A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

ABSTRACT

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.     

Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6

In aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate how competing mechanisms can explain the seemingly contradictory statements about the structure and dynamics of ion-coordinated solvent in aqueous solutions of two interesting and technologically important electrolytes, NaBF₄ and NaPF₆. While the static structural data (i.e. radial, radial-angular and spatial distribution functions, as well as hydrogen bonding statistics) unequivocally point at very weak anion–water hydrogen bonding in both salts, dynamic analyses (in particular, orientational anisotropy decay and solvent residence times) reveal quite significant retardation of water rotation and mobility due to solute coordination. Additionally, rotational immobilisation of coordinated solvent molecules is clearly unrelated to the hydrogen bond strength between them, as demonstrated by the interatomic oxygen–oxygen distance distributions for coordinated and bulk water.     

Dissociation of liquid water on defective rutile TiO<Subscript>2</Subscript> (110) surfaces using <Emphasis Type="Italic">ab initio</Emphasis> molecular dynamics simulations

In order to obtain a comprehensive understanding of both thermodynamics and kinetics of water dissociation on TiO₂, the reactions between liquid water and perfect and defective rutile TiO₂ (110) surfaces were investigated using ab initio molecular dynamics simulations. The results showed that the free-energy barrier (~4.4 kcal/mol) is too high for a spontaneous dissociation of water on the perfect rutile (110) surface at a low temperature. The most stable oxygen vacancy (Vo₁) on the rutile (110) surface cannot promote the dissociation of water, while other unstable oxygen vacancies can significantly enhance the water dissociation rate. This is opposite to the general understanding that Vo₁ defects are active sites for water dissociation. Furthermore, we reveal that water dissociation is an exothermic reaction, which demonstrates that the dissociated state of the adsorbed water is thermodynamically favorable for both perfect and defective rutile (110) surfaces. The dissociation adsorption of water can also increase the hydrophilicity of TiO₂.     

Velocity imaging spectrometer for negative fragment ions: application to dynamics of O2 and N2O ion-pair dissociation

A velocity imaging spectrometer has been developed to observe negative ions from molecular ion-pair dissociation. The imaging spectrometer is equipped with a pair of permanent magnets. The resulting magnetic field prevents efficiently the electrons from reaching the detector, without seriously affecting negative ions’ trajectories. The performance of the imaging spectrometer is demonstrated by the observations of photoelectrons from O₂ and He, and O⁻ from O₂. Application to ion-pair dissociation of O₂ and N₂O is presented, and it proves that the present imaging method provides useful information on the assignments of superexcited states and on the dynamics of ion-pair dissociation.     

Chemical reactions between CF2HCl and NH3 induced by IR double-beam excitation

Infrared multiphoton dissociation experiments with two wavelengths in different mixtures of chlorodifluoromethane and ammonia have been carried out. It is shown that the presence of ammonia in the sample induces a decrease in the chlorodifluoromethane dissociation yield. It has been observed that the distinct chemical reaction channels are differently activated as the time delay between the two laser pulses is varied. The ratio of the obtained products in the infrared multiphoton dissociation changes with the composition of the initial mixture and are not compatible with the mechanism suggested by Sugita and Arai for this reaction in single IR wavelength excitation if it is assumed to be the only contributing mechanism other than that for direct CF₂HCl dissociation and subsequent C₂F₄ formation from the resulting CF₂ radicals. It appears that, although for simultaneous two-wavelength irradiation the presence of an accumulated solid NH₄Cl deposit does not significantly influence the reaction, this is no longer the case when time delays are introduced between the two beams.     

Substituent effects on the formation of sulfonyl cations from sulfonyl chlorides: comparisons of solvolysis kinetic data with calculated gas phase energies

Suitable theoretical methods are validated for organosulfur compounds using experimental data for gas phase enthalpies of formation, proton affinities (PA) and heterolytic bond dissociation enthalpies (HBDEs). From enthalpies of chloride anion transfers from neutral chlorides to acyl, sulfonyl or cumyl cations in the gas phase, it is calculated that (i) similar aromatic substituent effects are expected for heterolyses of acyl, sulfonyl and cumyl chlorides; (ii) HBDEs for loss of chloride increase by over 70 kcal mol^?1 from 4‐MeOC₆H₄COCl to SO₂Cl₂. Rate constants for solvolyses of 4‐Z‐substituted arenesulfonyl chlorides (Z = OMe, Me, H, Cl, NO₂) in 97% w/w 2,2,2‐trifluoroethanol (TFE)–water are reported. Substituent effects are smaller than observed for identical solvolyses of acyl and cumyl chlorides, and are much smaller than those predicted theoretically for gas phase unimolecular heterolysis (explained by variable amounts of nucleophilic solvent assistance). Copyright © 2007 John Wiley & Sons, Ltd.     

Some measures for making a traditional halogen bond be chlorine-shared or ion-pair one in FCl•NH3 complex

ABSTRACT

The Cl···N halogen bond (XB) in FCl·NH₃ is tuned from a traditional one to a chlorine-shared or an ion-pair one with three methods. The first method is to put this complex into different clusters of (FCl·NH₃)(H₂O)₆. The second method is to add solvents with different dielectric constants around this complex. The third method is to impose a proper external electric field on this complex. The traditional XB has the negative quantity [r₁(F–Cl) ? r₂(Cl–N)], while the chlorine-shared and ion-pair XBs exhibit the positive r₁ ? r₂, both having the ion-pair character of smaller and larger than 85%, respectively.     

Etching reaction of methylchloride molecule on the GaAs (0 0 1)-2 × 4 surface

Adsorption process of methylchloride (CH₃Cl) on the GaAs (0 0 1)-2 × 4 surface was studied by a scanning tunnelling microscopy (STM) measurement. The arsenic rich 2 × 4 surface, which was prepared by molecular beam epitaxy (MBE), was exposed to a supersonic molecular beam of CH₃Cl with a kinetic energy of 0.06 eV. New bright spots appeared on the CH₃Cl exposed surface. They were largely observed at the “B-type” step edge and divided into two types according to their locations. It was suggested that new spots were due to weakly adsorbed CH₃Cl molecules without any dissociation. The adsorption mechanism of CH₃Cl molecule was also studied by an ab initio Hartree-Fock calculation, which explained the experimental results well.     

Molecular dynamics study on the dissociation of methane hydrate via inorganic salts

Hydrate plugging is a hidden threat to the safe exploitation of oil and gas. Inorganic salts are widely used as thermodynamic inhibitors to effectively prevent the hydrate formation. This study uses a molecular dynamics method to explore the mechanism of the hydrate dissociation via inorganic salts on the micro-scale. We simulated the dissociating process of methane hydrate under different concentration series of NaCl, KCl and CaCl₂ solutions at 273 K, and analysed the changes of ionic structure, transport parameters and kinetic energy in the system of inorganic salt/hydrate. The simulation results successfully revealed the step-by-step dissociation of hydrate, and the differences in dissociation rates among the different inhibitors. The energy needed for hydrate dissociation alters for different inorganic solutions; the energy reaches maximum when KCl is the inhibitor, and lowest when the concentration of CaCl₂ exceeds 30% w/w. We calculated the coordination numbers of all components, including oxygen atoms, cations and anions, and also their diffusion coefficients; analysed the effects of the three inorganic salts on the simulated hydrate structure and its transport; in addition, investigated the mechanism of hydrate dissociation via inorganic salts.     

Effect of water–methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; a molecular dynamics study

Continuing an ongoing study, molecular dynamics (MD) simulations were performed to investigate the effects of methanol concentration on Nafion morphology, such as the size of solvent cluster, solvent location, and polymer structure via the sandwich model. Our survey shows that high methanol concentrations resulted in increment of solvent cluster size in Nafion membrane. The sulfonic acid clusters also befall much in order as subsequent layers of such ionic clusters are formed. The number of neighbouring hydronium ions around a sulfur atom is independent of methanol concentration, but the first shell of hydronium and water around sulfonic acid clusters is broader. Although methanol would prefer to interact with water molecules rather than sulfonic acid groups, gathering of methanol molecules via hydrophobic self-aggregation is preferred. Methanol is located closer to the hydrophobic part of the polymer than water, while water is located closer to the hydrophilic part of the polymer. It was found that methanol distributes specifically more than water in nano-channels. Investigation of solvent dynamics in nano-channels shows that diffusion coefficients (D) of water, methanol, and hydronium decrease with increasing methanol concentration and they may be ordered as follows: D _Water?>?D _Methanol?>?D _Hydronium (D _Water?≈?1.6–2.0D _Methanol and D _Methanol?≈?2.1–3.0D _Hydronium).     

Theoretical studies on atmospheric chemistry of HFE‐347mcc3: reactions with OH radicals and Cl atoms

Detailed theoretical investigation has been performed on the mechanism, kinetics and thermochemistry of the gas phase reactions of CF₃CF₂CF₂OCH₃ (HFE‐347mcc3) with OH radicals and Cl atoms using M06‐2X/6‐31 + G(d,p) level of theory. Reaction profiles are modeled including the formation of pre‐reactive and post‐reactive complexes at entrance and exit channels, respectively. Using group‐balanced isodesmic reactions, the standard enthalpies of formation for species are also reported. The calculated bond dissociation energy for C―H bond is in good agreement with previous data. The rate constants of the two reactions are determined for the first time in a wide temperature range of 250–1000 K. At 298 K, the calculated rate coefficients are in good agreement with the experimental results. The atmospheric life time of HFE‐347mcc3 is estimated to be 4.4 years. Copyright © 2014 John Wiley & Sons, Ltd.     

Dispersive liquid–liquid microextraction based on solidification of floating organic drop for separation and preconcentration of malachite green before its determination by flow injection spectrophotometry

ABSTRACT

A simple and fast dispersive liquid–liquid microextraction based on solidification of floating organic drop has been developed for the separation and preconcentration of malachite green in water samples prior to its determination by flow injection spectrophotometry. Sodium lauryl sulfate, an anionic surfactant, was used for the ion-pair formation with malachite green. The factors affecting the ion-pair formation and extraction were optimized. Under the optimized conditions (volume of 1-undecanol as the extraction solvent, 40 μL; the volume of ethanol as the disperser solvent, 100 μL; sodium lauryl sulfate concentration, 7.5 × 10^?7 mol L^?1, and the pH of the sample, ～3.0), the calibration graph was linear over the range of 0.8–25 µg L^?1 with the detection limit of 0.3 µg L^?1 and the preconcentration factor of 750. The relative standard deviation at 7 µg L^?1 (n = 6) was found to be 2.1%. The developed method was successfully applied to the determination of malachite green in river water and fish farming water samples.     

Aqueous electrolyte surfaces in strong electric fields: molecular insight into nanoscale jets and bridges

Exposing aqueous surfaces to a strong electric field gives rise to interesting phenomena, such as formation of a floating water bridge or an eruption of a jet in electrospinning. In an effort to account for the phenomena at the molecular level, we performed molecular dynamics simulations using several protocols on both pure water and aqueous solutions of sodium chloride subjected to an electrostatic field. All simulations consistently point to the same mechanisms which govern the rearrangement of the originally planar surface. The results show that the phenomena are primarily governed by an orientational reordering of the water molecules driven by the applied field. It is demonstrated that, for pure water, a sufficiently strong field yields a columnar structure parallel to the field with an anisotropic arrangement of the water molecules with their dipole moments aligned along the applied field not only in the surface layer but over the entire cross section of the column. Nonetheless, the number of hydrogen bonds per molecule does not seem to be affected by the field regardless of its strength and molecule’s orientation. In the electrolyte solutions, the ionic charge is able to overcome the effect of the external field tending to arrange the water molecules radially in the first coordination shell of an ion. The ion–water interaction interferes thus with the water–electric field interaction, and the competition between these two forces (i.e., strength of the field versus concentration) provides the key mechanism determining the stability of the observed structures.     

Dissociation and kinetic of hydrochloric acid in mixed isomeric alcoholic-aqueous solvents — A conductance study

The effect of water and the effect of time on the conductance behavior of dilute solutions of hydrochloric acid in n-butanol–water and iso-butanol–water mixtures with the alcohol percentages; 97.00%, 97.50%, 98.00%, 98.50%, 99.00%, 99.50%, 99.70% and 99.98% at 298 K are reported. The data were analysed with a computer program for the Lee–Wheaton conductivity equation. The molar conductance (Λ), limiting molar conductance (Λ₀), dissociation constants (K_d), and the standard free energy of dissociation (?G^°_d) were calculated and discussed. The kinetic of hydrochloric acid conductance was also discussed and the results showed a first order interaction between HCl and the alcoholic solvents. In agreement with previous experiments in alcohol–water mixtures the limiting molar conductance decreases when water is added to the alcohol and then increases again. The results show that, the dissociation constant decreased as the relative permittivity of the solvent decreased.     

The SN3–SN2 spectrum. Rate constants and product selectivities for solvolyses of benzenesulfonyl chlorides in aqueous alcohols

Rate constants for a wide range of binary aqueous mixtures and product selectivities (S) in ethanol–water (EW) and methanol–water (MW) mixtures, are reported at 25 °C for solvolyses of benzenesulfonyl chloride and the 4‐chloro‐derivative. S is defined as follows using molar concentrations: S = ([ester product]/[acid product]) × ([water solvent]/[alcohol solvent]). Additional selectivity data are reported for solvolyses of 4‐Z‐substituted sulfonyl chlorides (Z = OMe, Me, H, Cl and NO₂) in 2,2,2‐trifluoroethanol–water. To explain these results and previously published data on kinetic solvent isotope effects (KSIEs) and on other solvolyses of 4‐nitro and 4‐methoxybenzenesulfonyl chloride, a mechanistic spectrum involving a change from third order to second order is proposed. The molecularity of these reactions is discussed, along with new term ‘S_N3–S_N2 spectrum’ and its connection with the better established term ‘S_N2–S_N1 spectrum’. Copyright © 2009 John Wiley & Sons, Ltd.     

Enhancing the relaxivity of paramagnetic coordination complexes through the optimization of the molecular electrostatic potential

The low relaxivity of paramagnetic coordination complexes limits their use as contrast agents in magnetic resonance imaging (MRI). To address this problem, we study the relationship between the molecular structure of these complexes and their relaxivity. While others have investigated the vibrational modes as molecular determinants of the electronic spin relaxation time, we focus on the analysis of the molecular electrostatic potential (MEP) of the paramagnetic coordination complex. Electrostatic forces dominate the interaction between the coordination complex and water. Hence, in addition to steric forces, the molecular electrostatic potential should be a determinant of the lifetime of the water-metal link (t_m), the internuclear distance between the water hydrogens and the metal (R), and the number of water molecules attached to the metal in the inner and outer spheres of coordination. We compute the molecular electrostatic potential for a series of model metalloporphyrins because their physical and biologic properties are well known, and they are putative magnetic resonance imaging contrast agents with affinity to neoplastic tissue. Replacing the sulfonato groups in MnTPPS4 with carboxylate groups in the ortho position of the phenyl rings attached to the meso carbons results in an electrostatic focusing field that should reduce R and increase t_m. Similar substitutions involving polar groups, including one modeled after a well-known picket-fence porphyrin, are not strong enough to generate a focusing field. Instead, these polar groups should modulate the water-metal interactions through steric interactions. Molecular dynamic simulations show a large outer sphere of coordination around the paramagnet that extends almost three times the distance of the inner sphere of coordination.     

Electron-attachment spectroscopy: formation and dissociation of negative ions in the fluorochloroethylenes

The formation and dissociation of negative ions in C₂Cl₄, C₂FCl₃, 1,1-C₂F₂Cl₂, 1,2-C₂F₂Cl₂ (isomeric mixture), C₂F₃Cl and C₂F₄ have been studied employing (dissociative) electron-attachment spectroscopy with nearly monoenergetic electrons in the energy range 0–15 eV. All six compounds show low-lying resonances (below 4eV) associated with various dissociation channels leading to one negative and one neutral fragment. It is found that the resonance energy increases if Cl is replaced by F. Electron affinities in the limit of the unknown excess energy are given for the radicals C₂Cl₃, C₂F₂Cl₂, C₂F₂Cl and C₂F₃. For C₂Cl₄ and C₂F₂Cl₂ long-lived parent molecular anions are observed. Only tetrafluoroethylene gives fragments by cleavage of the double bond, as a result of the perfluoro effect.     

Palladium‐catalyzed cyclization of 2‐alkynyl‐N‐ethanoyl anilines to indoles: synthesis,structural, spectroscopic,and mechanistic study

This study reports a facial regio‐selective synthesis of 2‐alkyl‐N‐ethanoyl indoles from substituted‐N‐ethanoyl anilines employing palladium (II) chloride, which acts as a cyclization catalyst. The mechanistic trait of palladium‐based cyclization is also explored by employing density functional theory. In a two‐step mechanism, the palladium, which attaches to the ethylene carbons, promotes the proton transfer and cyclization. The gas‐phase barrier height of the first transition state is 37 kcal/mol, indicating the rate‐determining step of this reaction. Incorporating acetonitrile through the solvation model on density solvation model reduces the barrier height to 31 kcal/mol. In the presence of solvent, the electron‐releasing (–CH₃) group has a greater influence on the reduction of the barrier height compared with the electron‐withdrawing group (–Cl). These results further confirm that solvent plays an important role on palladium‐catalyzed proton transfer and cyclization. For unveiling structural, spectroscopic, and photophysical properties, experimental and computational studies are also performed. Thermodynamic analysis discloses that these reactions are exothermic. The highest occupied molecular orbital?lowest unoccupied molecular orbital gap (4.9–5.0 eV) confirms that these compounds are more chemically reactive than indole. The calculated UV–Vis spectra by time‐dependent density functional theory exhibit strong peaks at 290, 246, and 232 nm, in good agreement with the experimental results. Moreover, experimental and computed ¹H and ¹³C NMR chemical shifts of the indole derivatives are well correlated. Copyright © 2015 John Wiley & Sons, Ltd.     

Piperidine‐appended imidazolium ionic liquids as task‐specific catalysts: computational study,synthesis, and multinuclear NMR

Imidazolium ionic liquids (IMILs) with a piperidine moiety appended via variable length methylene spacers (with n = 1–4) were studied computationally to assess their potential to act as internal base for N‐heterocyclic carbene (NHC) generation. Proton transfer energies computed by B3LYP/6‐311+G(2d,p) were least endothermic for the basic‐IL with n = 3, whose optimized structure showed the shortest C₂‐H‐‐‐‐N(piperidine) distance. Inclusion of counter anion (Cl or NTf₂) caused dramatic conformational changes to enable close contact between the acidic C₂‐H and the anions. To examine the prospect for internal C₂‐H‐‐‐‐N coordination, multinuclear NMR data (¹H, ¹⁵N, and ¹³C) were computed by gauge independent atomic orbitals–density functional theory (GIAO‐DFT) in the gas phase and in several solvents by the PCM method for comparison with the experimental NMR data for the basic ILs (with n = 2–4) synthesized in the laboratory. These studies indicate that interactions with solvent and counter ion are dominant forces that could disrupt internal C₂‐H‐‐‐‐N coordination/proton transfer, making carbene generation from these basic‐ILs unlikely without an added external base. Therefore, the piperidine‐appended IMILs appear suitable for application as dual solvent/base in organic/organometallic transformations that require the use of mild base, without the necessity to alkylate at C‐2 to prevent N‐heterocyclic carbene formation. Copyright © 2016 John Wiley & Sons, Ltd.