Showing papers in "Journal of Physical Chemistry B in 2009"
TL;DR: The SMD model may be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space, including, for example, the conductor-like screening algorithm.
Abstract: We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute−solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonho...
10,945 citations
TL;DR: mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations, and concludes that it is not the nature of the interactions but the connectivity of the molecules that determines the structural and thermodynamic behavior of water.
Abstract: Water and silicon are chemically dissimilar substances with common physical properties. Their liquids display a temperature of maximum density, increased diffusivity on compression, and they form tetrahedral crystals and tetrahedral amorphous phases. The common feature to water, silicon, and carbon is the formation of tetrahedrally coordinated units. We exploit these similarities to develop a coarse-grained model of water (mW) that is essentially an atom with tetrahedrality intermediate between carbon and silicon. mW mimics the hydrogen-bonded structure of water through the introduction of a nonbond angular dependent term that encourages tetrahedral configurations. The model departs from the prevailing paradigm in water modeling: the use of long-ranged forces (electrostatics) to produce short-ranged (hydrogen-bonded) structure. mW has only short-range interactions yet it reproduces the energetics, density and structure of liquid water, and its anomalies and phase transitions with comparable or better accu...
816 citations
TL;DR: Simple backbone energy corrections are determined for two force fields to reproduce the fraction of helix measured in short peptides at 300 K, showing that the dependence of the helix content on temperature is too weak, a problem shared with other force fields.
Abstract: Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
775 citations
TL;DR: A connection between the structural changes in IL resulting from turning off polarization and slowing down of ion dynamics has been found and accurate description/prediction of thermodynamic and transport properties of alkanes, fluoroalkanes, oligoethers and dimethyl ketone is provided.
Abstract: A many-body polarizable force field has been developed and validated for ionic liquids (ILs) containing 1-methyl-3-alkylimidazolium, 1-alkyl-2-methyl-3-alkylimidazolium, N-methyl-N-alkylpyrrolidinium, N-alkylpyridinium, N-alkyl-N-alkylpiperidinium, N-alkyl-N-alkylmorpholinium, tetraalkylammonium, tetraalkylphosphonium, N-methyl-N-oligoetherpyrrolidinium cations and BF4−, CF3BF3−, CH3BF3−, CF3SO3−, PF6−, dicyanamide, tricyanomethanide, tetracyanoborate, bis(trifluoromethane sulfonyl)imide (Ntf2− or TFSI−), bis(fluorosulfonyl)imide (FSI−) and nitrate anions. Classical molecular dynamics (MD) simulations have been performed on 30 ionic liquids at 298, 333, and 393 K. The IL density, heat of vaporization, ion self-diffusion coefficient, conductivity, and viscosity were found in a good agreement with available experimental data. Ability of the developed force field to predict ionic crystal cell parameters has been tested on four ionic crystals containing Ntf2− anions. The influence of polarization on the struc...
604 citations
TL;DR: The proposed methodology departs from the traditional single-parameter procedures for estimating nonspecific solvent effects by splitting them into a polarizability term and a dipolarity term, and is applied to understanding for the indole chromophore the feasible inversion of the electronic nature for the first electronic excited state due to solvent effects.
Abstract: This paper reports a methodology for analyzing the solvent effect from empirical measurements of solvent acidity (SA), basicity (SB), dipolarity (SdP), and polarizability (SP). The proposed methodology departs from the traditional single-parameter procedures for estimating nonspecific solvent effects by splitting them into a polarizability term and a dipolarity term. In this work, we examined the SA, SB, SP, and SdP values for 160 solvents, the gas phase (the absence of solvent) being the origin of these scales. As shown in this paper, this information allows one not only to accurately describe the solvent effect experienced by any solute—whether polar or nonpolar and exhibiting some or no specific interaction with the solvent—but also to understand the nature of the well-known solvent parameters ET(30), π*, S′, and SPP, which are frequently used to describe the overall nonspecific contribution of solvents in terms of a single parameter. The high potential of the proposed empirical methodology is illustra...
548 citations
TL;DR: An increasing number of studies have reported computations of the standard (absolute) binding free energy of small ligands to proteins using molecular dynamics simulations and explicit solvent molecules that are in good agreement with experiments, suggesting that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future.
Abstract: An increasing number of studies have reported computations of the standard (absolute) binding free energy of small ligands to proteins using molecular dynamics (MD) simulations and explicit solvent molecules that are in good agreement with experiments. This encouraging progress suggests that physics-based approaches hold the promise of making important contributions to the process of drug discovery and optimization in the near future. Two types of approaches are principally used to compute binding free energies with MD simulations. The most widely known is the alchemical double decoupling method, in which the interaction of the ligand with its surroundings are progressively switched off. It is also possible to use a potential of mean force (PMF) method, in which the ligand is physically separated from the protein receptor. For both of these computational approaches, restraining potentials may be activated and released during the simulation for sampling efficiently the changes in translational, rotational, and conformational freedom of the ligand and protein upon binding. Because such restraining potentials add bias to the simulations, it is important that their effects be rigorously removed to yield a binding free energy that is properly unbiased with respect to the standard state. A review of recent results is presented, and differences in computational methods are discussed. Examples of computations with T4-lysozyme mutants, FKBP12, SH2 domain, and cytochrome P450 are discussed and compared. Remaining difficulties and challenges are highlighted.
501 citations
TL;DR: The correlations among the various properties led to the following conclusions: (1) the reliability of the ion force fields is significantly affected by the specific choice of water model, and (2) Ion−ion interactions are very important to accurately simulate the properties, especially solubility.
Abstract: The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation−anion, water−cation, and water−anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali−halide salts were generally lower than the true s...
471 citations
465 citations
TL;DR: Results show that covalently functionalizing graphene with the reverse saturable absorption chromospheres porphyrin and fullerene can enhance the nonlinear optical performance in the nanosecond regime.
Abstract: The nonlinear optical properties of two novel graphene nanohybrid materials covalently functionalized with porphyrin and fullerene were investigated by using the Z-scan technique at 532 nm in the nanosecond and picosecond time scale. Results show that covalently functionalizing graphene with the reverse saturable absorption chromospheres porphyrin and fullerene can enhance the nonlinear optical performance in the nanosecond regime. The covalently linked graphene nanohybrids offer performance superior to that of the individual graphene, porphyrin, and fullerene by combination of a nonlinear mechanism and the photoinduced electron or energy transfer between porphyrin or fullerene moiety and graphene.
435 citations
TL;DR: Various ways that electronic energy transfer is promoted by mechanisms beyond those explicitly considered in Forster RET theory are considered.
Abstract: After photoexcitation, energy absorbed by a molecule can be transferred efficiently over a distance of up to several tens of angstroms to another molecule by the process of resonance energy transfer, RET (also commonly known as electronic energy transfer, EET). Examples of where RET is observed include natural and artificial antennae for the capture and energy conversion of light, amplification of fluorescence-based sensors, optimization of organic light-emitting diodes, and the measurement of structure in biological systems (FRET). Forster theory has proven to be very successful at estimating the rate of RET in many donor-acceptor systems, but it has also been of interest to discover when this theory does not work. By identifying these cases, researchers have been able to obtain, sometimes surprising, insights into excited-state dynamics in complex systems. In this article, we consider various ways that electronic energy transfer is promoted by mechanisms beyond those explicitly considered in Forster RET theory. First, we recount the important situations when the electronic coupling is not accurately calculated by the dipole-dipole approximation. Second, we examine the related problem of how to describe solvent screening when the dipole approximation fails. Third, there are situations where we need to be careful about the separability of electronic coupling and spectral overlap factors. For example, when the donors and/or acceptors are molecular aggregates rather than individual molecules, then RET occurs between molecular exciton states and we must invoke generalized Forster theory (GFT). In even more complicated cases, involving the intermediate regime of electronic energy transfer, we should consider carefully nonequilibrium processes and coherences and how bath modes can be shared. Lastly, we discuss how information is obscured by various forms of energetic disorder in ensemble measurements and we outline how single molecule experiments continue to be important in these instances.
423 citations
TL;DR: The SM6, SM8, and SMD quantum mechanical aqueous continuum solvation models are applied to predict free energies of aQueous solvation for 61 molecules in the SAMPL1 test set, and it is suggested that the uncertainty in the target solvation free energies for these molecules may be quite large.
Abstract: The SM6, SM8, and SMD quantum mechanical aqueous continuum solvation models are applied to predict free energies of aqueous solvation for 61 molecules in the SAMPL1 test set described elsewhere (Guthrie. J. Phys. Chem. B 2009, 113, 4501−4507). For direct comparison to other models, frozen geometries, provided by Guthrie, were used together with the M06-2X density functional and the 6-31G(d) basis set. For the bulk electrostatic component of the solvation free energy, SM6 and SM8 employ a generalized Born model that uses polarized discrete partial atomic charges to model the electron density, with these charges being calculated by the CM4 and CM4M class IV charge models, respectively; SMD uses the polarized continuous quantum mechanical charge density. If five sulfonylureas are removed from the SAMPL1 set, the root-mean-square deviations (RMSDs) of SM6, SM8, and SMD on the remaining 56 molecules are 2.4, 2.6, and 2.5 kcal mol−1, respectively. The SM6, SM8, and SMD RMSDs on the five sulfonylureas are 14.2, ...
TL;DR: It is shown that the partition coefficients obtained between the IL and the K(3)PO(4)-aqueous rich phases were substantially larger than those typically obtained withpolymers-inorganic salts or polymers-polysaccharides aqueous systems.
Abstract: Extractive fermentation using aqueous biphasic systems (ABS) is a promising separation process since it provides a nondenaturing environment for biomolecules and improves the stability of cells. Due to environmental concerns and toxicity issues related with common volatile organic solvents, ionic liquids (ILs), a new class of nonvolatile alternative solvents, are being currently investigated for extraction purposes. In this work, a wide range of imidazolium-based ILs was studied aiming at obtaining new insights regarding their ability toward the formation of ABS and their capacity to the extraction of biomolecules. On the basis of the IL cations 1-ethyl-3-methylimidazolium and 1-butyl-3-methylimidazolium, the IL anion influence on ABS formation was assessed through their combination with chloride, bromide, acetate, hydrogensulfate, methanesulfonate, methylsulfate, ethylsulfate, trifluomethanesulfonate, trifluoroacetate, and dicyanamide. Ternary phase diagrams (and respective tie-lines) formed by these hyd...
TL;DR: This work quantifies the biological importance of fundamental physical processes, such as the excitonic Hamiltonian evolution and phonon-induced decoherence, by their contribution to the efficiency of the primary photosynthetic event.
Abstract: The role of quantum coherence in the dynamics of photosynthetic energy transfer in chromophoric complexes is not fully understood. In this work, we quantify the biological importance of fundamental physical processes, such as the excitonic Hamiltonian evolution and phonon-induced decoherence, by their contribution to the efficiency of the primary photosynthetic event. We study the effect of spatial correlations in the phonon bath and slow protein scaffold movements on the efficiency and the contributing processes. To this end, we develop two theoretical approaches based on a Green's function method and energy transfer susceptibilities. We investigate the Fenna-Matthews-Olson protein complex, in which we find a contribution of coherent dynamics of about 10% in the presence of uncorrelated phonons and about 30% in the presence of realistically correlated ones.
TL;DR: The observed glass transition temperature (Tg) defines the operating window for the thermal annealing and explains the long-term instability of both the morphology and the photovoltaic performance of the P3HT/PCBM solar cells.
Abstract: In this work, the phase diagram of poly(3-hexyl thiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) blends is measured by means of standard and modulated temperature differential scanning calorimetry. Blends were made by solvent-casting from chlorobenzene, as blends cast from toluene or 1,2-dichlorobenzene prove to retain effects of phase segregation during casting, hindering the determination of the phase diagram. The film morphology of P3HT/PCBM blends cast from chlorobenzene results from a dual crystallization behavior, in which the crystallization of each component is hindered by the other component. A single glass transition is observed for all compositions. The glass transition temperature (Tg) increases with increasing concentration of PCBM: from 12.1 degrees C for pure P3HT to 131.2 degrees C for pure PCBM. The observed Tg defines the operating window for the thermal annealing and explains the long-term instability of both the morphology and the photovoltaic performance of the P3HT/PCBM solar cells.
TL;DR: Simulations of PEO grafted to a nonadsorbing surface yield a mushroom to brush transition that is well described by the Alexander-de Gennes formalism.
Abstract: A coarse-grained (CG) model for polyethylene oxide (PEO) and polyethylene glycol (PEG) developed within the framework of the MARTINI CG force field (FF) using the distributions of bonds, angles, and dihedrals from the CHARMM all-atom FF is presented. Densities of neat low molecular weight PEO agree with experiment, and the radius of gyration Rg = 19.1 A ± 0.7 for 76-mers of PEO (Mw ≈ 3400), in excellent agreement with neutron scattering results for an equal sized PEG. Simulations of 9, 18, 27, 36, 44, 67, 76, 90, 112, 135, and 158-mers of the CG PEO (442 < Mw < 6998) at low concentration in water show the experimentally observed transition from ideal chain to real chain behavior at 1600 < Mw < 2000, in excellent agreement with the dependence of experimentally observed hydrodynamic radii of PEG. Hydrodynamic radii of PEO calculated from diffusion coefficients of the higher Mw PEO also agree well with experiment. Rg calculated from both all-atom and CG simulations of PEO76 at 21 and 148 mg/cm3 are found to ...
TL;DR: It is shown that this picture is consistent with both ultrafast anisotropy and NMR experimental results and that the transition state excluded volume theory yields quantitative predictions of the rotational slowdown for diverse hydrophobic solutes of varying size over a wide concentration range.
Abstract: The dynamics of water molecules next to hydrophobic solutes is investigated, specifically addressing the recent controversy raised by the first time-resolved observations, which concluded that some water molecules are immobilized by hydrophobic groups, in strong contrast to previous NMR conclusions Through molecular dynamics simulations and an analytic jump reorientation model, we identify the water reorientation mechanism next to a hydrophobic solute and provide evidence that no water molecules are immobilized by hydrophobic solutes Their moderate rotational slowdown compared to bulk water (eg, by a factor of less than 2 at low solute concentration) is mainly due to slower hydrogen-bond exchange The slowdown is quantitatively described by a solute excluded volume effect at the transition state for the key hydrogen-bond exchange in the reorientation mechanism We show that this picture is consistent with both ultrafast anisotropy and NMR experimental results and that the transition state excluded vol
TL;DR: MWCNT-g-CMC has much higher sorption ability in the removal of UO(2)(2+) than raw MWCNT and is a suitable material in the preconcentration and solidification of heavy metal ions from large volume of aqueous solutions.
Abstract: Carboxymethyl cellulose (CMC) is grafted on multiwalled carbon nanotubes (MWCNT) by using plasma techniques. The CMC grafted MWCNT (MWCNT-g-CMC) is characterized by using Fourier transform infrared spectra (FT-IR), Raman spectra, powder X-ray diffraction (XRD), thermogravimetric analysis (TGA)−differential thermal analysis (DTA), scanning electron microscopy (SEM), and N2-BET methods in detail. The application of MWCNT-g-CMC in the removal of UO22+ from aqueous solution is investigated. MWCNT-g-CMC has much higher sorption ability in the removal of UO22+ than raw MWCNT. The MWCNT-g-CMC is a suitable material in the preconcentration and solidification of heavy metal ions from large volume of aqueous solutions.
TL;DR: A comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric-isothermal ensemble indicates that both PBE and BLYP functionals under predict the density and over structure the liquid.
Abstract: We present herein a comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric−isothermal ensemble Our results indicate that both PBE and BLYP functionals under predict the density and over structure the liquid Adding the dispersion correction due to Grimme(1, 2) improves the predicted densities for both BLYP and PBE in a significant manner Moreover, the addition of the dispersion correction for BLYP yields an oxygen−oxygen radial distribution function in excellent agreement with experiment Thus, we conclude that one can obtain a very satisfactory model for water using BLYP and a correction for dispersion
TL;DR: The observation of quantum coherence using two-dimensional electronic spectroscopy is employed to directly measure the 14 lowest electronic energy levels in light-harvesting complex II (LHCII), the most abundant antenna complex in plants containing approximately 50% of the world's chlorophyll.
Abstract: The near-unity efficiency of energy transfer in photosynthesis makes photosynthetic light-harvesting complexes a promising avenue for developing new renewable energy technologies. Knowledge of the energy landscape of these complexes is essential in understanding their function, but its experimental determination has proven elusive. Here, the observation of quantum coherence using two-dimensional electronic spectroscopy is employed to directly measure the 14 lowest electronic energy levels in light-harvesting complex II (LHCII), the most abundant antenna complex in plants containing approximately 50% of the world’s chlorophyll. We observe that the electronically excited states are relatively evenly distributed, highlighting an important design principle of photosynthetic complexes that explains the observed ultrafast intracomplex energy transfer in LHCII.
TL;DR: Recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils are described.
Abstract: Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.
TL;DR: A simple first-principles-based simulation model (combining quantum mechanics with Marcus-Hush theory) that provides the quantitative structural relationships between angular resolution anisotropic hole mobility and molecular structures and packing is reported.
Abstract: We report a simple first-principles-based simulation model (combining quantum mechanics with Marcus−Hush theory) that provides the quantitative structural relationships between angular resolution anisotropic hole mobility and molecular structures and packing. We validate that this model correctly predicts the anisotropic hole mobilities of ruberene, pentacene, tetracene, 5,11-dichlorotetracene (DCT), and hexathiapentacene (HTP), leading to results in good agreement with experiment.
TL;DR: From observations on the relative depths of the free energies of the contact ion pair and the solvent-shared ion pair, along with related solvent structure analyses, a good correlation is found with this proposition: small-small and large- Large should associate in water, and small-large should be more dissociated.
Abstract: Using classical molecular dynamics simulations, we study ion−ion interactions in water. We study the potentials of mean force (PMF) for the full set of alkali halide ion pairs, and in each case, we test different parameter sets for modeling both the water and the ions. Altogether, we compared 300 different PMFs. We also calculate association equilibrium constants (KA) and compare them to two types of experiments. Of additional interest here was the proposition of Collins called the “law of matching water affinities”, where the relative affinity of ions in solution depends on the matching of cation and anion sizes. From observations on the relative depths of the free energies of the contact ion pair (CIP) and the solvent-shared ion pair (SIP), along with related solvent structure analyses, we find a good correlation with this proposition: small−small and large−large should associate in water, and small−large should be more dissociated.
TL;DR: A new force field (43A1-S3) for simulation of membranes by the Gromacs simulation package is introduced and correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP 1 atm simulations is demonstrated.
Abstract: We introduce a new force field (43A1-S3) for simulation of membranes by the Gromacs simulation package. Construction of the force fields is by standard methods of electronic structure computations for bond parameters and charge distribution and specific volumes and heats of vaporization for small-molecule components of the larger lipid molecules for van der Waals parameters. Some parameters from the earlier 43A1 force field are found to be correct in the context of these calculations, while others are modified. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP 1 atm simulations. 43-A1-S3 compares favorably with other force fields used in conjunction with the Gromacs simulation package with respect to the breadth of phenomena that it accurately reproduces.
TL;DR: An overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies is provided, pointing out that the approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
Abstract: Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
TL;DR: The results show that clathrates do not need the presence of a guest molecule to grow, but they need the guest to nucleate from liquid water, and nucleation of empty clathrate from supercooled liquid water would be extremely challenging if not impossible to attain in experiments.
Abstract: We use molecular dynamics simulations with the monatomic water (mW) model to investigate the phase diagram, metastability, and growth of guest-free water clathrates of structure sI and sII. At 1 atm pressure, the simulated guest-free water clathrates are metastable with respect to ice and stable with respect to the liquid up to their melting temperatures, 245 ± 2 and 252 ± 2 K for sI and sII, respectively. We characterize the growth of the sI and sII water crystals from supercooled water and find that the clathrates are unable to nucleate ice, the stable crystal. We computed the phase relations of ice, guest-free sII clathrate, and liquid water from −1500 to 500 atm. The resulting phase diagram indicates that empty sII may be the stable phase of water at pressures lower than approximately −1300 atm and temperatures lower than 275 K. The simulations show that, even in the region of stability of the empty clathrates, supercooled liquid water crystallizes to ice. This suggests that the barrier for nucleation...
TL;DR: It is found that Li+ complexation significantly stabilizes the highly polar cis-trans DMC conformation relative to the nearly nonpolar gas-phase low energy cis-cis conformer, and a slight preference for DMC in the cation solvation shell for EC:DMC ( 1 wt:1 wt) electrolytes is found.
Abstract: Quantum chemistry studies of ethylene carbonate (EC) and dimethyl carbonate (DMC) complexes with Li+ and LiPF6 have been conducted. We found that Li+ complexation significantly stabilizes the highly polar cis−trans DMC conformation relative to the nearly nonpolar gas-phase low energy cis−cis conformer. As a consequence, the binding of Li+ to EC in the gas phase is not as favorable relative to binding to DMC as previously reported. Furthermore, quantum chemistry studies reveal that, when complexation of LiPF6 ion pairs is considered, the DMC/LiPF6 complex is about 1 kcal/mol more stable than the EC/LiPF6 complex. The EC3DMC(cis−cis)/Li+ complex was found to be the most energetically stable among ECnDMCm/Li+ (n + m = 4) investigated complexes followed by EC4/Li+. Results of the quantum chemistry studies of these complexes were utilized in the development of a many-body polarizable force field for EC:DMC/LiPF6 electrolytes. Molecular dynamics (MD) simulations of EC/LiPF6, DMC/LiPF6, and mixed solvent EC:DMC/...
TL;DR: An overview of the full multiple spawning method for multistate quantum dynamics, together with hybrid quantum mechanical/molecular mechanical potential energy surfaces using both semiempirical and ab initio QM methods, and a comparison of the excited-state dynamics of several biological chromophores in solvent and protein environments are presented.
Abstract: Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical photochemistry occurs in solution and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biological chromophores in solvent and protein environments. Aqueous solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their respective CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.
TL;DR: Nine ILs with the same cation, 1-octyl-3-methylimidazolium [C(8)C(1)Im](+), but very different anions are investigated, finding an enrichment of the cation alkyl chains is found at the expense of the polar cation head groups and the anions in the first molecular layer.
Abstract: Angle-resolved X-ray photoelectron spectroscopy has been used to study the influence of different types of anions on the surface composition of ionic liquids (ILs). We have investigated nine ILs with the same cation, 1-octyl-3-methylimidazolium [C8C1Im]+, but very different anions. In all cases, an enrichment of the cation alkyl chains is found at the expense of the polar cation head groups and the anions in the first molecular layer. This enhancement effect decreases with increasing size of the anion, which means it is most pronounced for the smallest anions and least pronounced for the largest anions. A simple model is proposed to explain the experimental observations.
TL;DR: The pH dependence of the zeta potentials of oil drops has been measured by two very different techniques: on a single drop in a rotating electrophoresis cell and on about 1014 submicrometer drops in a 2 vol % emulsion by an electroacoustic method to give similar results with a sigmoidal pH dependence characterized by an isoelectric point at pH 2−3 and a half adsorption point about pH 5.5.
Abstract: Despite claims, based largely on molecular dynamics simulations, that the surface of water at the air/water interface is acidic, with a positive charge, there is compelling experimental evidence that it is in fact basic, with a negative charge due to the specific adsorption of hydroxide ions. The oil/water interface behaves similarly. The pH dependence of the zeta potentials of oil drops has been measured by two very different techniques: on a single drop in a rotating electrophoresis cell and on about 1014 submicrometer drops in a 2 vol % emulsion by an electroacoustic method to give similar results with a sigmoidal pH dependence characterized by an isoelectric point at pH 2−3 and a half adsorption point about pH 5.5, or at 10−8.5 M hydroxide ion. This indicates that hydroxide ion is absorbed much more strongly than other anions. The pH dependence of a single N2 bubble has also been measured and has the same pH dependence, independently of whether HCl or HI is used to adjust the pH. These similarities be...
TL;DR: The translational motion of the terminal carbon atoms in the alkyl chains of the imidazolium cations on the time scale of a few nanoseconds is significantly faster than that of the atoms inThe imidzolium rings and anions, which suggests that the dynamics of atoms inthe polar domains of the ionic liquids is significantly different from that in the nonpolar domains.
Abstract: Molecular dynamics simulations of a series of ionic liquids [1-alkyl-3-methylimidazolium (alkyl = methyl, ethyl, butyl, hexyl, and octyl), 1-butylpyridinium, N-butyl-N,N,N-trimethylammonium and N-butyl-N-methylpyrrolidinium cations combined with a (CF(3)SO(2))(2)N(-) anion ([mmim][TFSA], [emim][TFSA], [bmim][TFSA], [C(6)mim][TFSA], [C(8)mim][TFSA], [bpy][TFSA], [(n-C(4)H(9))(CH(3))(3)N][TFSA], and [bmpro][TFSA]) and a 1-butyl-3-methylimidazolium combined with BF(4)(-), PF(6)(-), CF(3)CO(2)(-), CF(3)SO(3)(-), and (C(2)F(5)SO(2))(2)N(-) anions ([bmim][BF(4)], [bmim][PF(6)], [bmim][CF(3)CO(2)], [bmim][CF(3)SO(3)], and [bmim][BETA])] were carried out using the OPLS force field for ionic liquids. The force field was refined on the basis of ab initio molecular orbital calculations of isolated ions and experimental densities for four ionic liquids. The densities calculated for the 13 ionic liquids agreed with the experimental values within a 2% error. The self-diffusion coefficients calculated for the ions in the 13 ionic liquids were compared with the experimental values obtained by the NMR measurements. Although the calculated self-diffusion coefficients were about 1 order smaller than the experimental ones, the cation and anion dependence (the effects of alkyl chain length in imidazolium, cation structures, and anion species) of the experimental self-diffusion coefficients was reproduced by the simulations quite well in most cases. The translational motion of the terminal carbon atoms in the alkyl chains of the imidazolium cations on the time scale of a few nanoseconds is significantly faster than that of the atoms in the imidazolium rings and anions, which suggests that the dynamics of atoms in the polar domains of the ionic liquids is significantly different from that in the nonpolar domains. The factors determining the self-diffusion coefficients of the ions are also discussed.