QM/MM calculations with deMon2k.

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted. In the first, deMon2k is interfaced with the CHARMM MM code (CHARMM-deMon2k); in the second MM is coded directly within the deMon2k software; and in the third the Chemistry in Ruby (Cuby) wrapper is used to drive the calculations. Cuby is also used in the context of constrained-DFT/MM calculations. Each of these implementations is described briefly; pros and cons are discussed and a few recent applications are described briefly. Applications include solvated ions and biomolecules, polyglutamine peptides important in polyQ neurodegenerative diseases, copper monooxygenases and ultra-rapid electron transfer in cryptochromes.

Insights into the oxygen-based ligand of the low pH component of the Cu(2+)-amyloid-ß complex.

In spite of significant experimental effort dedicated to the study of Cu(2+) binding to the amyloid beta (Aß) peptide, involved in Alzheimer's disease, the nature of the oxygen-based ligand in the low pH component of the Cu(2+)-Aß(1-16) complex is still under debate. This study reports density-functional-theory-based calculations that explore the potential energy surface of Cu(2+) complexes including N and O ligands at the N-terminus of the Aß peptide, with a focus on evaluating the role of Asp1 carboxylate in copper coordination. Model conformers including 3, 6, and 17 amino acids have been used to systematically study several aspects of the Cu(2+)-coordination such as the Asp1 side chain conformation, local peptide backbone geometry, electrostatic and/or hydrogen bond interactions, and number and availability of Cu(2+) ligands. Our results show that the Asp1 peptide carbonyl binds to Cu(2+) only if the coordination number is less than four. In contrast, if four ligands are available, the most stable structures include the Asp1 carboxylate in equatorial position instead of the Asp1 carbonyl group. The two lowest energy Cu(2+)-Aß(1-17) models involve Asp1 COO(-), the N-terminus, and His6 and His14 as equatorial ligands, with either a carbonyl or a water molecule in the axial position. These models are in good agreement with experimental data reported for component I of the Cu(2+)-Aß(1-16) complex, including EXAFS- and X-ray-derived Cu(2+)-ligand distances, Cu(2+) EPR parameters, and (14)N and (13)C superhyperfine couplings. Our results suggest that at low pH, Cu(2+)-Aß species with Asp1 carboxylate equatorial coordination coexist with species coordinating the Asp1 carbonyl. Understanding the bonding mechanism in these species is relevant to gain a deeper insight on the molecular processes involving copper-amyloid-ß complexes, such as aggregation and redox activity.

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters.

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

A comparative study of structural, acidic and hydrophilic properties of Sn-BEA with Ti-BEA using periodic density functional theory.

Periodic density functional theory has been employed to characterize the differences in the structural, Lewis acidic and hydrophilic properties of Sn-BEA and Ti-BEA. We show that the incorporation of Sn increases the Lewis acidity of BEA compared to the incorporation of Ti. Hence, the present work gives insight into the role of Sn in increasing the efficiency of the oxidation reactions. The results also justify that the percentage of Sn substituted in BEA is less than Ti. The structural analysis shows that the first coordination shell of Sn is larger than that of Ti. However, the second coordination of both sites remains the same. The water adsorption properties of these substituted zeolites are quantified. Moreover, we explain the higher Lewis acidity of Sn than the Ti site on the basis of the Fukui functions and charge population analysis.

Interaction between n-Alkane Chains: Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.

Theoretical study of Cu(I)Y zeolite: structure and electronic properties.

The structural and electronic properties of the accessible Cu(I) site of a faujasite-type zeolite have been studied, by use of large cluster models and a density functional theory-based methodology. We demonstrate that the local ideal C(3) symmetry of the Cu(I) site II is broken. The Cu(I) cation is bonded to the zeolite framework by one bond of about 2.26 A and two shorter ones of 2.07 A. We demonstrate that only one cation position exists at this site. This result is also confirmed by a molecular electrostatic potential analysis. We show that local properties at site II, as well as the global properties of the solid (frontier orbitals), do not depend on the Al and cation distribution and only slightly on the cocation nature. Taking into account the present results and well-known experimental data, we propose that specific catalytic behaviors are correlated with local response properties, such as the local acid strength or, in other reactions, specific local architecture or confinement.

Theoretical study of N2O reduction by CO in Fe-BEA Zeolite.

Quantum mechanical (QM) and QM/molecular mechanics (MM) studies of the full catalytic cycle of N(2)O reduction by CO in Fe-BEA zeolite, that is, oxidation of BEA-Fe by N(2)O and reduction of BEA-Fe-alphaO by CO, is presented. A large QM cluster, representing half of the channel of the BEA zeolite, is used. The contribution of the MM embedding to the calculated activation energies is found to be negligible. The minimum-energy paths for N(2)O decomposition and reduction with CO are calculated using the nudged elastic band (NEB) method. Calculated and experimental activation energies are in good agreement. The two possible orientations for the gaseous molecules adsorbing on the Fe site that are found lead to different activation energies.

Structural, electronic, and bonding properties of zeolite Sn-beta: a periodic density functional theory study.

The structural, electronic, and the bonding properties of the zeolite Sn-beta (Sn-BEA) have been investigated by using the periodic density functional theory. Each of the nine different T-sites in BEA were substituted by Sn atoms and all the nine geometries were completely optimized by using the plane-wave basis set in conjunction with the ultra-soft pseudopotential. On the basis of the structural and the electronic properties, it has been demonstrated that the substitution of Sn atoms in the BEA framework is an endothermic process and hence the incorporation of Sn in the BEA is limited. The lowest unoccupied molecular orbitals (LUMO) energies have been used to characterize the Lewis acidity of each T-site. On the basis of the relative cohesive energy and the LUMO energy, the T2 site is shown to be the most favorable site for the substitution Sn atoms in the BEA framework.

Comparative density functional theory study of the binding of ligands to Cu+ and Cu2+: Influence of the coordination and oxidation state.

BP86, B3LYP and MP2 methods, generally used to study large systems containing transition metals, were compared for their ability to accuratly evaluate bond dissociation energies of copper complexes. Various [Cu-L]+ and [Cu-L]2+ complexes in which L are small ligands and the higher coordinated complexes, [Cu(NH3)(4)]+ and [Cu(NH3)4]2+ were studied. For monoligated complexes, the BDEs calculated by the three methods differed by 2 to 60 kcal/mol, the larger differences being obtained for [Cu-L]2+ complexes. The BDEs calculated using the B3LYP functional were in general close to the experimental values whereas the BDEs calculated using the BP86 functional were too high and the BDEs calculated using the MP2 were too low. If we rank the whole ligands according to their increased bond strength, the resulting orders obtained with the three methods are different for the [Cu-L]+ complexes, the B3LYP giving the same order as the experimental one. This result indicates that the BDEs of [Cu-L]+ complexes are better modeled using the B3LYP than using the BP86 and MP2 methods. For [Cu-L]2+, B3LYP also gave the most reliable results whereas BP86 gave too large BDEs and MP2 gave too small BDEs. However, symmetries of ground states can be different using DFT and post-Hartree-Fock methods. For [Cu-N2O]2+ the use of the B1LYP provides a better symmetry of the complex than the B3LYP, as has been recently shown in the literature for [Cu-H2O]2+. MP2 led to an incorrect bent structure for [Cu-N2]2+ in contrast to a linear structure obtained with the other methods, including CCSD(T). However, due to the lack of experimental data for [Cu-L]2+ complexes and to contrasted results for the methods, it is not possible to conclude definitely. For the high coordinated complexes [Cu(NH3)4]+ and [Cu(NH3)4]2+, the PBE calculation method was used in addition to the BP86, B3LYP and MP2. The BDE values were very close to each other when there is no change of the oxidation state during the reaction. On the basis of these calculations, the choice of the method was less crucial for high coordinated complexes [Cu(NH3)4]+ and [Cu(NH3)4]2+ so long as the oxidation state remained the same during the reaction. In contrast, when [Cu(NH3)4]2+ is reduced in [Cu(NH3)3]+ and NH3, the BDE calculated using the four methods were markedly different.

Calculated magnetic properties for the characterization of zeolite active sites.

Detailed structures of zeolite catalysts, including Al and cation distribution, framework and catalytic site geometries, are not fully accessible from experiment. Since the magnetic properties of framework elements and extra-framework cations are strongly dependent on their environment, the combined use of magic angle spinning NMR or ESR techniques with quantum chemical calculations is very useful to establish the local structure around specific sites. General effects of Al and B substitution in the zeolite framework, coupled with H(+) or Na(+) counter-ions, on the (29)Si, (27)Al and (11)B NMR spectra were studied, using a density functional theory (DFT)-based methodology, for a model of the zeolite mazzite. In agreement with experiment, the exchange of Na(+) by H(+) in the boron compound is accompanied by a change of B coordination from tetrahedral to trigonal, with a characteristic downfield shift of around 10 ppm, whereas the presence of water restores the tetrahedral boron and its NMR chemical shift. Further, ESR spectra of zeolites exchanged with open-shell cations provide useful data on the metal coordination and its reactivity compared with calculated model ESR properties. The ESR hyperfine coupling constants, calculated using DFT, for models of different Cu sites of a Cu(II)-Y zeolite, with and without H(2)O or NH(3), show a clear correlation between the Cu spin population and its coordination, involving the participation of the zeolite framework in the reactivity.

Selective catalytic reduction of NO by NH3 on Cu-faujasite catalysts: an experimental and quantum chemical approach.

The selective catalytic reduction (SCR) of NO by NH3 in the presence of O2 on Cu-faujasite (Cu-FAU) has been studied. Substitution of some Cu2+ with H+ and Na+ cations, compensating for the negative charge of the zeolite framework, forms the various CuHNa-FAU studied. The amount of Cu was held constant and the proportion of H+ and Na+ varied in the sample. The substitution of Na+ for H+ increases sharply the SCR rate by lowering the temperature of reaction by about 150 K. It is proposed that the rate increase mainly comes from an unhindered migration of Cu from hidden to active sites and a modification of the redox properties of Cu species. The former was demonstrated by diffuse reflectance IR spectroscopy of adsorbed CO. The change in redox properties was demonstrated by a faster oxidation of Cu+ to Cu2+ (rate-determining step). Quantum chemical calculations on model clusters of CuHNa-FAU indicate that the faster rate of oxidation can be explained by a higher lability of protons in the absence of Na, which can be then removed from the catalyst more easily to yield H2O during the oxidation process.