Search PubMed⌕ Search

Biomedical subjects

Walter Thiel

Publications and source records attributed to Walter Thiel.

At least 55 records · Page 3Linked to original sources
PubMed2004

Theoretical studies on the smallest fullerene: from monomer to oligomers and solid States.

Hybrid B3LYP and density-functional-based tight-binding (DFTB) computations on the solid-state structures and electronic properties of the C(20) fullerene monomer and oligomers are reported. C(20) cages with C(2), C(2h), C(i), D(3d), and D(2h) symmetries have similar energies and geometries. Release of the very high C(20) strain is, in theory, responsible for the ready oligomerization and the formation of different solid phases. Open [2+2] bonding is preferred both in the oligomers and in the infinite one-dimensional solids; the latter may exhibit metallic character. Two types of three-dimensional solids, the open [2+2] simple cubic and the body-centered cubic (bcc) forms, are proposed. The energy of the latter is lower due to the better oligomer bonding. The open [2+2] simple cubic solid should be a conductor, whereas the bcc solids are insulators. The most stable three-dimensional solid-state structure, an anisotropically compressed form of the bcc solid, has a HOMO-LUMO gap of approximately 2 eV and a larger binding energy than that of the proposed C(36) solid.

Journal Article↗
PubMed2004

Learning from directed evolution: theoretical investigations into cooperative mutations in lipase enantioselectivity.

Molecular modeling with classical force-fields has been used to study the reactant complex and the tetrahedral intermediate in lipase-catalyzed ester hydrolysis in 20 enzyme/substrate combinations. The R and S enantiomers of alpha-methyldecanoic acid ester served as substrates for the wild-type lipase from Pseudomonas aeruginosa and nine selected mutants. After suitable preparation of initial structures from an available wild-type crystal structure, each system was subjected to 1 ns CHARMM force-field molecular dynamics simulations. The resulting geometric and energetic changes allow interpretation of some experimentally observed effects of mutations, particularly with regard to the "hot spots" at residues 155 and 162. The replacement S155F enhances S enantiopreference through a steric relay involving Leu162. The double mutation S53P + L162G improves S enantioselectivity by creating a new binding pocket for the S enantiomer with an additional stabilizing hydrogen bond to His83. The simulations provide insight into remote and cooperative effects of mutations.

Catalysis↗
PubMed2003

Active species of horseradish peroxidase (HRP) and cytochrome P450: two electronic chameleons.

The active site of HRP Compound I (Cpd I) is modeled using hybrid density functional theory (UB3LYP). The effects of neighboring amino acids and of environmental polarity are included. The low-lying states have porphyrin radical cationic species (Por(*)(+)). However, since the Por(*)(+) species is a very good electron acceptor, other species, which can be either the ligand or side chain amino acid residues, may participate in electron donation to the Por(*)(+) moiety, thereby making Cpd I behave like a chemical chameleon. Thus, this behavior that was noted before for Cpd I of P450 is apparently much more wide ranging than initially appreciated. Since chemical chameleonic behavior property was found to be expressed not only in the properties of Cpd I itself, but also in its reactivity, the roots of this phenomenon are generalized. A comparative discussion of Cpd I species follows for the enzymes HRP, CcP, APX, CAT (catalase), and P450.

Binding Sites↗
PubMed2003

Spherical sila- and germa-homoaromaticity.

Guided by the 2(N + 1)2 electron-counting rule for spherical aromatic molecules, we have designed various spherical sila- and germa-homoaromatic systems rich in group 14 elements. Their aromaticity is revealed by density-functional computations of their structures and the nucleus-independent chemical shifts (NICS). Besides the formerly used endohedral inclusion strategy, spherical homoaromaticity is another way to stabilize silicon and germanium clusters.

Journal Article↗
PubMed2003

A theoretical and structural investigation of thiocarbon anions.

Density functional theory energies, geometries, and population analyses as well as nucleus-independent chemical shifts (NICS) have been used to investigate the structural and magnetic evidence for cyclic CnSn(2-) and CnSn (n = 3-6) electron delocalization. Localized molecular orbital contributions to NICS, computed by the individual gauge for localized orbitals method, dissect pi effects from the sigma single bonds and lone pair influences. CnSn(2-) (n = 3-5) structures in Dnh symmetry are minima. Their aromaticity decreases with increasing ring size. C3S3(2-) is both sigma and pi aromatic, while C4S4(2-) and C5S5(2-) are much less aromatic. NICS(0)pi, the C-C(pi) contribution to NICS(0) (i.e., at the ring center), decreases gradually with ring size. In contrast, cyclic C6S6(2-) prefers D2h symmetry due to the balance between aromaticity, strain energy, and the S-S bond energies and is as aromatic as benzene. The theoretical prediction that C6S6(6-) has D6h minima was confirmed by X-ray structure analysis. Comparisons between thiocarbons and oxocarbons based on dissected NICS analysis show that CnSn(2-) (n = 3-5) and C6S6(6-) are less aromatic in Dnh symmetry than their oxocarbon analogues.

Journal Article↗
PubMed2003

Density functional calculations on the binding of dinitrogen to the FeFe cofactor in Fe-only nitrogenase: FeFeco(mu 6-N2) as intermediate in nitrogen fixation.

The geometries and stabilities of the FeFe cofactor at different oxidation states and its complexes with N(2) have been determined by density functional calculations. These calculations support an EPR-inactive resting state of the FeFe cofactor with four Fe(2+) and four Fe(3+) sites (4Fe(2+)4Fe(3+)). FeFeco(mu(6)-N(2)) with a central dinitrogen ligand is predicted to be the most stable complex of the FeFe cofactor with N(2). It is easily formed by penetration of N(2) into the trigonal Fe(6) prism of the FeFe cofactor with an approximate barrier of 4 kcal mol(-1). The present DFT results suggest that an FeFeco(mu(6)-N(2)) entity is a plausible intermediate in dinitrogen fixation by nitrogenase. CO is calculated to bind even more strongly than N(2) to the FeFe cofactor so that CO may inhibit the reduction of nitrogen by Fe-only nitrogenase.

Iron↗
PubMed2003

Fullerene anions of different sizes and shapes: a 13C NMR and density-functional study.

A combined experimental and theoretical study was conducted on numerous higher fullerene anions with different sizes and shapes, C76-D2, C78-C2v, C78-D3, C84-D2, and C84-D2d. The corresponding fullerenes were reduced by lithium metal to diamagnetic multiply charged anions. The centers of gravity of the 13C NMR spectra of all the multiply charged anions were deshielded, relative to those of the neutral fullerenes. The results of density functional (DFT) computations of the 13C NMR spectra and the molecular orbitals (MOs) of possible polyanion reduction products suggest that hexaanions were the species formed.

Journal Article↗
PubMed2003

Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach.

The graphical unitary group approach has been applied in an efficient implementation of a general multireference configuration interaction (MRCI) method for use with small active molecular orbital spaces in a semiempirical framework. Gradients can be computed analytically for molecular orbitals from a closed-shell or a half-electron open-shell Hartree-Fock calculation. CPU times for single point energy and gradient calculations are reported. The code allows MRCI geometry optimizations of large molecules, as illustrated for the singlet ground state and the four lowest triplet states of fullerene C(76).

Journal Article↗
PubMed2003

Structures and magnetic properties of mono-doped fullerenes C59Xn and C59X(6mn)m (X=Bm, N+, P+, As+, Si): isoelectronic analogues of C60 and C60(6m).

Structures of mono-doped fullerenes, C59Xn and C59X(6mn)m (X=Bm, N+, P+, As+, Si), the isoelectronic analogues to C60 and C606m with 60 and 66 pi-electrons, have been investigated at the B3LYP/6-31G* level of density functional theory. On the basis of the computed nucleus independent chemical shifts (NICS) at the cage center and also at the center of individual rings as magnetic criteria, heterofullerenes with 60 pi-electrons are as aromatic as the parent C60, while those with 66 pi-electrons are much less aromatic than C606m. The very distinct endohedral chemical shifts of the 66 pi-electron systems may be useful to identify the heterofullerenes through their endohedral 3He NMR chemical shifts.

Arsenic↗
PubMed2003

The structure and stability of Si60 and Ge60 cages: a computational study.

Structural studies of fullerene-like Si(60) and Ge(60) cages using ab initio methods were augmented by density functional tight-binding molecular dynamics (DFTB-MD) simulations of finite temperature effects. Neither the perfect I(h) symmetry nor the distorted T(h) structures are true minima. The energies of both are high relative to distorted, lower symmetry minima, C(i) and T, respectively, which still preserve C(60)-type connectivity. Both Si(60) and Ge(60) favor C(i) symmetry cages in which Si and Ge vertexes exhibit either near-trigonal or pyramidal geometries. These structural variations imply significant reactivity differences between different positions. The small magnetic shielding effects (NICS) indicate that aromaticity is not important in these systems. The inorganic fullerene cages have lower stabilities compared with their carbon analogs. Si(60) is stable towards spontaneous disintegration up to 700 K according to DFTB-MD simulations, and thus has potential for experimental observation. In contrast, Ge(60) preserves its cage structure only up to 200 K.

Journal Article↗
PubMed2002

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.

Photoactive yellow protein (PYP) is a prototype of the PAS domain superfamily of signaling proteins. The signaling process is coupled to a three-state photocycle. After the photoinduced trans-cis isomerization of the chromophore, 4-hydroxycinnamic acid (pCA), an early intermediate (pR) is formed, which proceeds to a second intermediate state (pB) on a sub-millisecond time scale. The signaling process is thought to be connected to the conformational changes upon the formation of pB and its recovery to the ground state (pG), but the exact signaling mechanism is not known. Experimental studies of PYP by solution NMR and X-ray crystallography suggest a very flexible protein backbone in the ground as well as in the signaling state. The relaxation from the pR to the pB state is accompanied by the protonation of the chromophore's phenoxyl group. This was found to be of crucial importance for the relaxation process. With the goal of gaining a better understanding of these experimental observations on an atomistic level, we performed five MD simulations on the three different states of PYP: a 1 ns simulation of PYP in its ground state [pG(MD)], a 1 ns simulation of the pR state [pR(MD)], a 2 ns simulation of the pR state with the chromophore protonated (pRprot), a 2 ns simulation of the pR state with Glu46 exchanged by Gln (pRGln) and a 2 ns simulation of PYP in its signaling state [pB(MD)]. Comparison of the pG simulation results with X-ray and NMR data, and with the results obtained for the pB simulation, confirmed the experimental observations of a rather flexible protein backbone and conformational changes during the recovery of the pG from the pB state. The conformational changes in the region around the chromophore pocket in the pR state were found to be crucially dependent on the strength of the Glu46-pCA hydrogen bond, which restricts the mobility of the chromophore in its unprotonated form considerably. Both the mutation of Glu46 with Gln and the protonation of the chromophore weaken this hydrogen bond, leading to an increased mobility of pCA and large structural changes in its surroundings. These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant.

Bacterial Proteins↗
PubMed2002

Mechanism of olefin metathesis with catalysis by ruthenium carbene complexes: density functional studies on model systems.

Gradient-corrected (BP86) density functional calculations were used to study alternative mechanisms of the metathesis reactions between ethene and model catalysts [(PH(3))(L)Cl(2)Ru[double bond]CH(2)] with L=PH3 (I) and L=C(3)N(2)H(4)=imidazol-2-ylidene (II). On the associative pathway, the initial addition of ethene is calculated to be rate-determining for both catalysts (Delta G(22-25)*[double bond] kcal mol(-1)). The dissociative pathway starts with the dissociation of phosphane, which is rather facile (Delta G(298)* is approximately equal to 5-10 kcal mol(-1)). The resulting active species (L)Cl(2)Ru[double bond]CH(2) can coordinate ethene cis or trans to L. The cis addition is unfavorable and mechanistically irrelevant (Delta G(298)* is approximately equal to 21-25 kcal mol(-1)). The trans coordination is barrierless, and the rate-determining step in the subsequent catalytic cycle is either ring closure of the complex to yield the ruthenacyclobutane (catalyst I, Delta G(298)*=12 kcal mol(-1)), or the reverse reaction (catalyst II, ring opening, Delta G(298)*=10 kcal mol(-1)), that is, II is slightly more active than I. For both catalysts, the dissociative mechanism with trans olefin coordination is favored. The relative energies of the species on this pathway can be tuned by ligand variation, as seen in (PMe(3))(2)Cl(2)Ru[double bond]CH(2) (III), in which phosphane dissociation is impeded and olefin insertion is facilitated relative to I. The differences in calculated relative energies for the model catalysts I-III can be rationalized in terms of electronic effects. Comparisons with experiment indicate that steric effects must also be considered for real catalysts containing bulky substituents.

Journal Article↗
PubMed2002

The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations.

The primary oxidant of cytochrome P450 enzymes, Compound I, is hard to detect experimentally; in the case of cytochrome P450(cam), this intermediate does not accumulate in solution during the catalytic cycle even at temperatures as low as 200 K (ref 4). Theory can play an important role in characterizing such elusive species. We present here combined quantum mechanical/molecular mechanical (QM/MM) calculations of Compound I of cytochrome P450(cam) in the full enzyme environment as well as density functional studies of the isolated QM region. The calculations assign the ground state of the species, quantify the effect of polarization and hydrogen bonding on its properties, and show that the protein environment and its specific hydrogen bonding to the cysteinate ligand are crucial for sustaining the Fe-S bond and for preventing the full oxidation of the sulfur.

Cytochrome P-450 Enzyme System↗
PubMed2002

[Supplement to the conservation of an entire cadaver according to W. Thiel].

Ten years after publishing the method "The preservation of complete human cadavers in native colours" by W Thiel an improved variant, due to the experiences throughout this time, will be described for the general embalming of corpses and a relating to the apparatus establishment for the preservation of brain in situ.

Autopsy↗