| 1. |
- Ahlstrand, Emma, et al.
(författare)
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Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands
- 2013
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Ingår i: International Journal of Quantum Chemistry. - Hoboken, NJ : Wiley. - 0020-7608 .- 1097-461X. ; 113:23, s. 2554-2562
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Tidskriftsartikel (refereegranskat)abstract
- Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.
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| 2. |
- Ai, Yuejie, 1982-, et al.
(författare)
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Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:10, s. 2366-2377
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Tidskriftsartikel (refereegranskat)abstract
- We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.
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| 3. |
- Bengtson, Charlotta, et al.
(författare)
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Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex
- 2016
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 116, s. 1763-1771
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Tidskriftsartikel (refereegranskat)abstract
- The Fenna-Matthews-Olson (FMO) complex - a pigment protein complex involved in photosynthesis in green sulfur bacteria - is remarkably efficient in transferring excitation energy from light harvesting antenna molecules to a reaction center. Recent experimental and theoretical studies suggest that quantum coherence and entanglement may play a role in this excitation energy transfer (EET). We examine whether bipartite quantum nonlocality, a property that expresses a stronger-than-entanglement form of correlation, exists between different pairs of chromophores in the FMO complex when modeling the EET by the hierarchically coupled equations of motion method. We compare the results for nonlocality with the amount of bipartite entanglement in the system. In particular, we analyze in what way these correlation properties are affected by different initial conditions. It is found that bipartite nonlocality only exists when the initial conditions are chosen in an unphysiological manner and probably is absent when considering the EET in the FMO complex in its natural habitat. It is also seen that nonlocality and entanglement behave quite differently in this system. In particular, for localized initial states, nonlocality only exists on a very short time scale and then drops to zero in an abrupt manner. As already known from previous studies, quantum entanglement between chromophore pairs on the other hand is oscillating and exponentially decaying and follow thereby a pattern more similar to the chromophore population dynamics. The abrupt disappearance of nonlocality in the presence of nonvanishing entanglement is a phenomenon we call nonlocality sudden death; a striking manifestation of the difference between these two types of correlations in quantum systems.
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| 4. |
- Björkman, Torbjörn, et al.
(författare)
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Adaptive Smearing for Brillouin Zone Integration
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:5, s. 1025-1030
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Tidskriftsartikel (refereegranskat)abstract
- We suggest a simple scheme for automatically determining the width parameter of smearing methods of the Brillouin zone integration in electronic structure calculation. The scheme retains one free parameter that at any time can be eliminated by choosing a denser k-space mesh until the desired accuracy is obtained. The tests are carried out in the context of Methfessel-Paxton smearing. This adaptive Gaussian smearing (AGS) is easily implemented, variational with respect to partial occupancies and free from spurious occupancies that are negative or larger than one. Its convergence properties are similar to those obtained with the modified tetrahedron method for energy resolution of >= 0.1 meV.
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| 5. |
- Blomberg, Margareta R. A.
(författare)
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How Quantum Chemistry Can Solve Fundamental Problems in Bioenergetics
- 2015
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 115:18, s. 1197-1201
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Tidskriftsartikel (refereegranskat)abstract
- Three different enzymes are discussed, cytochrome c oxidase, involved in aerobic respiration, cytochrome c dependent nitric oxide reductase, involved in denitrification (anaerobic respiration), and photosystem II, involved in photosynthesis. For all three systems, free energy profiles for the entire catalytic cycle are obtained from quantum mechanical calculations on large cluster models of the active sites, using hybrid density functional theory with the B3LYP* functional. The free energy pro-files are used to solve different fundamental problems concerning energy conservation, enzymatic reaction mechanisms and structure, and also to explain experimental results that seem to be in conflict with each other. Possible future applications to related problems using similar methodology are suggested.
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| 6. |
- Bondarchuk, S. V., et al.
(författare)
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Theoretical study of the triplet state aryl cations recombination : A possible route to unusually stable doubly charged biphenyl cations
- 2013
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 113:24, s. 2580-2588
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Tidskriftsartikel (refereegranskat)abstract
- The self-recombination reactions of 4-aminophenyl cations and parent phenyl cations, each in ground triplet states, are studied within the framework of density functional theory. Only the total zero spin (singlet state) is chosen, as the quintet and triplet counterparts are nonreactive in these systems. The recombination products are the benzidine and biphenyl doubly charged cations. These species are unexpectedly stable. The transition state of the 4-aminophenyl cations reaction is located at the distance of about 4.0 Å between the ipso-carbon atoms. The activation barrier is predominantly formed by electrostatic repulsion between two cations and is estimated to be 27.6 kcal mol−1 [B3LYP/6–311+G(d,p)]. Similar results are obtained for the phenyl cations recombination. The general importance of the participation of other aryl cations in analogous organic reactions is discussed.
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| 7. |
- Boström, Jonas, et al.
(författare)
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Analytical gradients of the second-order Møller–Plesset energy using Cholesky decompositions
- 2014
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 114:5, s. 321-327
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Tidskriftsartikel (refereegranskat)abstract
- An algorithm for computing analytical gradients of the second-order Møller–Plesset (MP2) energy using density fitting (DF) is presented. The algorithm assumes that the underlying canonical Hartree–Fock reference is obtained with the same auxiliary basis set, which we obtain by Cholesky decomposition (CD) of atomic electron repulsion integrals. CD is also used for the negative semidefinite MP2 amplitude matrix. Test calculations on the weakly interacting dimers of the S22 test set (Jurečka et al., Phys. Chem. Chem. Phys. 2006, 8, 1985) show that the geometry errors due to the auxiliary basis set are negligible. With double-zeta basis sets, the error due to the DF approximation in intermolecular bond lengths is better than 0.1 pm. The computational time is typically reduced by a factor of 6–7.
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| 8. |
- Brändas, Erkki J.
(författare)
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Arrows of time and fundamental symmetries in chemical physics
- 2013
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Ingår i: International Journal of Quantum Chemistry. - New York : Wiley-Blackwell. - 0020-7608 .- 1097-461X. ; 113:3, s. 173-184
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Tidskriftsartikel (refereegranskat)abstract
- The field of chemical and physical processes, using principal microscopic techniques, should today allegedly be identified as a fundamental branch of physics. The discipline, by tradition known as chemical physics, is undergoing rapid progress. This assessment, illustrated by the advances presented at this Congress, is characterized by modern developments and novel trends with a concrete bearing on original theoretical understanding, with the possibility to go beyond traditional interpretations and explanations. In this vein, we do not only consider nonrelativistic treatments of various types of molecules including interactions between these and polymers, theoretical examinations of chemical reactions, surface states and interface states, disordered phenomena etc., but also recent progress together with non-Hermitean extensions to quantum mechanics and statistical mechanics. The latter leads to a united edifice of theoretical constructions including the law of self-reference, which emerges in analogy with the illustrious Godel theorem(s) of mathematical logic, that is, the assertion of the inherent limitations of all nontrivial axiomatic systems. The current development begets the foundation of temporal processes and associated invariance principles including the valuation of the various arrows of time. The present conjugate operator array formulation supports the possible gravitational origin of molecular chirality and other principal symmetry violations.
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| 9. |
- Brändas, Erkki J.
(författare)
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Godelian Structures and Self-Organization in Biological Systems
- 2011
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:7-8, s. 1321-1332
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Tidskriftsartikel (refereegranskat)abstract
- In 1986, Seel and Ladik asked, which role Godel's incompleteness theorem should have in a basic theory of biology. Recently, the author has tried to collect the conditions, which such a meta-theory must fulfill. A further argument concerned the deeper connection between classical canonical forms of so-called (triangular) Jordan blocks in the description of open quantal systems far from equilibrium and those of self-referential contradictions and paradoxes in philosophy and mathematical logic. Related examples were quoted from the emergence of self-organization in so-called dissipative structures with applications to both fundamental-and of higher order levels of organization. To bring this analogy closer together, we have developed a quantum logical formalism, describing such a Godelian situation, via the characterization of a well-defined "truth matrix." In this setting, the modus operandi of exploiting self-referential traits and paradoxical inconsistencies emphasize the possibility of a meta-code in complicated enough (biological) systems. In conclusion, we will revisit situations were the aforementioned self-referential property, together with the laws of physics and chemistry will guide our understanding of biology. We will finally consider subsequent implications on the various positions on artificial intelligence.
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| 10. |
- Brändas, Erkki J.
(författare)
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Non-hermitian quantum mechanics
- 2012
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 112:15, s. 2764-2765
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Recension (övrigt vetenskapligt/konstnärligt)
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