Additional force field in cooling process of cellular Al alloy

The foaming process of Al alloy is similar to that of Al, but there is a solid-liquid state zone in the solidification process of cellular Al alloy which does not exist in the case of Al. In the unidirectional solidification of cellular Al alloy, the proportion of the solid phase gradually reduces from the solid front to the liquid front. This will introduce a force and result in a serious quick shrinkage. By the mathematic and physical mode, the solidification of the cellular Al alloy is studied. The data measured by experiment are close to the result calculated by the mode. This kind of shrinkage can be solved by suitable cooling method in appropriate growth stage. The compressive strength of the cellular Al alloy made by this way is 40% higher than that of cellular Al.     

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.     

Estimation of the NF bond distance in NF4+ from its general valence force field

The estimate of the bond length in NF₄⁺ from the published general valence force field was revised and a value of 1.31 Å is suggested.     

Evaluating force field accuracy with long-time simulations of a β-hairpin tryptophan zipper peptide

We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic β-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 μs of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 φ and ψ dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.     

Atomic force microscopy observation of the condensates of the spermidine-DNA complexes

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An improved anharmonic force field for SF6 which includes FF nonbonded interactions

An anharmonic force field for SF₆ in which nonbonded FF interactions are explicitly included has been explored. The FF interaction force constants were modeled with a Lennard—Jones potential using values of the parameters transfered from quadratic force-constant calculations. A Morse function was used to model the anharmonicity in the valence-bond stretching coordinates. The parameters of the model have been adjusted by least squares to some of the available experimental data and have been used to predict energies of excited vibrational states in the v₃ manifold.     

Assessment of density functionals and force field methods on anion–π interaction in heterocyclic calix complexes

The performance of ten density functionals and four force field methods in describing non-covalent interactions have been assessed by studying the interaction energies and structures of the four anion–π complexes involving tetraoxacalix[2]arene[2]triazine and various anions. Their structures are optimized at MP2/6-311++G(d,p) level, and interaction energies are obtained at DF-MP2-F12/aug-cc-pVDZ level. The result shows that the functional M06-2X predicts the most reliable interaction energy, followed by wB97XD and BHandH. B97D slightly overestimates the interaction energy. Other functionals and force field methods seriously overestimate the interaction energy. For the structures, three functionals M06-2X, wB97XD and BH and H predict the most reliable results, followed by B97D. The force field methods predict the largest deviations. The present work suggests that the functional M06-2X is a reliable method to describe energies and structural properties of the large molecules involving the anion–π interactions.     

Analytic energy gradient in combined second-order Møller-Plesset perturbation theory and polarizable force field calculation

Second-order M?ller-Plesset perturbation theory (MP2) is used to describe electronic correlation on the basis of Hartree-Fock (HF) variational calculations that incorporate induced dipole polarizable force fields (i.e., QM/MMpol style HF and MP2). The Z-vector equations for regular closed shell and open shell MP2 methods (RMP2, ZAPT2, and UMP2) are extended to include induced dipole contributions to determine the MP2 response density so that nuclear gradient and other properties can be efficiently evaluated. A better estimation of the induced dipole polarization energy can be obtained using the MP2 relaxed density. QM/MMpol style MP2 molecular dynamics simulations are performed for the ground state and first triplet state of acetone solvated by 1024 polarizable water molecules. A switching function is used to ensure energy conservation in QM/MM simulation under periodic boundary condition.     

On the effect of thermophoretic force,gravitational force,and particle–particle interactions in field-flow fractionation

The theoretical calculations confirmed that the gravitational force cannot be neglected in all field-flow fractionation techniques separating nanometer-sized colloidal particles whenever particle diameter is approximately 200?nm and larger. Particle–particle repulsive interactions, mostly electrostatic repulsions, influence substantially concentration distribution established by any effective field acting across the fractionation channel, as confirmed explicitly for thermophoretic force generated by temperature gradient in microthermal field-flow fractionation. The ionic strength of the carrier liquid causes the screening of the electrostatic double layer around the dispersed particles and thus influences the retention. The attractive particle–particle forces occur when the zeta potential of the particles approaches to 0?mV, the electrostatic repulsions are screened, and the aggregation of the particles is observed. The pH influences differently the size and zeta potential of the plain polystyrene latex particles and of the particles modified on the surface by the groups –COOH and –NH₂. The role of a detergent in carrier liquid is non-negligible, as demonstrated by its presence or absence in carrier liquid.     

Very empirical treatment of solvation and entropy: a force field derived from Log Po/w

A non-covalent interaction force field model derived from the partition coefficient of 1-octanol/water solubility is described. This model, HINT for Hydropathic INTeractions, is shown to include, in very empirical and approximate terms, all components of biomolecular associations, including hydrogen bonding, Coulombic interactions, hydrophobic interactions, entropy and solvation/desolvation. Particular emphasis is placed on: (1) demonstrating the relationship between the total empirical HINT score and free energy of association, G _interaction; (2) showing that the HINT hydrophobic-polar interaction sub-score represents the energy cost of desolvation upon binding for interacting biomolecules; and (3) a new methodology for treating constrained water molecules as discrete independent small ligands. An example calculation is reported for dihydrofolate reductase (DHFR) bound with methotrexate (MTX). In that case the observed very tight binding, G _interaction–13.6 kcal mol^–1, is largely due to ten hydrogen bonds between the ligand and enzyme with estimated strength ranging between –0.4 and –2.3 kcal mol^–1. Four water molecules bridging between DHFR and MTX contribute an additional –1.7 kcal mol^–1 stability to the complex. The HINT estimate of the cost of desolvation is +13.9 kcal mol^–1.     

A vibrational molecular force field of model compounds with biological interest—III. Harmonic dynamics of α- and β-d-galactose in the crystalline state

The infrared spectra of α- and β-d-galactose were recorded, both in the mid-IR range (4000-500 cm⁻¹) and in the far-IR (500-50 cm⁻¹). The Raman spectra were also obtained. These spectra constitute the basis of a crystalline-state force field established for these two molecules through a normal coordinate analysis. A modified Urey—Bradley—Shimanouchi force field was combined with an intermolecular potential energy function which includes van der Waals interactions, electrostatic terms and an explicit hydrogen bond function. The force constants were varied, so as to obtain an agreement between the observed vibrational frequencies and the calculated ones of α-d-galactose. The force field obtained was then applied to α-d-galactose O-d5 and β-d-galactose, in order to test its transferability. The computed potential energy distribution was found to be compatible with previous assignments for d-glucose, particularly for the modes involving C6 and COH groups. For β-d-galactose the same force field was used with changing the force constants due to the C1 and C6 groups.     

Substituent effect on the anharmonic force constant Ksδδ of the amino group in p-X anilines

The values of the anharmonic stretch-bend-bend force constant of the amino group in five p-substituted anilines is determined from the spectral parameters of the Fermi resonance doublet ν_s—2δ in tetrahydrofuran solutions. A large substituent effect on K_sδδ is observed with a linear dependence on σ_p. The unperturbed frequencies ν°_s show a weak negative dependence in σ_p in tetrahydrofuran, reflecting a solvent effect on the substituent one.     

The vibrational spectra of amides—II. The force field and isotopic shifts of N,N-dimethyl formamide

The effects of ¹⁶O → ¹⁸O substitution on the vibrational frequencies of N,N-dimethylformamide have been studied. To understand these and the effects of previously measured shift data due to ¹³C, ²H and ¹⁵N ab initio calculations of frequencies and intensities have been carried out at the 3-21G level. Accord between theory and experiment is generally good. A surprising result is the prediction of a weak band near 2000 cm⁻¹ in DMF due to in-plane interaction between the methyl umbrella modes and the anti-symmetric CN stretch. This abnormally high frequency is explained as arising due to the planar trigonal C₃N entity. Previous problems in reproducing isotope shifts are shown to be due to this mode being previously assigned near 1500 cm⁻¹. The effects of suppressing reference to one of a set of internal valence angles involved in a redundancy are explored. It is shown that the principal effect is to add the diagonal quadratic constant for that coordinate to all other quadratic terms involving pairs of the angles involved in the redundancy. This results in large, almost equal, interaction constants amongst this set. Such effects are seen in the present work. The ab initio field is shown to be compatible with ab initio fields of mono N-methyl amides extant in the literature.     

Improved intermolecular force field for crystalline oxohydrocarbons including O?HO hydrogen bonding

An improved intermolecular force field of the (exp‐6‐1) type was obtained by fitting a training set of 124 observed oxohydrocarbon crystal structures and seven observed heats of sublimation. All of these structures, when energy minimized, showed cell edge length shifts of 3% or less. Especially good results were obtained for modeling carbohydrate crystal structures. The fitted crystal structures are a subset of a database of 180 structures systematically selected from the CSD library according to functional group and threshold accuracy criteria. Energy minimization results are also presented for 56 structures not in the training set, which showed cell edge length shifts larger than 3%. The previously published W99 force field, using C(4), C(3), and H(1) potentials, was slightly modified and adopted for hydrocarbon portions of the molecules. Oxygen atoms with one bond, O(1), and those with two bonds, O(2), were assigned separate parameters. Hydrogen atoms bonded to oxygen were assigned exponential repulsion functions and divided into two types: in hydroxy groups, H(2); and in carboxyl groups, H(3). Wavefunctions of HF 6‐31g** quality were calculated for every molecule and the molecular electric potential (MEP) was modeled with net atomic charges. Methylene bisector charges were used for all CH₂ and CH₃ groups, and ring center site charges were added if necessary to fit the MEP. For some structures, upward scaling of the MEP to simulate intermolecular polarization gave better results. MEP interaction generally gave a satisfactory representation of weak C HO hydrogen bonding. Medium strength C HO hydrogen bonding was modeled by reducing the repulsion of the involved hydrogen atoms. Crystal structures of several biologically interesting molecules were modeled with the force field, yielding good results. These molecules include aspirin, sucrose, β‐cellobiose, β‐lactose, progesterone, testosterone, prostaglandin E1, cholesterol acetate, and stearic acid. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 1–20, 2001     

Charge transport at the protein–electrode interface in the emerging field of BioMolecular Electronics

The emerging field of BioMolecular Electronics aims to unveil the charge transport characteristics of biomolecules with two primary outcomes envisioned. The first is to use nature's efficient charge transport mechanisms as an inspiration to build the next generation of hybrid bioelectronic devices towards a more sustainable, biocompatible and efficient technology. The second is to understand this ubiquitous physicochemical process in life, exploited in many fundamental biological processes such as cell signalling, respiration, photosynthesis or enzymatic catalysis, leading us to a better understanding of disease mechanisms connected to charge diffusion. Extracting electrical signatures from a protein requires optimised methods for tethering the molecules to an electrode surface, where it is advantageous to have precise electrochemical control over the energy levels of the hybrid protein–electrode interface. Here, we review recent progress towards understanding the charge transport mechanisms through protein–electrode–protein junctions, which has led to the rapid development of the new BioMolecular Electronics field. The field has brought a new vision into the molecular electronics realm, wherein complex supramolecular structures such as proteins can efficiently transport charge over long distances when placed in a hybrid bioelectronic device. Such anomalous long-range charge transport mechanisms acutely depend on specific chemical modifications of the supramolecular protein structure and on the precisely engineered protein–electrode chemical interactions. Key areas to explore in more detail are parameters such as protein stiffness (dynamics) and intrinsic electrostatic charge and how these influence the transport pathways and mechanisms in such hybrid devices.     

Effect of the direction of the earth’s magnetic field lines on corrosive wear

In this work, the effect of the direction of the Earth’s magnetic field lines on the corrosive wear of steel samples in an aggressive medium was studied, and a study algorithm and a data processing algorithm were described.     

Palladium: a future key player in the nanomedical field?

Metal nanostructures offer invaluable possibilities for targeted drug delivery, detection/diagnosis and imaging. Whereas iron, gold, silver and platinum nanoarchitectures have largely dominated this field to date, several hurdles impede the widespread application of those nanopharmaceuticals in a clinical context. Therefore, technologies based on alternative metals are now being evaluated for their potential in medical applications. Palladium nanostructures are characterized by remarkable catalytic and optical properties. However, until recently, very few studies have taken advantage of these unique characteristics for applications in the biomedical field. Very recently, palladium nanostructures have been reported as prodrug activator, as photothermal agents and for anti-cancer/anti-microbial therapy. With only a handful of reports available, the pharmaceutical applications of palladium nanostructures reviewed here are in their infancy. Yet their interesting performance and toxicity profiles may qualify them as future key players in the nanomedical field.     

Investigating detailed mechanism of hydrogen molecules adsorbing on single-wall carbon nanotubes using fitted force field parameters containing carbon–carbon interactions

The nonbonded and bonded force field parameters for carbon atoms in single-wall carbon nanotubes (SWNT) are fitted by means of quantum chemistry calculations with considering the periodic boundary conditions. The nonbonded parameters between carbon atoms and hydrogen atoms are fitted as well. All the fitted parameters are verified by comparing to quantum chemistry results and by calculating Young's modulus. Adsorption of Hydrogen molecules are then carried out on a bundle of self-assembled SWNTs. The adsorption isotherms are consistent to the Freundlich equation. Both hydrogen molecules adsorbed outside and inside the SWNTs are counted. According to our result, hydrogen molecules adsorbed inside the SWNTs are more stable at a relatively high temperature and are playing an important part in total amount of the adsorbed molecules. While C(10,10) have the highest adsorption capacities in most of the temperatures, hydrogen molecules inside C(5,5) are the most stable of all the four kinds of SWNTs. Thus, balancing adsorption capacities and strength of interaction can be important in choosing SWNT for gas adsorption. Besides, we deduct an equation that can describe the relation between hydrogen pressure and amount of SWNTs based on our simulation results. The hydrogen pressure may decrease by adding SWNTs in the system. The fitting method in our system is valid to SWNTs and can be tested in further studies of similar systems. © 2018 Wiley Periodicals, Inc.