Quantum-mechanical coherence in cell microtubules: a realistic possibility?

We discuss the possibility of quantum-mechanical coherence in Cell MicroTubules (MT), based on recent developments in quantum physics. We focus on potential mechanisms for 'energy-loss-free' transport along the microtubules, which could be considered as realizations of Frohlich's ideas on the role of solitons for superconductivity and/or biological matter. In particular, by representing the MT arrangements as cavities, we review a novel scenario, suggested in collaboration with D.V. Nanopoulos, concerning the formation of macroscopic (or mesoscopic) quantum-coherent states, as a result of the (quantum-electromagnetic) interactions of the MT dimers with the surrounding molecules of the ordered water in the interior of the MT cylinders. We suggest specific experiments to test the above-conjectured quantum nature of the microtubular arrangements inside the cell. These experiments are similar in nature to those in atomic physics, used in the detection of the Rabi-Vacuum coupling between coherent cavity modes and atoms. Our conjecture is that a similar Rabi-Vacuum-splitting phenomenon occurs in the absorption (or emission) spectra of the MT dimers, which would constitute a manifestation of the dimer coupling with the coherent modes in the ordered-water environment (dipole quanta), which emerge due to the phenomenon of 'super-radiance'.     

Hydrogen–hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods

The nature of H‐H interaction between ortho‐hydrogen atoms in planar biphenyl is investigated by two different atomic energy partitioning methods, namely fractional occupation iterative Hirshfeld (FOHI) and interacting quantum atoms (IQA), and compared with the traditional virial‐based approach of quantum theory of atoms in molecules (QTAIM). In agreement with Bader's hypothesis of H? H bonding, partitioning the atomic energy into intra‐atomic and interatomic terms reveals that there is a net attractive interaction between the ortho‐hydrogens in the planar biphenyl. This falsifies the classical view of steric repulsion between the hydrogens. In addition, in contrast to the traditional QTAIM energy analysis, both FOHI and IQA show that the total atomic energy of the ortho‐hydrogens remains almost constant when they participate in the H‐H interaction. Although, the interatomic part of atomic energy of the hydrogens plays a stabilizing role during the formation of the H? H bond, it is almost compensated by the destabilizing effects of the intra‐atomic parts and consequently, the total energy of the hydrogens remains constant. The trends in the changes of intra‐atomic and interatomic energy terms of ortho‐hydrogens during H? H bond formation are very similar to those observed for the H₂ molecule. © 2014 Wiley Periodicals, Inc.     

Self-Consistent-Field potential-energy surfaces for hydrogen atom pairs within small palladium clusters

An ab initio electronic structure study is presented of hydrogen–hydrogen interactions in an electronic environment perturbed by the presence of palladium atom clusters. In particular, we investigated changes in the interatomic potential when the atomic centers are trapped inside an fcc palladium octahedral hole and when they are separated from each other by a (111) plane of palladium atoms. The (111) plane was modeled with a cluster of three palladium atoms. Self-consistent field (SCF ) level calculations were performed, and palladium atom pseudopotentials were employed to make the systems studied computationally tractable. For pairs of atoms placed within the octahedral hole, various lines of approach were considered [along the (100), (110), and (111) directions]. Lattice deformations and electronic excitations were examined for their effect on the interatomic potential.     

The ellipsoidal Gaussian basis in molecular orbital theory

The ellipsoidal Gaussian basis function used in a minimal valence atomic orbital representation is compared with the double-zeta spherical Gaussian basis orbital representation for some seventeen molecules made up of first row atoms and hydrogen. Except for acetylene the double-zeta basis gives consistently better total electronic energies and generally better property values than the optimized ellipsoidal single zeta basis. Difference molecular density contour maps comparing the two basis sets, as well as other one-electron property values, indicate that the ellipsoidal basis exaggerates the transfer of charge from the atomic regions to the interatomic and lone pair regions of molecules. Apparently, the forced complete elliptization of the valence atomic orbital in the single-zeta representation does not allow the basis set sufficient flexibility to simultaneously represent both the basically spherical atomic part of these orbitals and the non-spherical molecular bond formation. Other properties and aspects of the ellipsoidal Gaussian basis are also discussed.     

Phenomenological Theory of Cluster Orbitals and Electronic Structures of Molecules

A method for calculation of the energy structures of molecules is developed. The method is based on construction of a matrix of interactions between the atoms in the molecules with allowance made for their symmetric arrangement in space. Matrices are parametrized by comparison of the matrix eigenvalues with the experimental values for reference molecules (methane, benzene, ammonia, water, etc.). Interaction matrices are given for molecules with different types of bonding. Eigenvalues of the molecular energy, eigenfunctions of all molecular orbitals, bond angles, atomic orbital charges, etc. are determined. The dependence of the energy levels of MH₂ molecules (M = O, S, Se, and Te) on the interatomic interaction parameter is given. The dependences of the molecular parameters on the nature of atom M are analyzed.     

Anisotropy in the interaction of ultracold dysprosium

The nature of the interaction between ultracold atoms with a large orbital and spin angular momentum has attracted considerable attention. It was suggested that such interactions can lead to the realization of exotic states of highly correlated matter. Here, we report on a theoretical study of the competing anisotropic dispersion, magnetic dipole-dipole, and electric quadrupole-quadrupole forces between two dysprosium atoms. Each dysprosium atom has an orbital angular momentum of L = 6 and a magnetic moment of μ = 10 μ(B). We show that the dispersion coefficients of the ground state adiabatic potentials lie between 1865 a.u. and 1890 a.u., creating a non-negligible anisotropy with a spread of 25 a.u. and that the electric quadrupole-quadrupole interaction is weak compared to the other interactions. We also find that for interatomic separations R < 50a(0) both the anisotropic dispersion and magnetic dipole-dipole potential are larger than the atomic Zeeman splittings for external magnetic fields of order 10 G to 100 G. At these separations the atomic angular momentum can be reoriented. We finish by describing two scattering models for these inelastic m-changing collisions. A universal scattering theory is used to model loss due to the anisotropy in the dispersion and a Born approximation is used to model losses from the magnetic dipole-dipole interaction for the (164)Dy isotope. These models find loss rates that are of the same order of magnitude as the experimental value.     

Interatomic magnetizability: a QTAIM-based approach toward deciphering magnetic aromaticity

Interatomic magnetizability provides insight into the extent of electronic current density between two adjacent atomic basins. By studying a number of well-known aromatic, nonaromatic, and antiaromatic molecules, it is demonstrated that interatomic magnetizability (bond magnetizability) not only is able to verify the exact nature of aromaticity/antiaromaticity among different molecules, but also can distinguish the correct aromaticity order among sets of aromatic/antiaromatic molecules. The interatomic magnetizability is a direct measure of the current flux between two adjacent atomic basins and is the first QTAIM-derived index that evaluates aromaticity based on a response property, that is, magnetizability. Bond magnetizability is easy to compute, straightforward to interpret, and can be employed to evaluate the pure π- or σ-orbital contributions to magnetic aromaticity.     

Polarisable multipolar electrostatics from the machine learning method Kriging: an application to alanine

We present a polarisable multipolar interatomic electrostatic potential energy function for force fields and describe its application to the pilot molecule MeNH-Ala-COMe (AlaD). The total electrostatic energy associated with 1, 4 and higher interactions is partitioned into atomic contributions by application of quantum chemical topology (QCT). The exact atom–atom interaction is expressed in terms of atomic multipole moments. The machine learning method Kriging is used to model the dependence of these multipole moments on the conformation of the entire molecule. The resulting models are able to predict the QCT-partitioned multipole moments for arbitrary chemically relevant molecular geometries. The interaction energies between atoms are predicted for these geometries and compared to their true values. The computational expense of the procedure is compared to that of the point charge formalism.     

Evolution of the properties of Al(n)N(n) clusters with size

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.     

Electron localization and delocalization in open-shell molecules

Localization and delocalization indices derived in the framework of the quantum Atoms in Molecules theory have recently been used to analyze the electron-pair structure of closed-shell molecules. Here we report calculations of localization and delocalization indices for open-shell molecules at the Hartree-Fock (HF) level. Several simple doublet and triplet radical molecules are studied. In general, interatomic delocalization between bonded atoms is heavily dependent on the order and polarity of the bond. Unpaired electrons also have a significant effect on the interatomic delocalization indices. Indeed, for many radicals, the analysis of the spin components reveals that the interatomic delocalization is very different for alpha and beta spin electrons in many cases. In general, at the HF level, the results can be rationalized in terms of orbital contributions. However, the definition of localization and delocalization indices is completely general, and they could be calculated at any level of theory, provided that the one- and two-electron densities are available.     

Fully retarded van der Waals interaction between dielectric nanoclusters

The van der Waals (dispersion) interaction between an atom and a cluster or between two clusters at large separation is calculated by considering each cluster as a point particle, characterized by a polarizability tensor. For the extreme limit of very large separation, the fully retarded regime, one needs to know just the static polarizability in order to determine the interaction. This polarizability is evaluated by including all many-body (MB) intracluster atomic interactions self-consistently. The results of these calculations are compared with those obtained from various alternative methods. One is to consider each cluster as a collection of many atoms and evaluate the sum of two-body interatomic interactions, a common assumption. An alternative method is to include three-body atomic interactions as a MB correction term in the total energy. A comparison of these results reveals that the contribution of the higher-than-three-body MB interactions is always attractive and non-negligible even at such a large separation, in contrast to common assumptions. The procedure employed is quite general and is applicable, in principle, to any shape or size of dielectric cluster. We present numerical results for clusters composed of atoms with polarizability consistent with silica, for which the higher-than-three-body MB correction term can be as high as 42% of the atomic pairwise sum. This result is quite sensitive to the anisotropy and orientation of the cluster, in contrast to the result found in the additive case. We also present a power law expansion of the total van der Waals interaction as a series of n-body interaction terms.