Ivano Tavernelli

Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics—Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections

We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using ab initio molecular dynamics simulations with density functional theory. The lack of London dispersion forces in generalized gradient approximations (GGAs) is remedied by means of dispersion-corrected atom-centered potentials (DCACPs) or damped atom-pairwise dispersion corrections of the C6R(-6) form. We compare results from simulations using GGA density functionals (BLYP, PBE, and revPBE) with data from their van der Waals (vdW) corrected counterparts. As pointed out previously, all vdW-corrected BLYP simulations give rise to highly mobile water whose softened structure is closer to experimental data than the one predicted by the bare BLYP functional. Including vdW interactions in the PBE functional, on the other hand, has little influence on both structural and dynamical properties of water. Augmenting the revPBE functional with either damped atom-pairwise dispersion corrections or DCACP evokes opposite behaviors. The former further softens the already under-structured revPBE water, whereas the latter makes it more glassy. These results demonstrate the delicacy needed in describing weak interactions in molecular liquids.

Importance of van der Waals interactions in liquid water.

We present ab initio molecular dynamics studies on liquid water using density functional theory in conjunction with either dispersion-corrected atom-centered potentials or empirical van der Waals corrections. Our results show that improving the description of van der Waals interactions in DFT-GGA leads to a softening of liquid waters structure with higher mobility. The results obtained with dispersion-corrected atom-centered potentials are especially encouraging. In particular, the radial distribution functions are in better agreement with experiment, and the self-diffusion coefficient increases by more than three-fold compared with the one predicted by the BLYP functional. This work demonstrates that van der Waals interactions are essential in fine-tuning both structural and dynamical properties of liquid water.

Mixed time-dependent density-functional theory/classical trajectory surface hopping study of oxirane photochemistry

We present a mixed time-dependent density-functional theory (TDDFT)/classical trajectory surface hopping (SH) study of the photochemical ring opening in oxirane. Previous preparatory work limited to the symmetric CC ring-opening pathways of oxirane concluded that the Tamm-Dancoff approximation (TDA) is important for improving the performance of TDDFT away from the equilibrium geometry. This observation is supported by the present TDDFT TDA/SH calculations which successfully confirm the main experimentally derived Gomer-Noyes mechanism for the photochemical CO ring opening of oxirane and, in addition, provide important state-specific information not easily accessible from experiments. In particular, we find that, while one of the lowest two excited states is photochemically relatively inert, excitation into the other excited state leads predominantly to rapid ring opening, cyclic-C(2)H(4)O-->(*)CH(2)CH(2)O(*). This is followed by hopping to the electronic ground state where hot (4000 K) dynamics leads to further reactions, namely, (*)CH(2)CH(2)O()-->CH(3)CHO-->(*)CH(3)+(*)CHO and CH(4)+CO. We note that, in the dynamics, we are not limited to following minimum energy pathways and several surface hops may actually be needed before products are finally reached. The performance of different functionals is then assessed by comparison of TDDFT and diffusion Monte Carlo potential energy curves along a typical TDDFT TDA/SH reaction path. Finally, although true (S(0),S(1)) conical intersections are expected to be absent in adiabatic TDDFT, we show that the TDDFT TDA is able to approximate a conical intersection in this system.

Acid-induced degradation of phosphorescent dopants for OLEDs and its application to the synthesis of tris-heteroleptic iridium(III) bis-cyclometalated complexes.

Investigations of blue phosphorescent organic light emitting diodes (OLEDs) based on [Ir(2-(2,4-difluorophenyl)pyridine)(2)(picolinate)] (FIrPic) have pointed to the cleavage of the picolinate as a possible reason for device instability. We reproduced the loss of picolinate and acetylacetonate ancillary ligands in solution by the addition of Brønsted or Lewis acids. When hydrochloric acid is added to a solution of a [Ir(C^N)(2)(X^O)] complex (C^N = 2-phenylpyridine (ppy) or 2-(2,4-difluorophenyl)pyridine (diFppy) and X^O = picolinate (pic) or acetylacetonate (acac)), the cleavage of the ancillary ligand results in the direct formation of the chloro-bridged iridium(III) dimer [{Ir(C^N)(2)(μ-Cl)}(2)]. When triflic acid or boron trifluoride are used, a source of chloride (here tetrabutylammonium chloride) is added to obtain the same chloro-bridged iridium(III) dimer. Then, we advantageously used this degradation reaction for the efficient synthesis of tris-heteroleptic cyclometalated iridium(III) complexes [Ir(C^N(1))(C^N(2))(L)], a family of cyclometalated complexes otherwise challenging to prepare. We used an iridium(I) complex, [{Ir(COD)(μ-Cl)}(2)], and a stoichiometric amount of two different C^N ligands (C^N(1) = ppy; C^N(2) = diFppy) as starting materials for the swift preparation of the chloro-bridged iridium(III) dimers. After reacting the mixture with acetylacetonate and subsequent purification, the tris-heteroleptic complex [Ir(ppy)(diFppy)(acac)] could be isolated with good yield from the crude containing as well the bis-heteroleptic complexes [Ir(ppy)(2)(acac)] and [Ir(diFppy)(2)(acac)]. Reaction of the tris-heteroleptic acac complex with hydrochloric acid gives pure heteroleptic chloro-bridged iridium dimer [{Ir(ppy)(diFppy)(μ-Cl)}(2)], which can be used as starting material for the preparation of a new tris-heteroleptic iridium(III) complex based on these two C^N ligands. Finally, we use DFT/LR-TDDFT to rationalize the impact of the two different C^N ligands on the observed photophysical and electrochemical properties.

Mixed time-dependent density-functional theory/classical photodynamics study of oxirane photochemistry

We present a mixed time-dependent density-functional theory (TDDFT)/classical trajectory surface hopping (SH) study of the photochemical ring opening in oxirane. Previous preparatory work limited to the symmetric CC ring-opening pathways of oxirane concluded that the Tamm-Dancoff approximation (TDA) is important for improving the performance of TDDFT away from the equilibrium geometry. This observation is supported by the present TDDFT TDA/SH calculations which successfully confirm the main experimentally derived Gomer-Noyes mechanism for the photochemical CO ring opening of oxirane and, in addition, provide important state-specific information not easily accessible from experiments. In particular, we find that, while one of the lowest two excited states is photochemically relatively inert, excitation into the other excited state leads predominantly to rapid ring opening, cyclic-C(2)H(4)O-->(*)CH(2)CH(2)O(*). This is followed by hopping to the electronic ground state where hot (4000 K) dynamics leads to further reactions, namely, (*)CH(2)CH(2)O()-->CH(3)CHO-->(*)CH(3)+(*)CHO and CH(4)+CO. We note that, in the dynamics, we are not limited to following minimum energy pathways and several surface hops may actually be needed before products are finally reached. The performance of different functionals is then assessed by comparison of TDDFT and diffusion Monte Carlo potential energy curves along a typical TDDFT TDA/SH reaction path. Finally, although true (S(0),S(1)) conical intersections are expected to be absent in adiabatic TDDFT, we show that the TDDFT TDA is able to approximate a conical intersection in this system.

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa

We have coupled hybrid quantum mechanics (density functional theory; Car–Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu2+ + e− → Cu+ half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite-temperature fluctuations of the protein structure are both essential for a correct quantitative description of the electronic properties of this system. We report a redox potential shift with respect to copper in water of 0.2 eV (experimental 0.16 eV) and a reorganization free energy λ = 0.76 eV (experimental 0.6–0.8 eV). The electrostatic field of the protein plays a crucial role in fine tuning the redox potential and determining the structure of the solvent. The inner-sphere contribution to the reorganization energy is negligible. The overall small value is mainly due to solvent rearrangement at the protein surface.

Trajectory-Based Nonadiabatic Dynamics with Time- Dependent Density Functional Theory

Understanding the fate of an electronically excited molecule constitutes an important task for theoretical chemistry, and practical implications range from the interpretation of atto- and femtosecond spectroscopy to the development of light-driven molecular machines, the control of photochemical reactions, and the possibility of capturing sunlight energy. However, many challenging conceptual and technical problems are involved in the description of these phenomena such as 1) the failure of the well-known Born-Oppenheimer approximation; 2) the need for accurate electronic properties such as potential energy surfaces, excited nuclear forces, or nonadiabatic coupling terms; and 3) the necessity of describing the dynamics of the photoexcited nuclear wavepacket. This review provides an overview of the current methods to address points 1) and 3) and shows how time-dependent density functional theory (TDDFT) and its linear-response extension can be used for point 2). First, the derivation of Ehrenfest dynamics and nonadiabatic Bohmian dynamics is discussed and linked to Tullys trajectory surface hopping. Second, the coupling of these trajectory-based nonadiabatic schemes with TDDFT is described in detail with special emphasis on the derivation of the required electronic structure properties.

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

Limited searching in the conformational space is one of the major obstacles for investigating protein dynamics by numerical approaches. For this reason, classical all-atom molecular dynamics (MD) simulations of proteins tend to be confined to local energy minima, particularly when the bulk solvent is treated explicitly. To overcome this problem, we have developed a novel replica exchange protocol that uses modified force-field parameters to treat interparticle nonbonded potentials within the protein and between protein and solvent atoms, leaving unperturbed those relative to solvent-solvent interactions. We have tested the new protocol on the 18-residue-long tip of the P domain of calreticulin in an explicit solvent. With only eight replicas, we have been able to considerably enhance the conformational space sampled during a 100 ns simulation, compared to as many parallel classical molecular dynamics simulations of the same length or to a single one lasting 450 ns. A direct comparison between the various simulations has been possible thanks to the implementation of the weighted histogram analysis method, by which conformations simulated with modified force-field parameters can be assigned different weights. Interatom, inter-residue distances in the structural ensembles obtained with our novel replica exchange approach and by classical MD simulations compare equally well with those derived from NMR data. Rare events, such as unfolding and refolding, occur with reasonable statistical frequency. Visiting of conformations characterized by very small Boltzmann weights is also possible. Despite their low probability, such regions of the conformational space may play an important role in the search for local potential-energy minima and in dynamically controlled functions.

Molecular dynamics in electronically excited states using time-dependent density functional theory

We describe two different implementations of time-dependent density functional theory (TDDFT) for use in excited state molecular dynamics simulations. One is based on the linear response formulation (LR-TDDFT), whereas the other uses a time propagation scheme for the electronic wave functions (P-TDDFT). Photo-induced cis–trans isomerization of C=C, C=N and N=N double bonds is investigated in three model compounds, namely the 2,4-pentadiene-1-iminium cation (PSB), formaldimine and diimide. For formaldimine and diimide, the results obtained with both schemes are in agreement with experimental data and previously reported theoretical results. Molecular dynamics simulations yield new insights into the relaxation pathways in the excited state. For PSB, which is a model system for the retinal protonated Schiff base involved in the visual process, the forces computed from the LR-TDDFT S1 surface lead to an increased bond length alternation and, consequently, to single bond rotation. On the contrary, P-TDDFT dynamics lead to a decreased bond length alternation, in agreement with CASPT2 and restricted open-shell Kohn–Sham (ROKS) calculations.

DNA structural distortions induced by ruthenium-arene anticancer compounds.

Organometallic ruthenium(II)-arene (RA) compounds combine a rich structural diversity with the potential to overcome existing chemotherapeutic limitations. In particular, the two classes of compounds [Ru(II)(eta(6)-arene)X(en)] and [Ru(II)(eta(6)-arene)(X)2(pta)] (RA-en and RA-pta, respectively; X = leaving group, en = ethylenediamine, pta = 1,3,5-triaza-7-phosphaadamantane) have become the focus of recent anticancer research. In vitro and in vivo studies have shown that they exhibit promising new activity profiles, for which their interactions with DNA are suspected to be a crucial factor. In the present study, we investigate the binding processes of monofunctional RA-en and bifunctional RA-pta to double-stranded DNA and characterize the resulting structural perturbations by means of ab initio and classical molecular dynamics simulations. We find that both RA complexes bind easily through their ruthenium center to the N7 atom of guanine bases. The high flexibility of DNA allows for fast accommodation of the ruthenium complexes into the major groove. Once bound to the host, however, the two complexes induce different DNA structural distortions. Strain induced in the DNA backbone from RA-en complexation is released by a local break of a Watson-Crick base-pair, consistent with the experimentally observed local denaturation. The bulkier RA-pta, on the other hand, bends the DNA helix toward its major groove, resembling the characteristic DNA distortion induced by the classic anticancer drug cisplatin. The atomistic details of the interactions of RA complexes with DNA gained in the present study shed light on some of the anticancer properties of these compounds and should assist future rational compound design.