Publications by authors named "Evert Jan Baerends"

76 Publications

Origin of the Enhanced Binding Capability toward Axial Nitrogen Bases of Ni(II) Porphyrins Bearing Electron-Withdrawing Substituents: An Electronic Structure and Bond Energy Analysis.

Inorg Chem 2020 Aug 29;59(16):11528-11541. Epub 2020 Jul 29.

Università della Basilicata, Dipartimento di Scienze, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy.

Axial coordination to metalloporphyrins is important in many biological and catalytic processes. Experiments found the axial coordination of nitrogenous bases to nickel(II) porphyrins to be strongly favored by electron-withdrawing substituents such as perfluorophenyls at the meso carbon positions. Careful analysis of the electronic structure reveals that the natural explanation in terms of density change of the nickel(II) porphyrin system (in particular the metal), does not apply. Electron density changes, by the assumed inductive or polarizing effects on the metal or on the porphyrin ring system, are slight. The effect is caused by a remarkable through-space electric field effect on the metalloporphyrin system, originating from the charge distribution inside the perfluorphenyl groups (mostly the C-F dipoles).
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http://dx.doi.org/10.1021/acs.inorgchem.0c01327DOI Listing
August 2020

Density functional approximations for orbital energies and total energies of molecules and solids.

J Chem Phys 2018 Aug;149(5):054105

Section Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands.

The relation of Kohn-Sham (KS) orbital energies to ionization energies and electron affinities is different in molecules and solids. In molecules, the local density approximation (LDA) and generalized gradient approximations (GGA) approximate the exact ionization energy (I) and affinity (A) rather well with self-consistently calculated (total energy based) I and A, respectively. The highest occupied molecular orbital (HOMO) energy and lowest unoccupied molecular orbital (LUMO) energy, however, differ significantly (by typically 4-6 eV) from these quantities, ϵ(mol)>-I(mol)≈-I(mol), ϵ(mol)<-A(mol)≈-A(mol). In solids, these relations are very different, due to two effects. The (almost) infinite extent of a solid makes the difference of orbital energies and (L)DFA calculated ionization energy and affinity disappear: in the solid state limit, ϵ(solid)=-I(solid) and ϵ(solid)=-A(solid). Slater's relation ∂E/∂n = ϵ for local density functional approximations (LDFAs) [and Hartree-Fock (HF) and hybrids] is useful to prove these relations. The equality of LDFA orbital energies and LDFA calculated -I and -A in solids does not mean that they are good approximations to the exact quantities. The LDFA total energies of the ions with a delocalized charge are too low, hence I(solid) < I and A(solid) > A, due to the local-approximation error, also denoted delocalization error, of LDFAs in extended systems. These errors combine to make the LDFA orbital energy band gap considerably smaller than the exact fundamental gap, ϵ(solid)-ϵ(solid)=I(solid)-A(solid)
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http://dx.doi.org/10.1063/1.5026951DOI Listing
August 2018

Comment on "Kohn-Sham exchange-correlation potentials from second-order reduced density matrices" [J. Chem. Phys. 143, 244116 (2015)].

J Chem Phys 2016 Jul;145(3):037101

Section Theoretical Chemistry, Faculty of Exact Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1063/1.4958622DOI Listing
July 2016

Light-induced water splitting by titanium-tetrahydroxide: a computational study.

Phys Chem Chem Phys 2015 Aug;17(31):20308-21

VU University Amsterdam, Theoretical Chemistry, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

Water oxidation by Ti(OH)4 in the ground and excited states was investigated using density functional (ΔSCF, TDDFT) methods gauged by the coupled cluster (CCSD, CCSD(T)) calculations. O2 and H2 are generated in a reaction sequence that starts with Ti(OH)4 reacting with H2O. This reaction can proceed by either nucleophilic attack by H2O or by H-atom abstraction from H2O. The nucleophilic attack has high energy barriers (40-120 kcal mol(-1)) in both the ground and excited states. On the other hand, H abstraction is effected by Ti(OH)4 in the excited state with a low energy barrier (4-8 kcal mol(-1)), generating OH˙. This is the rate-limiting barrier in the chain of O2 formation reactions proposed in this work. The production of free OH˙ radicals is not energetically feasible in the ground state. By absorbing two photons, two hydroxyl radicals are produced, which then form H2O2. By a stepwise H-abstraction from H2O2 and OOH˙, O2 is generated by absorbing two more photons. In each H-abstraction reaction a Ti(OH)4 is consumed and a Ti(OH)3H2O is produced. H2 production can proceed thermally from the latter in a very exothermic (68-105 kcal mol(-1)) bimolecular reaction. The solvent effects, modelled by explicit water molecules, have a limited influence on the reactivity.
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http://dx.doi.org/10.1039/c5cp01812aDOI Listing
August 2015

Real-space representation of electron correlation in π-conjugated systems.

J Chem Phys 2015 May;142(20):204311

Afdeling Theoretische Chemie, FEW, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

π-electron conjugation and aromaticity are commonly associated with delocalization and especially high mobility of the π electrons. We investigate if also the electron correlation (pair density) exhibits signatures of the special electronic structure of conjugated systems. To that end the shape and extent of the pair density and derived quantities (exchange-correlation hole, Coulomb hole, and conditional density) are investigated for the prototype systems ethylene, hexatriene, and benzene. The answer is that the effects of π electron conjugation are hardly discernible in the real space representations of the electron correlation. We find the xc hole to be as localized (confined to atomic or diatomic regions) in conjugated systems as in small molecules. This result is relevant for density functional theory (DFT). The potential of the electron exchange-correlation hole is the largest part of vxc, the exchange-correlation Kohn-Sham potential. So the extent of the hole directly affects the orbital energies of both occupied and unoccupied Kohn-Sham orbitals and therefore has direct relevance for the excitation spectrum as calculated with time-dependent DFT calculations. The potential of the localized xc hole is comparatively more attractive than the actual hole left behind by an electron excited from a delocalized molecular orbital of a conjugated system.
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http://dx.doi.org/10.1063/1.4921725DOI Listing
May 2015

The importance of large-amplitude motions for the interpretation of mid-infrared vibrational absorption and circular dichroism spectra: 6,6'-dibromo-[1,1'-binaphthalene]-2,2'-diol in dimethyl sulfoxide.

J Phys Chem A 2014 Jul 18;118(26):4766-77. Epub 2014 Jun 18.

Department of Chemistry, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amstrdam, The Netherlands.

Using the 6,6'-dibromo-[1,1'-binaphthalene]-2,2'-diol molecule and its vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra measured in deuterated dimethyl sulfoxide as example, we present a first detailed study of the effects induced in VCD spectra by the large-amplitude motions of solvent molecules loosely bound to a solute molecule. We show that this type of perturbation can induce significant effects in the VA and VCD spectra. We also outline a computational procedure that can effectively model the effects induced in the spectra and at the same time provide detailed structural information regarding the relative orientations of moieties involved in a solute-solvent molecular complex.
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http://dx.doi.org/10.1021/jp4114738DOI Listing
July 2014

Solvent induced enhancement of enantiomeric excess: a case study of the Henry reaction with cinchona thiourea as the catalyst.

Phys Chem Chem Phys 2014 Apr;16(16):7315-23

Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

Enantiomeric excess (ee) in asymmetric catalysis may be strongly dependent on the solvent. The reaction product may range from an almost racemic mixture to an ee of over 90% for different solvents. We study this phenomenon for the C-C coupling reaction between nitromethane and benzaldehyde (the Henry reaction) with cinchona thiourea as the catalyst, where solvents that are strong Lewis bases induce a high ee. We show that the effect of the solvent does not consist of a change in the reaction mechanism. Instead, the solvation "prepares" the molecule, which is very flexible, in a specific conformation. The reaction barriers in this conformer are not lower than for other conformers, but are sufficiently differentiated between the enantiomers to give rise to a large ee. It is the strong Lewis basicity of the solvent that leads to the clear preference in solution for the "asymmetric" conformer. Although general rules or predictions for how solvent effects could be harnessed to produce a desired ee in general would be hard to formulate, this study does show that it is in this case (and presumably in many other cases as well) specific solute-solvent interactions rather than effects of the dielectric continuum of the solvent that are the root cause of the solvent effect. This is in agreement with experiment for the Henry reaction.
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http://dx.doi.org/10.1039/c3cp55267eDOI Listing
April 2014

A frontier orbital study with ab initio molecular dynamics of the effects of solvation on chemical reactivity: solvent-induced orbital control in FeO-activated hydroxylation reactions.

J Am Chem Soc 2013 Jun 7;135(24):8857-67. Epub 2013 Jun 7.

STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, United Kingdom.

Solvation effects on chemical reactivity are often rationalized using electrostatic considerations: the reduced stabilization of the transition state results in higher reaction barriers and lower reactivity in solution. We demonstrate that the effect of solvation on the relative energies of the frontier orbitals is equally important and may even reverse the trend expected from purely electrostatic arguments. We consider the H abstraction reaction from methane by quintet [EDTAH(n)·FeO]((n-2)+), (n = 0-4) complexes in the gas phase and in aqueous solution, which we examine using ab initio thermodynamic integration. The variation of the charge of the complex with the protonation of the EDTA ligand reveals that the free energy barrier in gas phase increases with the negative charge, varying from 16 kJ mol(-1) for [EDTAH4·FeO](2+) to 57 kJ mol(-1) for [EDTAHn·FeO](2-). In aqueous solution, the barrier for the +2 complex (38 kJ mol(-1)) is higher than in gas phase, as predicted by purely electrostatic arguments. For the negative complexes, however, the barrier is lower than in gas phase (e.g., 45 kJ mol(-1) for the -2 complex). We explain this increase in reactivity in terms of a stabilization of the virtual 3σ* orbital of FeO(2+), which acts as the dominant electron acceptor in the H-atom transfer from CH4. This stabilization originates from the dielectric screening caused by the reorientation of the water dipoles in the first solvation shell of the charged solute, which stabilizes the acceptor orbital energy for the -2 complex sufficiently to outweigh the unfavorable electrostatic destabilization of the transition-state relative to the reactants in solution.
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http://dx.doi.org/10.1021/ja311144dDOI Listing
June 2013

Assessment of density functional methods for reaction energetics: iridium-catalyzed water oxidation as case study.

J Comput Chem 2013 Apr 30;34(10):870-8. Epub 2012 Dec 30.

VU University Amsterdam, Theoretical Chemistry, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

We investigate basis set convergence for a series of density functional theory (DFT) functionals (both hybrid and nonhybrid) and compare to coupled-cluster with single and double excitations and perturbative triples [CCSD(T)] benchmark calculations. The case studied is the energetics of the water oxidation reaction by an iridium-oxo complex. Complexation energies for the reactants and products complexes as well as the transition state (TS) energy are considered. Contrary to the expectation of relatively weak basis set dependence for DFT, the basis set effects are large, for example, more than 10 kcal mol(-1) difference from converged basis for the activation energy with "small" basis sets (DZ/6-31G** for Ir/other atoms, or SVP) and still more than 6 kcal mol(-1) for def2-TZVPP/6-31G**. Inclusion of the dispersion correction in DFT-D3 schemes affects the energies of reactant complex (RC), TS, and product complex (PC) by almost the same amount; it significantly improves the complexation energy (the formation of RC), but has little effect on the activation energy with respect to RC. With converged basis, some pure GGAs (PBE-D3, BP86-D3) as well as the hybrid functional B3LYP-D3 are very accurate compared to benchmark CCSD(T) calculations.
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http://dx.doi.org/10.1002/jcc.23212DOI Listing
April 2013

Understanding solvent effects in vibrational circular dichroism spectra: [1,1'-binaphthalene]-2,2'-diol in dichloromethane, acetonitrile, and dimethyl sulfoxide solvents.

J Phys Chem A 2012 Aug 7;116(32):8366-73. Epub 2012 Aug 7.

Department of Chemistry, VU University Amsterdam, Amsterdam, The Netherlands.

We present a combined experimental and computational investigation of the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of [1,1'-binaphthalene]-2,2'-diol. First, the sensitive dependence of the experimental VA and VCD spectra on the solvent is demonstrated by comparing the experimental spectra measured in CH(2)Cl(2), CD(3)CN, and DMSO-d(6) solvents. Then, by comparing calculations performed for the isolated solute molecule to calculations performed for molecular complexes formed between solute and solvent molecules, we identify three main types of perturbations that affect the shape of the VA and VCD spectra when going from one solvent to another. These sources of perturbations are (1) perturbation of the Boltzmann populations, (2) perturbation of the electronic structure, and (3) perturbation of the normal modes.
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http://dx.doi.org/10.1021/jp303891xDOI Listing
August 2012

On the equivalence of conformational and enantiomeric changes of atomic configuration for vibrational circular dichroism signs.

J Phys Chem A 2012 Apr 22;116(13):3454-64. Epub 2012 Mar 22.

Department of Chemistry, VU University Amsterdam, The Netherlands.

We study systematically the vibrational circular dichroism (VCD) spectra of the conformers of a simple chiral molecule, with one chiral carbon and an "achiral" alkyl substituent of varying length. The vibrational modes can be divided into a group involving the chiral center and its direct neighbors and the modes of the achiral substituent. Conformational changes that consist of rotations around the bond from the next-nearest neighbor to the following carbon, and bond rotations further in the chain, do not affect the modes around the chiral center. However, conformational changes within the chiral fragment have dramatic effects, often reversing the sign of the rotational strength. The equivalence of the effect of enantiomeric change of the atomic configuration and conformational change on the VCD sign (rotational strength) is studied. It is explained as an effect of atomic characteristics, such as the nuclear amplitudes in some vibrational modes as well as the atomic polar and axial tensors, being to a high degree determined by the local topology of the atomic configuration. They reflect the local physics of the electron motions that generate the chemical bonds rather than the overall shape of the molecule.
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http://dx.doi.org/10.1021/jp212545zDOI Listing
April 2012

Hydroxylation catalysis by mononuclear and dinuclear iron oxo catalysts: a methane monooxygenase model system versus the Fenton reagent Fe(IV)O(H2O)5(2+).

Inorg Chem 2012 Jan 19;51(1):63-75. Epub 2011 Dec 19.

Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

Hydroxylation of aliphatic C-H bonds is a chemically and biologically important reaction, which is catalyzed by the oxidoiron group FeO(2+) in both mononuclear (heme and nonheme) and dinuclear complexes. We investigate the similarities and dissimilarities of the action of the FeO(2+) group in these two configurations, using the Fenton-type reagent [FeO(2+) in a water solution, FeO(H(2)O)(5)(2+)] and a model system for the methane monooxygenase (MMO) enzyme as representatives. The high-valent iron oxo intermediate MMOH(Q) (compound Q) is regarded as the active species in methane oxidation. We show that the electronic structure of compound Q can be understood as a dimer of two Fe(IV)O(2+) units. This implies that the insights from the past years in the oxidative action of this ubiquitous moiety in oxidation catalysis can be applied immediately to MMOH(Q). Electronically the dinuclear system is not fundamentally different from the mononuclear system. However, there is an important difference of MMOH(Q) from FeO(H(2)O)(5)(2+): the largest contribution to the transition state (TS) barrier in the case of MMOH(Q) is not the activation strain (which is in this case the energy for the C-H bond lengthening to the TS value), but it is the steric hindrance of the incoming CH(4) with the ligands representing glutamate residues. The importance of the steric factor in the dinuclear system suggests that it may be exploited, through variation in the ligand framework, to build a synthetic oxidation catalyst with the desired selectivity for the methane substrate.
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http://dx.doi.org/10.1021/ic200754wDOI Listing
January 2012

Cu(bipy)2+/TEMPO-catalyzed oxidation of alcohols: radical or nonradical mechanism?

Inorg Chem 2011 Dec 3;50(23):11896-904. Epub 2011 Nov 3.

Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.

In the oxidation of alcohols with TEMPO as catalyst, the substrate has alternatively been postulated to be oxidized but uncoordinated TEMPO(+) (Semmelhack) or Cu-coordinated TEMPO(•) radical (Sheldon). The reaction with the Cu(bipy)(2+)/TEMPO cocatalyst system has recently been claimed, on the basis of DFT calculations, to not be a radical reaction but to be best viewed as electrophilic attack on the alcohol C-H(α) bond by coordinated TEMPO(+). This mechanism combines elements of the Semmelhack mechanism (oxidation of TEMPO to TEMPO(+)) and the Sheldon proposal ("in the coordination sphere of Cu"). The recent proposal has been challenged on the basis of DFT calculations with a different functional, which were reported to lead to a radical mechanism. We carefully examine the results for the two functionals and conclude from both the calculated energetics and from an electronic structure analysis that the results of the two DFT functionals are consistent and that both lead to the proposed mechanism with TEMPO not acting as radical but as (coordinated) positive ion.
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http://dx.doi.org/10.1021/ic200725kDOI Listing
December 2011

Electron pair density in the lowest 1Σ(u)(+) and 1Σ(g)(+) states of H2.

J Chem Phys 2011 Aug;135(7):074111

School of Science, Huzhou University, Zhejiang 10083, China.

We demonstrate and advocate the use of observable quantities derived from the two-electron reduced density matrix - pair densities, conditional densities, and exchange-correlation holes--as signatures of the type of electron correlation in a chemical bond. The prototype cases of the lowest (1)Σ(u)(+) and (1)Σ(g)(+) states of H(2), which exhibit large variation in types of bonding, ranging from strongly ionic to covalent, are discussed. Both the excited (1)Σ(g)(+) and (1)Σ(u)(+) states have been interpreted as essentially consisting of (natural) orbital configurations with an inner electron in a contracted 1sσ(g) orbital and an outer electron in a diffuse (united atom type, Rydberg) orbital. We show that nevertheless totally different correlation behavior is encountered in various states when comparing them at a common internuclear distance. Also when following one state along the internuclear distance coordinate, strong variation in correlation behavior is observed, as expected. Switches between ionic to covalent character of a state occur till very large distances (40 bohrs for states approaching the 1s3[script-l] asymptotic limit, and 282 bohrs for states approaching the 1s4[script-l] limit).
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http://dx.doi.org/10.1063/1.3624571DOI Listing
August 2011

On the origin dependence of the angle made by the electric and magnetic vibrational transition dipole moment vectors.

Phys Chem Chem Phys 2011 Sep 12;13(36):16126-9. Epub 2011 Aug 12.

Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

The concept of robustness of rotational strengths of vibrational modes in a VCD spectrum has been introduced as an aid in assignment of the absolute configuration with the help of the VCD spectrum. The criteria for robustness have been based on the distribution around 90° of the angles ξ(i) between electric and magnetic transition dipoles of all the modes i of a molecule. The angles ξ(i) (not, of course, the rotational strengths) are, however, dependent on the choice of origin. The derived criteria are for the center of mass chosen as the origin of the coordinate system. We stress in this note that application of the derived criteria assumes that excessive translation of the coordinate origin is not applied. Although the ξ(i) angles are not very sensitive to the position of the origin, very small displacements (a few Å) are not a problem, excessive translation of the origin does have considerable effect on the ξ(i) angles. In this note we quantify this effect and demonstrate how the distribution of ξ(i) angles is affected. Although it is possible to recalibrate the robustness criteria for the angles for a specific (large) displacement, we recommend that such displacement simply be avoided. It is to be noted that some modeling software does yield output with excessively displaced coordinate origin; this should be checked and corrected.
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http://dx.doi.org/10.1039/c1cp21442jDOI Listing
September 2011

An abiotic analogue of the diiron(IV)oxo "diamond core" of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(II)/EDTA solutions: thermodynamics and electronic structure.

Phys Chem Chem Phys 2011 Sep 21;13(33):15272-82. Epub 2011 Jul 21.

STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX, UK.

We study the generation of a dinuclear Fe(IV)oxo species, [EDTAH·FeO·OFe·EDTAH](2-), in aqueous solution at room temperature using Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). This species has been postulated as an intermediate in the multi-step mechanism of autoxidation of Fe(II) to Fe(III) in the presence of atmospheric O(2) and EDTA ligand in water. We examine the formation of [EDTAH·FeO·OFe·EDTAH](2-) by direct cleavage of O(2), and the effects of solvation on the spin state and O-O cleavage barrier. We also study the reactivity of the resulting dinuclear Fe(IV)oxo system in CH(4) hydroxylation, and its tendency to decompose to mononuclear Fe(IV)oxo species. The presence of the solvent is shown to play a crucial role, determining important changes in all these processes compared to the gas phase. We show that, in water solution, [EDTAH·FeO·OFe·EDTAH](2-) (as well as its precursor [EDTAH·Fe·O(2)·Fe·EDTAH](2-)) exists as stable species in a S = 4 ground spin state when hydrogen-bonded to a single water molecule. Its structure comprises two facing Fe(IV)oxo groups, in an arrangement similar to the one evinced for the active centre of intermediate Q of soluble Methane Monooxygenase (sMMO). The inclusion of the water molecule in the complex decreases the overall symmetry of the system, and brings about important changes in the energy and spatial distribution of orbitals of the Fe(IV)oxo groups relative to the gas phase. In particular, the virtual 3σ* orbital of one of the Fe(IV)oxo groups experiences much reduced repulsive orbital interactions from ligand orbitals, and its consequent stabilisation dramatically enhances the electrophilic character of the complex, compared to the symmetrical non-hydrated species, and its ability to act as an acceptor of a H atom from the CH(4) substrate. The computed free energy barrier for H abstraction is 28.2 kJ mol(-1) (at the BLYP level of DFT), considerably below the gas phase value for monomeric [FeO·EDTAH](-), and much below the solution value for the prototype hydrated ferryl ion [FeO(H(2)O)(5)](2+).
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http://dx.doi.org/10.1039/c1cp21244cDOI Listing
September 2011

Counterpoise correction is not useful for short and Van der Waals distances but may be useful at long range.

J Comput Chem 2011 Oct 6;32(13):2896-901. Epub 2011 Jul 6.

The Institute of Atomic and Molecular physics, Sichuan University, Chengdu, Sichuan 610065, China.

This article investigates the errors in supermolecule calculations for the helium dimer. In a full CI calculation, there are two errors. One is the basis set superposition error (BSSE), the other is the basis set convergence error (BSCE). Both of the errors arise from the incompleteness of the basis set. These two errors make opposite contributions to the interaction energies. The BSCE is by far the largest error in the short range and larger than (but much closer to) BSSE around the Van der Waals minimum. Only at the long range, the BSSE becomes the larger error. The BSCE and BSSE largely cancel each other over the Van der Waals well. Accordingly, it may be recommended to not include the BSSE for the calculation of the potential energy curve from short distance till well beyond the Van der Waals minimum, but it may be recommended to include the BSSE correction if an accurate tail behavior is required. Only if the calculation has used a very large basis set, one can refrain from including the counterpoise correction in the full potential range. These results are based on full CI calculations with the aug-cc-pVXZ (X = D, T, Q, 5) basis sets.
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http://dx.doi.org/10.1002/jcc.21872DOI Listing
October 2011

Signatures of counter-ion association and hydrogen bonding in vibrational circular dichroism spectra.

Phys Chem Chem Phys 2011 May 4;13(19):8811-25. Epub 2011 Apr 4.

Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

We study the effect of counter-ion complexation on the example of Cl(-) ions interacting with the [Co(en)(3)](3+) complex. The H-bonding of the N-H groups of the ethylenediamine (en) ligands with the Cl(-) ions may lead to giant enhancement of the VCD intensity for the N-H stretches, but may also lead to VCD sign changes in the finger print region of N-H wagging, twisting and scissoring motions. Such sign changes should not be mistaken for signatures of the presence of the other enantiomer. We elucidate the mechanism for the sign changes and give a recommendation on how to deal with this problem. We also show that the experimental spectrum is only in good accord with the calculations if complexation of 5 Cl(-) ions (two axial, three equatorial) is assumed, but not with two (axial) or three (equatorial) Cl(-) ions, thus showing the potential of VCD to be used as an experimental probe for complexation.
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http://dx.doi.org/10.1039/c0cp02701dDOI Listing
May 2011

Counterintuitive Coulomb hole around the bond midplane.

J Chem Phys 2010 May;132(20):204102

School of Science, Huzhou University, Zhejiang 10083, China.

The Coulomb hole does not have its largest depth around an electron in or near the bond midplane. It splits into two parts, localized on both nuclear sites forming the bond. Even counterintuitive positive values of the "hole" around such a position may be observed. This happens when the Fermi hole is deeper than the total exchange-correlation hole at the reference electron position. This Coulomb "heap" is shown to arise from correlation effects on the one-electron density rather than correlation effects in the pair density. Left-right correlation tends to enhance the effect of the nuclear attraction, contracting the electron density around the nuclear positions and depleting the bond center region. Possible alternative definitions of the Coulomb hole are discussed, including one based on the exact Kohn-Sham exchange hole. Approximate density functional theory methods (generalized gradient approximation) are not accurate enough to realize the advantages of this definition.
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http://dx.doi.org/10.1063/1.3429608DOI Listing
May 2010

Is [FeO](2+) the active center also in iron containing zeolites? A density functional theory study of methane hydroxylation catalysis by Fe-ZSM-5 zeolite.

Inorg Chem 2010 Apr;49(8):3866-80

Dipartimento di Chimica, Università della Basilica, Via N. Sauro 85, 85100 Potenza, Italy.

Arguments are put forward that the active alpha-oxygen site in the Fe-ZSM-5 catalyst consists of the FeO(2+) moiety. It is demonstrated that this zeolite site for FeO(2+) indeed obeys the design principles for high reactivity of the FeO(2+) moiety proposed earlier: a ligand environment consisting of weak equatorial donors (rather oxygen based than nitrogen based) and very weak or absent trans axial donor. The alpha-oxygen site would then owe its high reactivity to the same electronic structure features that lends FeO(2+) its high activity in biological systems, as well as in the classical Fenton chemistry.
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http://dx.doi.org/10.1021/ic1000073DOI Listing
April 2010

A new analytical potential energy surface for the adsorption system CO/Cu(100).

J Chem Phys 2010 Feb;132(7):074108

Laboratoire de Chimie Quantique, Institut de Chimie, UMR 7177 CNRS/UdS, Université de Strasbourg 4, rue Blaise Pascal, 67000 Strasbourg, France.

Electronic structure data and analytical representations of the potential energy surface for the adsorption of carbon monoxide on a crystalline copper Cu(100) substrate are reviewed. It is found that a previously published and widely used analytical hypersurface for this process [J. C. Tully, M. Gomez, and M. Head-Gordon, J. Vac. Sci. Technol. A 11, 1914 (1993)] represents rather poorly the data obtained from a slab type calculation of the electronic structure. A new, global analytical representation of the potential energy surface for this process is derived via a nonlinear adjustment of parameters. It is more general and fits qualitatively better the electronic structure data. Key characteristic elements of the new surface are the "top" equilibrium adsorption site in the perpendicular arrangement Cu-C-O with Cu-C and C-O distances of 184 and 115 pm, the desorption energy of 0.76 eV and the barrier for lateral diffusion of 33 meV, including approximative corrections for the variation of zero point energy. Anharmonic vibrational fundamentals and overtones are also calculated from six dimensional variational calculations. All these values agree equally well or better with experimental data than previous published theoretical data within estimated uncertainties. The analytical representation is compact and robust, and may be used to describe other adsorption processes of diatomic molecules, including dissociative chemisorption.
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http://dx.doi.org/10.1063/1.3308481DOI Listing
February 2010

A VCD robust mode analysis of induced chirality: the case of pulegone in chloroform.

Chirality 2009 ;21 Suppl 1:E287-97

Theoretical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

Vibrational modes in an achiral molecule may acquire rotational strength by complexation to a chiral molecule, as happens for achiral solvent molecules complexed to a chiral solute. We investigate this transfer of chirality in vibrational circular dichroism for the pulegone molecule in CDCl(3) solvent from the point of view of the robustness concept introduced recently. It turns out that the transfer of chirality yields nonrobust modes, which means that, although they are observed in vibrational circular dichroism (VCD) experiments, the sign of these modes cannot be predicted reliably with standard (Density Functional Theory) VCD calculations. This limits the usefulness of the induced chirality phenomenon for obtaining information on the intermolecular interactions that give rise to it.
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http://dx.doi.org/10.1002/chir.20817DOI Listing
May 2010

Activation of the C-H bond by electrophilic attack: theoretical study of the reaction mechanism of the aerobic oxidation of alcohols to aldehydes by the Cu(bipy)(2+)/2,2,6,6-tetramethylpiperidinyl-1-oxy cocatalyst system.

Inorg Chem 2009 Dec;48(24):11909-20

Theoretical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

We have investigated the reaction mechanism of the selective aerobic oxidation of primary alcohols into aldehydes using a bipy-copper complex and the 2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO) radical as cocatalysts (Gamez et al. Chem. Commun. 2003, 2412-2415) and compared it to the well-known oxidation by the TEMPO(+) ion. Our theoretical investigation shows that (a) the oxidation of alcohols to aldehydes by uncoordinated TEMPO(+) takes place by electrophilic attack on the C-H(alpha) bond of the alcohol; (b) the Cu(bipy)(2+) complex has two functions, namely, (1) it acts as a template that brings TEMPO and the (deprotonated) alcohol in proximity by coordinating these moieties in adjacent coordination sites, and (2) it oxidizes the TEMPO radical to (coordinated) TEMPO(+) ion. The H abstraction from alcohol by TEMPO(+) then proceeds as an intramolecular reaction, very much analogous to one of the reaction pathways with free TEMPO(+) and with a remarkably low barrier. We stress that compared to other A-H bonds (A = C, N, O, F), the relatively high-lying C-H bonds are particularly susceptible to electrophilic attack, and notably the C-H(alpha) bond next to the O in an alcohol is so because it is pushed up by an O lone pair. Electrophilic attack, being common to the particular catalytic system studied in this paper and the well-known biotic and abiotic oxidation catalysis by heme and non-heme complexes of the ferryl (Fe(IV)O(2+)) ion, appears to be a unifying electronic structure principle of C-H(alpha) hydroxylation and oxidation reactions.
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http://dx.doi.org/10.1021/ic902155mDOI Listing
December 2009

O2 activation in a dinuclear Fe(II)/EDTA complex: spin surface crossing as a route to highly reactive Fe(IV)oxo species.

J Phys Chem A 2009 Oct;113(43):11926-37

Department of Chemistry, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy.

We study the cleavage of O2 in gas phase [(EDTAH)Fe(O2)Fe(EDTAH)]2-, a proposed intermediate in the aqueous Fe(II)-to-Fe(III) autoxidation reaction in the presence of atmospheric dioxygen and EDTA ligand. The role of the exchange coupling between the locally high-spin Fe centers in the O-O dissociation is investigated. Using results from broken symmetry (BS) density functional theory (DFT) calculations, we show that the system can be modeled as two high-spin (HS) S = 5/2 Fe(III) d5 centers coupled through a bridging peroxo O2(2-) ligand, consistent with hypotheses advanced in the literature. We show that in this electronic configuration the O-O cleavage reaction is forbidden by (spin) symmetry. Dissociation of the O2(2-) group to the product ground state may only take place if the system is allowed to undergo a transition to a state of lower spin multiplicity (S = 4) as the O-O bond is stretched. We show that the exchange coupling between the two Fe ions in [(EDTAH)Fe(O2)Fe(EDTAH)]2- plays only a minor role in defining the chemistry of O2 activation in this system. The peroxo/oxo interconversion involves a state outside the Heisenberg spin ladder of the initial S = 5 state. In this S = 4 state, the dinuclear complex evolves to two oxo complexes, [EDTAH x Fe(IV)O]-, with an overall energy barrier of only approximately 86 kJ mol(-1). According to recent theoretical work, the latter species are exceptionally strong oxidants, making them ideal candidate catalysts for organic oxidations (including C-H bond hydroxylation). We highlight the (spin) symmetry forbidden nature of the reaction on the S = 5 surface and its symmetry allowed character in the electronic configuration with S = 4.
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http://dx.doi.org/10.1021/jp9033672DOI Listing
October 2009

Homolytic versus heterolytic dissociation of alkalimetal halides: the effect of microsolvation.

Chemphyschem 2009 Dec;10(17):2955-65

Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.

Herein we report density functional calculations of homolytic and heterolytic dissociation energies of the diatomic alkalimetal halides MX (M=Li, Na, K, Rb, and Cs and X=F, Cl, Br, I, and At) and their corresponding microsolvated structures MX(H(2)O)(n) (n=1 to 4). Our results show that the homolytic dissociation energy of the MX(H(2)O)(n) species increases with the number of water molecules involved in the microsolvated salts. On the other hand, the heterolytic dissociation energy follows exactly the opposite trend. As a result, while for the isolated diatomic alkalimetal halides, homolytic dissociation is always favored over heterolytic dissociation, the latter is preferred for CsF and CsCl already for n=2, and for n=4 it is the preferential mode of dissociation for more than half of the species studied.
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http://dx.doi.org/10.1002/cphc.200900480DOI Listing
December 2009

Robust normal modes in vibrational circular dichroism spectra.

Phys Chem Chem Phys 2009 Aug 27;11(29):6107-18. Epub 2009 May 27.

Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

The use of calculations of the rotational strengths of normal modes in order to determine the absolute configuration (AC) of a molecule, by comparing a calculated vibrational circular dichroism (VCD) spectrum to an experimental one, can be made much more reliable when the vibrational modes are classified as either robust or non-robust. The robust modes are the ones with a robust sign of the rotational strength in the sense that it will not change by small perturbations in either experiment or calculation. The signs of non-robust modes may change. Clearly only robust modes should be used to establish the AC. We recommend that programs which calculate VCD spectra should provide, per normal mode, information that indicates the robustness of a mode, and therefore its usefulness for the AC determination. Such information consists of the angle xi between the electric and magnetic dipole transition moments, and the magnitudes of these dipole transition moments.
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http://dx.doi.org/10.1039/b823558aDOI Listing
August 2009

Double excitation effect in non-adiabatic time-dependent density functional theory with an analytic construction of the exchange-correlation kernel in the common energy denominator approximation.

Phys Chem Chem Phys 2009 Jun 23;11(22):4640-6. Epub 2009 Apr 23.

Theoretische Chemie, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.

Time-dependent density functional (response) theory (TDDF(R)T) is applied almost exclusively in its adiabatic approximation (ATDDFT), which is restricted to predominantly single electronic excitations and neglects additional roots of the TDDFT eigenvalue problem stemming from the interaction between single and double excitations. We incorporate the effect of the latter interaction into a non-adiabatic frequency-dependent and spatially non-local Hartree-exchange-correlation (Hxc) kernel fCEDAHxc (r1, r2, omega), the explicit analytical expression of which is derived for interacting single and double excitations well separated from the other excitations, within the common energy denominator approximation (CEDA) for the Kohn-Sham (KS) and interacting density response functions, chis and chi, respectively. The kernel fCEDAHxc (r1, r2, omega) obtained from the direct analytical inverse of chiCEDAs and chiCEDA is a sum of the delta-function and non-local orbital-dependent spatial terms with frequency-dependent factors, with which fCEDAHxc acquires a modulated quadratic dependence on omega. The effective incorporation in fCEDAHxc of the complete manifold of excited states (through the delta function term) represents an extension of the kernel reported by Maitra, Zhang, Cave, and Burke [J. Chem. Phys., 2004, 120, 5932]. In the TDDFT eigenvalue equations considered in the diagonal approximation, fCEDAHxc generates two excitation energies omegaq and omegaq+1, which both correspond to the same single KS excitation omegasq, thus producing the effect of the single-double excitation interaction.
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http://dx.doi.org/10.1039/b903123eDOI Listing
June 2009

What singles out the FeO2+ moiety? A density-functional theory study of the methane-to-methanol reaction catalyzed by the first row transition-metal oxide dications MO(H2O)(p)2+, M = V-Cu.

Inorg Chem 2009 Apr;48(8):3628-38

Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

Metaloxo species are often postulated as key active species in oxidative catalysis. Among all, the quintet FeO2+ moiety is particularly widespread and active: aliphatic C-H bonds undergo hydroxylation easily through a H-abstraction/O-rebound mechanism. The high electrophilicity of quintet FeO2+ originates from its electronic structure: a low lying vacant sigma* can accept electronic density from the aliphatic C-H bond. What singles out this quintet FeO2+? Its lowest vacant acceptor orbital energy? its shape (sigma* vs pi*)? or has its biological importance more simply arisen from the high iron abundance? To answer those questions, we have performed density-functional theory calculations to study systematically the methane-to-methanol reaction catalyzed by MO(H2O)(p)2+ complexes (M = V, Cr, Mn, Fe, Co, p = 5 and M = Ni, Cu, p = 4) in gas phase. We show here that the lower the MO2+ acceptor orbital lies in energy, the lower the H-abstraction barrier is in general. However, a sigma* acceptor orbital is much more efficient than a pi* acceptor orbital for a given energy. Finally, we found that indeed, the FeO2+ moiety is particularly efficient but also CoO2+ and MnO2+ could be good candidates to perform C-H hydroxylation.
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http://dx.doi.org/10.1021/ic802095mDOI Listing
April 2009

Enhancement of IR and VCD intensities due to charge transfer.

Phys Chem Chem Phys 2009 Mar 21;11(10):1526-38. Epub 2009 Jan 21.

Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.

Donor-acceptor interactions such as the one between the Cl(-) base and the N-H sigma* acceptor orbitals encountered in the complexation of Cl(-) counterions to the [Co(en)(3)](3+) transition metal complex, have been shown to cause huge enhancement (between 1 and 2 orders of magnitude) of the VCD intensities of N-H stretching modes. This effect has been fully analyzed, and could be attributed to increased charge flow from the Cl(-) donors when the N-H bonds become stretched. The transfer of charge counteracts the movement of negative electronic charge that happens along with the motion of the H nuclei, effectively reversing the electronic part of the electric dipole transition moment (EDTM) in the direction of the charge flow (z, say), and of the magnetic transition dipole moment (MDTM) in the perpendicular direction. The consequences for the IR and VCD intensity follow: IR intensity is strongly increased if the EDTM is polarized in the z direction, e.g. in A(2) modes, but not so much if it is polarized in the xy plane (E modes), the VCD is strongly enhanced if the EDTM and MTDM are polarized in the xy plane (in E modes), but less so when they are polarized in the z direction (in A(2) modes). The explanation holds generally for complexation phenomena of this sort, including the donor-acceptor part of hydrogen bonding interactions, e.g. with solvent molecules.
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http://dx.doi.org/10.1039/b816151hDOI Listing
March 2009

Generation of ferryl species through dioxygen activation in iron/EDTA systems: a computational study.

Inorg Chem 2009 Jan;48(2):527-40

Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

The ferryl species (oxidoiron(IV), FeO(2+)) is a ubiquitous, highly oxidative intermediate in oxidation catalysis. We study theoretically its abiotic generation, in the form of the singularly active complex of FeO(2+) with the EDTAH(n)(-4+n), n = 0-4 ligands, from O(2) and Fe(2+)-EDTA complexes. The calculations are for the gas phase using generalized gradient corrected (BLYP and OPBE) Density Functional Theory (DFT). We examine the effects of ligand protonation on the coordination geometry and electronic structure of the chelated Fe(2+) ion, on its affinity to bind dioxygen, and on the generation of dinuclear Fe/EDTA/O(2) complexes, whose formation has been hypothesized on the basis of kinetic measurements of Fe(II)/Fe(III) autoxidation reactions in aqueous solution. We also consider the homolytic cleavage of the O-O bond within one such complex, [Fe x EDTAH x O(2) x EDTAH x Fe](2-), and we show that this reaction leads to a pair of Fe(IV)O/EDTA systems with an energetic barrier comparable to those computed for model systems of active sites of enzymes involved in dioxygen activation, such as methane monooxygenase. Our study supports the recently advanced hypothesis that high valent iron compounds capable of oxidizing organic substrates may be produced as a byproduct of the Fe(II)/Fe(III) autoxidation in aqueous Fe/EDTA/O(2) solutions at ambient conditions. We also identify the origin of the enhanced O(2) activation ability in the monoprotonated [Fe x EDTAH](-) complex, compared to other ligand protonation states, which has been observed in kinetic measurements.
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http://dx.doi.org/10.1021/ic800998nDOI Listing
January 2009
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