Presence Of Additional Water Molecules Research Articles

Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity

Antifreeze proteins (AFPs) inhibit ice growth by adsorbing onto specific ice planes. Microbial AFPs show diverse antifreeze activity and ice plane specificity, while sharing a common molecular scaffold. To probe the molecular mechanisms responsible for AFP activity, we here characterized the antifreeze activity and crystal structure of TisAFP7 from the snow mold fungus Typhula ishikariensis. TisAFP7 exhibited intermediate activity, with the ability to bind the basal plane, compared with a hyperactive isoform TisAFP8 and a moderately active isoform TisAFP6. Analysis of the TisAFP7 crystal structure revealed a bound-water network arranged in a zigzag pattern on the surface of the protein’s ice-binding site (IBS). While the three AFP isoforms shared the water network pattern, the network on TisAFP7 IBS was not extensive, which was likely related to its intermediate activity. Analysis of the TisAFP7 crystal structure also revealed the presence of additional water molecules that form a ring-like network surrounding the hydrophobic side chain of a crucial IBS phenylalanine, which might be responsible for the increased adsorption of AFP molecule onto the basal plane. Based on these observations, we propose that the extended water network and hydrophobic hydration at IBS together determine the TisAFP activity.

Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules.

In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.

Relationship Between Phase Solubility Diagrams and Crystalline Structures During Dissolution of Cimetidine/Cyclodextrin Complex Crystals

Cyclodextrins (CDs) form complex crystals with drugs and improve physicochemical properties of drugs. However, only few reports have summarized relationships between crystal structures of drug/CD and dissolution behavior. In this study, we developed cimetidine (CIM)/CD complex crystals to achieve sustained drug release and investigated the relationship between the dissolution behavior of CIM/CD complexes and their crystal structures. CIM and 3 types of CDs (α-, β-, and γ-CD) formed a complex crystal when subjected to solvent mixing. The CIM/CD complexes had a highly reduced dissolution rate compared to that of the physical mixture of CIM and CD. β-CD improved the solubility of CIM, whereas γ-CD decreased its solubility. Based on the phase solubility diagram, CIM and α-, β-, and γ-CD indicated A-type positive (AP) and AL deviation, and B-type limited solubility (BS) profiles, respectively. In γ-CD, the saturated concentration of CIM decreased owing to the formation of a low-solubility complex with CIM. CIM/α-CD formed cage-type crystals, and CIM/β-CD and CIM/γ-CD formed channel-type crystals. The dissolution rate constant (k) of CIM/α-CD and CIM/β-CD were 0.045 and 0.04 h−1, respectively. CIM/γ-CD and CIM/β-CD displayed channel-type crystals; however, the channel-type crystals of CIM/γ-CD were stabilized by the presence of additional water molecules.

Predicting the Formation of Sulfur-Based Brønsted Acids from the Reactions of SOx with H2O and H2S.

We have performed an extensive computational investigation of the potential energy surfaces for the reactions of SOx (x = 2 or 3) with H2S and H2O in the gas phase and in aqueous solution at the CCSD(T)/CBS level of theory plus a self-consistent reaction field approach. Formation of a gas-phase H2SO4 from the hydrolysis of SO3 at lower temperatures requires the presence of additional water molecules. When additional waters are introduced, the barrier for H2SO4 formation is significantly reduced, and a barrierless transition occurs with only three excess waters as well as in aqueous solution. In a mixture of H2O, H2S, and SO3, formation of H2S2O3 has a lower barrier in the gas phase than does the formation of H2SO4. In aqueous solution, no barrier is predicted, and both are likely to be formed. Introduction of an additional water to the SO3 + H2S reaction results in a decrease in barrier height, nearly identical to the ∼18 kcal/mol catalytic effect of the first additional water in SO3 hydrolysis, with the barrier for H2S2O3 formation disappearing altogether in aqueous solution. Formation of H2SO3 by the way of SO2 hydrolysis is unlikely. Excess waters reduce the barrier for SO2 hydrolysis; however, the overall endothermicity is increased as waters are added. The formation of H2S2O2 from SO2 and H2S via an isostructural pathway to SO2 hydrolysis is unlikely, with additional water molecules resulting in a small increase in the overall endothermicity and a catalytic effect smaller than that observed for the SO3 reactions. The results of this work have implications pertaining to the formation of H2SO4, H2S2O3, H2SO3, and H2S2O2 in the atmospheres of Earth and Venus. These results also question the existence of H2S2O2 as an intermediate in the Claus process.

Classical dynamics simulations of interstellar glycine formation via $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2}\hbox {O}$$ CH 2 = NH + CO + H 2 O reaction

Formation of simple organic species such as glycine in the interstellar medium and transportation to earth via meteorites is considered to be a possible route for ‘Origin of Life’ on earth. Glycine formation has been proposed to occur via two different pathways involving formaldehyde ( $$\hbox {HCHO}$$ ) and methanimine ( $$\hbox {CH}_{2} = \hbox {NH}$$ ) as key intermediates. In the second pathway, which is the topic of this paper, $$\hbox {CH}_{2} = \hbox {NH}$$ reacts with $$\hbox {CO}$$ and $$\hbox {H}_{2} \hbox {O}$$ forming neutral glycine. In a recent article (Nhlabatsi et al. in Phys. Chem. Chem. Phys. 18:375, 2016), detailed electronic structure calculations were reported for the reaction between $$\hbox {CH}_{2} = \hbox {NH}$$ , $$\hbox {CO}$$ and $$(\hbox {H}_{2} \hbox {O})_n$$ , $$n = 1, 2, 3$$ , and 4, forming glycine in the interstellar media. The presence of additional water molecule(s) for this reaction reduces reaction barrier - thus exhibiting a catalytic effect. This effect was described in terms of efficient proton transfer mediated by the additional water molecule through a relay transport mechanism. In the present article, we report ab initio classical trajectory simulations for the interstellar formation of glycine for the above mentioned reaction with $$n = 1$$ and 2. The trajectories were generated on-the-fly over a density functional B3LYP/6-31++G(3df,2pd) potential energy surface. Our simulations indicate that the above proposed catalytic effect by the additional water molecule(s) may not be a classical effect. Synopsis: Glycine formation in the interstellar media via the $$\hbox {CH}_{2} = \hbox {NH} + \hbox {CO} + \hbox {H}_{2} \hbox {O}$$ reaction was investigated by classical chemical dynamics simulations. This reaction has a large barrier which reduces in presence of additional water molecules. Our simulations indicate that the proposed catalytic effect by the additional water molecules may not be a classical effect.

Theoretical study of HNCO formation from atomic nitrogen and carbon monoxide in the presence of water

The formation of HNCO has been studied through DFT calculations in comparison with experimental IR measurements. Four different pathways starting from atomic nitrogen, water and carbon monoxide molecules were considered. Among them, the direct formation of NCO in the presence of water corresponds to the most favourable with a relative energy of 11.8kcal/mol. IR frequencies were found to be in a good agreement with experimental measurements in presence of additional water molecules. Accordingly the most stable reaction path was studied by including an additional water molecule. The results show that the maximum relative energy is lowered to 5.5kcal/mol owing to the stabilization through H-bonds with water molecules. As such the presence of water seems mandatory to lower maximum energy states and favours the reaction to occur at low temperatures in astrophysical environments.

Adaptively Compressed Exchange Operator for Large-Scale Hybrid Density Functional Calculations with Applications to the Adsorption of Water on Silicene.

Density functional theory (DFT) calculations using hybrid exchange-correlation functionals have been shown to provide an accurate description of the electronic structures of nanosystems. However, such calculations are often limited to small system sizes due to the high computational cost associated with the construction and application of the Hartree-Fock (HF) exchange operator. In this paper, we demonstrate that the recently developed adaptively compressed exchange (ACE) operator formulation [J. Chem. Theory Comput. 2016, 12, 2242-2249] can enable hybrid functional DFT calculations for nanosystems with thousands of atoms. The cost of constructing the ACE operator is the same as that of applying the exchange operator to the occupied orbitals once, while the cost of applying the Hamiltonian operator with a hybrid functional (after construction of the ACE operator) is only marginally higher than that associated with applying a Hamiltonian constructed from local and semilocal exchange-correlation functionals. Therefore, this new development significantly lowers the computational barrier for using hybrid functionals in large-scale DFT calculations. We demonstrate that a parallel planewave implementation of this method can be used to compute the ground-state electronic structure of a 1000-atom bulk silicon system in less than 30 wall clock minutes and that this method scales beyond 8000 computational cores for a bulk silicon system containing about 4000 atoms. The efficiency of the present methodology in treating large systems enables us to investigate adsorption properties of water molecules on Ag-supported two-dimensional silicene. Our computational results show that water monomer, dimer, and trimer configurations exhibit distinct adsorption behaviors on silicene. In particular, the presence of additional water molecules in the dimer and trimer configurations induces a transition from physisorption to chemisorption, followed by dissociation on Ag-supported silicene. This is caused by the enhanced effect of hydrogen bonds on charge transfer and proton transfer processes. Such a hydrogen bond autocatalytic effect is expected to have broad applications for silicene as an efficient surface catalyst for oxygen reduction reactions and water dissociation.

The effect of water content on chain dynamics in nafion membranes measured by neutron spin echo and dielectric spectroscopy

ABSTRACTNeutron spin‐echo spectroscopy has been used to measure the time‐scale of fluctuations associated with the inter‐chain correlation peak observed in the diffraction pattern of the perfluorosulfonate ionomer, Nafion®. We have successfully measured the chain dynamics as a function of water content and temperature and have demonstrated that the chain dynamics become faster with increasing temperature. The addition of water also results in shorter relaxation times due to a plasticization of the chain motions. At water contents above aλ≈ 6, the chain dynamics seem to approach a plateau and the relaxation times of the chains are no longer being plasticized by the presence of additional water molecules. The increased mobility in molecular relaxations induced by the presence of water points to the molecular origins of the temperature‐ and humidity‐dependent softening mechanisms in Nafion and other perfluorinated sulfonic acid membrane materials. Moreover, these results show that there is a strong inter‐dependence of the dynamics of water and the polymer chains in Nafion membranes. © 2014 Wiley Periodicals, Inc. J. Polym. Sci. Part B: Polym.2014,52, 624–632

A computational study on the structures of methylamine–carbon dioxide–water clusters: evidence for the barrier free formation of the methylcarbamic acid zwitterion (CH3NH2+COO−) in interstellar water ices

We investigated theoretically the interaction between methylamine (CH(3)NH(2)) and carbon dioxide (CO(2)) in the presence of water (H(2)O) molecules thus simulating the geometries of various methylamine-carbon dioxide complexes (CH(3)NH(2)/CO(2)) relevant to the chemical processing of icy grains in the interstellar medium (ISM). Two approaches were followed. In the amorphous water phase approach, structures of methylamine-carbon dioxide-water [CH(3)NH(2)/CO(2)/(H(2)O)(n)] clusters (n = 0-20) were studied using density functional theory (DFT). In the crystalline water approach, we simulated methylamine and carbon dioxide interactions on a fragment of the crystalline water ice surface in the presence of additional water molecules in the CH(3)NH(2)/CO(2) environment using DFT and effective fragment potentials (EFP). Both the geometry optimization and vibrational frequency analysis results obtained from these two approaches suggested that the surrounding water molecules which form hydrogen bonds with the CH(3)NH(2)/CO(2) complex draw the carbon dioxide closer to the methylamine. This enables, when two or more water molecules are present, an electron transfer from methylamine to carbon dioxide to form the methylcarbamic acid zwitterion, CH(3)NH(2)(+)CO(2)(-), in which the carbon dioxide is bent. Our calculations show that the zwitterion is formed without involving any electronic excitation on the ground state surface; this structure is only stable in the presence of water, i.e. in a methyl amine-carbon dioxide-water ice. Notably, in the vibrational frequency calculations on the methylcarbamic acid zwitterion and two water molecules we find the carbon dioxide asymmetric stretch is drastically red shifted by 435 cm(-1) to 1989 cm(-1) and the carbon dioxide symmetric stretch becomes strongly infrared active. We discuss how the methylcarbamic acid zwitterion CH(3)NH(2)(+)CO(2)(-) might be experimentally and astronomically identified by its asymmetric CO(2) stretching mode using infrared spectroscopy.