Polymer-clay nanocomposites: a multiscale molecular modeling approach

A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.     

The tetracycline: Mg2+ complex: a molecular mechanics force field

Tetracycline (Tc) is an important antibiotic, which binds specifically to the ribosome and several proteins, in the form of a Tc-:Mg2+ complex. To model Tc:protein and Tc:RNA interactions, we have developed a molecular mechanics force field model of Tc, which is consistent with the CHARMM force field for proteins and nucleic acids. We used structures from the Cambridge Crystallographic Data Base to identify the main Tc conformations that are likely to be present in solution and in biomolecular complexes. A conformational search was also done, using the MM3 force field to perform simulated annealing of Tc. Several resulting, low-energy structures were optimized with an ab initio model and used in developing the new Tc force field. Atomic charges and Lennard-Jones parameters were derived from a supermolecule ab initio approach. We considered the ab initio energies and geometries of a probe water molecule interacting with Tc at 36 different positions. We considered both a neutral and a zwitterionic Tc form, with and without bound Mg2+. The final rms deviation between the ab initio and force field energies, averaged over all forms, was just 0.35 kcal/mol. The model also reproduces the ab initio geometry and flexibility of Tc. As further tests, we did simulations of a Tc crystal, of Tc:Mg2+ and Tc:Ca2+ complexes in aqueous solution, and of a solvated complex between Tc:Mg2+ and the Tet repressor protein (TetR). With slight, ad hoc adjustments, the model can reproduce the experimental, relative, Tc binding affinities of Mg2+ and Ca2+. It performs well for the structure and fluctuations of the Tc:Mg2+:TetR complex. The model should therefore be suitable to investigate the interactions of Tc with proteins and RNA. It provides a starting point to parameterize other compounds in the large Tc family.     

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains

To establish force-field-based (molecular) modeling capability that will accurately predict condensed-phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas-phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2-azidoethanamines that have been synthesized and tested for use as hydrazine-alternative fuels.     

Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization

The ability of force fields to reproduce relative conformational energies for seven molecules is probed. The correlation against LMP2/cc‐pVTZ results for standard force field employing fixed partial charges deteriorates as the molecules become more polar. Inclusion of multipole moments and intramolecular polarization can improve the correlation, and both contributions are of similar importance. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Understanding the optical spectroscopy of amphiphilic molecular rectifiers: a density functional approach

We present results of first principles density functional theory calculations of the electronic and atomic structural properties of model Z-type Langmuir-Blodgett (LB) layers comprising amphiphilic quinolinium tricyanoquinodimethanide (Q3CNQ) chromophores. We find that the chromophore electronic ground state is not as clearly "zwitterionic" as required by models to explain electrical rectification purportedly seen in such systems. The computed visible region transitions are not what have been assumed to be the intervalence charge transfer bands seen in the visible region of molecules in Z-type LB films. Our own LB deposition and spectroscopic studies suggest that almost all visible region features previously seen may be ascribed to aggregates. The calculated lowest energy electronic excitation between HOMO and LUMO levels, which is located in the near infrared region, has a transition moment aligned approximately 9° off the molecular long axis, and has a normalized oscillator strength of 1 order of magnitude higher than those of the visible region transitions. This most dominant feature has been neglected from discussions of Langmuir-Blodgett layer rectification but our own deposition studies show no sign of this feature, indicating that the structure of the modeled system differs from that of typical experimental structures. The model indicates that such idealized LB layer structures cannot confidently be invoked to explain their experimental optical or electrical properties.     

Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations

This study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura-Morokuma (KM) energy decomposition analysis at the HF/6-31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed.     

An extensible and systematic force field,ESFF, for molecular modeling of organic,inorganic, and organometallic systems

ESFF is a rule-based force field designed for modeling organic, inorganic, and organometallic systems. To cover this broad range of molecular systems, ESFF was developed in an extensible and systematic manner. Several unique features were introduced including pseudoangle and a dot product function representing torsion energy terms. The partial atomic charges that are topology-dependent are determined from ab initio (DFT) calculated electronegativity and hardness for valence orbitals. The van der Waals parameters are charge-dependent, and correlated with the ionization potential for atoms in various valence states. To obtain a set of well-defined and physically meaningful parameters, ESFF employs semiempirical rules to translate atomic-based parameters to parameters typically associated with a covalent valence force field. The atomic parameters depend not only on atom type, but also on internal type, thus resulting in a more accurate force field. This article presents the theory and the method used to develop the force field. The force field has been applied to molecular simulations of a wide variety of systems including nucleic acids, peptides, hydrocarbons, porphyrins, transition metal complexes, zeolites, and organometallic compounds. Agreement with the experimental results indicates that ESFF is a valuable tool in molecular simulations for understanding and predicting both crystal and gas phase molecular structures.     

Quantitative analysis of poly- and perfluoroalkyl compounds in water matrices using high resolution mass spectrometry: Optimization for a laser diode thermal desorption method

An alternative analysis technique for the quantitation of 15 poly- and perfluoroalkyl substances (PFASs) in water matrices is reported. Analysis time between each sample was reduced to less than 20 s, all target molecules being analyzed in a single run with the use of laser diode thermal desorption atmospheric pressure chemical ionization (LDTD/APCI) coupled with high resolution accurate mass (HRMS) orbitrap mass spectrometry. LDTD optimal settings were investigated using either one-factor-at-a-time or experimental design methodologies, while orbitrap parameters were optimized simultaneously by means of a Box–Behnken design. Following selection of an adequate sample concentration and purification procedure based on solid-phase extraction and graphite clean-up, the method was validated in an influent wastewater matrix. Environmentally significant limits of detection were reported (0.3–4 ng L⁻¹ in wastewater and 0.03–0.2 ng L⁻¹ in surface water) and out of the 15 target analytes, 11 showed excellent accuracies (±20% of the target values) and recovery rates (75–125%). The method was successfully applied to a selection of environmental samples, including wastewater samples in 7 locations across Canada, as well as surface and tap water samples from the Montreal region, providing insights into the degree of PFAS contamination in this area.     

Liquid chromatography/mass spectrometry analysis of perfluoroalkyl carboxylic acids and perfluorooctanesulfonate in bivalve shells: Extraction method optimization

Different extraction methods, including extraction by organic solvents with and without acetic acid digestion, and mixed inorganic acid digestion coupled with solid phase extraction (SPE), were developed for the analysis of perfluorinated carboxylic acids (PFCAs) and perfluorooctanesulfonate (PFOS) in bivalve shells. The extracts were separated, identified and quantified by liquid chromatography–electrospray ionization–tandem mass spectrometry (LC–ESI–MS/MS). The method utilizing mixed acid digestion coupled with SPE performed more efficiently than other extraction methods. Matrix recoveries of the optimized methods ranged from 92% to 104%, with limits of detection of 0.05–0.43 ng/g. The optimized method was successfully applied to the analysis of PFCAs and PFOS in shell samples of two bivalves from Bohai Bay, China. PFCAs and PFOS concentrations in the shells ranged from 0.3 ng/g to 4.1 ng/g, 1–50 times lower than those in the soft tissues of bivalves for most target analytes. No relationship between PFCAs and PFOS in shells and in soft tissues was found; this is explained by the different contaminant uptake mechanism of shells and soft tissues.     

Polymerization of acrylates and bulky methacrylates with the use of zirconocene precursors: Block copolymers with methyl methacrylate

The polymerization behavior of cyclohexyl methacrylate and trimethylsilyloxyethyl methacrylate with the catalytic system Cp₂ZrMe₂/B(C₆F₅)₃/ZnEt₂ was examined. Block copolymers of these bulky methacrylates with methyl methacrylate (MMA), having high molecular weights and relatively narrow molecular weight distributions, were prepared. n‐Butyl acrylate and tert‐butyl acrylate were polymerized with various catalytic systems based on zirconocene complexes. These polymerizations seemed to proceed to a nonquantitative yield, producing polymers with high molecular weights and relatively low polydispersities. This behavior indicated the presence of termination reactions in the initiation step, which appeared to be faster than the propagation step. Block copolymers of these acrylates with MMA were synthesized with the catalytic system rac‐Et(Ind)₂ZrMe₂/[B(C₆F₅)₄]⁻[Me₂NHPh]⁺/ZnEt₂, starting from the polymerization of MMA. The block copolymers produced were well defined in most cases, as indicated by size exclusion chromatography, NMR, and differential scanning calorimetry measurements. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3337–3348, 2005     

Synthesis of 3,6-dioxa-Δ-4-trifluoromethyl perfluorooctyl trifluoromethyl sulfonimide: bis[(perfluoroalkyl)sulfonyl] superacid monomer and polymer

A new type of ion exchange polymer, bis[(perfluoroalkyl)sulfonyl]imide ionomers (PFSI), were developed by the copolymerization of sodium 3,6-dioxa-Δ⁷-4-trifluoromethyl perfluorooctyl trifluoromethyl sulfonimide with tetrafluoroethylene (TFE) using an aqueous redox initiation system in an emulsion type polymerization. These polymers have been prepared in various equivalent weights and processed into functional membranes. The new ionomers exhibit excellent chemical and thermal stability. The materials have high potential for electrochemical applications especially as solid polymer electrolytes (SPE) in proton exchange membrane (PEM) fuel cells.     

Theoretical modeling of open-shell molecules in solution: a QM/MM molecular dynamics approach

In this work, the GLOB model, an effective and reliable computational approach well suited for ab initio and QM/MM molecular dynamics simulations of complex molecular systems in solution, has been applied to study two representative open-shell systems, the cobalt(II) ion and the glycine radical in aqueous solution, with special reference to their structural and magnetic properties. The main structural features of the solvent cage around the cobalt ion and the hydrogen bonding patterns around the neutral and zwitterionic forms of the glycine radical have been investigated in some detail. The general good agreement with experiments supports the use of the present model to investigate more challenging and biological/technological relevant open-shell systems.     

Force-field modeling through quantum mechanical calculations: molecular dynamics simulations of a nematogenic molecule in its condensed phases

Interaction energy of the 4-n-pentyloxy-4'-cyanobiphenyl (5OCB) dimer is computed at MP2 level, for many geometrical arrangements using the Fragmentation Reconstruction Method (FRM). DFT calculations are performed for a number of geometries of the monomer. The resulting database is used to parameterize an atomistic intra- and inter-molecular force-field suitable for classical bulk simulations. Several structural and dynamical properties in 5OCB isotropic and liquid crystalline phases are computed from molecular dynamics simulation mainly in the NPT ensemble. Lengthy runs (more than 70 ns) and large sample sizes (up to 806 molecules) were used to determine the nematic to isotropic transition temperature up to a precision of few K. Good agreement was found in most of the investigated properties, thus validating the accuracy of the proposed model potential, only derived by quantum mechanical calculations.     

Scaling of quantum-mechanical molecular force fields

Comparative analysis of various methods of empirical scaling of quantum-mechanical harmonic molecular force fields has been performed. The efficiency of using each particular scaling technique was shown to depend on the theoretical level of the quantum-mechanical calculation. The Pulay method of scaling (congruent transformation of the force constant matrix) is applicable in the case where the relative accuracies of determination of diagonal and off-diagonal quantum-mechanical force constants are approximately equal. This requirement is satisfied for a quantum-mechanical force field determined close to the HartreeFock limit. This makes it possible to carry out its correction with maximum retention of the peculiarities inherent in the molecule under investigation.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 840–807, April, 1996.     

Optimization of a molecular mechanics force field for polyoxometalates based on a genetic algorithm

A stochastic technique based on genetic algorithms was implemented to develop new force fields by optimizing molecular mechanics (MM) parameters. These force fields have been optimized for inorganic compounds such as polyoxometalates (POMs) and especially for type‐I polymolybdate and polytungstate clusters. Focussing on the methodology of the development of the force fields, they were tested for the prediction of structural parameters, comparing the MM optimized structures with the geometry obtained after an optimization based on density functional theory. Results show that the genetic algorithm converges toward an optimum combination of parameters which successfully reproduces POMs structures with a high degree of accuracy. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.     

Spontaneous three-dimensional nanostructure formation of perfluoroalkyl terminated liquid crystal: a molecular dynamics simulation study

Structure formation of a perfluoroalkyl terminated liquid crystal molecule was studied by molecular dynamics simulations. Two distinct structures with smectic-C-like layers and with bundles (blocks) of collapsed layers were spontaneously formed depending on the simulation temperatures. The bundles in the latter structure were somewhat positionally ordered (with respect to the small angle spots in its structure function) and orientationally isotropic overall even though the molecules making each bundle were well oriented. These characteristics of the simulated system well correspond to the cubic phase of the real system, and an even more precisely correspond to the proposed cubic structure model with respect to its hierarchical structure.