Rotational states of the ammonium ion in cubic lattice

The ammonium ion in the alkali halide lattice has the hindered rotational state. The rotational potential is expressed as crystal field, which depends upon only one rotational motion. The tetrahedral ion receives an octahedral field in this system. Four fundamental types of orientation appear due to the symmetry of ion and that of field. As the barrier height increases, the rotational levels approach to the librational levels with tunnel splitting. In particular, the tunneling part in the ground librational level is calculated using both free rotor bases and orientationally localized states. The level structure with the degeneracy is elucidated, which is peculiar in each type of orientation. Thermal properties are shown as model calculations. This revised version was published online in August 2006 with corrections to the Cover Date.     

Biosynthesis of platinum nanoparticles by Escherichia coli MC4100: can such nanoparticles exhibit intrinsic surface enantioselectivity?

The biomanufacture of two types of platinum bionanoparticle (bioNP) using Escherichia coli MC4100(1% and 20% by mass metal loading) together with a method for both liberating the nanoparticles (NPs) from the bacterial layer and their subsequent critical cleaning is reported. The possibility of an enantiomeric excess of chiral kink sites forming on the surface of the Pt nanoparticles produced by the bacteria was investigated using the electrooxidation of D- and L-glucose as the chiral probe. Transmission electron microscopy revealed that the Pt bioNPs (after recovery and cleaning) were typically 2.3 ± 0.7 nm (1% loading) and 4.5 ± 0.7 nm (20% loading) in diameter. The D- and L-glucose electrooxidation measurements did not give rise to any chiral response using either of the Pt bioNPs types but did display differing CV profiles. This suggested that the overall surface morphology of each bioNP could be controlled by the degree of metal loading but that no enantiomeric excess of intrinsically chiral surface kink sites was present.     

CO organization at ambient pressure on stepped Pt surfaces: first principles modeling accelerated by neural networks

Step and kink sites at Pt surfaces have crucial importance in catalysis. We employ a high dimensional neural network potential (HDNNP) trained using first-principles calculations to determine the adsorption structure of CO under ambient conditions (T = 300 K and P = 1 atm) on these surfaces. To thoroughly explore the potential energy surface (PES), we use a modified basin hopping method. We utilize the explored PES to identify the adsorbate structures and show that under the considered conditions several low free energy structures exist. Under the considered temperature and pressure conditions, the step edge (or kink) is totally occupied by on-top CO molecules. We show that the step structure and the structure of CO molecules on the step dictate the arrangement of CO molecules on the lower terrace. On surfaces with (111) steps, like Pt(553), CO forms quasi-hexagonal structures on the terrace with the top site preferred, with on average two top site CO for one multiply bonded CO, while in contrast surfaces with (100) steps, like Pt(557), present a majority of multiply bonded CO on their terrace. Short terraced surfaces, like Pt(643), with square (100) steps that are broken by kink sites constrain the CO arrangement parallel to the step edge. Overall, this effort provides detailed analysis on the influence of the step edge structure, kink sites, and terrace width on the organization of CO molecules on non-reconstructed stepped surfaces, yielding initial structures for understanding restructuring events driven by CO at high coverages and ambient pressure.

A neural network potential trained using first-principles calculations enables to understand the adsorption configurations of carbon monoxide on stepped Pt surfaces at ambient pressure.     

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks

Bending with high curvature is one of the major mechanical properties of double‐stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D‐shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti‐Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.     

Deformation structures in solid-state extruded polyethylene

Deformation structures resembling kink bands have previously been reported in a number of oriented semicrystalline polymers which have undergone various modes of deformation. In the present work, such structures have been observed and studied in solid-state extruded polyethylene which has been processed to give a biaxial, “single crystal” texture. Deformation of this material by bending followed by unbending has been observed to lead to shear during the bending stage and to void formation during the unbending stage. The kink bands which form during this treatment exhibit a single morphology regardless of the axis of bending so long as the direction of compression during bending is parallel to the original extrusion direction. Besides intracrystalline slip, which is known to contribute at least in part to the process of kink band formation, mechanisms involving interlamellar slip and interfibrillar slip are also considered. These mechanisms are considered in terms of three distinct experimental observations: the relationship between the kink boundary and the x-ray long period, the process of void formation during unbending, and the single characteristic morphology of the kink bands.     

Biodistribution study of free and microencapsulated 6‐methylcoumarin in Wistar rats by HPLC

A sensitive, specific and reproducible HPLC method has been developed and validated for the quantitative determination of 6‐methylcoumarin (6MC) in plasma and other tissues in Wistar rats. A C₁₈ column was used with UV detection at 321 nm and a gradient system consisting of methanol‐deionized water was used as mobile phase. The retention time for 6MC was 14.921 min and no interfering peaks were observed for any of the matrices. Linear relationships (r² > 0.997) were obtained between the peak height ratios and the corresponding biological sample concentrations over the range 0.4–12.8 µg/mL. Precision and accuracy were evaluated; the coefficient of variation and the relative error for all of the organs were <2 and 7%, respectively. The limit of quantitation was 0.20 µg/mL for the heart and 0.30 µg/mL for the other tissues evaluated. This HPLC method was successfully used in the determination of 6MC in the biodistribution study after administration of 200 mg/kg of both 6MC‐free and 6MC‐loaded polymeric microparticles. In this study, extensive 6MC was found, in both free and microencapsulated forms, in all the organs tested. The 6MC‐free showed a range of between 1.7 and 11.5 µg/g, while the microencapsulated 6MC showed concentrations of between 6.35 and 17.7 µg/g, suggesting that 6MC improved absorption rate. Copyright © 2014 John Wiley & Sons, Ltd.     

Second-order many-body perturbation study of solid hydrogen fluoride under pressure

A linear-scaling, embedded-fragment, second-order many-body perturbation (MP2) method with basis sets up to aug-cc-pVTZ is applied to the antiparallel structure of solid hydrogen fluoride and deuterium fluoride under 0-20 GPa of ambient pressure. The optimized structures, including the lattice parameters and molar volume, and phonon dispersion as well as phonon density of states (DOS), are determined as a function of pressure. The basis-set superposition errors are removed by the counterpoise correction. The structural parameters at 0 GPa calculated by MP2 agree accurately with the observed, making the predicted values at higher pressures a useful pilot for future experiments. The corresponding values obtained by the Hartree-Fock method have large, systematic errors. The MP2/aug-cc-pVDZ frequencies of the infrared- and Raman-active vibrations of the three-dimensional solids are in good agreement with the observed and also justify previous vibrational analyses based on one-dimensional chain models; the non-coincidence of the infrared and Raman mode pairs can be explained as factor-group (Davydov) splitting. The exceptions are one pair of modes in the librational region, for which band assignments based on a one-dimensional chain model need to be revised, as well as the five pseudo-translational modes that exist only in a three-dimensional treatment. The observed pressure dependence of Raman bands in the stretching region, which red-shift with pressure, is accounted for by theory only qualitatively, while that in the pseudo-translational region is reproduced with quantitative accuracy. The present calculation proves to be limited in explaining the complex pressure dependence of the librational modes. The hydrogen-amplitude-weighted phonon DOS at 0 GPa is much less structured than the DOS obtained from one-dimensional models and may be more realistic in view of the also broad, structureless observed inelastic neutron scattering spectra. All major observed peaks can be straightforwardly assigned to the calculated peaks in the DOS. With increasing pressure, MP2 predicts further broadening of bands and breach of the demarcation between the pseudo-translational and librational bands.     

Cooperative motion in amorphous polymers; application to the study of free-radical migration in solids

A Monte Carlo method has been used for studying the effect of the motion of some submolecular structures on the migration of radical centres and on the free-radical decay and its dependence on density. Motions of crank, crankshaft, kink, and double kink type are considered. A cooperative type of motions is also taken into account. The results show that cooperative motions support diffusion of radical centres and thus also the free-radical decay but, at higher densities, the cooperation of motions is restricted. The density of the system, where the decay of radicals is followed, affects the rate of the decay, its increase causes radical decay retardation. This is in line with the high pressure effect, which also retards the radical decay rate.     

Molecular-dynamics simulations of dimethylsulfoxide-methanol mixtures

We present molecular-dynamics (MD) computer simulation results for the local structures, hydrogen (H)-bond distribution, and dynamical properties of methanol (MeOH) and dimethylsulfoxide (DMSO) binary mixtures at ambient conditions over the entire composition range. The simulated heat of mixing and site-site pair distribution functions suggest that the intermolecular structures of the pure liquids are not markedly altered upon mixing. Nevertheless, H-bonding statistics show that aggregates of the type 1DMSO:1MeOH are formed and represent the predominant form of molecular association in these mixtures. Only a small fraction (10%) of DMSO molecules in MeOH-rich mixtures (85% in mole) forms H-bonding trimers of type 1DMSO:2MeOH. No evidence of other types of interspecies association is found. The self-diffusion coefficient for DMSO (MeOH) increases (decreases) upon mixing. The characteristic reorientation time tau1 of both species increases in the mixture, but the composition dependence is weak. The frequency spectrum of MeOH reorientational time-correlation function shows significant redshifts of the principal librational band as DMSO is added to the system, whereas the librational band of DMSO shows small alterations upon mixing. Our results are discussed in the light of previous simulation analyses for a similar system, DMSO-water mixtures, and compared with available experimental results.     

Observation of the Low‐Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces

Using the helium nanodroplet isolation setup at the ultrabright free‐electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm^?1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in‐plane and out‐of‐plane librational modes. This experimental data set provides a sensitive test for state‐of‐the‐art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high‐level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full‐dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.     

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions

This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free‐energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free‐energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels–Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG values of 20.1 and 21.4 kcal mol^?1 in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free‐energy surfaces for the Cope elimination of N,N‐dimethyl‐3‐phenylbutan‐2‐amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6‐hydroxybenzo‐isoxazole‐3‐carboxylic acid in aqueous, dimethyl sulfoxide, and CH₃CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol^?1 from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute–solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG value similar to the experimental values, as well as that for a small droplet with 34 molecules. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

An analysis of the influence of vibrations on electric field gradient tensors in solid hydrates

A method is described for calculating the influence of vibrational motion on the electric field gradient tensors at deuterons in solid hydrates using librational tensors. The method is applied to model calculations to illustrate the effect of normal modes which involve a mixture of standard wagging, twisting and rocking modes.     

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase

The rate enhancement provided by the chorismate mutase (CM) enzyme for the Claisen rearrangement of chorismate to prephenate has been investigated by application of the concept of near attack conformations (NACs). Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82% and 100% of chorismate conformers were found to be NAC structures in water and in the CM active site, respectively. Consequently, the conversion of non-NACs to NACs does not contribute to the free energy of activation from preorganization of the substrate into NACs. The FEP calculations yielded differences in free energies of activation that well reproduce the experimental data. Additional calculations indicate that the rate enhancement by CM over the aqueous phase results primarily from conformational compression of NACs by the enzyme and that this process is enthalpically controlled. This suggests that preferential stabilization of the transition state in the enzyme environment relative to water plays a secondary role in the catalysis by CM.     

Tilt grain boundaries in a diblock copolymer ordered nanocomposite lamellar phase

A hybrid self-consistent field theory/density functional theory method is applied to predict tilt (kink) grain boundary structures between lamellar domains of a symmetric diblock copolymer with added spherical nanoparticles. Structures consistent with experimental observations are found and theoretical evidence is provided in support of a hypothesis regarding the positioning of nanoparticles. Some particle distributions are predicted for situations not yet examined by experiment.     

Determination of microcystins in biological samples from freshwater fish

A new HPLC–DAD method has been developed to identify and quantify free microcystins (MC) in biological samples from fish (intestine and liver). The toxins were extracted from 500 mg sample with a mixture of methanol–water (85 : 15, v/v) and the extracts obtained were purified employing immunoaffinity columns (IAC). The purification step was optimised by a full factorial 3² design. MC were separated using conventional C18 column and an acetonitrile-acidified water (pH 3) gradient. Detection and quantification limits resulted equal for the two toxins assayed (MC-RR and MC-LR) and were 0.15 and 0.5 µg g^?1, respectively. The accuracy for each MC in liver samples were 96% (range 80–113%) for MC-RR and 101% (range 93–118%) for MC-LR. The results were slightly lower for intestine samples, with recoveries ranging between 85% (75–93%) for MC-RR and 88% (80–97%) for MC-LR. The proposed method was applied for the determination of free MC in fish intoxicated with these toxins, in order to determine its utility to evaluate the potential risks for human health if MC-contaminated fish are consumed. The results showed the transference of MC-LR from cyanobacterial cells to fish tissues.     

Librational relaxation and IR line broadening of matrix isolated CO

The IR line profile corresponding to the fundamental vibrational transition of CO isolated in an Ar matrix has been studied as a function of the temperature. The spectrum consists of two superimposed bands, a sharp one and a broad one whose linewidths are respectively 0.45 and 2.7 cm^?1 at 10 K. The strong temperature dependence of the CO lineshape is mainly due to the large change in the intensity ratio of the two components. Such a behaviour is accounted for by relaxation of librational populations. The calculated contributions of the processes connecting the ground and first excited librational states to the IR linewidth are of the same order of magnitude as the values experimentally measured. However the experimental lineshape of the sharp component being rather gaussian than lorentzian, it is concluded that librational relaxation contributes significantly to the broadening of the infrared CO band but not exclusively.     

Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations

The Kemp decarboxylation reaction for benzisoxazole-3-carboxylic acid derivatives has been investigated using QM/MM calculations in protic and dipolar aprotic solvents. Aprotic solvents have been shown to accelerate the rates of reaction by 7-8 orders of magnitude over water; however, the inclusion of an internal hydrogen bond effectively inhibits the reaction with near solvent independence. The effects of solvation and intramolecular hydrogen bonding on the reactants, transition structures, and the rate of reaction are elucidated using two-dimensional potentials of mean force (PMF) derived from free energy perturbation calculations in Monte Carlo simulations (MC/FEP). Free energies of activation in six solvents have been computed to be in close agreement with experiment. Solute-solvent interaction energies show that poorer solvation of the reactant anion in the dipolar aprotic solvents is primarily responsible for the observed rate enhancements over protic media. In addition, a discrepancy for the experimental rate in chloroform has been studied in detail with the conclusion that ion-pairing between the reactant anion and tetramethylguanidinium counterion is responsible for the anomalously slow reaction rate. The overall quantitative success of the computations supports the present QM/MM/MC approach, which features PDDG/PM3 as the QM method.     

Monte Carlo simulation of cutaneous reflectance and fluorescence measurements--the effect of melanin contents and localization

Melanin content and distribution in skin were studied by examining a patient with white, brown and blue skin tones expressed on skin affected by vitiligo. Both diffuse reflectance and autofluorescence spectra of the three distinction skin sites were measured and compared. Monte Carlo simulations were then performed to help explain the measured spectral differences. The modeling is based on a six-layer skin optical model established from published skin optical parameters and by adding melanin content into different locations in the model skin. Both the reflectance and fluorescence spectra calculated by Monte Carlo (MC) simulation were approximately in agreement with experimental results. The study suggests that: (1) trichrome vitiligo skin may be an ideal in vivo model for studying the effect of skin melanin content and distribution on skin spectroscopy properties. (2) Based on the skin optical model and MC simulation, the content and distribution of melanin in skin, or other component of skin could be simulated and predicted. (3) Both reflectance and fluorescence spectra provided information about superficial skin structures but fluorescence spectra are capable of providing information from deeper cutaneous structures. (4) The research method, including the spectral ratio method, the method of adding and modifying the melanin content in skin optical models, and MC simulation could be applied in other non-invasive optical studies of the skin.     

Implementation and performance of the artificial force induced reaction method in the GRRM17 program

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.