| 1. |
- Jensen, Kasper, et al.
(författare)
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The axial N-base has minor influence on Co-C bond cleavage in cobalamins
- 2002
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Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 585:1, s. 239-255
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the properties of cobalamin complexes with imidazolate using the density functional B3LYP method, In particular, we have compared imidazolate (Imm) with imidazole and 5,6-dimethylbenzimidazole (DMB), and studied how constraints in the axial Co-N bond length may affect the strength of the Co-C bond. The results show that the optimum Co-N-Imm bond is similar to0.2 Angstrom shorter than that of imidazole. There is no indication from crystal structures that the histidine ligand would be deprotonated in the enzymes. However, it is likely that it attains some imidazolate character through its hydrogen bond to a conserved aspartate residue. The Co-N bond with imidazolate is three times more rigid than that with imidazole or DMB, but twice as flexible as the Co-C bond. Constraints in the Co-N-Imm bond length give rise to a larger change in the corrin conformation than imidazole, but smaller than for DMB. The resulting effect for the Co-C bond dissociation energy is larger for imidazolate than for imidazole or DMB. However, even the largest reasonable distortion can only enhance catalysis by 15 kJ mol(-1). Therefore, we conclude that, irrespective of the nature of the N-base, constraints in the axial Co-N bond lengths cannot be the main reason for the catalytic power of cobalamin enzymes.
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| 2. |
- Ryde, Ulf, et al.
(författare)
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Quantum refinement - a combination of quantum chemistry and protein crystallography.
- 2003
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Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 632:1-3, s. 259-275
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Forskningsöversikt (refereegranskat)abstract
- The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.
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| 3. |
- Andres, J, et al.
(författare)
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Transition structures for hydride transfer reactions in vacuo and their role in enzyme catalysis
- 1996
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Ingår i: Journal of Molecular Structure: THEOCHEM. - : Elsevier. - 0166-1280. ; 371, s. 299-312
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Forskningsöversikt (refereegranskat)abstract
- A general discussion as to the role of in vacuo transition structure in enzyme catalysis is presented. Quantum mechanical aspects are emphasized. The transition structures defined as saddle points of index one (SPi-1) for the hydride transfer step on different model enzyme systems from flavoproteins to dehydrogenases have been characterized with analytical gradients at different levels of theory: semi-empirical; ab initio with different basis sets within the Hartree-Fock scheme; density functional theory using different approaches. Quantum chemical characteristics of the SPi-1 are used to discuss hydride transfer step in enzyme catalyzed reactions and mechanistic implications. With the exception of dihydrofolate reductase, the results for all other systems studied suggest that the endo relative orientation imposed by the active site on the reactants is essential for polarizing the CdHt bond and situating the system in the quadratic region of the endo SPi-1. The geometry and transition vector components are both model independent and weakly dependent on the level of theory used in their determination. Comparisons of the SPi-1 geometries with available X-ray coordinates show that the SPi-1 can be fitted without any stress at the active site. The geometrical arrangement of the SPi-1 results in optimal frontier LUMO orbital interactions, and the transition vector amplitudes show primary and secondary isotope effects to be strongly coupled. A comparison between simple and sophisticated molecular models shows that there is a minimal molecular model associated with geometrical parameters describing the essentials of the chemical interconversion step. For hydride transfer, the corresponding transition vector is an invariant feature.
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| 4. |
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| 5. |
- Dong, XC, et al.
(författare)
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A theoretical study of the cationic dimerization and polymerization of isobutene
- 1997
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Ingår i: Journal of Molecular Structure. - 0166-1280. ; 392, s. 111-124
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Tidskriftsartikel (refereegranskat)abstract
- The initial steps in the radiation-induced polymerization of isobutene have been studied by quantum chemical ab initio and semiempirical calculations. The addition of an isobutene cation to a neutral isobutene molecule to form a dimer radical cation is found to be a strongly exothermic reaction, by 29-32 kcal mol(-1) depending on the computational method. A 17 kcal mol(-1) barrier towards a one-hydrogen-shift isomerization reaction, yielding a 2,5-dimethyl-2-hexene radical cation, is obtained at the PMP2/6-31G(d, p) level, which is significantly higher than the value of 6 kcal mol(-1) obtained before for the corresponding isomerization of the ethene dimer radical cation. The further steps of the polymerization of isobutene are investigated in terms of addition reactions between a neutral isobutene moiety and the addition complex formed in the step before. The positive charge and the radical centres are found to be located in opposite ends of each of the radical cationic intermediate complexes, the positive charge centre being energetically the most favourable site of attachment. The overall reaction is thermodynamically favourable and has a high spatial selectivity. The polymer chain has a high structural symmetry and no cross-linking.
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| 6. |
- Guo, J. D., et al.
(författare)
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A theoretical study of the photo-oxidation of a fluorene-based two-photon chromophore
- 2003
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 635, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- The infrared and optical absorption spectra of a fluorene-based two-photon chromophore AF50 (N,N-diphenyl-7-2-(4-pyridinyl)-ethenyl-9,9-di-n-decyl-9H-fluorene-2-amine) and its photo-oxidation products after ultra-violet exposure have been calculated using hybrid density functional theory. Our calculations have provided very useful information about the nature of the read/write process of AF50 and its possible final products.
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| 7. |
- Jansik, B., et al.
(författare)
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Relativistic effects on linear and non-linear polarizabilities of the furan homologues
- 2003
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 633:03-feb, s. 237-246
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Tidskriftsartikel (refereegranskat)abstract
- First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H4, X = O, S, Se, Te, at three different levels of theory; time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these.
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| 8. |
- Jansik, B., et al.
(författare)
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Relativistic effects on linear and non-linear polarizabilities of the furan homologues
- 2003
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Ingår i: Journal of Molecular Structure. - 0166-1280. ; 633:2-3, s. 237-246
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Tidskriftsartikel (refereegranskat)abstract
- First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H 4, X = O, S, Se, Te, at three different levels of theory, time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these. © 2003 Elsevier B.V. All rights reserved.
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| 9. |
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| 10. |
- MURRAY, JS, et al.
(författare)
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CORRELATIONS BETWEEN MOLECULAR ELECTROSTATIC POTENTIALS AND SOME EXPERIMENTALLY-BASED INDEXES OF REACTIVITY
- 1992
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Ingår i: Journal of Molecular Structure. - UNIV NEW ORLEANS, DEPT CHEM, NEW ORLEANS, LA 70148 USA. : ELSEVIER SCIENCE BV. - 0166-1280. ; 88, s. 29-45
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Tidskriftsartikel (refereegranskat)abstract
- The key role that electrostatics plays in molecular reactive behavior is demonstrated in this work, which surveys and further explores correlations that we found between the molecular electrostatic potential V(r) calculated by an ab initio SCF-MO approach (a gas-phase property) and experimentally-based indices of reactivity (derived from solution studies). In our relationships involving negative V(r), we find in all cases that spatial minima (V(min)) provide correlations of higher quality than surface minima (V(S,min)). Relationships between V(min) and the hydrogen-bond-acceptor parameter-beta, and V(S,max) and the hydrogen-bond-donor parameter-alpha, confirm the physical validity of the empirically-derived solvatochromic parameters-alpha and beta. Correlations between the V(min) of NH2-X molecules and the substituent constants sigma(I), and sigma(I) + sigma(R) (when sigma(R) > 0) for the substituents X show how electrostatic properties reflect the electron-attracting tendencies of substituent groups. Whereas good relationships exist between the pK(a) values of some limited groups of molecules and their conjugate base V(min), we find that the average local ionization energy IBAR-(r) is better suited as a general measure of aqueous acidity.
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