Molecular dynamics studies of the Nafion®, Dow® and Aciplex® fuel-cell polymer membrane systems

The Nafion, Dow and Aciplex systems – where the prime differences lies in the side-chain length – have been studied by molecular dynamics (MD) simulation under standard pressure and temperature conditions for two different levels of hydration: 5 and 15 water molecules per (H)SO₃ end-group. Structural features such as water clustering, water-channel dimensions and topology, and the dynamics of the hydronium ions and water molecules have all been analysed in relation to the dynamical properties of the polymer backbone and side-chains. It is generally found that mobility is promoted by a high water content, with the side-chains participating actively in the H₃O⁺/H₂O transport mechanism. Nafion, whose side-chain length is intermediate of the three polymers studied, is found to have the most mobile polymer side-chains at the higher level of hydration, suggesting that there could be an optimal side-chain length in these systems. There are also some indications that the water-channel network connectivity is optimal for high water-content Nafion system, and that this could explain why Nafion appears to exhibit the most favourable overall hydronium/water mobility. Figure The simulation box for Aciplex with 5 water molecules per sulphonate end-group (yellow spheres). The polymer backbone is black; while side-chains are brown. The water-channel iso-surfaces are represented as blue clouds     

Alpha particle chemistry. On the formation of stable complexes between He2+ and other simple species: implications for atmospheric and interstellar chemistry

The possibility that stable complexes may be formed between alpha particles (He²⁺) and small molecules is investigated using QCISD quantum mechanical calculations. Implications for their presence in the terrestrial atmosphere and/or in interstellar space are discussed. Figure Optimized structure of a stable H₂OHe²⁺ complex     

Hydration of counterions interacting with DNA double helix: a molecular dynamics study

In the present work, molecular dynamics simulations have been carried out to study the dependence of counterion distribution around the DNA double helix on the character of ion hydration. The simulated systems consisted of DNA fragment d(CGCGAATTCGCG) in water solution with the counterions Na⁺, K⁺, Cs⁺ or Mg²⁺. The characteristic binding sites of the counterions with DNA and the changes in their hydration shell have been determined. The results show that due to the interaction with DNA at least two hydration shells of the counterions undergo changes. The first hydration shell of Na⁺, K⁺, Cs⁺, and Mg²⁺ counterions in the bulk consists of six, seven, ten, and six water molecules, respectively, while the second one has several times higher values. The Mg²⁺ and Na⁺ counterions, constraining water molecules of the first hydration shell, mostly form with DNA water-mediated contacts. In this case the coordination numbers of the first hydration shell do not change, while the coordination numbers of the second one decrease about twofold. The Cs⁺ and K⁺ counterions that do not constrain surrounding water molecules may be easily dehydrated, and when interacting with DNA their first hydration shell may be decreased by three and five water molecules, respectively. Due to the dehydration effect, these counterions can squeeze through the hydration shell of DNA to the bottom of the double helix grooves. The character of ion hydration establishes the correlation between the coordination numbers of the first and the second hydration shells.

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Graphical Abstract Hydration of counterions interacting with DNA double helix

     

G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene

Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane’s unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affinities. Our results indicate that the cis form of triazene has a specific enthalpy of combustion of −15.2 kJ g⁻¹ and the trans form has a specific enthalpy of combustion of −14.7 kJ g⁻¹. Figure Structures of cis- and trans-triazane, N₃H₃     

Theoretical study of spin-spin coupling across the hydrogen (O-H⋯N) bond in adenosine derivatives

The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes. The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH₂OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the ^4h J _NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models. Figure Coupling constants in 8-bromo-2′,3′-O-isopropylideneadenosine Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides

Nitrile hydratase (NHase) is an enzyme containing non-corrin Co³⁺ in the non-standard active site. NHases from Pseudonocardia thermophila JCM 3095 catalyse hydration of nitriles to corresponding amides. The efficiency of the enzyme is 100 times higher for aliphatic nitriles then aromatic ones. In order to understand better this selectivity dockings of a series of aliphatic and aromatic nitriles and related amides into a model protein based on an X-ray structure were performed. Substantial differences in binding modes were observed, showing better conformational freedom of aliphatic compounds. Distinct interactions with postranslationally modified cysteines present in the active site of the enzyme were observed. Modeling shows that water molecule activated by a metal ion may easily directly attack the docked acrylonitrile to transform this molecule into acryloamide. Thus docking studies provide support for one of the reaction mechanisms discussed in the literature. Figure Crystalographic structure of Pseudonocardia thermophila JCM 3095 nitrile hydratase (a) and the non-standard active site (b)     

An insight into hydration structure of sodium glycinate from <Emphasis Type="Italic">ab initio</Emphasis> quantum chemical study

The hydration structure of sodium glycinate (Na⁺GL^?) is probed by the Monte-Carlo multiple minimum (MCMM) method combined with quantum mechanical (QM) calculations at the MP2/6-311++G(d,p) level. In the gas phase, the energy of [Na⁺GL^?]_β is more than 30 kJ mol^?1 higher than [Na⁺GL^?]_α. With higher degrees of hydration, our results indicate that the most stable conformers of [Na⁺GL^?]?(H₂O)₈ were derived from [Na⁺GL^?]_β instead of [Na⁺GL^?]_α. The stable conformers determined by the conductor-like polarizable continuum model (CPCM) also show that [Na⁺GL^?]_β is more stable than [Na⁺GL^?]_α in the liquid phase. By analyzing the hydration process, water…water hydrogen bonding interaction will be more preferable than ion…water interaction as the number of water molecules increases. According to the electronic density at the bond critical point on the Na-X bonds (X?=?O1, O2, N) in the low-energy conformers, Na⁺GL^? will be dissociated as Na⁺ and GL^? in the bulk water, which is not predicted by the CPCM model. The structure features and the charge redistribution of Na⁺GL^? will provide a physical explanation for the weakening Na-O1 interaction.

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Graphical Abstract Hydration structure of sodium glycinate from ab initio quantum chemical study

     

Theoretical study of [ XN5 ]− (X=O, S, Se, Te) systems

A series of [XN₅]⁻ (X=O, S, Se, Te) compounds has been examined with ab initio and Density Functional Theory (DFT) methods. The five-membered nitrogen ring series of structures are global minima and may exist or be characterized due to their significant dissociation barriers (29.7–32.7 kcal mol⁻¹). Nucleus-independent chemical shifts (NICS) criteria and the presence of (4n+2) π-electrons confirmed that the five-membered nitrogen ring in their structures exhibits characteristics of aromaticity. Thus, the strong stability of the five-membered nitrogen ring structures may be attributed partially to their aromaticity.      

G2, G3, and complete basis set calculations on the thermodynamic properties of triazane

As a follow-up study to our study on tetrazane (N₄H₆), we present computed thermodynamic properties of triazane (N₃H₅). Calculated properties include optimized geometries, infrared vibrations, enthalpy of formation, enthalpy of combustion, and proton affinities. We have also mapped the potential energy surface as the molecule is rotated about the N-N bond. We have predicted a specific enthalpy of combustion for triazane of about -20 kJ g⁻¹. Figure Schematic diagram of the dielectric barrier discharge (left) and typical temporal profiles of voltage and current, as obtained from the simulations (right)     

Conformational stability and three-dimensional model of the δ-opioid pharmacophore for the extended antiparallel dimer structure of Met-enkephalin in water

The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly² and Phe⁴ groups. The three-dimensional model of the δ-opioid pharmacophore for this dimer structure was also established. Such a model was demonstrated to match the δ-opioid pharmacophore query derived from the non-peptides SIOM, TAN-67, and OMI perfectly. This result thus strongly supports the assumption that the dimer structure of Met-enkephalin is a possible δ-receptor binding conformation. Figure Schematic model of the extended antiparallel dimer structure of Met-enkephalin     

Computational modeling of the adsorption and •OH initiated photochemical and photocatalytic primary oxidation of nitrobenzene

The adsorption and primary oxidation step for the photodegradation of nitrobenzene (NB) have been studied computationally using MSINDO SCF MO method. The method performs efficiently for extended surface models such as Ti₃₆O₉₀H₃₆. Molecular dynamics simulations have revealed that NB is linked to TiO₂ surface at the titanium ion via the oxygen atoms of NO₂ group. In addition, the computed vibrational density of states for the adsorbed NB molecule is in reasonably good agreement with the available experimental data and theoretical results. In order to identify the primary photochemical and photocatalytic ^•OH initiated photooxidation intermediates, we have employed two different theoretical approaches, frontier orbital theory and Wheland localization theory. It has been found that the meta- hydroxynitrocyclohexadienyl radical is energetically more favored than para- and ortho-hydroxynitrocyclohexadienyl radicals for the photochemical photolysis, whereas in the case of photocatalysis, the ^•OH radical attack is unselective and all three possible isomers have comparable stabilities. Figure Minimum energy adsorption conformation of nitrobenzene onto TiO₂ (100) surface     

The platinum-olefin binding energy in series of (PH<Subscript>3</Subscript>)<Subscript>2</Subscript>Pt(olefin) complexes - a theoretical study

Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics bearing coordinated olefins with general formula (R¹R²C = CR³R⁴)Pt(PH₃)₂ [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin substituents. Figure Representation of (CH₂ = CHR)Pt(PPh₃)₂ and the stability chart     

First report of a planar and a quasi-planar Al<Subscript>13</Subscript><Superscript>+</Superscript> cluster having localized antiaromatic deltas within an aromatic sea: NICS,ELF, AIM,and AdNDP bonding analysis

A perfectly planar Al₁₃⁺ cluster (CI) and a quasi-planar Al₁₃⁺ cluster (CII) have been found for the first time. Both clusters have a triangular core surrounded by a set of ten Al atoms in the form of a ring. These cationic clusters have substantial aromatic character. The planar CI cluster has local antiaromatic patches within global aromatic sea. It is doubly aromatic having both σ and π aromatic character. The quasi-planar CII cluster is also aromatic but it has more σ-delocalization.

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Graphical abstract Planar and quasi-planar Al₁₃⁺ clusters with triangular core surrounded by a ring of ten atoms.

     

A B3LYP and MP2 theoretical investigation into host-guest interaction between calix[4]arene and Li+ or Na+

The DFT-B3LYP and MP2 methods with 6-311G** and 6-311++G** basis sets have been applied to study the complexation energies of the host-guest complexes between the cone calix[4]arene and Li⁺ or Na⁺ on the B3LYP optimized geometries. A comparison of the complexation energies obtained from the MP2(full) with those from MP2(fc) method is also carried out. The result shows that it is essential to introduce the diffuse basis set into the geometry optimizations and complexation energy calculations of the alkali-metal cation-π interaction complexes of calix[4]arene, and the D _e values show a maximum of 21.13 kJ mol⁻¹ (14.45% of relative error) between the MP2(full)/6-311++G** and MP2(fc)/6-311++G** method. For Li⁺ cation, the complexation is mainly energetically stabilized by the lower rim/cation (namely O–Li⁺) interaction. However, binding energies and NBO analyses confirm that Na⁺ cation prefers to enter the calix[4]arene cavity and the cation-π interaction is predominant, which contradicts the previous low-level theoretical studies. Furthermore, the complexation with Li⁺ is preferred over that with Na⁺ by at least 12.70 kJ mol⁻¹ at MP2(full)/6-311++G**//B3LYP/6-311++G** level.      

3D-QSAR and docking studies of 3-arylquinazolinethione derivatives as selective estrogen receptor modulators

3D-QSAR and molecular docking analysis were performed to explore the interaction of estrogen receptors (ERα and ERβ) with a series of 3-arylquinazolinethione derivatives. Using the conformations of these compounds revealed by molecular docking, CoMFA analysis resulted in the first quantitative structure-activity relationship (QSAR) and first quantitative structure-selectivity relationship (QSSR) models predicting the inhibitory activity against ERβ and the selectivity against ERá. The q² and R² values, along with further testing, indicate that the obtained 3D-QSAR and 3D-QSSR models will be valuable in predicting both the inhibitory activity and selectivity of 3-arylquinazolinethione derivatives for these protein targets. A set of 3D contour plots drawn based on the 3D-QSAR and 3D-QSSR models reveal modifications of substituents at C2 and C5 of the quinazoline which my be useful to improve both the activity and selectivity of ERβ/ ERα. Results showed that both the steric and electrostatic factors should appropriately be taken into account in future rational design and development of more active and more selective ERβ inhibitors for the therapeutic treatment of osteoporosis. Figure Structures of ERβ binding with compounds 1aar, 1ax and 1aag obtained from molecular docking     

TCNE-aniline charge transfer complex: ab initio and TDDFT investigations in gas phase

The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site is a C≡N and C=C bond center in the TCNE and, –NH₂ and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy, estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the reported experimental value in chloroform medium. TCNE-aniline at ground state. TCNE-aniline at excited state     

DFT investigation of the 1-octene metathesis reaction mechanism with the Phobcat precatalyst

The productive self-metathesis reaction of 1-octene in the presence of the Phobcat precatalyst [RuCl₂(Phoban-Cy)₂(=CHPh)] using density functional theory was investigated and compared to the Grubbs 1 precatalyst [RuCl₂(PCy₃)₂(=CHPh)]. At the GGA-PW91/DNP level, the geometry optimization of all the participating species and the PES scans of the various activation and catalytic cycles in the dissociative mechanism were performed. The formation of the catalytically active heptylidene species is kinetically and thermodynamically favored, while the formation of trans-tetradecene is thermodynamically favored.      

Molecular model for host–guest interaction of tetraamino-<Emphasis Type="Italic">tert</Emphasis>-butylthiacalix[4]arene and tetraamino-<Emphasis Type="Italic">tert</Emphasis>-butylcalix[4]arene receptors with carboxylate and dicarboxylate guests: an ONIOM study

Geometry optimizations of tetraamino-tert-butylthiacalix[4]arene (tatbtc4a) and tetraamino-tert-butylcalix[4]arene (tatbc4a) complexes with acetate, oxalate, malonate, succinate, glutarate, adipate, and pimelate were carried out using the integrated MO:MO method. Thermodynamic quantities, preorganization energies and complexation energies of these complexes were obtained at the ONIOM(B3LYP/6-31G(d):AM1) level of theory. The relative stabilities of the tatbtc4a and tatbc4a complexes with carboxylate guests are reported. The complexes tatbtc4a/malonate and tatbc4a/oxalate were found to be the most stable species. The selectivity of the tatbtc4a receptor toward to malonate with respect to oxalate, in terms of selectivity coefficient, is 9.90×10². Figure Atom labeling of tatbtc4a/oxalate complex as a representative of host-guest system.     

On the performance of ruthenium dyes in dye sensitized solar cells: a free cluster approach based on theoretical indexes

The performance of ruthenium dye sensitized solar cells (DSSC) with different types of ligand was studied by means of a theoretical model where the ruthenium complex is bound to two [Ti(OH)₃]⁺ units, instead of the more usual cluster TiO₂ model. Electron injection is proposed to proceed from a thermalized ³MLCT state rather than from higher vibrational excited states. The efficiency of the dye linked to the two [Ti(OH)₃]⁺ units was determined in terms of a global index (ξ), calculated as the product of three theoretical indexes (F_I) built from the results of time-dependent density functional theory (TDDFT) calculations. The index considers the harvested and delivered energy (F₁), the charge transferred to the semiconductor (F₂), and dye regeneration (F₃). The results show that this set of parameters is unique for each dye, and allows the comparative evaluation of the performance of a series of dyes, with a different ancillary ligand at each stage of the cell operation. The method provides insights that can help explain the improved performance of N3 and black dyes compared to other dyes.

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Graphical abstract Calculated global efficiency for complexes C1–C6. Inset General structure of the interacting model

     

Localized and delocalized perfluorosemibullvalenes

On the basis of the experimental Gibbs free-energy barrier of the degenerate Cope arrangement in semibullvalene, B3P86 shows the best agreement, while B3LYP and MP2 underestimate and CCSD(T) overestimates the barrier. The substituent effect proposal by Hoffmann has been verified. In contrast to semibullvalenes with either localized energy-minimum structures or delocalized transition-state structures, perfluorosemibullvalene has both localized and delocalized energy-minimum structures that are very close in energy. Localized and delocalized perfluorosemibullvalenes Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.