Maria Francesca Iozzi

The Dalton quantum chemistry program system

Dalton is a powerful general‐purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self‐consistent‐field, Møller–Plesset, configuration‐interaction, and coupled‐cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic‐structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge‐origin‐invariant manner. Frequency‐dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one‐, two‐, and three‐photon processes. Environmental effects may be included using various dielectric‐medium and quantum‐mechanics/molecular‐mechanics models. Large molecules may be studied using linear‐scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms.

Influence of External Force on Properties and Reactivity of Disulfide Bonds

The mechanochemistry of the disulfide bridge--that is, the influence of an externally applied force on the reactivity of the sulfur-sulfur bond--is investigated by unrestricted Kohn-Sham theory. Specifically, we apply the COGEF (constrained geometry simulates external force) approach to characterize the mechanochemistry of the disulfide bond in three different chemical environments: dimethyl disulfide, cystine, and a 102-atom model of the I27 domain in the titin protein. Furthermore, the mechanism of the thiol-disulfide reduction reaction under the effect of an external force is investigated by considering the COGEF potential for the adduct and transition-state clusters. With the unrestricted Becke-three-parameter-Lee-Yang-Parr (UB3LYP) exchange-correlation functional in the 6-311++G(3df,3pd) orbital basis, the rupture force of dimethyl disulfide is 3.8 nN at a disulfide bond elongation of 35 pm. The interaction with neighboring groups and the effect of conformational rigidity of the protein environment have little influence on the mechanochemical characteristics. Upon stretching, we make the following observations: the diradical character of the disulfide bridge increases; the energy difference between the singlet ground state and low-lying triplet state decreases; and the disulfide reduction is promoted by an external force in the range 0.1-0.4 nN. Our model of the interplay between force and reaction mechanism is in qualitative agreement with experimental observations.

Assessment of theoretical methods for the determination of the mechanochemical strength of covalent bonds

The performance of some commonly used quantum-chemical methods in accurately and reliably describing the influence of applying an external mechanical force has been investigated for a set of small molecules. By applying coupled-cluster CCSD(T) theory in an extended basis set as benchmark, all methods tested provide a good qualitative description of the physical process, although the quantitative agreement varies considerably. Hartree–Fock (HF) theory overestimates both the values of the bond-breaking point and the rupture force, typically by 20–30%. The same applies to density-functional theory (DFT) based on the local density approximation (LDA). By introducing the generalized gradient approximation (GGA) in the form of the BLYP and PBE functionals, only a slight overestimation is observed. Moreover, these pure DFT methods perform better than the hybrid B3LYP and CAM-B3LYP methods. The excellent agreement observed between the CCSD(T) method and multiconfigurational methods for bond distances significantly beyond the bond-breaking point shows that the essence of mechanical bond breaking is captured by single-reference-based methods. Comparisons of accurate numerical bond-dissociation curves with simple analytical forms show that Morse-type curves provide useful approximate bond-breaking points and rupture forces, accurate to within 10%. By contrast, polynomial curves are much less useful. The outcome of kinetic calculations to estimate the dissociation probability as a function of the applied force depends strongly on the description of the potential-energy curve. The most probable rupture forces calculated by numerical integration appear to be significantly more accurate than those obtained from simple analytical expressions based on fitted Morse potentials.

Communication: Analytic gradients in the random-phase approximation

The relationship between the random-phase-approximation (RPA) correlation energy and the continuous algebraic Riccati equation is examined and the importance of a stabilizing solution is emphasized. The criterion to distinguish this from non-stabilizing solutions can be used to ensure that physical, smooth potential energy surfaces are obtained. An implementation of analytic RPA molecular gradients is presented using the Lagrangian technique. Illustrative calculations indicate that RPA with Hartree-Fock reference orbitals delivers an accuracy similar to that of second-order Mo̸ller-Plesset perturbation theory.

A new chiral, poly-imidazole N8-ligand and the related di- and tri-copper(II) complexes: synthesis, theoretical modelling, spectroscopic properties, and biomimetic stereoselective oxidations

The new poly-imidazole N(8) ligand (S)-2-piperazinemethanamine-1,4-bis[2-((N-(1-acetoxy-3-(1-methyl-1H-imidazol-4-yl))-2-(S)-propyl)-(N-(1-methyl-1H-imidazol-2-ylmethyl)))ethyl]-N-(phenylmethyl)-N-(acetoxy), also named (S)-Pz-(C2-(HisIm))(2) (L), containing three chiral (S) centers, was obtained by a multi-step synthesis and used to prepare dinuclear [Cu(2)(L)](4+) and trinuclear [Cu(3)(L)](6+) copper(II) complexes. Low-temperature EPR experiments performed on [Cu(2)(L)](4+) demonstrated that the two S = ½ centers behaved as independent paramagnetic units, while the EPR spectra used to study the trinuclear copper complex, [Cu(3)(L)](6+), were consistent with a weakly coupled three-spin ½ system. Theoretical models for the two complexes were obtained by DFT/RI-BP86/TZVP geometry optimization, where the structural and electronic characteristics nicely supported the EPR experimental findings. In addition, the theoretical analysis unveiled that the conformational flexibility encoded in both [Cu(2)(L)](4+) and [Cu(3)(L)](6+) arises not only from the presence of several σ-bonds and the bulky residues attached to the (S)-Pz-(C2-(HisIm))(2) ligand scaffold, but also from the poor coordination ability of the tertiary amino groups located in the ligand side-chains containing the imidazole units towards the copper(II) ions. Both the dinuclear and trinuclear complexes are efficient catalysts in the stereoselective oxidation of several catechols and flavonoid compounds, yielding the corresponding quinones. The structural features of the substrate-catalyst adduct intermediates were assessed by searching the conformational space of the molecule through MMFF94/Monte Carlo (MMFF94/MC) methods. The conformational flexibility of the bound ligand in the complexes proves to be beneficial for substrate binding and recognition. For the dinuclear complex, chiral recognition of the optically active substrates derives from weak electrostatic interactions between bound substrates and folded regions of the ligand scaffold. For the trinuclear complex, in the case of L/D-Dopa, the chiral recognition has a remarkable stereoselectivity index of 75%, the highest so far reported for this type of reaction. Here the dominant contribution to stereoselectivity arises from the direct interaction between a donor group (the Dopa carboxylate) far from the substrate reaction site (the catechol ring) with the additional (third) copper center not involved in the oxidative catalysis. On the other hand, in the case of bulky substrates, such as L/D-catechin, the observed poor substrate recognition is associated with much weaker interactions between the chiral regions of the complex and the chiral part of the substrate.

An efficient density-functional-theory force evaluation for large molecular systems

An efficient, linear-scaling implementation of Kohn-Sham density-functional theory for the calculation of molecular forces for systems containing hundreds of atoms is presented. The density-fitted Coulomb force contribution is calculated in linear time by combining atomic integral screening with the continuous fast multipole method. For higher efficiency and greater simplicity, the near-field Coulomb force contribution is calculated by expanding the solid-harmonic Gaussian basis functions in Hermite rather than Cartesian Gaussians. The efficiency and linear complexity of the molecular-force evaluation is demonstrated by sample calculations and applied to the geometry optimization of a few selected large systems.

Adsorption of CH3 COOH on TiO2: IR and theoretical investigations

Adsorption of organic molecules on TiO2 surfaces is widely used in a number of technological applications, from heterogeneous catalysis, in particular photodegradation of organic pollutants, to dye-sensitized solar cells (DSSCs), where in most cases the dye molecules are grafted to the anatase TiO2 surface through a carboxylic group. In particular, organic/TiO2 systems can be of relevant importance in the modeling of electronic devices, in which the molecular layer is able to finely tune the electric properties, as well as of highly efficient heterogeneous catalysts. A key step is the understanding of the nature of the carbon-oxygen-titanium bonds on such surfaces, which is the specific aim of our combined IR and ab initio study of the adsorption of CH3COOH on TiO2. The experimental determination of the CH3COOH frequency shifts due to the absorption on the P25 (Degussa) TiO2 surface was performed by means of a step-wise procedure, consisting of a preliminary outgassing at 600°C of TiO2, in order to have a high dehydroxilation degree of the surface, followed by IR measurements at increasing CH3COOH pressure and subsequent desorption. Frequency calculations to be compared with experimental results were performed within a cluster approach using GAUSSIAN03 package. In order to make such calculations feasible, we decided to use an ONIOM approach where the model system, i.e., the small portion corresponding to CH3COOH plus the surface atoms, is treated at DFT level while the real system, comprising the bulk atoms, at MSINDO level. Once properly tested the ONIOM approach to characterize the interaction of TiO2 with CH3COOH, we computed the vibrational frequencies and compared them with the results of the IR experiments, providing some insight for the interpretation of the experimental complex vibrational pattern.

Structural changes induced by dehydration in the crystalline layered silicate Na-RUB-18: a computational/experimental combined study

Na-RUB-18 layered silicate (Na8Si32O64(OH)8·32H2O) is prepared following the procedure reported in the literature (: K. Kosuge and A. Tsunashima, J. Chem. Soc., Chem. Commun., 1995, 2427) and its significant structural modifications induced by progressive removal of hydration water molecules are studied for the first time by a combined experimental (TGA and variable temperature XRD and FTIR) and theoretical approach. A novel structure of a partially de-hydrated Na-RUB-18 obtained upon heating at 75 °C under inert gas flow, which leads to a reversible phase transformation in agreement with XRD and FTIR results, is found. TGA indicates that at this stage, two of the four hydration water molecules per Na ion are lost. Theoretical results based on DFT calculations suggest that the apical water molecules of the solvated octahedrally coordinated sodium ion, forming weak H-bonds with the silicate oxygen atoms, are removed at this stage. As a consequence of the dehydration, the silicate layers get closer, and, similarly to that observed for zeolites, the sodium ions move towards lattice oxygen atoms, to restore their coordination shell. A combination of IR spectroscopy and computational models is used to describe the vibrational properties of silanol/silanolate (SiOH⋯SiO)−1 bridges, which are responsible for the proton conduction of Na-RUB-18. The method described can be of general utility to refine structures which are not fully accessible to standard X-ray structure analysis.

A polarizable continuum approach for the study of heterogeneous dielectric environments

We present a computational method, exploiting some features of the polarizable continuum model (PCM) to describe heterogeneous media; it belongs to the family of electrostatic embedding mixed methods, such as the more common quantum-mechanical (QM)/molecular mechanics approaches, with the electrostatic long range effects accounted for by a polarized continuum instead of atomic point charges. Provided effective dielectric constants are determined for the various parts of the system, the method is much faster than its atomistic counterpart, and allows for high-level QM calculations on the fragment of interest, using all the highly efficient computational tools developed for homogeneous PCM. Two case studies (the calculation of the pKa of solvent exposed acidic residues in a model protein, and the calculation of the electron spin resonance spectrum of a typical spin probe partially embedded in a membrane) are analyzed in some detail, to illustrate the application of the method to complex systems.

Photoemission study of ferrocenes: Insights into the electronic structure of Si-based hybrid materials

We present here the results of synchrotron radiation-excited UV-photoemission investigation and DFT calculations on vinylferrocene (VFC), a redox molecule suitable for applications in molecular electronics. A detailed assignment is discussed of the valence photoelectron spectra (UPS), which provides new data on the electronic structure and offers a partial re-interpretation of previous assignments on VFC based on theoretical and experimental evidences. Furthermore, the present results can allow for a meaningful comparison of photoemission results from the corresponding hybrid obtained by covalently attaching VFC to Si oriented surfaces.