Atomic partitioning of the dissociation energy of the P-O(H) bond in hydrogen phosphate anion (HPO4(2-)): disentangling the effect of Mg2+

This paper has three goals: (1) to provide a first step in understanding the atomic basis of the role of magnesium in facilitating the dissociation of the P-O bond in phosphorylated biochemical fuel molecules (such as ATP or GTP), (2) to compare second-order M?ller-Plesset perturbation theory (MP2) results with those obtained at the more economical density functional theory (DFT) level for a future study of larger more realistic models of ATP/GTP, and (3) to examine the calculation of atomic total energies from atomic kinetic energies within a Kohn-Sham implemention of DFT, as compared to ab initio methods. A newly described method based on the quantum theory of atoms in molecules (QTAIM), which is termed the "atomic partitioning of the bond dissociation energy" (APBDE), is applied to a simple model of phosphorylated biological molecules (HPO42-). The APBDE approach is applied in the presence and in the absence of magnesium. It is found that the P-O(H) bond in the magnesium complex is shorter, exhibits a higher stretching frequency, and has a higher electron density at the bond critical point than in the magnesium-free hydrogen phosphate anion. Though these data would seem to suggest a stronger P-O(H) bond in the magnesium complex compared to the magnesium-free case, the homolytic breaking of the P-O(H) bond in the complex is found to be easier, i.e., has a lower BDE. This effect is the result of the balance of several atomic contributions to the BDE induced by the magnesium cation, which stabilizes the dissociation product more than it stabilizes the intact model molecule.     

Structure,magnetic and magnetoresistance properties of Pr0.67Sr0.33MnO3 manganite oxide prepared by ball milling method

A sample of Pr_0.67Sr_0.33MnO₃ nanoparticles was synthesized by the ball milling method. X-ray diffraction pattern of the sample showed orthorhombic system with Pnma space group. The average crystallite size of 110 nm was obtained by both Scanning Electron Microscopy and X-ray diffraction. Magnetic measurements showed para-to-ferromagnetic transition with a Curie temperature of T_C=269 K. Electrical investigations showed that all our samples exhibit a semi-conducting behavior above T_C and a metallic-like one at lower temperatures. The sample exhibited a large magnetoresistance of 30% at room temperature in an applied magnetic field of 2 T. The transport and the magnetic properties were interpreted in terms of the existence of magnetic polarons in the sample.     

Static and dynamic study of magnetic properties in FeNi film on flexible substrate, effect of applied stresses

The influence of an external electric field on the binding energies of the ground state and excited states with the third-harmonic-generation (THG) coefficient for spherical quantum dot (QD) with parabolic confinement is investigated theoretically. The energy levels and wave functions of electronic states in the QDs are calculated using by variational method within the effective-mass approximation. The numerical results demonstrate that the THG coefficient very sensitively depends on the magnitude of the electric field and the radius of the QDs. In addition, the THG coefficient also depends on the relaxation rate of the spherical QD with parabolic confinement and the position of impurity.     

On the connections between the quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT): a letter from Richard F. W. Bader to Lou Massa

A 31-year-old letter from Professor Richard F. W. Bader to Professor Lou Massa outlining the connections between the quantum theory of atoms in molecules (QTAIM) and density functional theory (DFT) especially with regard to the first Hohenberg-Kohn theorem is brought to light. This connection has not often been the topic of such a focused review by Bader and is presented here for the first time. The scientific importance of this letter is, in the opinion of the presenter, as timely today as it was back then in 1986. In Bader’s own opening words: “... that if I sent you a summary of what I think are the important connections between our work and density functional theory, ...”. He then takes us in a grand tour of the foundations of QTAIM culminating into the antecedents of a paper he later published with Professor Pierre Becker, whereby the Hohenberg-Kohn theorem is shown to operate at the level of an atom-in-a-molecule. Bader closes his letter by suggesting to Massa: “Study these two charge distributions – they are proof of the theorem of Hohenberg and Kohn”. By that Bader meant that when the charge distributions of two atoms or groups are identical within a given precision, then the kinetic and total energy contributions of these atoms to the corresponding molecular quantities are also identical. It is revealing to follow the intellectual threads weaved by Bader which provides us with a glimpse of his thought processes and intuition that guided him to some of his key discoveries. The lucidity, rigor, and clarity characteristic of Bader and the informality of style of a letter makes it of pedagogic and historic interest.

     

The Kernel energy method: Application to graphene and extended aromatics

The quantum chemistry of finite aperiodic graphene flakes is a matter of considerable interest because of the anticipated technological importance of such objects. Since real aperiodic graphene flakes will in general be composed of many thousands of carbon atoms, theoretical methods appropriate to such large molecules would need to be used for the ab initio quantum calculation of their properties. The Kernel energy method is discussed here, and it is shown to be accurately applicable to graphenes and analogous extended aromatic molecules. It is necessary to define the kernels of a graphene molecule in a new way because of the extensive aromaticity, which defines its electronic structure. The kernels used in the reconstruction of the full graphene sheet preserve the total number of π‐electrons, Clar sextets, and the approximate overall aromaticity. Sivaramakrishnan et al. [J Phys Chem A, 2005, 109, 1621] define similar “ring conserved isodesmic reactions (RCIR).” The principal innovation of this article is the suggestion that kernels may be mathematically extracted from an extended aromatic molecule such as graphene by a fissioning of aromatic bonds. Hartree Fock (HF) and Møller‐Plesset (MP2) chemical models using a Gaussian basis of 3‐21G orbitals are used to calculate the total energy of a graphene flake. This demonstration calculation is performed on a graphene flake in which dangling bonds are saturated with hydrogens (C₇₈H₂₆) composed of a total of 104 atoms arranged in 27 benzenoid rings. The KEM with both types of chemical model are shown to be accurate to nearly 1 kcal/mol, of a total energy, which is nearly 3000 atomic units, that is, with an absolute error within “chemical accuracy” and a relative error of the order of 5 × 10⁵% of the total energy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Effects of external electric fields on double proton transfer kinetics in the formic acid dimer

Molecules can be exposed to strong local electric fields of the order of 10(8)-10(10) V m(-1) in the biological milieu. The effects of such fields on the rate constant (k) of a model reaction, the double-proton transfer reaction in the formic acid dimer (FAD), are investigated. The barrier heights and shapes are calculated in the absence and presence of several static homogenous external fields ranging from 5.14 × 10(8) to 5.14 × 10(9) V m(-1) using density functional theory (DFT/B3LYP) and second order M?ller-Plesset perturbation theory (MP2) in conjunction with the 6-311++G(d,p) Pople basis set. Conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants at 25 °C. It is found that electric fields parallel to the long axis of the dimer (the line joining the two carbon atoms) lower the uncorrected barrier height, and hence increase the raw k. These fields also flatten the potential energy surface near the transition state region and, hence, decrease the multiplicative tunneling correction factor. The net result of these two opposing effects is that fields increase k(corrected) by a factor of ca. 3-4 (DFT-MP2, respectively) compared to the field-free k. Field strengths of ～3 × 10(9) V m(-1) are found to be sufficient to double the tunneling-corrected double proton transfer rate constant at 25 °C. Field strengths of similar orders of magnitudes are encountered in the scanning tunneling microscope (STM), in the microenvironment of a DNA base-pair, in an enzyme active site, and in intense laser radiation fields. It is shown that the net (tunneling corrected) effect of the field on k can be closely fitted to an exponential relationship of the form k = aexp(bE), where a and b are constants and E the electric field strength.     

Molecular model with quantum mechanical bonding information

The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.