Xavier Assfeld

Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method

Abstract In this Letter we extend to the ab initio level the principles of the local self consistent field method (LSCF) developed earlier within the semiempirical approximations. It allows quantum electronic computations on a fragment of a large molecule mostly depicted by a classical force field. The bond separating the quantum subsystem from the classical one is assumed to be represented by localized orbitals introduced as data. The molecular orbitals of this subsystem are developed on a basis of functions, orthogonal to the localized orbitals, which derive from the atomic orbitals of the usual basis set by a simple linear transformation. The algorithm of the LSCF method is obtained by a simple modification of the standard Hartree-Fock or DFT codes.

Time-dependent density functional theory investigation of the absorption, fluorescence, and phosphorescence spectra of solvated coumarins

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model, we have computed the electronic transitions of a large panel of coumarin dyes in their enol, keto, cationic, and anionic forms. Several processes have been studied: absorption, fluorescence, 0-0 phosphorescence, and triplet-triplet excitations. For each process, detailed comparison with experimental data has been carried out. Using the PBE06-31+G(d) scheme, it turns out that for a given electronic transition the experimental shifts resulting from the substitution of the coumarin core are nicely reproduced. Indeed, once a simple statistical correction is applied, the mean absolute errors on the absorption and fluorescence wavelengths are limited to 8 nm (0.09 eV) and 9 nm (0.07 eV), respectively. A valuable correlation between the experimental and theoretical phosphorescence auxochromic displacements has also been unravelled. The differences between the wavelengths of the various electronic processes of a given dye tend to be fairly predicted, especially for the fluorescence-phosphoresence shifts that are strongly overestimated by TD-DFT.

Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.

The pure quantum mechanics method, called Local Self‐Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post‐Hartree–Fock method, based on the restricted or unrestricted Hartree–Fock Slater determinant, and Kohn–Sham‐based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane.

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of the atom: for an sp(3) carbon atom, we consider the two core 1s electrons and treat that carbon as an atom with three electrons. This results in an LSCF+3 model. Similarly, a nitrogen atom with a lone pair of electrons available for conjugation is treated as an atom with five electrons (LSCF+5). This approach is particularly well suited to splitting peptide bonds and other bonds that include carbon or nitrogen atoms. To embed the induced polarization within the calculation, researchers must use a polarizable force field. However, because the parameters of the usual force fields include an average of the induction effects, researchers typically can obtain satisfactory results without explicitly introducing the polarization. When considering electronic transitions, researchers must take into account the changes in the electronic polarization. One approach is to simulate the electronic cloud of the surroundings by a continuum whose dielectric constant is equal to the square of the refractive index. This Electronic Response of the Surroundings (ERS) methodology allows researchers to model the changes in induced polarization easily. We illustrate this approach by modeling the electronic absorption of tryptophan in human serum albumin (HSA).

Toward a Quantitative Assessment of Electronic Transitions’ Charge-Transfer Character

We hereby report studies devoted to a topological descriptor of photoinduced electronic charge density variation. Our novel index, symbolized as ϕS, consists in the detachment and attachment densities overlap, where the detachment density physically depicts the electron density removed from the ground state of a molecule during the transition while the attachment density consists in the rearranged density in the excited state. Our method provides a simple and efficient way to quantitatively evaluate how easy the charge-separation is made upon the chromophores light absorption. Furthermore, this model can be applied for instance to address a comment on new push-pull dyes charge-transfer ability in order to assess their potentiality as candidates for light absorption-based devices. Moreover, the ϕS assessment allows us to perform some methodological diagnostic tests concerning the use of long-range corrected exchange-correlation functional in a time-dependent density functional theory (TDDFT) framework. This paper relates the ϕS descriptors mathematical foundations from various perspectives (detachment/attachment densities or natural transition orbitals), together with its application to several types of chromophores. Connections and divergences with a formerly proposed index are finally evidenced.

A theoretical study of Ru(II) polypyridyl DNA intercalators structure and electronic absorption spectroscopy of [Ru(phen)2(dppz)]2+ and [Ru(tap)2(dppz)]2+ complexes intercalated in guanine-cytosine base pairs.

The structural and spectroscopic properties of [Ru(phen)(2)(dppz)](2+) and [Ru(tap)(2)(dppz)](2+) (phen=1,10-phenanthroline; tap=1,4,5,8-tetraazaphenanthrene; dppz=dipyridophenazine ) have been investigated by means of density functional theory (DFT), time-dependent DFT (TD-DFT) within the polarized continuum model (IEF-PCM) and quantum mechanics/molecular mechanics (QM/MM) calculations. The model of the Delta and Lambda enantiomers of Ru(II) intercalated in DNA in the minor and major grooves is limited to the metal complexes intercalated in two guanine-cytosine base pairs. The main experimental spectral features of these complexes reported in DNA or synthetic polynucleotides are better reproduced by the theoretical absorption spectra of the Delta enantiomers regardless of intercalation mode (major or minor groove). This is especially true for [Ru(phen)(2)(dppz)](2+). The visible absorption of [Ru(tap)(2)(dppz)](2+) is governed by the MLCT(tap) transitions regardless of the environment (water, acetonitrile or bases pair), the visible absorption of [Ru(phen)(2)(dppz)](2+) is characterized by transitions to metal-to-ligand-charge-transfer MLCT(dppz) in water and acetonitrile and to MLCT(phen) when intercalated in DNA. The response of the IL(dppz) state to the environment is very sensitive. In vacuum, water and acetonitrile these transitions are characterized by significant oscillator strengths and their positions depend significantly on the medium with blue shifts of about 80 nm when going from vacuum to solvent. When the complex is intercalated in the guanine-cytosine base pairs the (1)IL(dppz) transition contributes mainly to the band at 370 nm observed in the spectrum of [Ru(phen)(2)(dppz)](2+) and to the band at 362 nm observed in the spectrum of [Ru(tap)(2)(dppz)](2+).

Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)2]2+.

The UV/Visible absorption properties of a polypyridyl ruthenium complex upon intercalation on DNA are studied at the mixed quantum mechanics molecular mechanics level of theory. Vertical excitation transitions are computed by time dependent density functional theory. Particular emphasis is put on the different levels at which the macromolecular environment is treated, and in particular on the analysis of the effect of mechanical, electrostatic and polarizable embedding. We show that with the highest level of theory the experimental absorption wavelengths are reproduced with a difference of only 2 or 3 nm for the low energy bands. The systematic analysis of the individual vertical transitions allows us to get much more insights into the role played by the environment, in particular, in metal to ligand and intra ligand charge transfer transitions that can lead to the production of DNA oxidative lesions exploitable in phototherapy.

Theoretical study of new ruthenium-based dyes for dye-sensitized solar cells.

Two relevant, recently reported, ruthenium-based complexes to be used as sensitizers in Grätzel photovoltaic cells are theoretically studied. The UV/vis absorption spectra have been computed within the time-dependent density functional theory formalism. The obtained excitation energies are compared with the experimental results, and the nature of the transition is analyzed in terms of the electronic density. A preliminary study on the performance of different functionals against the equation of motion coupled cluster is performed on a smaller model system.

Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: True orthogonality between ground and excited states

True orthogonality between single-determinant ground state and excited states is achieved through the use of the ab initio local self-consistent-field method. This method allows to optimize the electronic wave function under the constraint of orthogonality to one or several frozen spin–orbitals, virtuals or not. Core- and valence ionization energies of small molecules are computed and show the accuracy of this new scheme. First applications deal with core ionization of macromolecular systems, like proteins or polymers.

Improved Treatment of Surrounding Effects: UV/vis Absorption Properties of a Solvated Ru(II) Complex.

The UV/vis and circular-dichroism spectra of a bis-bipyridinyl ruthenium complex are computed at the density functional theory level and the time dependent density functional level of theory. The effects of the solvent, here water, have been taken into account, by polarizable continuum methods and by a hybrid quantum-mechanics/molecular-mechanics approach combined with molecular dynamics. The effects of the solvent have been decomposed in geometric, electrostatic, and polarization of the environment. The principal transitions have been analyzed by means of natural transition orbitals.