HCl reaction. After including the effect of full quadratic excitations at the coupled cluster level, in addition to core, relativistic, spin-orbit, and diagonal Born-Oppenheimer corrections, we found the values of reaction energy and barrier height to be -15.29 and +2.38 kcal mol-1, respectively. Employing this reaction energy and barrier height, we used variational transition state theory in conjunction with small curvature tunneling to calculate the rate constants within a temperature range from 138 to 1000 K. The calculated rate constants were found to be in good agreement with available experimental results throughout the whole temperature range.

Ammonolysis of ketene as a potential source of acetamide in the troposphere: a quantum chemical investigation.

Quantum chemical calculations at the CCSD(T)/CBS//MP2/aug-cc-pVTZ levels of theory have been carried out to investigate a potential new source of acetamide in Earth's atmosphere through the ammonolysis of the simplest ketene. It was found that the reaction can occur via the addition of ammonia at either the C[double bond, length as m-dash]C or C[double bond, length as m-dash]O bond of ketene. The potential energy surface as well as calculated rate coefficients indicate that under tropospheric conditions, ammonolysis would occur almost exclusively via ammonia addition at the C[double bond, length as m-dash]O bond with negligible contribution from addition at the C[double bond, length as m-dash]C bond. The reaction of ketene with water has also been investigated in order to compare between hydrolysis and ammonolysis, as the former is known to be responsible for the formation of acetic acid. The rate coefficient for the formation of acetamide was found to be ∼106 to 109 times higher than that for the formation of acetic acid from the same ketene source in the troposphere. By means of the relative rate of ammonolysis with respect to hydrolysis, it was shown that acetamide formation would dominate over acetic acid formation at various altitudes in the troposphere.

Effect of Ammonia and Formic Acid on the OH• + HCl Reaction in the Troposphere: Competition between Single and Double Hydrogen Atom Transfer Pathways.

Quantum chemical calculations at QCISD and CCSD(T) levels of theory have been performed to investigate the effect of NH3 and HCO2H on the reaction between OH• and HCl. Potential energy profiles indicate that both NH3 and HCO2H catalyzed reactions could proceed through two different channels, namely, single and double hydrogen atom transfer. Theoretically calculated rate constants for both the catalysts show that both NH3 and HCO2H catalyzed channels prefer a single hydrogen atom transfer path. Besides, both NH3 and HCO2H catalyzed paths have higher rate constant values as compared to that of the water catalyzed path.

Isomerization of methoxy radical in the troposphere: competition between acidic, neutral and basic catalysts.

A comprehensive investigation of the roles of acidic, neutral and basic catalysts in isomerization of methoxy radical in the troposphere has been carried out by quantum chemical calculations at the MP2 and CCSD(T) levels of theory. The effect of basic catalysts, namely ammonia and an ammonia-water complex, on the isomerization process has been studied for the very first time. In terms of rate coefficients ammonia was found to be a better catalyst than a water monomer whereas the ammonia-water complex was found to be more efficient over a water dimer but marginally less efficient than formic acid. Based on the effective rate constants under various tropospheric conditions, it was found that at 0 km altitude water dimers and ammonia-water complexes could compete with acid catalysts but at higher altitudes the acid catalysts would dominate their neutral and basic counterparts by a long distance.