Nanostructuration of CoSi by mechanical milling and mechanical alloying

CoSi is an inexpensive thermoelectric material for medium temperature (200–500 °C). Its power factor is as large as the state of the art materials; however, its thermal conductivity is too large. Then, improving its thermoelectric performances implies increasing the scattering of phonons, which can be performed by nanostructuring the material. In this paper we investigate the effect of nanostructuration on the structure, microstructure, lattice dynamics and stability of CoSi. We obtained powders of about 13 nm by mechanical milling bulk CoSi for only four hours or by mechanical alloying pure elements for twelve hours. Nanostructuration induces a 0.1% expansion of the lattice parameter. Raman spectroscopy, associated to ab initio calculations, highlights the effectiveness of nanostructuration on phonon scattering, showing a reduction of the phonon relaxation time by as much as 80%. Powders are stable up to 450 °C; then grains coarsen and a partial degradation of the material occurs, probably due to silicon sublimation. Our results indicate that nanostructuration should be considered when interested to reduce CoSi thermal conductivity.     

Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis

We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.     

Dynamic mechanical analysis

Using dynamic mechanical analysis (DMA) we have studied thermal degradation for a system containing a diglycidyl ether of bisphenol A (DGEBA) and 1,3-bisaminomethylcylohexane (1,3-BAC). The changes of dynamic mechanical properties during thermal degradation indicated a shift of the glass transition temperature (T _g) to higher temperatures and a decrease in the peak value of the dynamic loss factor (tan δ) with an increasing of aging time. The value of dynamic storage modulus (E′) at the rubbery state showed an increase with aging time, whiteE′ at the glassy state only underwent a moderate change with increased thermal degradation. From these results it can be argued that thermal degradation during the stage prior to the onset of the severe degradation involves structural changes in the epoxy system, as further crosslinking and loss of dangling chains in the crosslinked network.     

Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method

 Hybrid potentials have become a common tool in the study of many condensed-phase processes and are the subject of much active research. An important aspect of the formulation of a hybrid potential concerns how to handle covalent bonds between atoms that are described with different potentials and, most notably, those at the interface of the quantum mechanical (QM) and molecular mechanical (MM) regions. Several methods have been proposed to deal with this problem, ranging from the simple link-atom method to more sophisticated hybrid-orbital techniques. Although it has been heavily criticized, the link-atom method has probably been the most widely used in applications, especially with hybrid potentials that use semiempirical QM methods. Our aim in this paper has been to evaluate the link-atom method for ab initio QM/MM hybrid potentials and to compare the results it gives with those of previously published studies. Given its simplicity and robustness, we find that the link-atom method can produce results of comparable accuracy to other methods as long as the charge distribution on the MM atoms at the interface is treated appropriately. Received: 27 September 2002 / Accepted: 21 October 2002 / Published online: 8 January 2003 Correspondence to: M. J. Field e-mail: mjfield@ibs.fr Acknowledgements. The authors thank the Institut de Biologie Structurale – Jean-Pierre Ebel, the Commissariat à l'Energie Atomique and the Centre National de la Recherche Scientifique for support of this work.     

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.     

Study of the mechanical damping behavior of SBR-modified cement pastes by dynamic mechanical analyzer

Improvement in mechanical damping of SBR-modified cement pastes had been evaluated by dynamic mechanical analyzer. Specimens were fabricated and tested under 3-point flexure clamp at frequencies of 0.5–50 Hz or temperatures of ?30 to 70 °C. Significant improvement in damping was observed in cementitious-SBR composite specimens when SBR latex to cement ratio was 0.12, which is hypothesized to occur due to improvements in viscosity of cement paste. Furthermore, the SBR-modified cement pastes showed a decreased damping variation tendency with an increase of frequency. They also showed a peak damping variation tendency under the effect of the glass transition temperature. Based on the three element model, mechanical parameters are calculated by fitting the dynamic modulus of SBR-modified cement pastes.     

Multiaxial mechanical testing of plastics

This paper outlines the many problems associated with the testing of plastics and suggests a method of minimising these problems by the use of multiaxial testing techniques. It extends the multiaxial approach into the determination of the fatigue loading characteristics of a plastic. General design criteria of such machines, as well as details of a family of machines that have been developed for that purpose, are given.     

The mechanical degradation of polystyrene

The catastrophic failure of a polymeric material is preceded by a number of complex, partially understood events occurring on the molecular level. These events range from the flow of ordered regions to the cleavage of primary bonds in the chain. In recent years, stress-induced bond cleavage in polymers has received increased attention, many authors nothing the presence of free radicals and/or volatile products released upon fracture; a free-radical decomposition mechanism involving up to 10³ molecules per chain rupture also has been postulated. A special tensile stress–strain and shear apparatus was developed and located inside the ion-source housing of a time-of-flight mass spectrometer to characterize the volatile products released during mechanical degradation of polystyrene. Volatile compounds evolved during stress and fracture of polystyrene were monitored either continuously or by z-axis modulated oscilloscopic display. The polystyrene was purified by two methods: vacuum outgassing and fractional reprecipitation. Large amounts of styrene evolved from both the as-received and outgassed samples; however, essentially none was observed from the reprecipitated samples. Previous reports on monomer evolution during mechanical stress of polystyrene may be the result of residual monomer and not mechanical degradation products. The product of the surface density of primary radicals and the chain length for unzipping is less than 3 × 10¹⁰ radicals/mm² indicating a maximum radical concentration of approximately 10¹⁰ radicals/mm².     

Swelling of mechanical pulp fines

The objective of the study was to determine the swelling of different types of mechanical pulp fines. The physical and chemical characteristics of the fines were also examined. It was found that the degree of swelling correlates with the proportion of fibrillar material, that is fibrillar content of the fines. The fines with the lowest fibrillar content had a swelling comparable to mechanical pulp fibres (0.69g/g), whereas the fines with a high fibrillar content had a swelling comparable to neverdried kraft pulp fibres (1.41g/g). Hemicellulose content and charge could not explain the differences in swelling of different types of the mechanical pulp fines. While the lignin content appears to be an important factor in the degree of swelling of mechanical pulp fines, the results suggest that structural differences between the particles are also important. The bulk elastic modulus was determined by measuring the change in swelling for a known change in osmotic pressure. All the mechanical pulp fines had a high bulk elastic modulus compared to kraft fines. However, fibrillar fines had a lower bulk elastic modulus than flakelike fines. Mechanical pulp fines, both fibrillar and flakelike varieties, did not hornify appreciably. The swelling of both the fines and the fibre fractions increased slightly with the specific energy consumption in the refining.     

Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

We present a series of capping-potentials designed as link atoms to saturate dangling bonds at the quantum/classical interface within density functional theory-based hybrid QM/MM calculations. We aim at imitating the properties of different carbon-carbon bonds by means of monovalent analytic pseudopotentials. These effective potentials are optimized such that the perturbations of the quantum electronic density are minimized. This optimization is based on a stochastic scheme, which helps to avoid local minima trapping. For a series of common biomolecular groups, we find capping-potentials that outperform the more common hydrogen-capping in view of structural and spectroscopic properties. To demonstrate the transferability to complex systems, we also benchmark our potentials with a hydrogen-bonded dimer, yielding systematic improvements in structural and spectroscopic parameters.     

Quantum mechanical/molecular mechanical study on the mechanism of the enzymatic Baeyer-Villiger reaction

We report a combined quantum mechanical/molecular mechanical (QM/MM) study on the mechanism of the enzymatic Baeyer-Villiger reaction catalyzed by cyclohexanone monooxygenase (CHMO). In QM/MM geometry optimizations and reaction path calculations, density functional theory (B3LYP/TZVP) is used to describe the QM region consisting of the substrate (cyclohexanone), the isoalloxazine ring of C4a-peroxyflavin, the side chain of Arg-329, and the nicotinamide ring and the adjacent ribose of NADP(+), while the remainder of the enzyme is represented by the CHARMM force field. QM/MM molecular dynamics simulations and free energy calculations at the semiempirical OM3/CHARMM level employ the same QM/MM partitioning. According to the QM/MM calculations, the enzyme-reactant complex contains an anionic deprotonated C4a-peroxyflavin that is stabilized by strong hydrogen bonds with the Arg-329 residue and the NADP(+) cofactor. The CHMO-catalyzed reaction proceeds via a Criegee intermediate having pronounced anionic character. The initial addition reaction has to overcome an energy barrier of about 9 kcal/mol. The formed Criegee intermediate occupies a shallow minimum on the QM/MM potential energy surface and can undergo fragmentation to the lactone product by surmounting a second energy barrier of about 7 kcal/mol. The transition state for the latter migration step is the highest point on the QM/MM energy profile. Gas-phase reoptimizations of the QM region lead to higher barriers and confirm the crucial role of the Arg-329 residue and the NADP(+) cofactor for the catalytic efficiency of CHMO. QM/MM calculations for the CHMO-catalyzed oxidation of 4-methylcyclohexanone reproduce and rationalize the experimentally observed (S)-enantioselectivity for this substrate, which is governed by the conformational preferences of the corresponding Criegee intermediate and the subsequent transition state for the migration step.     

The catalytic activity of proline racemase: a quantum mechanical/molecular mechanical study

The enzyme proline racemase from the eukaryotic parasite Trypanosoma cruzi (responsible for endemic Chagas disease) catalyzes the reversible stereoinversion of chiral Calpha in proline. We employed a new combined quantum mechanical and molecular mechanical (QM/MM) potential to study the reaction mechanism of the enzyme. Three critical points were found: two almost isoenergetic minima (M1a and M2a), in which the enzyme is bound to L- and D-Pro, respectively, and a transition state (TSCa), unveiling a highly asynchronous concerted process. A systematic analysis was performed on the optimized geometries to point out the key role played by some residues in stabilizing the transition state.     

Prediction of the mechanisms of enzyme-catalysed reactions using hybrid quantum mechanical/molecular mechanical methods

The use of hybrid methods, involving both quantum mechanics and molecular mechanics, to model the mechanism of enzyme-catalysed reactions, is discussed. Two alternative approaches to treating the electrostatic interactions between the quantum mechanical and molecular mechanical regions are studied, involving either the inclusion of this term in the electronic Hamiltonian (QM/MM), or evaluating it purely classically (MO + MM). In the latter scheme, possible problems of using force fields that are standard for macromolecular modelling are identified. The use of QM/MM schemes to investigate the mechanism of the enzymes thymidine phosphorylase (ThdPase) and protein tyrosine phosphatase (PTP) is described. For both systems, transition states have been identified using a PM3 Hamiltonian. For ThdPase, concerted motion of the enzyme during the course of the reaction is suggested and, for PTP, a two-step dephosphorylation reaction is indicated, both with quite low barriers.     

Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent

Quantum mechanical/molecular mechanical (QM/MM) free energy calculation presents a significant challenge due to an excessive number of QM calculations. A useful approach for reducing the computational cost is that based on the mean field approximation to the QM subsystem. Here, we describe such a mean-field QM/MM theory for electronically polarizable systems by starting from the Hartree product ansatz for the total system and invoking a variational principle of free energy. The MM part is then recast to a classical polarizable model by introducing the charge response kernel. Numerical test shows that the potential of mean force (PMF) thus obtained agrees quantitatively with that obtained from a direct QM/MM calculation, indicating the utility of self-consistent mean-field approximation. Next, we apply the obtained method to prototypical reactions in several qualitatively different solvents and make a systematic comparison of polarization effects. The results show that in aqueous solution the PMF does not depend very much on the water models employed, while in nonaqueous solutions the PMF is significantly affected by explicit polarization. For example, the free energy barrier for a phosphoryl dissociation reaction in acetone and cyclohexane is found to increase by more than 10 kcal/mol when switching the solvent model from an empirical to explicitly polarizable one. The reason for this is discussed based on the parametrization of empirical nonpolarizable models.     

Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods

The pseudobond approach offers a smooth connection at the quantum mechanical/molecular mechanical interface which passes through covalent bonds. It replaces the boundary atom of the environment part with a seven-valence-electron atom to form a pseudobond with the boundary atom of the active part [Y. Zhang, T. S. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999)]. In its original formulation, the seven-valence-electron boundary atom has the basis set of fluorine and a parametrized effective core potential. Up to now, only the Cps(sp3)-C(sp3) pseudobond has been successfully developed; thus in the case of proteins, it can only be used to cut the protein side chains. Here we employ a different formulation to construct this seven-valence-electron boundary atom, which has its own basis set as well as the effective core potential. We have not only further improved Cps(sp3)-C(sp3) pseudobond, but also developed Cps(sp3)-C(sp2,carbonyl) and Cps(sp3)-N(sp3) pseudobonds for the cutting of protein backbones and nucleic acid bases. The basis set and effective core potential for the seven-valence-electron boundary atom are independent of the molecular mechanical force field. Although the parametrization is performed with density functional calculations using hybrid B3LYP exchange-correlation functional, it is found that the same set of parameters is also applicable to Hartree-Fock and MP2 methods, as well as DFT calculations with other exchange-correlation functionals. Tests on a series of molecules yield very good structural, electronic, and energetic results in comparison with the corresponding full ab initio quantum mechanical calculations.     

Accelerating quantum mechanical/molecular mechanical sampling using pure molecular mechanical potential as an importance function: the case of effective fragment potential

Acceleration of sampling from a quantum mechanical/effective fragment mechanical (QM/EFP) potential is explored with effective fragment potential (EFP) as an importance function. EFP, generated on the fly, is found to be an excellent choice for an importance function for a QM/EFP potential. This technique is used to find nine stationary points of a blocked amino acid with twelve waters in a semi-automated way.     

Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion–repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 38–50, 1998     

Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution

The procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential⁷ was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.