| 1. |
- Andersson, Kerstin
(författare)
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The electronic spectrum of VCr
- 2003
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Ingår i: Theoretical Chemistry Accounts. - Heidelberg : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 218-223
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectrum of VCr has been studied using the complete-active-space self-consistent field complete-active-space second-order perturbation theory approach. Potential-energy curves for 12 electronic states have been computed. Transition energies, with respect to the X(2)Delta ground state, for some of the calculated electronic states are (with possible experimental values within parentheses) 0.53 eV (0.56) for A(2)Sigma(+), 1.03 eV (1. 14) for A(4)Delta, 1.20 eV (1.14) for B(2)Delta, 1.45 eV (1.51) for B(4)Delta, 1.60 eV (1.51, 1.78) for C(2)Delta, and 1.61 eV (1.63) for A(4)Sigma(-).
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| 2. |
- Feierberg, Isabella, et al.
(författare)
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Computational modeling of enzymatic keto-enol isomerization reactions
- 2002
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 108:2, s. 71-84
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Tidskriftsartikel (refereegranskat)abstract
- Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the last few decades. Enzymes catalyzing these reactions, which normally involve labile enolic intermediates, need to overcome large pK a differences between the reacting groups as well as high intrinsic free-energy barriers. Here, we present an overview of results from recent computer simulation studies of keto-enol isomerization reactions catalyzed by the enzymes glyoxalase I, triosephopsphate isomerase and ketosteroid isomerase. For all three enzymes it is found that electrostatic stabilization of the transient enolate intermediates, either by charge–charge interactions or by hydrogen bonding, accounts for the main part of the activation free-energy barrier reduction. Another catalytic effect observed in all cases is the reduction of the reorganization energy by the enzyme active site. Some other factors that have been proposed to be important for these reactions are also discussed and evaluated.
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| 3. |
- Gonzalez-Luque, R, et al.
(författare)
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Theoretical characterization of the absorption spectra of phenanthrene and its radical cation
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 224-232
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Tidskriftsartikel (refereegranskat)abstract
- The vertical absorption spectra of phenanthrene and its radical cation have been studied theoretically by means of a multiconfigurational second-order perturbation approach. Singlet-singlet transition energies and oscillator strengths, and singlet-triplet excitation energies have been studied in the absorption spectrum of phenanthrene up to 6 eV. The absorption spectrum of the phenanthrene radical cation has been computed up to 3.4 eV. The results obtained confirm previous assignments and also lead to new interpretations of the main features of the spectra of these systems.
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| 4. |
- Gusarov, Sergey, et al.
(författare)
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Correlation potentials for a multiconfigurational-based density functional theory with exact exchange
- 2004
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 112:2, s. 84-94
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Tidskriftsartikel (refereegranskat)abstract
- A density functional theory based on a complete active space self consistent field (CASSCF) reference function with exact exchange is discussed. It is first shown that such a theory may be formulated with a correlation potential dependent on the density function and on the active space used. Auxiliary functions, such as the on-top two-particle density, are used to define uniquely the potential for different active spaces. The paper also analyses the correlation functional for some atomic and molecular cases. Large ab initio calculations are performed to obtain accurate density functions. A correlation potential is then fitted such that the reference CASSCF function gives the same density. The correlation potential values are saved in a data base for future analysis.
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| 5. |
- Hermida-Ramón, Jose Manuel, et al.
(författare)
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On the influence of the basis set superposition error on calculated vibrational frequencies
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 190-195
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Tidskriftsartikel (refereegranskat)abstract
- The relation between the so called basis set superposition error and intramolecular vibrational frequencies calculated at the Hartree Fock SCF level of approximation was investigated. A linear conformation of HF dimer was chosen as test system for the investigation. It was found that the direct basis set superposition error for the studied system is rather small. It was further found that the shifts are mainly determined by the geometry parameters of the system
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| 6. |
- Khan, MO, et al.
(författare)
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Nonlinear electric response of polyampholytes
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 110:3, s. 126-129
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Tidskriftsartikel (refereegranskat)abstract
- The behavior of polyampholytes (PAs) in electric fields is investigated by Monte Carlo simulations. In bulk it is found that the response of the PA depends on the charge sequence. For small repeating units of positive and negative charges the response is linear, while bigger units results in a nonlinear response in both the induced dipole moment and the resulting polymer conformation. This is reflected in how PAs modify colloidal suspensions, and while PAs always decrease the repulsion between charged colloidal particles, some net-neutral PAs can even induce an effective attraction between the colloidal particles.
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| 7. |
- Lindh, Roland, et al.
(författare)
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Bjorn's top ten
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 115-117
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Lindh, Roland, 1958-, et al.
(författare)
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Molecular integrals by numerical quadrature. I. Radial integration
- 2001
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 106:3, s. 178-187
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Tidskriftsartikel (refereegranskat)abstract
- This article presents a numerical quadrature intended primarily for evaluating integrals in quantum chemistry programs based on molecular orbital theory, in particular density functional methods. Typically, many integrals must be computed. They are divided up into different classes, on the basis of the required accuracy and spatial extent. Ideally, each batch should be integrated using the minimal set of integration points that at the same time guarantees the required precision. Currently used quadrature schemes are far from optimal in this sense, and we are now developing new algorithms. They are designed to be flexible; such that given the range of functions to be integrated, and the required precision, the integration is performed as economically as possible with error bounds within specification. A standard approach is to partition space into a see of regions, where each region is integrated using a spherically polar grid. This article presents a radial quadrature which allows error control, uniform error distribution and uniform error reduction with increased number of radial grid points. A relative error less than 10(-14) for all s-type Gaussian integrands with an exponent range of 14 orders of magnitude is achieved with about 200 grid points. Higher angular I quantum numbers, lower precision or narrower exponent ranges require fewer points. The quadrature also allows controlled pruning of the angular grid in the vicinity of the nuclei.
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| 9. |
- Lindh, Roland, 1958-, et al.
(författare)
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Semidirect parallel self-consistent field : the load balancing problem in the input/output intensive self-consistent field iterations
- 2003
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 156-164
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Tidskriftsartikel (refereegranskat)abstract
- The full capacity of contemporary parallel computers can, in the context of iterative ab initio procedures like, for example, self-consistent field (SCF) and multiconfigurational SCF, only be utilized if the disk and input/output (I/O) capacity are fully exploited before the implementation turns to an integral direct strategy. In a recent report on parallel semidirect SCF http://www.tc.cornell.edu/er/media/1996/collabrate.html, http://www.fp.mcs.anl.gd/grand-challenges/chem/non-direct/index.html it was demonstrated that super-linear speedups are achievable for algorithms that exploit scalable parallel I/O. In the I/O-intensive SCF iterations of this implementation a static load balancing, however, was employed, dictated by the initial iteration in which integral evaluation dominates the central processing unit activity and thus determines the load balancing. In the present paper we present the first implementation in which load balancing is achieved throughout the whole SCF procedure, i.e. also in subsequent iterations. The improved scalability of our new algorithm is demonstrated in some test calculations, for example, for 63-node calculation a speedup of 104 was observed in the computation of the two-electron integral contribution to the Fock matrix.
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| 10. |
- Lundberg, Marcus, 1974-, et al.
(författare)
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Modeling water exchange on monomeric and dimeric Mn centers
- 2003
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 110:3, s. 130-143
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Tidskriftsartikel (refereegranskat)abstract
- Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn-IV(H2O)(2)(OH)(4)] is only 9.6 kcal mol(-1), corresponding to a rate of 6 x 10(5) s(-1). It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H2O)(2)(OH)(2)Mn-IV(mu-O)(2)Mn-IV(H2O)(2) (OH)(2)] is 8.6 kcal mol(-1), while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol(-1). These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic 02 catalyst [(terpy)(H2O)Mn-IV(mu-O)(2)Mn-IV(O.)(terpy)](3+) (terpy=2,2':6,2"-terpyridine). The calculated reaction barrier is 14.7 kcal mol(-1).
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| 11. |
- Minaev, Boris, et al.
(författare)
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Solvent effects on optically detected magnetic resonance in triplet spin labels
- 2004
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 111:2-6, s. 168-175
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Tidskriftsartikel (refereegranskat)abstract
- We have calculated solvent effects on the zero-field splitting (ZFS) constants induced by electron spin-spin coupling (SSC) in the low-lying triplet states of azaaromatic molecules in solutions using multiconfiguration self-consistent-field wave functions and the polarizable continuum model. The second-order spin-orbit coupling (SOC) contribution to the splitting of the (3)pipi(*) states is found to be almost negligible, and the calculations therefore provide a good estimate of the ZFS parameters and their solvent dependence based only on the electron spin-spin coupling expectation values. The correlation between the shift in the ZFS and the phosphorescence frequency that has been observed in optically detected magnetic resonance experiments in low-temperature glasses is supported by our direct SSC calculations without taking SOC into account. This makes it possible to distinguish between the two theories that earlier were proposed to explain the inhomogeneous broadening of triplet state spectra, and discard the one that is exclusively based on the SOC-induced mixing of the singlet and triplet states.
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| 12. |
- Polo, Victor, et al.
(författare)
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Long-range and short-range Coulomb correlation effects as simulated by Hartree-Fock, local density approximation, and generalized gradient approximation exchange functionals
- 2003
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 109, s. 22-35
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Tidskriftsartikel (refereegranskat)abstract
- Exchange functionals used in density functional theory (DFT) are generally considered to simulate long-range electron correlation effects. It is shown that these effects can be traced back to the self-interaction error (SIE) of approximate exchange functionals. An analysis of the SIE with the help of the exchange hole reveals that both short-range (dynamic) and long-range (nondynamic) electron correlation effects are simulated by DFT exchange where the local density approximation (LDA) accounts for stronger effects than the generalized gradient expansion (GGA). This is a result of the fact that the GGA exchange hole describes the exact exchange hole close to the reference electron more accurately than the LDA hole does. The LDA hole is more diffuse, thus leading to an underestimation of exchange and stronger SIE effects, where the magnitude of the SIE energy is primarily due to the contribution of the core orbitals. The GGA exchange hole is more compact, which leads to an exaggeration of exchange in the bond and the nonbonding region and negative SIE contributions. Partitioning of the SIE into intra-/interelectronic and individual orbital contributions makes it possible to test the performance of a given exchange functional in different regions of the molecule. It is shown that Hartree-Fock exchange always covers some long-range effects via interelectronic exchange while self-interaction-corrected DFT is lacking these effects.
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| 13. |
- Roos, Björn, et al.
(författare)
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Relativistic atomic natural orbital type basis sets for the alkaline and alkaline-earth atoms applied to the ground-state potentials for the corresponding dimers
- 2004
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 111:2-6, s. 345-351
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Tidskriftsartikel (refereegranskat)abstract
- New basis sets of the atomic natural orbital (ANO) type have been developed for the atoms Li-Fr and Be-Ra. The ANOs have been obtained from the average density matrix of the ground states and the lowest excited states of the atom, the positive ion, and the dimer at its equilibirium geometry. Scalar realtivisitc effects are included through the use of a Douglas-Kroll Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of the ground-state potentials for the dimers. Computed bond energies are accurate to within 0.05 eV for the alkaline dimers and 0.02 eV for the alkaline-earth dimers (except for Be-2).
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| 14. |
- Rubio, Mercedes, et al.
(författare)
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Theoretical studies of isomers of C3H2 using a multiconfigurational approach
- 2000
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Ingår i: Theoretical Chemistry accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 105:1, s. 15-30
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Tidskriftsartikel (refereegranskat)abstract
- The C3H2 isomers are important molecules in interstellar space. An understanding of their electronic structure can contribute significantly to the interpretation of interstellar spectra. In a theoretical study of the C3H2 isomers a multiconfigurational treatment is of interest because many of the isomers are carbenes or diradicals. We present such an investigation of all possible C3H2 isomers. The most important features of their electronic and vibrational spectra are calculated. Earlier theoretical studies are reviewed and it is shown that the present study yields the same order of stability for the singlet and triplet states as most previous studies.
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| 15. |
- Ryde, Ulf, et al.
(författare)
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A theoretical study of the copper–cysteine bond in blue copper proteins
- 2001
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X. ; 105:6, s. 452-462
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Tidskriftsartikel (refereegranskat)abstract
- The accuracy of theoretical calculations on models of the blue copper proteins is investigated using density functional theory (DFT) Becke's three-parameter hybrid method with the Lee–Yang–Parr correlation functional (B3LYP) and medium-sized basis sets. Increasing the basis set to triple-zeta quality with f-type functions on all heavy atoms and enlarging the model [up to Cu(imidazole-CH3)2(SC2H5) (CH3SC2H5)0/+] has only a limited influence on geometries and relative energies. Comparative calculations with more accurate wave-function–based methods (second-order Møller–Plesset perturbation theory, complete-active-space second-order perturbation theory, coupled-cluster method, including single and double replacement amplitudes and in addition triple replacement perturbatively) and a variety of basis sets on smaller models indicate that the DFT/B3LYP approach gives reliable results with only a small basis set dependence, whereas the former methods strongly depend on the size of the basis sets. The effect of performing the geometry optimizations in a continuum solvent is quite small, except for the flexible Cu-SMet bond. The results of this study confirm the earlier results that neither the oxidized nor the reduced copper site in the blue proteins is strained to any significant degree (in energy terms) by the protein surrounding.
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| 16. |
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