On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data

We propose a method for calculating absolute free energies from Monte Carlo or molecular-dynamics data. The method is based on the identity that expresses the partition function Q as a Boltzmann average: 1Q=w(p,x)exp[betaH(p,x)], where w(p,x) is an arbitrary weight function such that its integral over the phase space is equal to 1. In practice, to minimize statistical errors the weight function is chosen such that the regions of the phase space where sampling statistics are poor are excluded from the average. The "ideal" weight function would be the equilibrium phase-space density exp[-betaH(p,x)]Q itself. We consider two methods for constructing the weight function based on different estimates of the equilibrium phase-space density from simulation data. In the first method, it is chosen to be a Gaussian function, whose parameters are obtained from the covariance matrix of the atomic coordinates. In the second, a clustering algorithm is used to attempt partitioning the data into clusters corresponding to different basins of attraction visited by the system. The weight function is then constructed as a superposition of Gaussians calculated for each cluster separately. We show that these strategies can be used to improve upon previous methods of estimating absolute entropies from covariance matrices.     

Entropic and electrostatic effects on the folding free energy of a surface-attached biomolecule: an experimental and theoretical study

Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged-but otherwise apparently inert-surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxylalkane-coated gold surface. We find that whereas surface attachment is destabilizing at low ionic strength, it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis, we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate.     

A planar chiral non-metallocenic analogue of the most popular N,N-dimethylbenzylaminate palladacycle

A racemic planar chiral tertiary amine pCp-CH₂NMe₂ (HL¹, pCp = [2.2]paracyclophane-4-yl) was prepared by aminomethylation of the bromide pCp-Br with Eschenmoser’s salt. Direct cyclopalladation of this new ligand with palladium(II) acetate results in the formation of the racemic CN-dimer rac-3 in a moderate yield of 64%. The enantiomerically pure dimer (S_pl, S_pl)-3 was obtained by the standard procedure of racemic palladacycle resolution using (S_C)-prolinate as a chiral derivatising agent. The ortho-palladated structure, absolute configuration of the chiral plane and stereochemical peculiarities of the new CN-palladacycle were established by means of NMR spectroscopy and an X-ray diffraction study of its (S_C)-prolinate derivative.     

Explicitly correlated second-order Møller-Plesset perturbation theory employing pseudospectral numerical quadratures

We implemented explicitly correlated second-order M?ller-Plesset perturbation theory with numerical quadratures using pseudospectral construction of grids. Introduction of pseudospectral approach for the calculation of many-electron integrals gives a possibility to use coarse grids without significant loss of precision in correlation energies, while the number of points in the grid is reduced about nine times. The use of complementary auxiliary basis sets as the sets of dealiasing functions is justified at both theoretical and computational levels. Benchmark calculations for a set of 16 molecules have shown the possibility to keep an error of second-order correlation energies within 1 milihartree (mH) with respect to MP2-F12 method with dense grids. Numerical tests for a set of 13 isogyric reactions are also performed.     

Magnetic Field Influence on the Gas Detonation Induced by Spark Discharge

The present paper describes the influence of magnetic field on the spark discharge utilized for initialization of detonation. The method of schlieren time-based scanning shows the increase of shock wave velocity in the case when magnetic field was applied to the area of electrical discharge in the air. The critical energy values are obtained for a direct initialization of detonation in hydrogen–air and hexane–air mixtures. Magnetic field has a significant influence on the deflagration–combustion transition in both mixtures at the critical energy values. Pressure and velocity of the shock front were measured by ICP pressure transducers, flame front was recorded by photo-diodes. Two cases were studied experimentally: external magnetic field is produced by inductance coils connected to capacitor; own magnetic field is induced directly by discharge current in the cables positioned in special way.     

Electrophilically Activated Nitroalkanes in Double Annulation of [1,2,4]Triazolo[4,3-a]quinolines and 1,3,4-Oxadiazole Rings

Nitroalkanes activated with polyphosphoric acid could serve as efficient electrophiles in reactions with amines and hydrazines, enabling various cascade transformations toward heterocyclic systems. This strategy was developed for an innovative synthetic protocol employing simultaneous or sequential annulation of two different heterocyclic cores, affording [1,2,4]triazolo[4,3-a]quinolines with 1,3,4-oxadiazole substituents.     

A 19F NMR Study of the Transmissive Ability of Boron-Containing Bridged Systems with Three- and Four-Coordinated Boron Atoms

Two series of model compounds, Ar₂BOC₆H₄F-4 and Ar₂B(Py)OC₆H₄F-4, containing three-and four-coordinated boron atoms, have been synthesized. It was established by ¹⁹F NMR technique that both systems possess a similar transmissive ability that is in intermolecular coordination with pyridine does not influence the transmissive properties of the boron-oxygen binuclear bridging group. The solvent polarity does not influence the electron transmission in the boron complexes studied.     

Correction to: Accelerating Reactive Transport Modeling: On-Demand Machine Learning Algorithm for Chemical Equilibrium Calculations

Transport in Porous Media - In the original publication of the article, Table 2 was published incorrectly.     

Synthesis of 2-(polyfluoromethyl)pyrimido-[1,2-a]benzimidazole-4-carbaldehyde derivatives

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