Showing papers in "Physical Chemistry Chemical Physics in 2006"
TL;DR: A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented and computation times for the Coulomb part are reduced by a factor of ca.15 kJ mol(-1) per atom.
Abstract: A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented. For each element only one auxiliary basis set is needed to approximate Coulomb energies in conjunction with orbital basis sets of split valence, triple zeta valence and quadruple zeta valence quality with errors of typically below ca. 0.15 kJ mol−1 per atom; this was demonstrated in conjunction with the recently developed orbital basis sets of types def2-SV(P), def2-TZVP and def2-QZVPP for a large set of small molecules representing (nearly) each element in all of its common oxidation states. These auxiliary bases are slightly more than three times larger than orbital bases of split valence quality. Compared to non-approximated treatments, computation times for the Coulomb part are reduced by a factor of ca. 8 for def2-SV(P) orbital bases, ca. 25 for def2-TZVP and ca. 100 for def2-QZVPP orbital bases.
4,876 citations
TL;DR: Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
Abstract: Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
2,527 citations
TL;DR: MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together.
Abstract: MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and different basis sets (aug-cc-pVDZ – aug-cc-pVTZ, aug-cc-pVTZ – aug-cc-pVQZ, cc-pVTZ – cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a difference between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the first screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.
1,672 citations
TL;DR: In this review article, a short overview on physicochemical aspects of ionic liquids, such as physical properties of ions, nanoparticles, nanotubes, batteries, spectroscopy, thermodynamics and catalysis of/in ions are given.
Abstract: Ionic liquids are defined today as liquids which solely consist of cations and anions and which by definition must have a melting point of 100 °C or below. Originating from electrochemistry in AlCl3 based liquids an enormous progress was made during the recent 10 years to synthesize ionic liquids that can be handled under ambient conditions, and today about 300 ionic liquids are already commercially available. Whereas the main interest is still focussed on organic and technical chemistry, various aspects of physical chemistry in ionic liquids are discussed now in literature. In this review article we give a short overview on physicochemical aspects of ionic liquids, such as physical properties of ionic liquids, nanoparticles, nanotubes, batteries, spectroscopy, thermodynamics and catalysis of/in ionic liquids. The focus is set on air and water stable ionic liquids as they will presumably dominate various fields of chemistry in future.
1,052 citations
TL;DR: A non-exhaustive literature survey on particle based crystallization pathways leading to single crystals via mesoscopic transformation with a focus on recent examples and studies, which are dedicated to a mechanistic understanding.
Abstract: In this review, we highlight particle based crystallization pathways leading to single crystals via mesoscopic transformation. In contrast to the classical mechanism of atom/molecule mediated growth of a single crystal, the particle mediated growth and assembly mechanisms are summarized as “non-classical crystallization”, including exiting processes like oriented attachment and mesocrystal formation. Detailed investigations of non-classical crystallization mechanisms are a recent development, but evidence for these pathways is rapidly increasing in the literature. A major driving force for these investigations originates from biomineralization, because it seems that these crystallization routes are frequently applied by natural organisms. We give a non-exhaustive literature survey on these two mechanisms with a focus on recent examples and studies, which are dedicated to a mechanistic understanding. Furthermore, conditions are introduced for which these non-classical crystallization mechanisms can be expected, as they are always an alternative reaction pathway to classical crystallization.
990 citations
TL;DR: In this article, the physical and chemical properties of ionic liquids for metal deposition have been discussed and the effect of composition and temperature on viscosity and conductivity is discussed.
Abstract: The electrodeposition of most of technologically important metals has been shown to be possible from a wide range of room temperature molten salts, more commonly known today as 'ionic liquids'. These liquids are currently under intense scrutiny for a wide variety of applications some of which have already been commercialized. Despite the fact that electrodeposition was the first application studied in these liquids no metal deposition processes have as yet been developed to an industrial scale. This review addresses the practical and theoretical aspects that need to be considered when choosing ionic liquids for metal deposition. It details the current understanding of the physical and chemical properties of these interesting fluids and highlights the areas that need to be considered to develop practical electroplating systems. The effect of composition and temperature on viscosity and conductivity are discussed together with the fundamental approaches required to synthesise new liquids.
685 citations
TL;DR: The big improvement compared to common density functionals is further demonstrated by the reduction of the maximum and minimum errors (outliers) and by much smaller errors for complicated molecular systems.
Abstract: Two hybrid density functionals that include a second-order perturbation correction for non-local correlation effects are tested for the full G3/05 test set. Very large AO basis sets including core-polarization/correlation functions have been employed that yield for the first time results quite close to the basis set limit for this set. The B2-PLYP functional and the new mPW2-PLYP approach with a modified exchange part give by far the lowest MAD over the whole G3/05 set ever reported for a DFT method (2.5 and 2.1 kcal mol−1, respectively). The big improvement compared to common density functionals is further demonstrated by the reduction of the maximum and minimum errors (outliers) and by much smaller errors for complicated molecular systems.
538 citations
TL;DR: The key issue of binding strengths is examined from a basic perspective by surveying the distinct classes of interactions (dispersion, electrostatics, orbital interactions) in first a general way, and then in the context of calculated binding affinities for a range of model systems.
Abstract: Intermolecular interactions between H2 and ligands, metals, and metal–ligand complexes determine the binding affinities of potential hydrogen storage materials (HSM), and thus their extent of potential for practical use. A brief survey of current activity on HSM is given. The key issue of binding strengths is examined from a basic perspective by surveying the distinct classes of interactions (dispersion, electrostatics, orbital interactions) in first a general way, and then in the context of calculated binding affinities for a range of model systems.
498 citations
TL;DR: Silver and gold nanorods with aspect ratios from 1 to 16 have been used as substrates for surface enhanced Raman spectroscopy (SERS) in colloidal solution and enhancement factors suggest that enhancement factors are a factor of 10-10(2) greater for substrates that have plasmon band overlap with the excitation source than for substrate whose plAsmon bands do not.
Abstract: Silver and gold nanorods with aspect ratios from 1 to 16 have been used as substrates for surface enhanced Raman spectroscopy (SERS) in colloidal solution. The nanorod aspect ratio is varied to give different degrees of overlap between the nanorod longitudinal plasmon band and excitation source in order to determine its effect on overall surface enhancement. Results suggest that enhancement factors are a factor of 10–102 greater for substrates that have plasmon band overlap with the excitation source than for substrates whose plasmon bands do not.
463 citations
TL;DR: The recently proposed CAM-B3LYP exchange-correlation energy functional, based on a partitioning of the r operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties.
Abstract: The recently proposed CAM-B3LYP exchange–correlation energy functional, based on a partitioning of the r−112 operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties. Rydberg and charge transfer excitation energies and static electronic polarisabilities are notably improved over the standard B3LYP functional; classical reaction barriers also improve. Ionisation potentials, bond lengths, NMR shielding constants and indirect spin–spin coupling constants are comparable with the two functionals. CAM-B3LYP atomisation energies and diatomic harmonic vibrational wavenumbers are less accurate than those of B3LYP. Future research directions are outlined.
458 citations
TL;DR: The results indicate that quantum dots with the smallest hydrodynamic sizes are best prepared by direct ligand exchange with hydrophilic molecules, but the resulting particles are less stable than those encapsulated in amphiphilic polymers.
Abstract: A number of procedures are currently available to encapsulate and solubilize hydrophobic semiconductor Quantum Dots (QDs) for biological applications Most of these procedures are based on the use of small-molecule coordinating ligands, amphiphilic polymers, or amphiphilic lipids However, it is still not clear how these different surface coating molecules affect the optical, colloidal, and chemical properties of the solubilized QDs Here we report a systematic study to examine the effects of surface coating chemistry on the hydrodynamic size, fluorescence quantum yield, photostability, chemical stability, and biocompatibility of water-soluble QDs The results indicate that quantum dots with the smallest hydrodynamic sizes are best prepared by direct ligand exchange with hydrophilic molecules, but the resulting particles are less stable than those encapsulated in amphiphilic polymers For stability against chemical oxidation, QDs should be protected with a hydrophobic bilayer For high stability under acidic conditions, the best QDs are prepared by using hyperbranched polyethylenimine For stability in high salt buffers, it is preferable to have uncharged, sterically-stabilized QDs, like those coated with polyethylene glycol (PEG) These insights are expected to benefit the development of quantum dots and related nanoparticle probes for molecular and cellular imaging applications
TL;DR: Experimental and theoretical studies of energy transfer in the photosynthetic light-harvesting complexes LH1, LH2, and LHCII performed during the past decade since the discovery of high-resolution structure are overviewed.
Abstract: We overview experimental and theoretical studies of energy transfer in the photosynthetic light-harvesting complexes LH1, LH2, and LHCII performed during the past decade since the discovery of high-resolution structure of these complexes. Experimental findings obtained with various spectroscopic techniques makes possible a modelling of the excitation dynamics at a quantitative level. The modified Redfield theory allows a precise assignment of the energy transfer pathways together with a direct visualization of the whole excitation dynamics where various regimes from a coherent motion of delocalized exciton to a hopping of localized excitations are superimposed. In a single complex it is possible to observe the switching between these regimes driven by slow conformational motion (as we demonstrate for LH2). Excitation dynamics under quenched conditions in higher-plant complexes is discussed.
TL;DR: In this paper, the authors applied density functional theory including dispersion corrections (DFT-D) to calculate intermolecular interaction energies in an extensive benchmark set consisting mainly of DNA base pairs and amino acid pairs, for which CCSD(T) complete basis set limit estimates are available.
Abstract: Density functional theory including dispersion corrections (DFT-D) is applied to calculate intermolecular interaction energies in an extensive benchmark set consisting mainly of DNA base pairs and amino acid pairs, for which CCSD(T) complete basis set limit estimates are available (JSCH-2005 database). The three generalized gradient approximation (GGA) density functionals B-LYP, PBE and the new B97-D are tested together with the popular hybrid functional B3-LYP. The DFT-D interaction energies deviate on average by less than 1 kcal mol−1 or 10% from the reference values. In only six out of 161 cases, the deviation exceeds 2 kcal mol−1. With one exception, the few larger deviations occur for non-equilibrium structures extracted from experimental geometries. The largest absolute deviations are observed for pairs of oppositely charged amino acids which are, however, not significant on a relative basis due to the huge interaction energies >100 kcal mol−1 involved. The counterpoise (CP) correction for the basis set superposition error with the applied triple-zeta AO basis sets varies between 0 and −1 kcal mol−1 (<5% of the interaction energy in most cases) except for four complexes, where it is up to −1.4 kcal mol−1. It is thus suggested to skip the laborious calculation of the CP correction in DFT-D treatments with reasonable basis sets. The three dispersion corrected GGAs considered differ mainly for the interactions of the hydrogen-bonded DNA base pairs, which are systematically too small by 0.6 kcal mol−1 in case of B97-D, while for PBE-D they are too high by 1.5 kcal mol−1, and for B-LYP-D by 0.5 kcal mol−1. The all in all excellent results that have been obtained at affordable computational costs suggest the DFT-D method to be a routine tool for many applications in organic chemistry or biochemistry.
TL;DR: It is shown that reported variations in the kinetics, structure and reaction mechanism for the water gas shift reaction on gold catalysts can now be understood and rationalised and it is proposed that the dominant surface intermediate is a function of reaction conditions.
Abstract: The production of hydrogen containing very low levels of carbon monoxide for use in polymer electrolyte fuel cells requires the development of catalysts that show very high activity at low temperatures where the equilibrium for the removal of carbon monoxide using the water–gas shift reaction is favourable. It has been claimed that oxide-supported gold catalysts have the required high activity but there is considerable uncertainty in the literature about the feasibility of using these catalysts under real conditions. By comparing the activity of gold catalysts with that of platinum catalysts it is shown that well-prepared gold catalysts are significantly more active than the corresponding platinum catalysts. However, the method of preparation and pre-treatment of the gold catalysts is critical and activity variations of several orders of magnitude can be observed depending on the methods chosen. It is shown that an intimate contact between gold and the oxide support is important and any preparative procedure that does not generate such an interaction, or any subsequent treatment that can destroy such an interaction, may result in catalysts with low activity. The oxidation state and structure of active gold catalysts for the water–gas shift reaction is shown to comprise gold primarily in a zerovalent metallic state but in intimate contact with the support. This close contact between small metallic gold particles and the support may result in the “atoms” at the point of contact having a net charge (most probably cationic) but the high activity is associated with the presence of metallic gold. Both in situ XPS and XANES appear unequivocal on this point and this conclusion is consistent with similar measurements on gold catalysts even when used for CO oxidation. In situ EXAFS measurements under water gas shift conditions show that the active form of gold is a small gold cluster in intimate contact with the oxide support. The importance of the gold/oxide interface is indicated but the possible role of special sites (e.g., edge sites) on the gold clusters cannot be excluded. These may be important for CO oxidation but the fact that water has to be activated in the water gas shift reaction may point towards a more dominant role for the interfacial sites. The mechanism of the water gas shift reaction on gold and other low temperature catalysts has been widely investigated but little agreement exists. However, it is shown that a single “universal” model is consistent with much of the experimental literature. In this, it is proposed that the dominant surface intermediate is a function of reaction conditions. For example, as the temperature is increased the dominant species changes from a carbonate or carboxylate species, to a formate species and eventually at high temperatures to a mechanism that is characteristic of a redox process. Similar changes in the dominant intermediate are observed with changes in the gas composition. Overall, it is shown that reported variations in the kinetics, structure and reaction mechanism for the water gas shift reaction on gold catalysts can now be understood and rationalised.
TL;DR: In this paper, the correlation between the internal structure and dynamics of polyelectrolyte multilayers and their functional properties was investigated and different concepts of multilayer formation like driving forces, adsorption kinetics, mode of growth and stability aspects were considered.
Abstract: The paper deals with the correlation between the internal structure and dynamics of polyelectrolyte multilayers on one hand and their functional properties on the other hand. It considers different concepts of multilayer formation like driving forces, adsorption kinetics, mode of growth and stability aspects. A further focus is the control of internal structure and dynamics which is of high impact with respect to the design of stimuli-responsive material.
TL;DR: Reaction paths that involve charge-separated intermediates or transition states are accelerated--by lowering the activation barrier-in the presence of ILs when compared with those performed in classical organic solvents.
Abstract: Among the various properties exhibited by ionic liquids (ILs)—especially those based on the imidazolium cation—their inherent ionic patterns, very low vapour pressure and pronounced self-organization in the solid, liquid and even in the gas phase are particularly interesting since this allows the use of these fluids as alternative and complementary media to classical organic solvents and water in many applications. Hence, reaction paths that involve charge-separated intermediates or transition states are accelerated—by lowering the activation barrier—in the presence of ILs when compared with those performed in classical organic solvents. It is also possible, for example, to observe, by electrochemical methods, transient species (ionic and radical) that are otherwise undetectible in water or in molecular organic solvents and to investigate the interactions and behaviour of molecular, biological and macromolecular species in solution using physical and chemical methods which require special conditions such as high-vacuum, and which have been traditionally limited to solid state chemistry.
TL;DR: The potential for developing parachor and molar refraction contribution data for ions as tools to predict ionic liquid physical properties is demonstrated.
Abstract: A simple method to predict the densities of a range of ionic liquids from their surface tensions, and vice versa, using a surface-tension-weighted molar volume, the parachor, is reported. The parachors of ionic liquids containing 1-alkyl-3-methylimidazolium cations were determined experimentally, but were also calculated directly from their structural compositions using existing parachor contribution data for neutral compounds. The calculated and experimentally determined parachors were remarkably similar, and the latter data were subsequently employed to predict the densities and surface tensions of the investigated ionic liquids. Using a similar approach, the molar refractions of ionic liquids were determined experimentally, as well as calculated using existing molar refraction contribution data for uncharged compounds. The calculated molar refraction data were employed to predict the refractive indices of the ionic liquids from their surface tensions. The errors involved in the refractive index predictions were much higher than the analogous predictions employing the parachor, but nevertheless demonstrated the potential for developing parachor and molar refraction contribution data for ions as tools to predict ionic liquid physical properties.
TL;DR: The behavior of platinum dissolution and deposition in the polymer electrolyte membrane of a membrane-electrode-assembly for a proton-exchange membrane fuel cell was studied and the electrochemically active surface area decreased depending on the cycle number and the upper potential limit.
Abstract: The behavior of platinum dissolution and deposition in the polymer electrolyte membrane of a membrane-electrode-assembly (MEA) for a proton-exchange membrane fuel cell (PEMFC) was studied using potential cycling experiment and high-resolution transmission electron microscopy (HRTEM). The electrochemically active surface area decreased depending on the cycle number and the upper potential limit. Platinum deposition was observed in the polymer electrolyte membrane near a cathode catalyst layer. Platinum deposition was accelerated by the presence of hydrogen transported through the membrane from an anode compartment. Platinum was transported across the membrane and deposited on the anode layer in the absence of hydrogen in the anode compartment. This deposition was also affected by the presence of oxygen in the cathode compartment.
TL;DR: Several recently developed detection techniques opened studies of individual metal nanoparticles (1-100 nm in diameter) in the optical far field hold great potential for nanoscience and for single-molecule labelling in biological assays and live cells.
Abstract: Several recently developed detection techniques opened studies of individual metal nanoparticles (1-100 nm in diameter) in the optical far field. Eliminating averaging over the broad size and shape distributions produced by even the best of current synthesis methods, these studies hold great promise for gaining a deeper insight into many of the properties of metal nanoparticles, notably electronic and vibrational relaxation. All methods are based on detection of a scattered wave emitted either by the particle itself, or by its close environment. Direct absorption and interference techniques rely on the particle's scattering and have similar limits in signal-to-noise ratio. The photothermal method uses a photo-induced change in the refractive index of the environment as an additional step to scatter a wave with a different wavelength. This leads to a considerable improvement in signal-to-background ratio, and thus to a much higher sensitivity. We briefly discuss and compare these various techniques, review the new results they generated so far, and conclude on their great potential for nanoscience and for single-molecule labelling in biological assays and live cells.
TL;DR: Measurements of the period of the extensional mode of the nanorods using time-resolved spectroscopy show a significant softening at high pump laser powers, however, the decrease in the period is less than expected from bulk Young's modulus vs. temperature data.
Abstract: The response of gold nanorods to both thermal and ultrafast laser-induced heating has been examined The thermal heating experiments show structural changes that occur on timescales ranging from hours to days At the highest temperature examined (250 degrees C) the nanorods are transformed into spheres within an hour On the other hand, no structural changes are observed in the laser-induced heating experiments up to temperatures of 700 +/- 50 degrees C This is attributed to thermal diffusion in the laser experiments Measurements of the period of the extensional mode of the nanorods using time-resolved spectroscopy show a significant softening at high pump laser powers However, the decrease in the period is less than expected from bulk Young's modulus vs temperature data
TL;DR: The scattering spectra of single gold nanorods with aspect ratios between 2 and 4 have been examined and show that the longitudinal plasmon resonance (electron oscillation along the long axis of the rod) broadens as the width of the rods decreases from 14 to 8 nm, attributed to electron surface scattering.
Abstract: The scattering spectra of single gold nanorods with aspect ratios between 2 and 4 have been examined by dark field microscopy. The results show that the longitudinal plasmon resonance (electron oscillation along the long axis of the rod) broadens as the width of the rods decreases from 14 to 8 nm. This is attributed to electron surface scattering. Analysis of the data using γ = γbulk + AνF/Leff, where Leff is the effective path length of the electrons and νF is the Fermi velocity, allows us to determine a value for the surface scattering parameter of A = 0.3. Larger rods with widths of 19 and 30 nm were also examined. These samples also show spectral broadening, which is attributed to radiation damping. The relative strengths of the surface scattering and radiation damping effects are in excellent agreement with recent work on spherical gold nanoparticles by Sonnichsen et al., Phys. Rev. Lett., 2002, 88, 077402; and by Berciaud et al., Nano Lett., 2005, 5, 515.
TL;DR: An overview of a number of representative polymer brush systems will be presented and their potential application for surfaces with controlled wettability, smart surfaces and nanoactuators will be explored in some detail.
Abstract: Polymer brushes are assemblies of macromolecules chemically tethered at one end to a substrate. They provide an alternative to self-assembled monolayers because of the intrinsically large size of the building blocks and the ensuing entropic contribution to the film morphology. In this article, an overview of a number of representative polymer brush systems will be presented and their potential application for surfaces with controlled wettability, smart surfaces and nanoactuators will be explored in some detail.
TL;DR: The evolution of the Ion imaging technique is traced, some of the more important breakthroughs with regards to improving image resolution and in image processing and analysis methods are highlighted, and the many applications to which the technique is now being applied are illustrated.
Abstract: Ion imaging methods are making ever greater impact on studies of gas phase molecular reaction dynamics. This article traces the evolution of the technique, highlights some of the more important breakthroughs with regards to improving image resolution and in image processing and analysis methods, and then proceeds to illustrate some of the many applications to which the technique is now being applied—most notably in studies of molecular photodissociation and of bimolecular reaction dynamics.
TL;DR: A first principles analysis of the origin of p-type semiconducting behaviour in Cu2O with 1.5 and 3% Cu vacancy concentrations demonstrates that the p- type semiconductor properties observed for Cu 2O are explained by a small concentration of Cu vacancies.
Abstract: Materials based on Cu2O are potential p-type transparent semiconducting oxides. Developing an understanding of the mechanism leading to p-type behaviour is important. An accepted origin is the formation of Cu vacancies. However, the way in which this mechanism leads to p-type properties needs to be investigated. This paper presents a first principles analysis of the origin of p-type semiconducting behaviour in Cu2O with 1.5 and 3% Cu vacancy concentrations. Plane wave density functional theory (DFT) with the Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional is applied. In order to investigate the applicability of DFT, we firstly show that CuO, with 50% Cu vacancies cannot be described with DFT and in order to obtain a consistent description of CuO, the DFT+U approach is applied. The resulting electronic structure is consistent with experiment, with a spin moment of 0.64 μB and an indirect band gap of 1.48 eV for U = 7 eV. However, for a 3% Cu vacancy concentration in Cu2O, the DFT and DFT+U descriptions of Cu vacancies are similar, indicating that DFT is suitable for a small concentration of Cu vacancies; the formation energy of a Cu vacancy is no larger than 1.7 eV. Formation of Cu vacancies produces delocalised hole states with hole effective masses consistent with the semiconducting nature of Cu2O. These results demonstrate that the p-type semiconducting properties observed for Cu2O are explained by a small concentration of Cu vacancies.
TL;DR: Different classes of amphiphiles that form reversed phases in excess solvent are reviewed, with an emphasis on linking phase behavior to amphiphile structure.
Abstract: Amphiphile lyotropic liquid crystalline self-assembly materials are being used for a diverse range of applications. Historically, the most studied lyotropic liquid crystalline phase is probably the one-dimensional (1-D) lamellar phase, which has been employed as a model system for biomembranes and for drug delivery applications. In recent years, the structurally more complex 2-D and 3-D ordered lyotropic liquid crystalline phases, of which reversed hexagonal (H2) and reversed cubic phases (v2) are two prominent examples, have received growing interest. As is the case for the lamellar phase, these phases are frequently stable in excess water, which facilitates the preparation of nanoparticle dispersions and makes them suitable candidates for the encapsulation and controlled release of drugs. Integral membrane protein crystallization media and templates for the synthesis of inorganic nanostructured materials are other applications for 2-D and 3-D amphiphile self-assembly materials. The number of amphiphiles identified as forming nanostructured reversed phases stable in excess solvent is rapidly growing. In this article, different classes of amphiphiles that form reversed phases in excess solvent are reviewed, with an emphasis on linking phase behavior to amphiphile structure. The different amphiphile classes include: ethylene oxide-, monoacylglycerol-, glycolipid-, phosphatidylethanolamine-, and urea-based amphiphiles.
TL;DR: A hybrid method to study problems that involve both bond rearrangements and van-der-Waals interactions is proposed, designed for a reaction between a small or medium sized substrate molecule and a very large chemical system.
Abstract: We propose use of a hybrid method to study problems that involve both bond rearrangements and van-der-Waals interactions. The method combines second-order Moller–Plesset perturbation theory (MP2) calculations for the reaction site with density functional theory (DFT) calculations for a large system under periodic boundary conditions. Hybrid MP2:DFT structure optimisation for a cluster embedded in the periodic model is the first of three steps in a multi-level approach. The second step is extrapolation of the MP2 energy to the complete basis set limit. The third step is extrapolating the high-level (MP2) correction to the limiting case of the full periodic structure. This is done by calculating the MP2 correction for a series of cluster models of increasing size, fitting an analytic expression to these energy corrections, and applying the fitted expression to the full periodic structure. We assume that, up to a constant, the high-level correction is described by a damped dispersion expression. Combining the results of all three steps yields an estimate of the MP2 reaction energy for the full periodic system at the complete basis set level. The method is designed for a reaction between a small or medium sized substrate molecule and a very large chemical system. For adsorption of isobutene in zeolite H-ferrierite, the energies obtained for the formation of different structures, the π-complex, the isobutoxide, the tert-butoxide, and the tert-butyl carbenium ion, are −78, −73, −48, and −21 kJ mol−1, respectively. This corresponds to corrections of the pure DFT (PBE functional) results by −62, −70, −67, and −29 kJ mol−1, respectively. Hence, the MP2 corrections are substantial and, perhaps more importantly, not the same for the different hydrocarbon species in the zeolite. Coupled-cluster (CCSD(T)) calculations change the MP2 energies by −4 kJ mol−1 (tert-butyl cation) or less (below ±1 kJ mol−1 for the other species).
TL;DR: In new results presented here, several improvements to the physics-based scoring method are explored including modifying the dielectric constant used for the protein and ligand interiors, and empirically scaling energy terms to compensate for deficiencies in the energy model.
Abstract: Ligand binding affinity prediction is one of the most important applications of computational chemistry. However, accurately ranking compounds with respect to their estimated binding affinities to a biomolecular target remains highly challenging. We provide an overview of recent work using molecular mechanics energy functions to address this challenge. We briefly review methods that use molecular dynamics and Monte Carlo simulations to predict absolute and relative ligand binding free energies, as well as our own work in which we have developed a physics-based scoring method that can be applied to hundreds of thousands of compounds by invoking a number of simplifying approximations. In our previous studies, we have demonstrated that our scoring method is a promising approach for improving the discrimination between ligands that are known to bind and those that are presumed not to, in virtual screening of large compound databases. In new results presented here, we explore several improvements to our computational method including modifying the dielectric constant used for the protein and ligand interiors, and empirically scaling energy terms to compensate for deficiencies in the energy model. Future directions for further improving our physics-based scoring method are also discussed.
TL;DR: The lithium transference number in TFSI-based ionic liquid electrolytes for lithium batteries should thus be strongly improved.
Abstract: The lithium solvation in (1 −
x)(EMI-TFSI), xLiTFSI ionic liquids where EMI+ is the 1-ethyl-3-methylimidazolium cation and TFSI− the bis(trifluoromethanesulfonyl)imide anion, is shown by Raman spectroscopy to involve essentially [Li(TFSI)2]− anionic clusters for 0 < x < 0.4, but addition of stoichiometric amounts of solvents S such as oligoethers changes the lithium solvation into [Li(S)m]+ cationic clusters; the lithium transference number in TFSI-based ionic liquid electrolytes for lithium batteries should thus be strongly improved.
TL;DR: The parallel implementation of second-order Møller-Plesset perturbation theory with the resolution-of-the-identity approximation (RI-MP2) extends the applicability of canonical MP2 to considerably larger systems.
Abstract: We present a parallel implementation of second-order Moller–Plesset perturbation theory with the resolution-of-the-identity approximation (RI-MP2). The implementation is based on a recent improved sequential implementation of RI-MP2 within the Turbomole program package and employs the message passing interface (MPI) standard for communication between distributed memory nodes. The parallel implementation extends the applicability of canonical MP2 to considerably larger systems. Examples are presented for full geometry optimizations with up to 60 atoms and 3300 basis functions and MP2 energy calculations with more than 200 atoms and 7000 basis functions.
TL;DR: DF-SCS-LMP2 is computationally inexpensive and represents an attractive method for the study of larger pi-stacked systems such as truncated sections of DNA.
Abstract: Potential energy curves for the parallel-displaced, T-shaped and sandwich structures of the benzene dimer are computed with density fitted local second-order Moller–Plesset perturbation theory (DF-LMP2) as well as with the spin-component scaled (SCS) variant of DF-LMP2. While DF-LMP2 strongly overestimates the dispersion interaction, in common with canonical MP2, the DF-SCS-LMP2 interaction energies are in excellent agreement with the best available literature values along the entire potential energy curves. The DF-SCS-LMP2 dissociation energies for the three structures are also compared with new complete basis set estimates of the interaction energies obtained from accurate coupled cluster (CCSD(T)) and DF-SCS-MP2 calculations. Since LMP2 is essentially free of basis set superposition errors, counterpoise corrections are not required. As a result, DF-SCS-LMP2 is computationally inexpensive and represents an attractive method for the study of larger π-stacked systems such as truncated sections of DNA.