Kazunari Matsumura

Effects of the higher electron correlation correction on the calculated intermolecular interaction energies of benzene and naphthalene dimers: Comparison between MP2 and CCSD(T) calculations

Abstract Intermolecular interaction energies of parallel and T-shape benzene dimers and parallel naphthalene dimer were calculated with MP2, MP3, MP4(SDQ), MP4(SDTQ), CCSD and CCSD(T) electron correlation corrections using several basis sets. The MP2 calculations considerably overestimated the attraction compared to the CCSD(T) ones. The MP2 correlation interaction energies, the differences between the HF and MP2 interaction energies, were 21–38% larger than the corresponding CCSD(T) ones. The MP4(SDQ) and CCSD calculations substantially underestimated the attraction compared to MP4(SDTQ) and CCSD(T), which indicated the importance of triple excitation. The estimated CCSD(T) interaction energies of the three dimers with reasonably large basis sets were −1.74, −2.50 and −5.69 kcal/mol, respectively.

Effects of basis set and electron correlation on the calculated interaction energies of hydrogen bonding complexes: MP2/cc-pV5Z calculations of H2O–MeOH, H2O–Me2O, H2O–H2CO, MeOH–MeOH, and HCOOH–HCOOH complexes

The MP2 intermolecular interaction energies of the title complexes were calculated with the Dunning’s correlation consistent basis sets (cc-pVXZ, X=D, T, Q, and 5) and the interaction energies at the basis set limit were estimated. The second-order Mo/ller–Plesset (MP2) interaction energies greatly depend on the basis sets used, while the Hartree–Fock (HF) energies do not. Small basis sets considerably underestimate the attractive interaction. The coupled cluster single double triple [CCSD(T)] interaction energies are close to the MP2 ones. The expected CCSD(T) interaction energies of the H2O–MeOH, H2O–Me2O, H2O–H2CO, MeOH–MeOH, and HCOOH–HCOOH complexes at the basis set limit are −4.90, −5.51, −5.17, −5.45, and −13.93 kcal/mol, respectively, while the HF/cc-pV5Z energies are −3.15, −2.58, −3.60, −2.69, and −11.29 kcal/mol, respectively. The HF calculations greatly underestimate the attractive energies and fail to predict the order of the bonding energies in these complexes. These results show that a larg...

Torsional potential of biphenyl: Ab initio calculations with the Dunning correlation consisted basis sets

The internal rotational barrier heights of biphenyl were calculated with the Dunning correlation consisted basis sets (up to cc-pVQZ, 960 basis functions) and the electron correlation correction by the second order Mo/ller-Plesset method (MP2). Although previous Hartree–Fock (HF) and MP2 calculations showed that the internal rotational barrier height at 0° (ΔE0) was substantially larger than that at 90° (ΔE90), our MP2/cc-pVQZ//MP2/6-31G* calculations showed that ΔE0 (2.28 kcal/mol) was close to ΔE90 (2.13 kcal/mol), which agreed with the estimation from experimental measurements. The calculations of benzene dimers suggested that the dispersion interaction increased the relative stability of the coplanar conformer. The basis sets employed in the previous calculations were not large enough to evaluate the attractive dispersion interaction. The underestimation of the stabilization of the coplanar conformer by the dispersion interaction would be one of the reasons for the overestimation of ΔE0 in the previou...

Lanthanide complex−oligo-DNA hybrid for sequence-selective hydrolysis of RNA

Iminodiacetate complexes of lanthanide(III) ions (lutetium, europium, thulium and lanthanum), attached to the 5′-end of a 15-mer DNA, hydrolyse a 39-mer RNA selectively at the 3′-side of its 15-mer sequence, which is complementary with the DNA.

Unprecedentedly fast hydrolysis of the RNA dinucleoside monophosphates ApA and UpU by rare earth metal ions

Rare earth metal(III) ions rapidly hydrolyse adenylyl(3′-5′)adenosine and uridyl(3′-5′)uridine at pH 8,30°C; the half-life of the former is 10 min with 0.01 mol dm–3 TmIII.

Cerium(IV)-oligoDNA hybrid as highly selective artificial nuclease

Abstract Cerium(IV) ion is attached to the 5′-end of a 19-mer DNA by use of iminodiacetate ligand. At pH 7.2 and 30 °C, the hybrid selectively cuts a 40-mer DNA, which has 19-mer sequence complementary with the DNA in the hybrid, at the target site (the 3′-side of the 19-mer portion of the substrate DNA). Cerium(IV) ion hydrolyzes thymidylyl(3′-5′)thymidine to thymidine without concurrent oxidative cleavage of the ribose, indicating that the selective scission by the hybrid proceeds via the hydrolysis of the phosphodiester linkage.

Hydrolysis of phosphatidylinositol by rare earth metal ion as a phospholipase C mimic

Abstract Phosphatidylinositol, a cell-membrane component responsible for the transduction of extracellular signals into cells, is hydrolyzed by rare earth metal chlorides (YCl3, LaCl3, EuCl3, CeCl3, and TmCl3) at pH 7.5–8.5 and 30°C. YCl3 has the largest activity. A key step in the cell-to-cell communication has been successfully mimicked. In contrast, non-rare earth metal ions such as Fe(III), Zn(II), and Cu(II) show no measurable activity, confirming the overwhelming superiority of rare earth metal(III) ions.

Blue/Red Linear Dichroic Emission from a Highly Anisotropic Crystal of Triarylmethane Dye Conjugated with Phenoxo-Zinc Complexes

We have developed a novel triphenylmethane-based hexanuclear zinc complex that exhibits peculiar photochemical and photophysical properties. Upon UV irradiation, the compound turned from colorless to reddish purple, while the color of emission turned from blue to red. The color change was attributed to an oxidation of the ligand part. It was suggested that an intramolecular energy-transfer mechanism operates to give rise to the red emission. The UV treatment of a single crystal results in simultaneous emission of orthogonally polarized blue and red light. This color switching, namely linear dichroic emission was so distinct that one can recognize with by sight through optical microscope. The columnar arrangement of molecules in the crystal clearly accounts for the observed polarization of the emission.

The mutual polarization of reactants: Fukui function description of the charge reorganization

Abstract The diagonal and off-diagonal Fukui functions (FFs) constitute the charge transfer FF that describes reorganization in the electron density due to charge transfer. In this Letter, we consider the mutual polarization of the reactants. We prove that the off-diagonal FF is related to charge reorganization due to the polarization process. The change in the electron density of a given reactant caused by a perturbation in the external potential (due to nuclei) is proportional to the off-diagonal FF. The self-consistent charge and configuration method for a subsystem is used to illustrate this concept numerically.

Solution-phase energy profiles for trigonal bipyramidal species postulated as intermediates for the hydrolysis of methyl ethylene phosphate

Abstract We present results of solution-phase ab initio and DFT investigations on the trigonal bipyramidal (TBP) intermediates postulated for the hydrolysis of methyl ethylene phosphate (MEP). A key intermediate for the hydrolysis would not be a TBP species with the hydroxyl group axial, but would be a TBP intermediate with the hydroxyl group equatorial. Considering the reaction pathways through this intermediate, not only exclusive ring opening in the dilute alkaline hydrolysis of MEP but also significant amount of exocyclic cleavage in the strong alkali can be rationalized. This interpretation is in accord with the mechanisms proposed by Lim et al. and by Lonnberg et al.