Pair interaction energy decomposition analysis

The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H2O)1024, the alpha helix, beta turn, and beta strand of polyalanine (ALA)10, as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.     

Change in a protein's electronic structure induced by an explicit solvent: an ab initio fragment molecular orbital study of ubiquitin

The effect of solvation on the electronic structure of the ubiquitin protein was analyzed using the ab initio fragment molecular orbital (FMO) method. FMO calculations were performed for the protein in vacuo, and the protein was immersed in an explicit solvent shell as thick as 12 A at the HF or MP2 level by using the 6-31G* basis set. The protein's physical properties examined were the net charge, the dipole moment, the internal energy, and the solvent interaction energy. Comparison of the computational results revealed the following changes in the protein upon solvation. First, the positively charged amino acid residues on the protein surface drew electrons from the solvent, while the negatively charged ones transfer electrons to the solvent. Second, the dipole moment of the protein was enhanced as a result of the polarization. Third, the internal energy of the protein was destabilized, but the destabilization was more than compensated for by the generation of a favorable protein-solvent interaction. Finally, the energetic changes were elicited both by the electron correlation effect of the first solvent shell and by the electrostatic effect of more distant solvent molecules. These findings were consistent with the picture of the solvated protein being a polarizable molecule dissolved in a dielectric media.     

Ion distribution in polyelectrolyte multilayers with standing-wave X-ray fluorescence

Absolute ion concentration and its profile across polyelectrolyte multilayer films were studied. The films were prepared by alternating adsorption of polyanions and polycations from aqueous solution. Standing-wave X-ray fluorescence was used to map the ion profile. The well-studied multilayer system PSS/PAH was investigated, and bromide ions were used as probe entities. The results show that the sign of the charge of the outermost layer and the washing procedure after finishing the preparation have a decisive effect on the ion concentration and the ion profile. Multilayers with PSS as the outermost layer contain fewer bromide ions than the PAH-terminated multilayers. Exposure to water washes the ions out, but even after 6 h of washing, not all of the bromide ions had been removed.     

Dispersible Shortened Boron Nitride Nanotubes with Improved Molecule‐Loading Capacity

The oxidation process of boron nitride nanotubes was thoroughly investigated, and a slow oxidation characteristic was clearly revealed. Subsequently, the controllable oxidation process was utilized to break the sturdy structure of the boron nitride nanotubes to fabricate shortened nanotubes. The shortened boronnitride nanotubes were found to possess good solubility in water and many organic solvents. Further experiments demonstrated remarkably improved molecule‐loading capacity of the shortened boron nitride nanotubes. These dispersible shortened boron nitride nanotubes might have the potential to be developed as effective delivery systems for various molecules, which may find applications in bio‐related fields.     

Deformation theory of objects in homotopy and derived categories III: Abelian categories

This is the third paper in a series. In Part I we developed a deformation theory of objects in homotopy and derived categories of DG categories. Here we show how this theory can be used to study deformations of objects in homotopy and derived categories of abelian categories. Then we consider examples from (noncommutative) algebraic geometry. In particular, we study noncommutative Grassmanians that are true noncommutative moduli spaces of structure sheaves of projective subspaces in projective spaces.     

New possible mode of ligand-metal cooperation in PC(sp3)P pincer complexes

Ligand-metal cooperation in iridium and platinum complexes bearing tricyclic dibenzobarrelene-based PC(sp(3))P pincer ligands is discussed. We demonstrated that the carbon-metal bond in these complexes may be efficiently cleaved and regenerated via 1,2-addition/elimination reactions.     

Ribosylation of adenosine: an orthogonally protected building block for the synthesis of ADP-ribosyl oligomers

A method to ribosylate adenosine on the 2' hydroxyl function in an α-selective fashion and in good yield is presented. Protective groups chosen for the acceptor and donor used in this glycosylation not only direct α-selectivity but also allow the construction of a fully orthogonally protected building block for the future assembly of oligo-ADP-ribosylated peptides and proteins.     

Formal and finite order equivalences

We show that two families of germs of real-analytic subsets in ${{\mathbb C}^{n}}$ are formally equivalent if and only if they are equivalent of any finite order. We further apply the same technique to obtain analogous statements for equivalences of real-analytic self-maps and vector fields under conjugations. On the other hand, we provide an example of two sets of germs of smooth curves that are equivalent of any finite order but not formally equivalent.     

Two-component natural spinors from two-step spin-orbit coupled wave functions

We developed an algorithm to obtain the natural orbitals (natural spinors) from the two-step spin-orbit coupled wave functions. These natural spinors are generally complex-valued, mixing two spin components, and they can have similar symmetry properties as the j-j spinors from the one-step spin-orbit coupling calculations, if the reduced density equally averages all the components of a multi-dimensional irreducible representation. Therefore, the natural spinors can serve as an approximation to the j-j spinors and any wave function analysis based on the j-j spinors can also be performed based on them. The comparison between the natural spinors and the j-j spinors of three representative atoms, Tl, At, and Lu, shows their close similarity and demonstrates the ability of the natural spinors to approximate the j-j spinors.     

Collisional stabilization of van der Waals states of ozone

The mixed quantum-classical theory developed earlier [M. Ivanov and D. Babikov, J. Chem. Phys. 134, 144107 (2011)] is employed to treat the collisional energy transfer and the ro-vibrational energy flow in a recombination reaction that forms ozone. Assumption is that the van der Waals states of ozone are formed in the O + O(2) collisions, and then stabilized into the states of covalent well by collisions with bath gas. Cross sections for collision induced dissociation of van der Waals states of ozone, for their stabilization into the covalent well, and for their survival in the van der Waals well are computed. The role these states may play in the kinetics of ozone formation is discussed.