Biomedical subjects

Bernd A Hess

Publications and source records attributed to Bernd A Hess.

9 recordsLinked to original sources

PubMed2005

Comparative analysis of local spin definitions.

This work provides a survey of the definition of electron spin as a local property and its dependence on several parameters in actual calculations. We analyze one-determinant wave functions constructed from Hartree-Fock and, in particular, from Kohn-Sham orbitals within the collinear approach to electron spin. The scalar total spin operators S2 and Sz are partitioned by projection operators, as introduced by Clark and Davidson, in order to obtain local spin operators SASB and SzA, respectively. To complement the work of Davidson and co-workers, we analyze some features of local spins which have not yet been discussed in sufficient depth. The dependence of local spin on the choice of basis set, density functional, and projector is studied. We also discuss the results of Sz partitioning and show that SzA values depend less on these parameters than SASB values. Furthermore, we demonstrate that for small organic test molecules, a partitioning of Sz with preorthogonalized Lowdin projectors yields nearly the same results as one obtains using atoms-in-molecules projectors. In addition, the physical significance of nonzero SASB values for closed-shell molecules is investigated. It is shown that due to this problem, SASB values are useful for calculations of relative spin values, but not for absolute local spins, where SzA values appear to be better suited.

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PubMed2005

Car-Parrinello molecular dynamics study of the initial dinitrogen reduction step in Sellmann-type nitrogenase model complexes.

We have studied reduction reactions for nitrogen fixation at Sellmann-type model complexes with Car-Parrinello simulation techniques. These dinuclear complexes are especially designed to emulate the so-called open-side FeMoco model. The main result of this work shows that in order to obtain the reduced species several side reactions have to be suppressed. These involve partial dissociation of the chelate ligands and hydrogen atom transfer to the metal center. Working at low temperature turns out to be one necessary pre-requisite in carrying out successful events. The successful events cannot be described by simple reaction coordinates. Complicated processes are involved during the initiation of the reaction. Our theoretical study emphasizes two experimental strategies which are likely to inhibit the side reactions. Clamping of the two metal fragments by a chelating phosphane ligand should prevent dissociation of the complex. Furthermore, introduction of tert-butyl substituents could improve the solubility and should thus allow usage of a wider range of (mild) acids, reductants, and reaction conditions.

Hydrogen↗

PubMed2005

Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods.

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PubMed2004

Resonance Raman spectra of uracil based on Kramers-Kronig relations using time-dependent density functional calculations and multireference perturbation theory.

The use of time-dependent density functional calculations for the optimization of excited-state structures and the subsequent calculation of resonance Raman intensities within the transform-theory framework is compared to calculations of Hartree-Fock/configuration interaction singles-type (CIS). The transform theory of resonance Raman scattering is based on Kramers-Kronig relations between polarizability tensor components and the optical absorption. Stationary points for the two lowest excited singlet states of uracil are optimized and characterized by means of numerical differentiation of analytical excited-state gradients. It is shown that the effect of electron correlation leads to substantial modifications of the relative intensities. Calculations of vibrational frequencies for ground and excited states are carried out, which show that the neglect of Duschinsky mixing and the assumption of equal wave numbers for ground and excited state are not in all cases good approximations. We also compare the transform-theory resonance Raman intensities with those obtained within a simple approximation from excited-state gradients at the ground-state equilibrium position, and find that they are in qualitative agreement in the case of CIS, but show some important differences in calculations based on density functional theory. Since the results from CIS calculations are in better agreement with experiment, we also present approximate resonance Raman spectra obtained using excited-state gradients from multireference perturbation theory calculations, which confirm the CIS gradients.

Journal Article↗

PubMed2004

Synthesis, structure, and dynamics of six-membered metallacoronands and metallodendrimers of iron and indium.

In the reaction of the N-substituted diethanolamines (H(2)L(1-3)) (1-3) with calcium hydride followed by addition of iron(III) or indium(III) chloride, the iron wheels [Fe(6)Cl(6)(L(1))(6)] (4) and [Fe(6)Cl(6)(L(2))(6)] (6) or indium wheels [In(6)Cl(6)(L(1))(6)] (5), [In(6)Cl(6)(L(2))(6)] (8) and [In(6)Cl(6)(L(3))(6)] (9) were formed in excellent yields. Exchange of the chloride ions of 6 by thiocyanate ions afforded [Fe(6)(SCN)(6)(L(2))(6)] (7). Whereas the structures of 4, 5 and 7 were determined unequivocally by single-crystal X-ray analyses, complexes 8 and 9 were characterised by NMR spectroscopy. Contrary to what is normally presumed, the scaffolds of six-membered metallic wheels are not generally rigid, but rather undergo nondissociative topomerisation processes. This was shown by variable temperature (VT) (1)H NMR spectroscopy for the indium wheel [In(6)Cl(6)(L(1))(6)] (5) and is highlighted for the enantiotopomerisation of one indium centre [ 1/6[S(6)-5]<==>[1/6[S(6)-5']]. The self-assembly of metallic wheels, starting from diethanolamine dendrons, is an efficient strategy for the convergent synthesis of metallodendrimers.

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PubMed2004

The structure of the second-order reduced density matrix in density matrix functional theory and its construction from formal criteria.

Some formal requirements for the second-order reduced density matrix are discussed in the context of density matrix functional theory. They serve as a basis for the ad hoc construction of the second-order reduced density matrix in terms of the first-order reduced density matrix and lead to implicit functionals where the occupation numbers of the natural orbitals are obtained as diagonal elements of an idempotent matrix the elements of which represent the variational parameters to be optimized. The numerical results obtained from a first realization of such an implicit density matrix functional give excellent agreement with the results of full configuration interaction calculations for four-electron systems like LiH and Be. Results for H2O taken as an example for a somewhat larger molecule are numerically less satisfactory but still give reasonable occupation numbers of the natural orbitals and indicate the capability of density matrix functional theory to cope with static electron correlation.

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PubMed2003

A quantum chemical study of racemization pathways in substituted chrysene derivatives.

The potential-energy surfaces of 5,11-disubstituted 6,12-dimethoxychrysene and chrysene-6,12-dione derivatives were investigated by means of density functional calculations. We report relative energies of all conformers and an identification of the racemisation pathways of the chiral equilibrium structures. By analysis of homodesmotic reactions we were able to obtain an estimate for the strain energy of the substituted compounds. This strain energy can be used as a means of measuring the steric effects exerted by the substituents.

Journal Article↗

PubMed2002

Iron carbonyl, nitrosyl, and nitro complexes of a tetrapodal pentadentate amine ligand: synthesis, electronic structure, and nitrite reductase-like reactivity.

The tetrapodal pentaamine 2,6-C5H3N[CMe(CH2NH2)2]2 (pyN4, 1) forms a series of octahedral iron(II) complexes of general formula [Fe(L)(1)]Xn with a variety of small-molecule ligands L at the sixth coordination site (L = X = Br, n = 1 (2); L = CO, X = Br, n = 2 (3); L = NO, X = Br, n = 2 (4); L = NO+, X = Br, n = 3 (5); L = NO2-, X = Br, n = 1 (6)). The bromo complex, which is remarkably stable towards hydrolysis and oxidation, serves as the precursor for all other complexes, which may be obtained by ligand exchange, employing CO, NO, NOBF4, and NaNO2, respectively. All complexes have been fully characterised, including solid-state structures in most cases. Attempts to obtain single crystals of 6 produced the dinuclear complex [Fe2[mu 2-(eta 1-N: eta 1-O)-NO2](1)2]Br2PF6 (7), whose bridging NO2- unit, which is unsupported by bracketing ligands, is without precedent in the coordination chemistry of iron. Compound 2 has a high-spin electronic configuration with four unpaired electrons (S = 2), while the carbonyl complex 3 is low-spin (S = 0), as are complexes 5, 6 and 7 (S = 0 in all cases); the 19 valence electron nitrosyl complex 4 has S = 1/2. Complex 4 and its oxidation product, 5 ([Fe(NO)]7 and [Fe(NO)]6 in the Feltham-Enemark notation) may be interconverted by a one-electron redox process. Both complexes are also accessible from the mononuclear nitro complex 6: Treatment with acid produces the 18 valence electron NO+ complex 5, whereas hydrolysis in the absence of added protons (in methanolic solution) gives the 19 valence electron NO. complex 4, with formal reduction of the NO2- ligand. This reactivity mimicks the function of certain heme-dependent nitrite reductases. Density functional calculations for complexes 3, 4 and 5 provide a description of the electronic structures and are compatible with the formulation of iron(II) in all cases; this is derived from the careful analysis of the combined IR, ESR and Mössbauer spectroscopic data, as well as structural parameters.

Journal Article↗

PubMed2002

Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene.

In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.

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