Force Field Analysis

Medical implants are increasingly often inserted into bone of frail patients, who are advanced in years. Due to age, severe trauma or pathology-related bone changes, osseous healing at the implant site is frequently limited. We were able to demonstrate that coating of endosseous implants with nanocrystalline diamond (NCD) allows stable functionalization by means of physisorption with BMP-2. Strong physisorption was shown to be directly related to the unique properties of NCD, and BMP-2 in its active form interacted strongest when NCD was oxygen-terminated. The binding of the protein was monitored under physiological conditions by single molecule force spectroscopy, and the respective adsorption energies were further substantiated by force-field-calculations. Implant surfaces refined in such a manner yielded enhanced osseointegration in vivo, when inserted into sheep calvaria. Our results further suggest that this technical advancement can be readily applied in clinical therapies with regard to bone healing, since primary human mesenchymal stromal cells strongly activated the expression of osteogenic markers when being cultivated on NCD physisorbed with physiological amounts of BMP-2.

We investigate whether the observed fine structure and asymmetry of non-averaged galactic rotation curves can be reconstructed directly from the observed HI distribution within the framework of a kinetic gas transport description. Using the observed HI density profiles separately for the approaching (north-eastern) side and the receding (south-western) side of the galaxy NGC 3198, we reconstruct the corresponding rotation curves based on the equation previously derived in Lipovka (2022). It is shown that the reconstructed curves reproduce not only the approximately flat large-scale behaviour of the observed rotation curves, but also their detailed local morphology and asymmetry separately for the northeastern and southwestern sides of the galactic disk. The obtained results indicate that the local structure of galactic rotation curves is closely connected with the local HI distribution and arises naturally as a consequence of kinetic gas transport processes in galactic disks.

Silica-based hybrid organic -inorganic (O/I) materials prepared by sol-gel chemistry exhibit unique chemical and physical properties. (3-glycidoxypropyl)trimethoxysilane (GPTMS)-based networks represent an archetype of this class of substances, with a vast range of applications. In the present study, a new computational recipe has been developed within Materials Studio w software platform to generate atomistic models of GPTMS crosslinked networks. The methodology is based on molecular mechanics/dynamics schemes and assumes close proximity as a criterion for crosslinking reaction to occur. The COMPASS force-field was selected for molecular model constructions, and two charge schemes -one obtained directly from the force field and one derived from quantum-chemical calculations -were employed and compared for the prediction of the final system thermophysical properties. Starting from fully-hydrolysed GPTMS molecules, a realistic 3D network was successfully constructed, including the presence of 4-and 6-membered cyclic structures. Mechanical moduli and specific heat values estimated from equilibrated structures were selected as benchmarks for model/procedure validation. Overall, the simulation results are reasonable and in the range of experimental data available in the literature on similar systems. Thus, the proposed computational strategy has a good potential in the design and optimisation of O/I hybrid materials.

A general all-atoms force field (FF) for atomistic simulation of low molecular weight hydrofluorocarbons (HFCs) was developed using state-of-art ab initio calculations and empirical parameterization techniques. The FF is based on ab initio quantum mechanical calculations for the valence parameters and on molecular dynamics (MD) simulations for the tuning of the Lennard-Jones (LJ) parameters describing the dispersion forces. Validation of the proposed FF has been made versus intramolecular properties of isolated molecules, vibrational spectra, and intermolecular properties of liquid state molecules such as cohesive energy, enthalpy of vaporization and density for molecules of interest. The reported results show that the present force filed enables accurate and simultaneous prediction of structural, conformational, vibrational and thermophysical properties for low molecular weight HFCs in isolation and in condensed phase. Detailed results of the parameterization and validation are reported.

The present paper reports the results obtained from MD calculations on the following systems: 1 Ž . Ž . chloro-fluoro-hydrocarbons CFHs of widespread use in the refrigerant industry e.g., R22, R32, R123, etc. Ž . and 2 selected polymers of industrial applications. In the case of CFHs, force field and quantum-mechanical techniques were employed in molecular modeling and for the calculation of geometrical and chemico-physical parameters. The Connolly surface algorithm, corrected for quantum-mechanical effects, was used in the evaluation of molecular surfaces and volumes. From these data, the parameters of the perturbed hard sphere chain equation of state, V U and A U , were obtained. The third parameter, E U , was calculated from extensive MD simulations under NPT conditions. For polymers, a more complicated preliminary procedure was necessary to model realistic amorphous polymeric chains. The Lattice Fluid equation parameters were then calculated from thorough MD simulations both under NVT and NPT conditions. The predicted thermophysical properties of both classes of substances are then discussed and compared with the relevant experimental data, were available.

In this paper we present a new procedure, based on quantumrmolecular QMrMM mechanics and Ž . molecular dynamics MD computer simulations, for estimating the Perturbed Hard Sphere Chain Theory Ž . Ž . Ž . PHSCT equation of state EOS parameters of a set of 14 alternative chloro-fluoro-hydrocarbons CFH of industrial relevance and to predict their thermophysical properties and PVT behavior. Force field and quantum-mechanical techniques were employed in molecular modeling and for the calculation of geometrical and chemico-physical parameters. The Connolly surface algorithm, corrected for quantum-mechanical effects, was used in the evaluation of molecular surfaces and volumes. From these data, the parameters of the PHSCT EOS, V U and A U , were obtained. The third parameter, E U , was calculated from extensive MD simulations under NPT conditions. The new, original method proposed in this work gives good results, is relatively inexpensive, is absolutely general and can be applied in principle to any EOS, provided the parameters have a physical meaning. The tuning of the energetic parameter to a generated data set accounts for the degree of empiricism introduced at a certain stage in the development of any EOS.

Several popular force fields, namely, CHARMM, AMBER, OPLS‐AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechanical potential energy curves for noncovalent interactions in the benzene dimer, the benzene‐CH4 complex, and the benzene‐H2S complex. All of the force fields are semi‐quantitatively correct, but none of them is consistently reliable quantitatively. Re‐optimization of Lennard‐Jones parameters and symmetry‐adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions) are employed for the empirical force fields. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009

We present an efficient algorithm for generating semiglobal potential energy surfaces of reactive systems. The method takes as input molecular mechanics force fields for reactants and products and a quadratic expansion of the potential energy surface around a small number of geometries whose locations are determined by an iterative process. These Hessian expansions might come, for example, from ab initio electronic structure calculations, density functional theory, or semiempirical molecular orbital theory. A 2×2 electronic diabatic Hamiltonian matrix is constructed from these data such that, by construction, the lowest eigenvalue of this matrix provides a semiglobal approximation to the lowest electronically adiabatic potential energy surface. The theory is illustrated and tested by applications to rate constant calculations for three gas-phase test reactions, namely, the isomerization of 1,3-cis-pentadiene, OH+CH4→H2O+CH3, and CH2Cl+CH3F→CH3Cl+CH2F.

Recent theoretical and experimental studies have shown that polarizable anions, such as iodide and bromide, preferentially accumulate close to the surface of electrolyte solutions. This finding is in sharp contrast to the previously prevailing idea that salts are dielectrically excluded from the free water surface and opens up new avenues for research in specific salt effects. In this work, we have verified the ability of a recently introduced polarizable water model, SWM4-DP, to reproduce this behavior, by simulations of a NaI/water slab, corresponding to a 1.2 M solution. The water and ion polarizabilities are modeled by classical Drude oscillator particles. As revealed by the simulations, a double layer is formed close to the free water surface, with the iodide ions located closer to the interface and the sodium ions at a neighboring, interior layer. Near the surface, all solution species acquire an induced dipole moment, that is perpendicular to the surface and points toward the exterior. The double charge layer causes ordering of water at a subsurface region. Simulations with a simpler system of a single iodide ion in a water slab show that the surface position is stabilized by induced charge interactions; in contrast, the charge-dipole interactions between the iodide permanent charge and the water permanent dipole moment favor the bulk position. Thus, the polarizabilities of ion and water are essential for explaining the increased preference of iodide for the air-water interface, in accordance with other studies.

Recent experiments and simulations show that large chaotropic anions favor solvation at the water surface, mainly due to induction interactions dominated by ionic polarizabilities. We compare the solvation free-energy components of iodide at the water surface and bulk with a recent, polarizable force field. The bulk position is stabilized by the interaction between the iodide permanent charge and the solvent permanent dipole moments; the surface is favored by the iodide polarizability and the reduced cavity accommodating the solute. The ionic solvation is not described satisfactorily by linear response; the non-linearity of the iodide induced dipole moment is discussed.

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According to Schrödinger's ideas, classical dynamics of point particles should correspond to the « geometrical optics » limit of a linear wave equation, in the same way as ray optics is the limit of wave optics. It is shown that, using notions of modern wave theory, the « geometrical optics » analogy leads to the correspondence between a classical Hamiltonian H and a « quantum » wave equation in a natural and general way. In particular, the correspondence is unambiguous also in the case where H contains mixed terms involving momentum and position. In the line of Schrödinger's ideas, it is also attempted to justify the occurrence, in QM, of eigenvalues problems, not merely for energy, but also for momentum. It is shown that the wave functions of pure momentum states can be defined in a physically more satisfying way than by assuming plane waves. In the case of a spatially uniform force field, such momentum states have a singularity and move undeformed according to Newton's second law. The mentioned unambiguous correspondence allows to uniquely extend the Klein-Gordon relativistic wave equation to the case where a constant gravitational field is present. It is argued that Schrödinger's wave mechanics can be extended to the case with a variable gravitational field only if one accepts that the wave equation is a preferred-frame one. From this viewpoint, generally-covariant extensions of the wave equations of QM seem rather formal. Finally, it is conjectured that there is no need for a quantum gravity.

Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of protein complex formation, and especially for those of weak or transient protein complexes.

Force field parameters for large scale computational modeling of sensitized TiO2-anatase surfaces are developed from ab initio molecular dynamics simulations and geometry optimization based on Density Functional Theory (DFT). The resulting force field, composed of Coulomb, van der Waals and harmonic interactions, reproduces the ab initio structures and the phonon spectra density profiles of TiO2-anatase nanostructures functionalized with catechol, a prototype of an aromatic linker commonly used to sensitize TiO2 nanoparticles with Ru(II)-polypyridyl dyes. In addition, simulations of interfacial electron injection and electron-hole relaxation dynamics demonstrate the capabilities of the resulting molecular mechanics forcefield, as applied in conjunction with mixed quantum-classical methods, for modeling quantum processes that are critical for the overall efficiency of sensitized-TiO2 solar cells.

Force field parameters for large scale computational modeling of sensitized TiO2-anatase surfaces are developed from ab initio molecular dynamics simulations and geometry optimization based on Density Functional Theory (DFT). The resulting force field, composed of Coulomb, van der Waals and harmonic interactions, reproduces the ab initio structures and the phonon spectra density profiles of TiO2-anatase nanostructures functionalized with catechol, a prototype of an aromatic linker commonly used to sensitize TiO2 nanoparticles with Ru(II)-polypyridyl dyes. In addition, simulations of interfacial electron injection and electron-hole relaxation dynamics demonstrate the capabilities of the resulting molecular mechanics force-field, as applied in conjunction with mixed quantum-classical methods, for modeling quantum processes that are critical for the overall efficiency of sensitized-TiO2 solar cells.

Force field parameters for large scale computational modeling of sensitized TiO2-anatase surfaces are developed from ab initio molecular dynamics simulations and geometry optimization based on Density Functional Theory (DFT). The resulting force field, composed of Coulomb, van der Waals and harmonic interactions, reproduces the ab initio structures and the phonon spectra density profiles of TiO2-anatase nanostructures functionalized with catechol, a prototype of an aromatic linker commonly used to sensitize TiO2 nanoparticles with Ru(II)-polypyridyl dyes. In addition, simulations of interfacial electron injection and electron-hole relaxation dynamics demonstrate the capabilities of the resulting molecular mechanics forcefield, as applied in conjunction with mixed quantum-classical methods, for modeling quantum processes that are critical for the overall efficiency of sensitized-TiO2 solar cells.

Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of lowresolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086-3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/ FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with C α root-mean-square-deviations below 3.5 Å as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low energy, are due to omission of protein-protein interactions. The results of this study represent a benchmark in force-field development, and may be useful for evaluation of the performance of different force fields.

The majority of mechanisms that can be deployed for optical micromanipulation are not especially amenable for extension into the nanoscale. At the molecular level, the rich variety of schemes that have been proposed to achieve mechanical effect using light commonly exploit specific chemical structures; familiar examples are compounds that can fold by cis-trans isomerization, or the mechanically interlocked architectures of rotaxanes. However, such systems are synthetically highly challenging, and few of them can realistically form the basis for a true molecular motor. Developing the basis for a very different strategy based on programmed electronic excitation, this paper explores the possibility of producing controlled mechanical motion through optically induced modifications of intermolecular force fields, not involving the limitations associated with using photochemical change, nor the high intensities required to produce and manipulate optical binding forces between molecules. Calculations reveal that significant, rapidly responsive effects can be achieved in relatively simple systems. By the use of suitable laser pulse sequences, the possibilities include the generation of continuous rotary motion, the ultimate aim of molecular motor design.

An accurate modeling of phonons, strain distributions, and Grüneisen coefficients is essential for the qualitative and quantitative design of modern nanoelectronic and nanooptoelectronic devices. The challenge is the development of a model that fits within an atomistic representation of the overall crystal yet remains computationally tractable. A simple model for introducing the anharmonicity of the interatomic potential into the Keating two-parameter valence-force-field model is developed. The new method is used for the calculation of acoustic phonon and strain effects in zinc-blende semiconductors. The model is fitted to the Grüneisen coefficients for long-wavelength acoustic phonons and reproduces the response to strain throughout the Brillouin zone in reasonable agreement with experiment.

The effect of wetting layers on the strain and electronic structure of InAs self-assembled quantum dots grown on GaAs is investigated with an atomistic valence-force-field model and an empirical tight-binding model. By comparing a dot with and without a wetting layer, we find that the inclusion of the wetting layer weakens the strain inside the dot by only 1% relative change, while it reduces the energy gap between a confined electron and hole level by as much as 10%. The small change in the strain distribution indicates that strain relaxes only little through the thin wetting layer. The large reduction of the energy gap is attributed to the increase of the confining-potential width rather than the change of the potential height. First-order perturbation calculations or, alternatively, the addition of an InAs disk below the quantum dot confirm this conclusion. The effect of the wetting layer on the wave function is qualitatively different for the weakly confined electron state and the strongly confined hole state. The electron wave function shifts from the buffer to the wetting layer, while the hole shifts from the dot to the wetting layer.

The quadratic, cubic, and semi-diagonal quartic force field of vinyl chloride has been calculated at the MP2 level of theory employing a basis set of triple-f quality. The spectroscopic constants derived from this force field are compared with the experimental values. To make this comparison more complete, the rotational constants of the lowest excited state, v 9 = 1 at 395 cm À1 have been determined by microwave spectroscopy and the m 12 band (around 618 cm À1 ) has been investigated by high-resolution infrared Fourier transform spectroscopy. The equilibrium structure has been derived from experimental ground state rotational constants and ab initio rovibrational interaction parameters. This semi-experimental structure is in excellent agreement with the ab initio structure calculated at the CCSD(T) level of theory using a basis set of quintuple-f quality and a core correlation correction. The experimental mass-dependent r m structures are also determined and their accuracy is discussed. The recommended equilibrium geometry is: r (C@C) = 1.3262(10), r (CACl) = 1.7263(10), r (CAH g ) = 1.0784(10), r (CAH c ) = 1.0795(10), r (CAH t ) = 1.0797(10), \(CCCl) = 122.77(10)°, \(CCH g ) = 123.86(10)°, \(CCH c ) = 121.80(10)°, \(CCH t ) = 119.29(10)°.