| 1. |
- Ahlstrand, Emma, et al.
(författare)
-
Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands
- 2013
-
Ingår i: International Journal of Quantum Chemistry. - Hoboken, NJ : Wiley. - 0020-7608 .- 1097-461X. ; 113:23, s. 2554-2562
-
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.
|
|
| 2. |
- Ai, Yuejie, 1982-, et al.
(författare)
-
Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies
- 2011
-
Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:10, s. 2366-2377
-
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.
|
|
| 3. |
- Arteca, Gustavo A., et al.
(författare)
-
Generalized electronic diabatic approach to structural similarity and the Hammond postulate
- 2007
-
Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 107:2, s. 382-395
-
Tidskriftsartikel (refereegranskat)abstract
- We revisit the notion of structural similarity along a reaction path within the context of a generalized electronic diabatic (GED) molecular model. In this approach, a reaction involving two closed-shell stable species is described as the evolution of a quantum state that superimposes at least three diabatic electronic species (reactant, product, and an open-shell transition state) coupled by an external electromagnetic field. Reactant and product amplitudes in this general state are also modulated by changing the geometry of a system of classical positive charges interacting with the electrons. By mapping these amplitudes over nuclear configurational space, we can follow the total quantum state along a reaction coordinate and establish its similarity to each of the diabatic species. As a result, chemical processes, and useful notions such as those of energy barriers and the Hammond postulate, emerge as consequence of Franck-Condon-like transitions between quantum states.
|
|
| 4. |
- Arteca, Gustavo A., et al.
(författare)
-
Generalized electronic diabatic approach to structural similarity in two-dimensional potential energy surfaces of various topologies
- 2008
-
Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 108:4, s. 651-666
-
Tidskriftsartikel (refereegranskat)abstract
- Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two-dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open-shell transition state) coupled in an external field. The "effective" 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential-energy-surface topologies (consistent with three-state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product.
|
|
| 5. |
|
|
| 6. |
- Arteca, Gustavo, et al.
(författare)
-
Simulating trends in reaction path geometry as a function of external fields : A generalized electronic diabatic model for two-dimensional energy surfaces
- 2008
-
Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 108:10, s. 1810-1820
-
Tidskriftsartikel (refereegranskat)abstract
- We introduce a protocol to represent quantum states as a linear superposition of model electronic diabatic basis states coupled in an external (static) elec. field. By considering an entire family of these models, we uncover trends in reaction-path geometry and the topol. of potential-energy surfaces, including all those that can be realized in a two-dimensional configurational space. Our approach can be used as a tool to model the key parameters (e.g., diabatic basis states, external field intensity) that yield desired geometrical characteristics in an actual potential energy surface. In this work, external agents such as laser fields, or a group of neighboring charges, are regarded as essential requirements to prompt, or trigger, the occurrence of a chem. process. In these cases, reaction path geometry can be modulated externally so as to yield processes that would appear to occur far from gas-phase geometries. This phenomenol. is intrinsically nonadiabatic. Our present approach accounts for the possibility of such features, i.e., the occurrence of quantum states whose electronic structures resemble products, while at geometries that are more similar to those of reactants.
|
|
| 7. |
- Bakker, Albert, et al.
(författare)
-
Interaction of aluminum(III) with water. An ab initio study
- 1999
-
Ingår i: International Journal of Quantum Chemistry. - 0020-7608 .- 1097-461X. ; 75:4-5, s. 659-669
-
Tidskriftsartikel (refereegranskat)abstract
- Hydrated Al(3+) ions [Al(H(2)O)(n)](3+), n = 1-6, were examined with ab Initio self-consistent field (SCF) calculations. The relative contributions of two-, three-, and higher-body terms to the total interaction energy for an [Al(H(2)O)(6)](3+) complex were calculated The sum of all three-body contributions amounts to - 30% of the sum of all pair-additive contributions and is opposite in sign. The three-body energy contributions were also derived for two types of [Al(H(2)O)(2)](3+) complexes. in the first type, both water molecules reside in the first hydration shell of Al(3+) and in the second type there is one in the first shell and one in the second. Altogether 15,500 triplets were investigated and analytical two- and three-body potential energy functions were derived via a fitting procedure. (C) 1999 John Wiley & Sons, Inc.
|
|
| 8. |
|
|
| 9. |
- Bengtson, Charlotta, et al.
(författare)
-
Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex
- 2016
-
Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 116, s. 1763-1771
-
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.
|
|
| 10. |
|
|
