| 1. |
- Chen, Shilu, et al.
(författare)
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Technical aspects of quantum chemical modeling of enzymatic reactions : the case of phosphotriesterase
- 2008
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 120:4-6, s. 515-522
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Tidskriftsartikel (refereegranskat)abstract
- Quantum chemical methods are today a powerful tool in the study of enzymatic reaction mechanisms. In this paper we evaluate the adequacy of some of the technical approximations frequently used in the modeling of enzyme reactions with high level methods. These include the choice of basis set for geometry optimizations and energy evaluation, the choice of dielectric constant to model the enzyme surrounding, and the effects of locking the centers of truncation. As a test case, we choose the phosphotriesterase enzyme, which is a binuclear zinc enzyme that catalyzes the hydrolysis of organophosphate triesters.
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| 2. |
- Eek, William, 1976, et al.
(författare)
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Simple analysis of atomic reactivity: Thomas-Fermi theory with nonergodicity and gradient correction
- 2006
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 115:4, s. 266-273
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Tidskriftsartikel (refereegranskat)abstract
- Covalent bonding has been found to be related to the relaxation of dynamical constraints on electronic motion in atoms and molecules. The corresponding strain energy in an atom is therefore a measure of its inherent reactivity. Here, such reactivities of the atoms H through Ne are estimated by the use of the Thomas-Fermi density functional theory which can be simply implemented using parametrized exponential electron densities in two different forms-the traditional form assuming complete ergodicity and a modified form which accounts for nonergodicity and therefore strain. The Thomas-Fermi functional is amended by the incorporation of gradient correction of the kinetic energy according to the von Weizsacker prescription. This correction, implemented within the nonergodic form of the Thomas-Fermi theory, is scaled to yield total atomic energies in agreement with the Hartree-Fock results. The scaling factor shows a variation from around 0.07 for Be to 0.1 for Ne. The reactivity, measured by the stabilization brought by going to the ergodic form of quantization within the Thomas-Fermi theory, is zero for He and Ne and shows a broad peak around oxygen in apparent agreement with chemical intuition. Molecular bonding efficiencies are studied for some small molecules and are found to be relatively large for hydrides and smaller for diatomic molecules such as Be-2 and F-2.
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| 3. |
- Gaenko, Alexander V, et al.
(författare)
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Ab initio DFT study of Z-E isomerization pathways of N-benzylideneaniline
- 2007
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 118:1, s. 271-279
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Tidskriftsartikel (refereegranskat)abstract
- The ground state properties and absorption spectra of N-benzylideneaniline (NBA) have been studied at the density functional (DFT) and at the time-dependent density functional (TD-DFT) level of the theory. The equilibrium geometries of the E and Z isomers in the ground state and their vibrational frequencies have been computed. Furthermore, the excitation energies of the lowest excited singlet and triplet states and the potential energy curves along the torsion and the inversion isomerization coordinates were evaluated. The results are discussed in light of the available experimental data.
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| 4. |
- Gräfenstein, Jürgen, 1963, et al.
(författare)
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The self-interaction error and the description of non-dynamic electron correlation in density functional theory
- 2009
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 123:3-4, s. 171-182
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Tidskriftsartikel (refereegranskat)abstract
- The self-interaction error (SIE) plays a central role in density functional theory (DFT) when carried out with approximate exchange-correlation functionals. Its origin, properties, and consequences for the development of standard DFT to a method that can correctly describe multi-reference electron systems by treating dynamic and non-dynamic electron correlation on an equal footing, is discussed. In this connection, the seminal work of Colle and Salvetti on wave function-based correlation functionals that do no longer suffer from a SIE is essential. It is described how the Colle–Salvetti correlation functional is an anchor point for the derivation of a functional multi-reference DFT method.
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| 5. |
- Himo, Fahmi
(författare)
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Quantum chemical modeling of enzyme active sites and reaction mechanisms
- 2006
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 116:03-jan, s. 232-240
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Tidskriftsartikel (refereegranskat)abstract
- Density functional methods, in particular the B3LYP functional, together with the explosive enhancement of computational power, have in the last 5 years or so made it possible to model enzyme active sites and reaction mechanisms in a quite realistic way. Many mechanistic problems have indeed been addressed and solved. This review gives a brief account of the methods and models used to study enzyme active sites and their reaction mechanisms using quantum chemical methods. Examples are given from our recent work in this field. Future perspectives of the field are discussed.
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| 6. |
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| 7. |
- Labet, Vanessa, et al.
(författare)
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Proton catalyzed hydrolytic deamination of cytosine : a computational study
- 2008
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Ingår i: Theoretical Chemistry accounts. - Berlin Heidelberg : Springer. - 1432-881X .- 1432-2234. ; 120:4-6, s. 429-435
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Tidskriftsartikel (refereegranskat)abstract
- Two pathways involving proton catalyzed hydrolytic deamination of cytosine (to uracil) are investigated at the PCM-corrected B3LYP/6-311G(d,p) level of theory, in the presence of an additional catalyzing water molecule. It is concluded that the pathway involving initial protonation at nitrogen in position 3 of the ring, followed by water addition at C4 and proton transfer to the amino group, is a likely route to hydrolytic deamination. The rate determining step is the addition of water to the cytosine, with a calculated free energy barrier in aqueous solution of G==140 kJ/mol. The current mechanism provides a lower barrier to deamination than previous work based on OH− catalyzed reactions, and lies closer to the experimental barrier derived from rate constants (Ea = 117 ± 4kJ/mol).
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| 8. |
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| 9. |
- Müller, Carsten, et al.
(författare)
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Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders
- 2007
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 117:1, s. 41-48
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Tidskriftsartikel (refereegranskat)abstract
- We present a computational approach, using quantum Monte Carlo, that provides some insight into the effect of electron correlation on chemical bonding between individual pairs of atoms. Our approach rests upon a recently suggested relation between the bond order and charge fluctuations with respect to atomic domains. Within the present implementation we have taken a compromise between conceptual rigour and computational simplicity. In a first step atomic domains were obtained from Hartree-Fock (HF) densities, using Bader’s definition of atoms in molecules. These domains were used in a second step in quantum Monte Carlo calculations to determine bond orders for pairs of atoms. Correlation effects have been studied by comparison of HF bond orders with those obtained from pure diffusion quantum Monte Carlo calculations. We illustrate this concept for C–O and C–S bonds in different molecular environments. Our results suggest an approximate linear relation between bond order and bond length for these kinds of bonds.
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| 10. |
- Pedersen, Thomas Bondo, et al.
(författare)
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Density fitting with auxiliary basis sets from Cholesky decompositions
- 2009
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 124:1-2, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Recent progress in the use of Cholesky decomposition techniques within the density fitting approximation of two-electron integrals is reviewed with emphasis on the theoretical background. Special attention is paid to the fact that errors due to the density fitting approximation can be controlled by constructing auxiliary basis sets by means of Cholesky decomposition of either the entire or certain subblocks of the molecular two-electron integral matrix. Finally, the prospects of trivial linear-scaling calculation of fitting coefficients in the Cholesky decomposition-based density fitting scheme are outlined.
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| 11. |
- Rubio Pons, Oscar, et al.
(författare)
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Ab initio calculations of vibronic activity in phosphorescence microwave double resonance spectra of para-dichlorobenzene
- 2005
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 113:1, s. 15-27
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Tidskriftsartikel (refereegranskat)abstract
- The phosphorescence spectrum of p-dichlorobenzene has been calculated using multiconfiguration self-consistent-field wave functions and the quadratic response technique. Attention has been paid to the intensity distribution of the singlet-triplet (B-3(1u)->(1)A(g)) transition through a number of vibronic subbands. The second order spin-orbit coupling (SOC) contribution to the spin splitting of the B-3(1u) ((3)pi pi*) state is found to be almost negligible, and the calculations therefore provide a good estimate for the zero-field splitting (ZFS) parameters based only on the electron spin-spin coupling expectation values. Nuclear quadrupole resonance constants for the different Cl isotopes are also calculated to accomplish the ZFS assignment. The electric dipole activity of the spin sublevels in the triplet singlet transitions to the ground-state vibrational levels is estimated by calculations of derivatives using distorted geometries which are shifted from the equilibrium position along different vibrational modes. A vibrational analysis of the phosphorescence spectrum, based on the SOC-induced mixing of the singlet and triplet states calculated along different vibrational modes, provides reasonable agreement with experimental data.
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| 12. |
- Vallet, V., et al.
(författare)
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Actinide chemistry in solution, quantum chemical methods and models
- 2006
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 115:2-3, s. 145-160
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical modeling of actinide complexes requires access to structural parameters, information on electronic, vibration and rotation energy levels and thermodynamics properties. This article presents a critical review of theoretical studies of actinide chemistry in gas-phase and in solution and a comparison with experimental data in order to assess the applicability and accuracy by which various electronic structure theories can predict the required quantities. The quality of the basis set, the importance of electron correlation, the description of solute-solvent interactions is discussed in some detail.
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| 13. |
- Wåhlin, Pernilla, 1968-, et al.
(författare)
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On the combined use of discrete solvent models and continuum descriptions of solvent effects in ligand exchange reactions : a case study of the uranyl(VI) aquo ion
- 2009
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 124:5-6, s. 377-384
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Tidskriftsartikel (refereegranskat)abstract
- Modeling of the solvent is important when using quantum chemical methods for the assignment of mechanisms from experimental studies of the exchange of water between metal aquo ions and the bulk solvent. In the present study, we have investigated if and how the mechanisms for water exchange in the UO2(OH2)(5)(2+)-H2O system is affected by the choice of chemical models for the second coordination sphere and physical models for describing the cavity in conductor-like polarizable continuum (CPCM) models. In the first case, we have compared models with one and five waters in the second coordination sphere. For both models, we have compared cavities in which each atom is assigned one spherical cavity and one in which the water molecules are described by a single spherical cavity (the United Atom model). There are significant differences in the relative energy of dissociative and associative intermediates; however, they are not large enough to affect the conclusion that the water exchange proceeds through an associative/interchange mechanism.
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| 14. |
- Zhang, Wenhua, et al.
(författare)
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Interaction of biomolecular systems with titanium-based materials: computational investigations
- 2009
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 123:3-4, s. 299-309
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio calculations and molecular dynamics simulations were performed to investigate the adsorption mode of various oligopeptides on titanium dioxide surfaces and to characterize their conformational behavior upon adsorption. The models were progressively improved obtaining a description compatible with the experimental observations.
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| 15. |
- Öhrn, Anders, et al.
(författare)
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Hybrid Monte Carlo simulations of vertical electronic transitions in acetone in aqueous solution
- 2007
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 117:3, s. 441-449
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Tidskriftsartikel (refereegranskat)abstract
- A simulation of the n -> pi* absorption and the pi -> n fluorescence of acetone in aqueous solution is reported. The model has an explicit solvent representation with an effective ab initio treatment of the solute. The model attempts to balance quantum chemistry, intermolecular interactions and statistical thermodynamics. It includes a non-electrostatic perturbation on the solute which models the solute-solvent exchange repulsion and the restriction put on the electronic structure of the solute by the antisymmetry to the solvent. The solvent shift to the absorption transition is found to be between 0.16 and 0.21 eV; the shift to the fluorescence transition is found to be between 0.02 and 0.05 eV. The simulation supports the conclusion that the first peak in the fluorescence spectrum of acetone is from a single molecule in equilibrium with the solvent, not from an excimer.
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