Hamiltonian replica exchange molecular dynamics using soft-core interactions

To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25 ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1 ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8 ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].     

Vanadium(V) tartrato complexes: speciation in the H3O+(OH-)/H2VO4-/(2R,3R)-tartrate system and X-ray crystal structures of Na4[V4O8(rac-tart)2].12H2O and (NEt4)4[V4O8((R,R)-tart)2].6H2O (tart = C4H2O6(4-))

A study of the aqueous H3O+(OH-)/H2VO4-/(2R,3R)-tartrate system has been performed at 273 K in a 1.0 mol/L Na+(Cl-) ionic medium using 51V NMR spectroscopy. In this relatively complicated system, more than 12 different species were observed. Ligand concentration, vanadate concentration, and pH variation studies were carried out, particularly for the range of pH 5.8-8.0 and for pH 2.4. Chemical shifts, vanadium-ligand stoichiometry, and also composition and formation constants for some, but not all, species are given. Despite some reduction of vanadium(V) to vanadium(IV) in an acidic medium at pH approximately 2.4, the stoichiometries of the principal species in solution at this pH were determined. Electrospray ionization mass spectra for some solutions were obtained and were in accordance with the conclusions drawn from the speciation studies. A series of crystalline vanadium(V) tartrato complexes M4[V4O8(tart)2].aq were also prepared and characterized. X-ray diffraction studies of Na4[V4O8(rac-tart)2].12H2O (1) and (NEt4)4[V4O8((R,R)-tart)2].6H2O (2) revealed unique tetranuclear [V4O8(tart)2]4- ions for which the {V4O4} rings have boat conformations.     

Large configuration interaction calculations of nuclear spin-spin coupling constants: III. Vibrational effects in ammonia

Large configuration interaction calculations of the proton—proton coupling constant for several geometrical configurations of the ammonia molecules are reported. The analytical expressions for the energy surface and the coupling constant as functions of two cartesian displacement coordinates are fitted to the calculated values. The potential is used for the calculation of the vibrational wavefunctions for ¹⁵NH₃ and ¹⁵ND₃ species and the vibrational averaging of the coupling constant is carried out using these functions. Though the value of the coupling constants shows a very strong geometry dependence, the vibrational corrections are found to be small. A possible correlation of the proton—proton coupling constant with an angular parameter in the NH₂ group in RNH₂ compounds is indicated.     

Secondary ion mass spectrometry and alpha-spectrometry of electrodeposited thorium films

The main aim of this work was the preparation of samples with thorium content on the steel discs by electrodeposition for determination of natural thorium isotope by alpha spectrometry and secondary ion mass spectrometry and finding out their possible linear correlation between these methods. The analysis of the composition of surface was other aim of study. Discs were measured by alpha spectrometer. After that, alpha spectrometry discs were analyzed by TOF-SIMS IV, which is installed in the International Laser Centre in Bratislava. The integral and normalized intensities of isotope of ²³²Th and intensities of ions of ThO⁺, ThOH⁺, ThO₂H⁺, Th₂O₄H⁺, ThO₂ ^?, ThO₃H^?, ThH₃O₃ ^? a ThN₂O₅H^? were measured. The linear correlation is between surface’s weights of Th and intensities of ions of Th⁺ from identified in SIMS spectra. We found out the chemical binding between thorium and oxygen and hydrogen on the surface of samples by SIMS method. Obtained intensities of ions ²³²ThO⁺, ²³²ThOH⁺, ²³²ThO₂H⁺ prove the presence of oxidized forms of thorium in the upper layers of surface. The oxidized ions predominate in univalent form of thorium up to deep about 3,000 nm.     

Synthesis and study of new rod-like mesogens containing 2-aminothiophene unit

We present a synthesis and mesomorphic properties of a new series of rod-like mesogens. All the compounds possess a substituted 2-aminothiophene unit as a main element in the structure attached to a stilbene moiety with a terminal alkyloxy chain (OR¹, OR² where R¹=C_nH_2n+1, R²=C_mH_2m+1; n, m ranging from 6 to 12). The synthesis of alkyloxybiphenyl substituted 2-aminothiophenes was carried out by the Gewald reaction and the appropriate reaction conditions were investigated. The liquid–crystalline properties were studied via polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction. These materials exhibit nematic and/or smectic A phases. The influence of structural changes (variation in alkyloxy chain length and symmetry of the molecule) on mesogenic behaviour is discussed. Evaluation of UV–vis, fluorescent and electrochemical properties are also included.     

Serum estradiol measurement by solid-phase chemiluminescence immunoassay and direct radioimmunoassay

Estradiol017β is determined in serum extracts by solid-phase chemiluminescence immunoassay. The results are compared with those obtained from unextracted serum in routine conditions with a commercial radioimmunoassay (r.i.a.) kit. For the chemiluminescence procedure, a purified monoclonal antibody to estradiol-6-carboxymethyloxime/bovine serum albumin and the homologous chemiluminescent marker conjugate estradiol-6-carboxymethyloxime aminobutylethylisoluminol are used. Bound and free ligand are separated by washing and simple centrifugation. Results obtained by the chemiluminescence assay (y) and by r.i.a. (x) on 170 serum specimens from women during ovulation induction showed good correlation (y = 1.01x ? 16 with r = 0.95). The methods are similar in selectivity, detection limit (ca. 10 ng l^?1) and precision (interassay relative standard deviation, 8–13%).     

CCSD(T) expectation value calculations of first-order properties

An expectation value approach to calculations of first-order properties using the non-iterative, triple-excitation amplitudes in the coupled cluster wave function is exploited. Three methods are suggested and analysed using the many body perturbation theory (MBPT) expansion arguments. The first method, in which non-iterative triple-excitation amplitudes are used in the expression for the expectation values, makes the wave function accurate through the second order of MBPT. In the second method, which is an extension of the first, effects of triple-excitation amplitudes are coupled with single- and double-excitation amplitudes. The correlated density matrix equivalent through the fourth order to that obtained when CCSDT-la amplitudes are used is employed in the third method. The suggested methods are tested on dipole moment and polarizability calculations for several diatomic closed-shell molecules and are compared to other related approaches. Received: 15 May 1997 / Accepted: 5 June 1997     

Pore Development during the Carbonization Process of Lignin Microparticles Investigated by Small Angle X-ray Scattering

Application of low-cost carbon black from lignin highly depends on the materials properties, which might by determined by raw material and processing conditions. Four different technical lignins were subjected to thermostabilization followed by stepwise heat treatment up to a temperature of 2000 °C in order to obtain micro-sized carbon particles. The development of the pore structure, graphitization and inner surfaces were investigated by X-ray scattering complemented by scanning electron microscopy and FTIR spectroscopy. Lignosulfonate-based carbons exhibit a complex pore structure with nanopores and mesopores that evolve by heat treatment. Organosolv, kraft and soda lignin-based samples exhibit distinct pores growing steadily with heat treatment temperature. All carbons exhibit increasing pore size of about 0.5–2 nm and increasing inner surface, with a strong increase between 1200 °C and 1600 °C. The chemistry and bonding nature shifts from basic organic material towards pure graphite. The crystallite size was found to increase with the increasing degree of graphitization. Heat treatment of just 1600 °C might be sufficient for many applications, allowing to reduce production energy while maintaining materials properties.     

Investigation of the Chemo- and Stereoselectivity of the Ketene-Claisen Rearrangement

A novel type of ketene-Claisen rearrangement in which the precursor of the rearrangement is generated in situ by reaction of optically active allyl thioethers with dichloroketene is described. A characteristic feature of this rearrangement is the excellent chemoselectivity in favor of allyl thioethers vs. allyl ethers, i.e., exclusive chirality transfer of the allylic sulfur moiety is observed with 12, 13 , and 25--27 . The cyclic, optically active allyl thioethers (+)-(R)- 4 and (?)-(S)- 4 and the open-chain allyl thioethers 11--13 rearrange with in situ generated dichloroketene to the optically active thioesters (?)-(S)- 28 , (+)-(R)- 28 , and 31-33 , respectively. A chirality-transfer of > 99% in the cyclic cases (+)-(R)- 4 and (?)-(S)- 4 , and 96--98 % in the open-chain cases 11--13 is observed. Furthermore, the dichloroketene-Claisen rearrangement is characterized by a high asymmetric 1,2-induction. The chiral allylic sulfides 25--27 give the optically active thioesters 36--38 with a 1,2-induction > 99% as determined by NMR-shift experiments.     

Microstructural model for prediction of stress–strain curves of amorphous and semicrystalline elastomers

A fundamental microstructural model was developed to calculate the stress–strain curves of rubbery amorphous polymers and of semicrystalline polymers with a rubbery amorphous phase by numerical simulations. The rubbery amorphous phase was treated by using a version of the theory of rubber elasticity with finite extensibility. Physical entanglements and chemical crosslinks were both allowed. Slippage was implemented by a Monte Carlo algorithm controlled by kinetic parameters such as the activation energy and activation volume for slippage. The crystalline phase was treated in a very idealized manner, including a crude representation of tie chains but not taking the internal structure of the crystallites into account. A two-dimensional embodiment of the model was implemented into software. For amorphous polymers, while lacking truly quantitative accuracy, the model showed sufficiently good agreement with the experimental trends to be used as a qualitative or semiquantitative predictive tool, and it is currently being used in this manner. The more complex semicrystalline version was less accurate and will need to be improved in future work. Most of the limitations of the semicrystalline version could be ascribed unambiguously to specific simplifications made in the software implementation to reduce the amount of computer time required for the calculations. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2715–2739, 1997