Biomedical subjects

Evert Jan Baerends

Publications and source records attributed to Evert Jan Baerends.

At least 19 recordsLinked to original sources

PubMed2006

Oxidative properties of FeO2+: electronic structure and solvation effects.

An electronic structure analysis is provided of the action of solvated FeO(2+), [FeO(H(2)O)(5)](2+), as a hydroxylation catalyst. It is emphasized that the oxo end of FeO(2+) does not form hydrogen bonds (as electron donor and H-bond acceptor) with H-bond donors nor with aliphatic C-H bonds, but it activates C-H bonds as an electron acceptor. It is extremely electrophilic, to the extent that it can activate even such poor electron donors as aliphatic C-H bonds, the C-H bond orbital acting as electron donor in a charge transfer type of interaction. Lower lying O-H bonding orbitals are less easily activated. The primary electron accepting orbital in a water environment is the 3sigma*alpha orbital, an antibonding combination of Fe-3d(z(2)) and O-2p(z), which is very low-lying relative to the pi*alpha compared with, for example, the sigma* orbital in O(2) relative to its pi*. This is ascribed to relatively small Fe-3d(z(2)) with O-2p(z) overlap, due to the nodal structure of the 3d(z(2)).The H-abstraction barrier is very low in the gas phase, but it is considerably enhanced in water solvent. This is shown to be due to strong screening effects of the dielectric medium, leading to relative destabilization of the levels of the charged [FeO(H(2)O)(5)](2+) species compared to those of the neutral substrate molecules, making it a less effective electron acceptor. The solvent directly affects the orbital interactions responsible for the catalytic reaction.

Journal Article↗

PubMed2006

Exploring the ability of frozen-density embedding to model induced circular dichroism.

In this study, we present calculations of the circular dichroism (CD) spectra of complexes between achiral and chiral molecules. Nonzero rotational strengths for transitions of the nonchiral molecule are induced by interactions between the two molecules, which cause electronic and/or structural perturbations of the achiral molecule. We investigate if the chiral molecule (environment) can be represented only in terms of its frozen electron density, which is used to generate an effective embedding potential. The accuracy of these calculations is assessed in comparison to full supermolecular calculations. We can show that electronic effects arising from specific interactions between the two subsystems can reliably be modeled by the frozen-density representation of the chiral molecule. This is demonstrated for complexes of 2-benzoylbenzoic acid with (-)-(R)-amphetamine and for a nonchiral, artificial amino acid receptor system consisting of ferrocenecarboxylic acid bound to a crown ether, for which a complex with l-leucine is studied. Especially in the latter case, where multiple binding sites and interactions between receptor and target molecule exist, the frozen-density results compare very well with the full supermolecular calculation. We also study systems in which a cyclodextrin cavity serves as a chiral host system for a small, achiral molecule. Problems arise in that case because of the importance of excitonic couplings with excitations in the host system. The frozen-density embedding cannot describe such couplings but can only capture the direct effect of the host electron density on the electronic structure of the guest. If couplings play a role, frozen-density embedding can at best only partially describe the induced circular dichroism. To illustrate this problem, we finally construct a case in which excitonic coupling effects are much stronger than direct interactions of the subsystem densities. The frozen density embedding is then completely unsuitable.

Journal Article↗

PubMed2006

Long-range solvent effects on the orbital interaction mechanism of water acidity enhancement in metal ion solutions: a comparative study of the electronic structure of aqueous Mg and Zn dications.

We study the dissociation of water coordinated to a divalent metal ion center, M2+ = Mg2+, Zn2+ using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. First, the proton affinity of a coordinated OH- group is computed from gas-phase Mg2+(H2O)5(OH-), which yields a relative higher gas-phase acidity for a Zn2+-coordinated as compared to a Mg2+-coordinated water molecule, DeltapKa(gp) = 5.3. We explain this difference on the basis of a gain in stabilization energy of the Zn2+(H2O)5(OH-) system arising from direct orbital interaction between the coordinated OH- and the empty 4s state of the cation. Next, we compute the acidity of coordinated water molecules in solution using free-energy thermodynamic integration with constrained AIMD. This approach yields pKa Mg2+ = 11.2 and pKa Zn2+ = 8.4, which compare favorably to experimental data. Finally, we examine the factors responsible for the apparent decrease in the relative Zn2+-coordinated water acidity in going from the gas-phase (DeltapKa(gp) = 5.3) to the solvated (DeltapKa = 2.8) regime. We propose two simultaneously occurring solvation-induced processes affecting the relative stability of Zn2+(H2O)5(OH-), namely: (a) reduction of the Zn 4s character in solution states near the bottom of the conduction band; (b) hybridization between OH- orbitals and valence-band states of the solvent. Both effects contribute to hindering the OH- --> Zn2+ charge transfer, either by making it energetically unfavorable or by delocalizing the ligand charge density over several water molecules.

Acids↗

PubMed2006

Assessment of a simple correction for the long-range charge-transfer problem in time-dependent density-functional theory.

The failure of the time-dependent density-functional theory to describe long-range charge-transfer (CT) excitations correctly is a serious problem for calculations of electronic transitions in large systems, especially if they are composed of several weakly interacting units. The problem is particularly severe for molecules in solution, either modeled by periodic boundary calculations with large box sizes or by cluster calculations employing extended solvent shells. In the present study we describe the implementation and assessment of a simple physically motivated correction to the exchange-correlation kernel suggested in a previous study [O. Gritsenko and E. J. Baerends J. Chem. Phys. 121, 655 (2004)]. It introduces the required divergence in the kernel when the transition density goes to zero due to a large spatial distance between the "electron" (in the virtual orbital) and the "hole" (in the occupied orbital). A major benefit arises for solvated molecules, for which many CT excitations occur from solvent to solute or vice versa. In these cases, the correction of the exchange-correlation kernel can be used to automatically "clean up" the spectrum and significantly reduce the computational effort to determine low-lying transitions of the solute. This correction uses a phenomenological parameter, which is needed to identify a CT excitation in terms of the orbital density overlap of the occupied and virtual orbitals involved. Another quantity needed in this approach is the magnitude of the correction in the asymptotic limit. Although this can, in principle, be calculated rigorously for a given CT transition, we assess a simple approximation to it that can automatically be applied to a number of low-energy CT excitations without additional computational effort. We show that the method is robust and correctly shifts long-range CT excitations, while other excitations remain unaffected. We discuss problems arising from a strong delocalization of orbitals, which leads to a breakdown of the correction criterion.

Journal Article↗

PubMed2006

Synergism of porphyrin-core saddling and twisting of meso-aryl substituents.

The structural chemistry of meso-aryl-substituted porhyrins has uncovered a bewildering variety of macrocycle distortions. Saddling angles range up to 40 degrees , while the plane of the phenyl groups at the meso positions may be anywhere between perpendicular to the porphyrin plane (theta = 90 degrees) and tilted to quite acute angles (theta = 30 degrees or even less). These two distortions appear to be correlated. This has naturally been explained by steric hindrance: when the phenyls rotate toward the porphyrin plane, for instance, coerced by packing forces, the pyrrole rings can alleviate the steric hindrance by tilting away to a saddled conformation. We demonstrate, however, that the two motions are intrinsically coupled by electronic factors and are correlated even in the absence of external forces. A saddling motion makes it sterically possible for the phenyl rings to rotate toward the porphyrin plane, which will always happen because of increasingly favorable pi-conjugation interaction with smaller angles theta. The considerable energy lowering due to pi conjugation counteracts the energy cost of the saddling, making the concerted saddling/rotation motion very soft. Unsubstituted meso-aryl porphyrins just do not distort, but an additional driving force may tip the balance in favor of the combined distortion motion. Internal forces having this effect are repulsion of the four hydrogens that occupy the central hole of the ring in porphyrin diacids but also steric repulsion in peripherally crowded porphyrins. These findings lead to a clarification and systematization of the observed structural variety, which indeed shows a remarkable correlation between saddling and phenyl ring tilting.

Models, Chemical↗

PubMed2006

A simple natural orbital mechanism of "pure" van der Waals interaction in the lowest excited triplet state of the hydrogen molecule.

A treatment of van der Waals (vdW) interaction by density-matrix functional theory requires a description of this interaction in terms of natural orbitals (NOs) and their occupation numbers. From an analysis of the configuration-interaction (CI) wave function of the 3Sigmau + state of H2 and the exact NO expansion of the two-electron triplet wave function, we demonstrate that the construction of such a functional is straightforward in this case. A quantitative description of the vdW interaction is already obtained with, in addition to the standard part arising from the Hartree-Fock determinant /1sigmag(r1)1sigmau(r2)/, only two additional terms in the two-electron density, one from the first "excited" determinant /2sigmag(r1)2sigmau(r2)/ and one from the state of 3Sigmau + symmetry belonging to the (1pig)1(1piu)1 configuration. The potential-energy curve of the 3Sigmau + state calculated around the vdW minimum with the exact density-matrix functional employing only these eight NOs and NO occupations is in excellent agreement with the full CI one and reproduces well the benchmark potential curve of Kolos and Wolniewicz [J. Chem. Phys. 43, 2429 (1965)]. The corresponding terms in the two-electron density rho2(r1,r2), containing specific products of NOs combined with prefactors that depend on the occupation numbers, can be shown to produce exchange-correlation holes that correspond precisely to the well-known intuitive picture of the dispersion interaction as an instantaneous dipole-induced dipole (higher multipole) effect. Indeed, (induced) higher multipoles account for almost 50% of the total vdW bond energy. These results serve as a basis for both a density-matrix functional theory of van der Waals bonding and for the construction of orbital-dependent functionals in density-functional theory that could be used for this type of bonding.

Journal Article↗

PubMed2006

First hyperpolarizability of a sesquifulvalene transition metal complex by time-dependent density-functional theory.

The first hyperpolarizability and electronic excitation spectrum of sesquifulvalene and a sesquifulvalene ruthenium complex have been computed and analyzed with use of time-dependent density-functional theory. A new orbital decomposition scheme is introduced that allows the computed first hyperpolarizability to be related to the electronic structure of complex molecules. The analysis shows that the first hyperpolarizability of sesquifulvalene is not associated with the first intense absorption, with HOMO-1 --> LUMO+1 character, but is dominated by the lowest energy transition, with HOMO --> LUMO character, despite its very low intensity. In the ruthenium complex, the analysis reveals that the strong enhancement of the nonlinear optical response compared to free sesquifulvalene should not be attributed to the effect of complexation on the hyperpolarizability of sesquifulvalene. The strong hyperpolarizability originates from MLCT transitions from ruthenium d-orbitals to an empty orbital located at the seven ring of sesquifulvalene, transitions that have no analogue in free sequifulvalene.

Journal Article↗

PubMed2006

Coupled-perturbed density-matrix functional theory equations. Application to static polarizabilities.

Starting from the variational equations for the natural occupation numbers and the recently proposed eigenequations for the natural spin-orbitals, we derive coupled-perturbed density-matrix equations that furnish a linear response of the one-electron reduced density matrix to a static perturbation when the total energy is a functional of the one-electron reduced density matrix. Cases when some occupation numbers achieve exactly 0 or 1 or when the total number of the particles in a system is not preserved are taken into consideration. The scheme is applied to computing static polarizabilities from two simple density-matrix functionals. The behavior of the functionals is erratic and they provide only little or no improvement over the coupled-perturbed Hartree-Fock results.

Journal Article↗

PubMed2005

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study.

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.

Algorithms↗

PubMed2005

Rotational effects in the dissociative adsorption of H2 on the Pt211 stepped surface.

Rotational effects in the dissociative adsorption of H2 on the Pt211 stepped surface have been studied using classical trajectory calculations on a six-dimensional, density-functional theory potential-energy surface. Reaction of rotating molecules via an indirect trapping mechanism exhibits an unexpected nonmonotonic dependence on the initial rotational quantum number J. Indirect reaction is first quenched with increasing J but is enhanced again for high J initial states. The quenching is attributed to rotational-to-translational energy transfer, which facilitates escape from the chemisorption wells responsible for molecular trapping. For high J, rotational and translational motions decouple, and the energy transfer is no longer possible, which leads again to trapping. Degeneracy-resolved calculations show that for high initial J, molecules rotating in a "cartwheel" fashion (mJ=0) are more likely to become trapped and react indirectly than "helicoptering" molecules (mJ=J). Experimental confirmation of this finding would lend strong support to the existence of the chemisorption wells that trap molecules prior to reaction.

Journal Article↗

PubMed2005

Structural, optical, and photophysical properties of nickel(II) alkylthioporphyrins: insights from experimental and DFT/TDDFT studies.

The ground- and excited-state properties of a Ni(II) porphyrin bearing peripheral alkylthio group, NiOMTP (OMTP = 2,3,7,8,12,13,17,18-octakis methylthio porphyrinate) have been investigated by steady-state and time-resolved absorption spectrometry and DFT/TDDFT theoretical methods. Several conformations corresponding to different deformations of the porphyrin core and to different orientations of the alkylthio groups have been theoretically explored. The nearly degenerate, purely ruffled D(2d) and hybrid (ruffled with a modest degree of saddling) D(2) conformations, both characterized by an up-down (ud) orientation of the vicinal methylthio groups are by far the preferred conformations in the "gas phase". In contrast to NiOEP, it is the orientation of the peripheral substituents rather than the type and degree of distortions of the porphyrin core that determines the stability of the NiOMTP conformers. The ground-state electronic absorption spectra of NiOMTP exhibit significant changes compared to its parent NiP and beta-alkylated analogues, such as NiOEP, resulting in a considerable red shift of the B and the Q bands, intensification and broadening of the Q band, and additional weak absorptions in the region between the Q and B bands. These spectral changes can be understood in terms of the electronic effects of the methylthio groups with nonplanar distortions of the porphyrin ring playing a very minor role. Transient absorption measurements with sub-picosecond resolution performed in toluene and TDDFT calculations reveal that following photoexcitation, NiOMTP deactivates by the pathway 1(pi,pi) --> 3(d(z2),d(x2-y2))--> ground state. The (d,d) state exhibits complex spectral evolution over ca. 8 ps, interpreted in terms of vibrational relaxation and cooling. The cold ligand-field excited state decays with a lifetime of 320 ps. At variance with the highly distorted nickel porphyrins but similar to the planar analogues, the (d,d) spectrum of NiOMTP has transient absorption bands immediately to the red of the bleaching of the ground-state Q and B bands.

Electrochemistry↗

PubMed2005

Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding.

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.

Journal Article↗

PubMed2005

An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151.

The absorption spectra of aminocoumarin C151 in water and n-hexane solution are investigated by an explicit quantum chemical solvent model. We improved the efficiency of the frozen-density embedding scheme, as used in a former study on solvatochromism (J. Chem. Phys. 2005, 122, 094115) to describe very large solvent shells. The computer time used in this new implementation scales approximately linearly (with a low prefactor) with the number of solvent molecules. We test the ability of the frozen-density embedding to describe specific solvent effects due to hydrogen bonding for a small example system, as well as the convergence of the excitation energy with the number of solvent molecules considered in the solvation shell. Calculations with up to 500 water molecules (1500 atoms) in the solvent system are carried out. The absorption spectra are studied for C151 in aqueous or n-hexane solution for direct comparison with experimental data. To obtain snapshots of the dye molecule in solution, for which subsequent excitation energies are calculated, we use a classical molecular dynamics (MD) simulation with a force field adapted to first-principles calculations. In the calculation of solvatochromic shifts between solvents of different polarity, the vertical excitation energy obtained at the equilibrium structure of the isolated chromophore is sometimes taken as a guess for the excitation energy in a nonpolar solvent. Our results show that this is, in general, not an appropriate assumption. This is mainly due to the fact that the solute dynamics is neglected. The experimental shift between n-hexane and water as solvents is qualitatively reproduced, even by the simplest embedding approximation, and the results can be improved by a partial polarization of the frozen density. It is shown that the shift is mainly due to the electronic effect of the water molecules, and the structural effects are similar in n-hexane and water. By including water molecules, which might be directly involved in the excitation, in the embedded region, an agreement with experimental values within 0.05 eV is achieved.

Journal Article↗

PubMed2005

Importance of vibronic effects on the circular dichroism spectrum of dimethyloxirane.

We present a theoretical study on the vibrational structure of a circular dichroism (CD) spectrum using time-dependent density-functional theory in combination with a Franck-Condon-type approach. This method is applied to analyze the complex CD spectrum of dimethyloxirane, which involves delicate cancellations of positive and negative CD bands. Our approach reveals that these cancellations are strongly affected by the shapes of the CD bands, and that it is vital for an accurate simulation of the spectrum to take the different envelopes of these bands into account. One crucial point in some former theoretical studies on this compound, which were restricted to vertical excitations, was the appearance of a strong negative CD band in the energy range of 7.0-7.5 eV, which is not present in the experimental spectrum. We can explain the disappearance of this 2B band by a strong vibrational progression along normal modes with C-O stretching character, so that the band extends over an energy range of almost 1.1 eV. Thus, it overlaps with many other (mostly positive) CD bands, leading to a cancellation of its intensity. The dominant vibrational features in the experimental spectrum can be assigned to the 1B, 3B, and 5B bands, which show several clear vibrational peaks and a total bandwidth of only 0.3-0.5 eV. In order to obtain close agreement between the simulated and the experimental spectrum we have to apply small shifts to the vertical excitation energies that enter the calculation. These shifts account both for possible errors in the time-dependent density-functional theory calculations and for the neglect of differential zero-point energy between ground and excited states in our gradient-based vertical Franck-Condon approach.

Journal Article↗

PubMed2005

The calculation of excitation energies based on the relativistic two-component zeroth-order regular approximation and time-dependent density-functional with full use of symmetry.

In the present work, we propose a relativistic time-dependent density-functional theory (TDDFT) based on the two-component zeroth-order regular approximation and a noncollinear exchange-correlation (XC) functional. This two-component TDDFT formalism has the correct nonrelativistic limit and affords the correct threefold degeneracy of triplet excitations. The relativistic TDDFT formalism is implemented into the AMSTERDAM DENSITY FUNCTIONAL program package for closed-shell systems with full use of double-group symmetry to reduce the computational effort and facilitate the assignments. The performance of the formalism is tested on some closed-shell atoms, ions, and a few diatomic molecules containing heavy elements. The results show that the fine structure of the excited states for most atoms and ions studied here can be accurately accounted for with a proper XC potential. For the excitation energies of the molecules studied here, the present formalism shows promise and the error encountered is comparable to that of nonrelativistic TDDFT calculations on light elements.

Journal Article↗

PubMed2005

An improved density matrix functional by physically motivated repulsive corrections.

An improved density matrix functional [correction to Buijse and Baerends functional (BBC)] is proposed, in which a hierarchy of physically motivated repulsive corrections is employed to the strongly overbinding functional of Buijse and Baerends (BB). The first correction C1 restores the repulsive exchange-correlation (xc) interaction between electrons in weakly occupied natural orbitals (NOs) as it appears in the exact electron pair density rho(2) for the limiting two-electron case. The second correction C2 reduces the xc interaction of the BB functional between electrons in strongly occupied NOs to an exchange-type interaction. The third correction C3 employs a similar reduction for the interaction of the antibonding orbital of a dissociating molecular bond. In addition, C3 applies a selective cancellation of diagonal terms in the Coulomb and xc energies (not for the frontier orbitals). With these corrections, BBC still retains a correct description of strong nondynamical correlation for the dissociating electron pair bond. BBC greatly improves the quality of the BB potential energy curves for the prototype few-electron molecules and in several cases BBC reproduces very well the benchmark ab initio potential curves. The average error of the self-consistent correlation energies obtained with BBC3 for prototype atomic systems and molecular systems at the equilibrium geometry is only ca. 6%.

Journal Article↗

PubMed2005

Mechanisms of H2 dissociative adsorption on the Pt(211) stepped surface.

We utilize classical trajectory calculations to study the reaction dynamics of the dissociative adsorption of H2 on the stepped Pt(211) surface. The potential-energy surface has been obtained through an accurate interpolation of density-functional theory data at the generalized gradient approximation level, using the corrugation reduction procedure. New techniques for visualizing the collective dynamics of trajectories are introduced to elucidate the reaction mechanisms involved. Reaction exhibits a nonmonotonic dependence on collision energy, first decreasing with energy, and then increasing. A strong component of direct nonactivated reaction exists at the top edge of the step over the entire range of energies. The inverse relationship between reaction and collision energy at low energies is attributed to trapping in weak chemisorption wells. These wells also influence the direct reaction at the step, leading to a strong asymmetric dependence on incidence angle. Reaction on the terrace is activated, and only contributes significantly at high energies. Agreement with experiments on Pt(533) [A. T. Gee, B. E. Hayden, C. Mormiche, and T. S. Nunney, J. Chem. Phys. 112, 7660 (2000); Surf. Sci. 512, 165 (2002)] is good, and we are able to suggest new interpretations of the experimental data.

Journal Article↗

PubMed2005

Combined theoretical and experimental deep-UV resonance raman studies of substituted pyrenes.

The results of time-dependent density functional theory (TDDFT) calculations of resonance Raman intensities are combined with experimental deep-ultraviolet resonance Raman measurements at a single wavelength, i.e., 244 nm, in order to test the possibility to distinguish several very similar compounds. Pyrene and three of its substituted derivatives, in which a single hydrogen atom has been replaced by a halogen atom, are compared. The fixed 244 nm excitation wavelength overlapped with the same electronic transition of the four pyrenes. Ground-state calculations using the BP86 exchange-correlation functional were used to predict the Raman frequencies, whereas excited-state calculations have been carried out employing the "statistical averaging of (model) orbital potentials" (SAOP) potential within a linear-response TDDFT framework in combination with the short-time approximation of resonance Raman intensities. In view of the simplistic theoretical approach, we find a surprisingly good agreement between the simulated and measured resonance Raman spectra of pyrene and its substituted analogues in terms of frequencies and intensities, which shows that the calculations can be used reliably to interpret the experimental spectra. With this combined information, it is possible to find criteria to distinguish the compounds under investigation, although many features of their vibrational spectra are similar.

Journal Article↗