Jahn and Tellers last case: the icosahedral sextet, gamma(9) x (g+2 h).
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Biomedical subjects
Arnout Ceulemans
Publications and source records attributed to Arnout Ceulemans.
Tryptophan rotamers as evidenced by X-ray, fluorescence lifetimes, and molecular dynamics modeling.
We investigated the native-state dynamics of the Bacillus caldolyticus cold-shock protein mutant Bc-Csp L66E, using fluorescence and appropriate molecular dynamics methods. Two fluorescence lifetimes were found, the amplitudes of which agree very well with tryptophan rotamer populations, obtained from parallel tempering calculations. Rotamer lifetimes were predicted by transition-state theory from high-temperature simulations. Transition pathways were extracted from the transition rates between individual rotameric states. The molecular dynamics also reveal the loop fluctuations in the native state.
Acrylamide↗
Multiquanta vortex entry and vortex-antivortex pattern expansion in a superconducting microsquare with a magnetic dot.
We investigate the nucleation of superconductivity in a microsquare with a magnetic dot on top. The cusplike behavior of the calculated normal-superconducting phase boundaries, T(c)(H), shows a transition between short-period to long-period oscillations when going from positive to negative applied fields, H. Vorticity changes by more than 1, indicating multiquanta vortex entries, have been detected along this asymmetric T(c)(H) boundary. The dot also expands dramatically the symmetry-consistent vortex-antivortex patterns, thus facilitating their experimental observation.
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Hydrogen bonding to pi-systems of indole and 1-methylindole: is there any OH...phenyl bond?
The weak hydrogen-bonded complexes between proton donors and the pi-cloud of indole and 1-methylindole (MI) are investigated theoretically by three different methods: DFT/B3LYP, MPW1B95, and MP2. This study addresses the question as to whether the 1:1 complex can only form between the proton and the pi-cloud of the pyrrole part of indole or if there also exists a 1:1 complex between the proton and the pi-cloud of the phenyl ring. For the water-indole system, the more elaborate MP2 and MPW1B95 methods yield only one minimum with a hydrogen bond to the pyrrole part and weak secondary interactions to the phenyl ring, in agreement with a recent criticism by Van Mourik (Chem. Phys. 2004, 304, 317-319) that the B3LYP functional is unable to account for the dispersion interaction. However, for the 1:1 complexes between MI and 2-propanol, all three methods indicate that both the five-membered and the six-membered rings of the indole chromophore can form pi-complexes. For the MI-trifluoroethanol (TFE) system, it is shown that the ethanol conformation is specific for the interaction site: for the complex to the five-membered ring, TFE is in the cis-gauche conformation, while for the complex to the six-membered ring site, it is in the trans conformation. These results are discussed as a function of local interactions in the systems.
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Magnetic anisotropy of [Mo(CN)7]4- anions and fragments of cyano-bridged magnetic networks.
Quantum chemistry calculations of CASSCF/CASPT2 level together with ligand field analysis are used for the investigation of magnetic anisotropy of [Mo(CN)7]4- complexes. We have considered three types of heptacyano environments: two ideal geometries, a pentagonal bipyramid and a capped trigonal prism, and the heptacyanomolybdate fragment of the cyano-bridged magnetic network K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O. At all geometries the first excited Kramers doublet is found remarkably close to the ground one due to a small orbital energy gap in the ligand field spectrum, which ranges between a maximal value in the capped trigonal prism (800 cm(-1)) and zero in the pentagonal bipyramid. The small value of this gap explains (i) the axial form of the g tensor and (ii) the strong magnetic anisotropy even in strongly distorted complexes. Comparison with available experimental data for the g tensor of the mononuclear precursors reveals good agreement with the present calculations for the capped trigonal prismatic complex and a significant discrepancy for the pentagonal bipyramidal one. The calculations for the heptacyanomolybdate fragment of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O give g(perpendicular)/g(parallel) approximately 0.5 and the orientation of the local anisotropy axis close to the symmetry axis of an idealized pentagonal bipyramid. These findings are expected to be important for the understanding of the magnetism of anisotropic Mo(III)-Mn(II) cyano-bridged networks based on the [Mo(CN)7]4- building block.
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Theoretical study on the group 2 atoms + N2O reactions.
The electronic structure aspects of the M (1S,3P) + N2O(X 1sigma+) (M = Be, Mg, Ca) reactions are investigated using the CASSCF/MRMP2 (complete active space SCF and the multireference Møller-Plesset perturbation theory of the second order) computational methodology. The lowest adiabatic 1 1A' and 1 3A' potential energy surfaces (PESs) favor the bending dissociation mechanism of N2O in all studied cases. The rate-limiting channels are determined by the classical barriers that decrease in the series Be (8.9) > Mg (7.0) > Ca (1.2) kcal/mol, whereas the spin-forbidden reaction channels are found to be less important. A comparison with elaborated kinetic results (Plane et al. J. Phys. Chem. 1990, 94, 5255; Gas-Phase Metal Reactions; Elsevier: Amsterdam, 1992; Vinckier et al. J. Phys. Chem. A 1999, 103, 5328) on the Ca (1S) + N2O(X 1sigma+) reaction is presented, and the differences in the kinetic behavior of the title reactions are discussed. Our results also indicate that the techniques based on the multiconfigurational wave functions are unavoidable if a correct topology of the PESs governing these reactions is needed.
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Definitive assignments of the visible-near-IR bands of porphyrin-naphthalocyanine rare-earth sandwich double- and triple-decker compounds by magnetic circular dichroism spectroscopy.
A series of heteroleptic rare-earth sandwich complexes [M(Nc)(OEP)] (M = La, Nd, Eu, Dy, and Lu; Nc = 2,3-naphthalocyaninate; OEP = octaethylporphyrinate) have been investigated by electronic absorption and magnetic circular dichroism (MCD) spectroscopy. The electronic absorption spectra of the neutral forms showed two characteristic transitions (bands I and II) in the near-IR region, both of which were systematically shifted depending on the size of their central metal. In the MCD spectra, a relatively intense Faraday A term and a significantly weak Faraday B term have been observed corresponding to bands II and I, respectively. The spectral features were successfully interpreted using a simple MO model by considering the relevant interactions of Gouterman's four orbitals of the constituent chromophores. The model succeeded in assigning the MCD spectra of the related compounds, the oxidized and reduced forms of the dimer ([M(Nc)(OEP)]+ and [M(Nc)(OEP)]-), and neutral forms of the triple-decker compounds (M2(Nc)(OEP)2, M = Nd, Eu). DFT calculations of the dimers supported the validity of this model.
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The E x e dynamic Jahn-Teller problem: a new insight from the strong coupling limit.
Correct boundary conditions for the E x e dynamic Jahn-Teller problem are considered explicitly for the first time to obtain approximate analytical solutions in the strong coupling limit. Numerical solutions for the decoupled equations using the finite difference method are also presented. The numerical solutions for the decoupled equations exhibit avoided crossings in the weak coupling region, which explains the oscillating behavior of the solutions obtained by Longuet-Higgins et al. for the coupled equations. The obtained analytical energy expressions show improved agreement with the numerical calculations as compared with the previous treatment in which the potentials were assumed to be harmonic. We demonstrate that the pseudorotational energy j(2)/(2g(2)), where g is the dimensionless vibronic coupling constant, and j total angular momentum: j=+/-1/2,+/-3/2,..., in the conventional strong coupling expression for the vibronic levels of the lower sheet is exact. Non-Hermitian first-order perturbation theory gives the energy which is correct up to 1/g(4). The asymptotic behavior of the wave function at the origin does not influence the corrected energy up to order of 1/g(4). At the same time the treatment of the upper sheet with correct boundary conditions gives solutions which are entirely different from the corresponding Slonczewski's solutions. Besides, the correct boundary conditions enable us to evaluate the nonadiabatic coupling between the lower and upper potential sheets. The energy correction due to the nonadiabatic coupling is estimated to be of order 1/g(6).
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Rationalization of supramolecular chirality in a bisporphyrin system.
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Chelating Agents↗
Ab initio study of small graphitic cones with triangle, square, and pentagon apex.
Accurate geometries of carbon nanocones of different sizes with a triangle, square or pentagon at the apex have been determined for the first time using a quantum chemical optimization method. The structure close to the apex is distorted from an ideal conical surface. The charging effect of the central defect is quite different from that predicted by tight-binding calculations. The symmetry behavior of the frontier orbitals and the size of the highest occupied molecular orbital-lowest unoccupied molecular orbital gap versus cone type and size is explained. The density of states quickly converges towards that of graphite when the size of the cone increases. In comparison to previous results in the literature it is found that the local densities of states of cones, that are locally different but belong to the same topo-combinatoric class, share common features.
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Recognition of chiral catechols using oxo-titanium phthalocyanine.
Oxo-titanium phthalocyanine (TiOPc) derivatives of catechin and hematoxylin (natural ortho-diol type chiral compounds) have been prepared and characterized by spectral and chromatographic techniques. It is demonstrated that the TiOPc unit is an excellent template for chiral recognition through its isolated Q-transitions. The formation of a helical dimeric complex with hematoxylin induces strong CD-activity in the Q-band region. Ab initio geometry optimizations were combined with a Kuhn-Kirkwood coupled-oscillator mechanism to obtain the absolute configuration of hematoxylin. In addition, it is shown that the described chiroptical recognition method is sensitive to slight conformational changes.
Catechols↗
Protein simulations: the absorption spectrum of barnase point mutants.
The near-UV absorption spectra of barnase double-point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared-Amber5.0, CHARMM-c27b1, and GROMOS96-using indole as the fluorescent probe. It was found that calculated absorption spectra reproduce experimental values very well, provided detailed charge cloud descriptions are included. These calculations further sustain the hypothesis that different tryptophan rotamers can be present in proteins. Molecular dynamics calculations of the double-point mutants also point to the structural effect of counter ions.
Bacillus↗
Mechanism of a strongly anisotropic MoIII-CN-MnII spin-spin coupling in molecular magnets based on the [Mo(CN)(7)](4-) heptacyanometalate: a new strategy for single-molecule magnets with high blocking temperatures.
Unusual spin coupling between Mo(III) and Mn(II) cyano-bridged ions in bimetallic molecular magnets based on the [Mo(III)(CN)(7)](4-) heptacyanometalate is analyzed in terms of the superexchange theory. Due to the orbital degeneracy and strong spin-orbit coupling on Mo(III), the ground state of the pentagonal-bipyramidal [Mo(III)(CN)(7)](4-) complex corresponds to an anisotropic Kramers doublet. Using a specially adapted kinetic exchange model we have shown that the Mo(III)-CN-Mn(II) superexchange interaction is extremely anisotropic: it is described by an Ising-like spin Hamiltonian JS(z)(Mo) S(z)(Mn) for the apical pairs and by the J(z)S(z)(Mo) S(z)(Mn) + J(xy)(Sx(Mo) Sx(Mn) + Sy(Mo) Sy(Mn)) spin Hamiltonian for the equatorial pairs (in the latter case J(z) and J(xy) can have opposite signs). This anisotropy resulted from an interplay of several Ising-like (Sz(Mo) Sz(Mn)) and isotropic (S(Mo)S(Mn)) ferro- and antiferromagnetic contributions originating from metal-to-metal electron transfers through the pi and sigma orbitals of the cyano bridges. The Mo(III)-CN-Mn(II) exchange anisotropy is distinct from the anisotropy of the g-tensor of [Mo(III)(CN)(7)](4-); moreover, there is no correlation between the exchange anisotropy and g-tensor anisotropy. We indicate that highly anisotropic spin-spin couplings (such as the Ising-like JS(z)(Mo) S(z)(Mn)) combined with large exchange parameters represent a very important source of the global magnetic anisotropy of polyatomic molecular magnetic clusters. Since the total spin of such clusters is no longer a good quantum number, the spin spectrum pattern can differ considerably from the conventional scheme described by the zero-field splitting of the isotropic spin of the ground state. As a result, the spin reorientation barrier of the magnetic cluster may be considerably larger. This finding opens a new way in the strategy of designing single-molecule magnets (SMM) with unusually high blocking temperatures. The use of orbitally degenerate complexes with a strong spin-orbit coupling (such as [Mo(III)(CN)(7)](4-) or its 5d analogues) as building blocks is therefore very promising for these purposes.
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An Ab initio study of the ligand field and charge-transfer transitions of Cr(CN)(6)(3-) and Mo(CN)(6)(3-).
High-level ab initio calculations on the excited states of Cr(CN)63- and Mo(CN)63- are reported. For the latter complex, a rather large 10 Dq value of 42 000 cm-1 is obtained, reflecting the increased covalency. The lowest lying charge-transfer transitions for both complexes are predicted to be of the type ligand-to-metal, an assignment in agreement with the photochemical behavior of Cr(CN)63-. A good correspondence between the well-known experimental spectrum of the chromium complex and the theoretical CASPT2 excitation energies is found.
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Origin of Ferromagnetism in Cyano-Bridged Compounds Containing d(1) Octacyanometallates Financial support by the Belgian National Science Foundation and Flemish Government under the Concerted Action Scheme, the ESF programme on molecular magnets, the Russian Foundation for Basic Research (Grant No. 01-02-32210), and the INTAS Grant 00-00565 are gratefully acknowledged. The authors thank Professor Silvio Decurtins and the members of his group for stimulating discussions and for sending us the structural data on the niobium compound prior the publication, and Dr. Høgni Weihe for useful discussions. We also thank Ken Somers for the help with the Figures.
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Topology-aided molecular design: the platonic molecules of genera 0 to 3.
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