The three channels of many-body perturbation theory: GW, particle-particle, and electron-hole T-matrix self-energies.

We derive the explicit expression of the three self-energies that one encounters in many-body perturbation theory: the well-known GW self-energy, as well as the particle-particle and electron-hole T-matrix self-energies. Each of these can be easily computed via the eigenvalues and eigenvectors of a different random-phase approximation linear eigenvalue problem that completely defines their corresponding response function. For illustrative and comparative purposes, we report the principal ionization potentials of a set of small molecules computed at each level of theory. The performance of these schemes on strongly correlated systems (B2 and C2) is also discussed.

Measuring the Elasticity of Poly-l-Proline Helices with Terahertz Spectroscopy.

The rigidity of poly-l-proline is an important contributor to the stability of many protein secondary structures, where it has been shown to strongly influence bulk flexibility. The experimental Young's moduli of two known poly-l-proline helical forms, right-handed all-cis (Form I) and left-handed all-trans (Form II), were determined in the crystalline state by using an approach that combines terahertz time-domain spectroscopy, X-ray diffraction, and solid-state density functional theory. Contrary to expectations, the helices were found to be considerably less rigid than many other natural and synthetic polymers, as well as differing greatly from each other, with Young's moduli of 4.9 and 9.6 GPa for Forms I and II, respectively.

Electron density analysis of large (molecular and periodic) systems: A parallel implementation.

A parallel implementation is presented of a series of algorithms for the evaluation of several one-electron properties of large molecular and periodic (of any dimensionality) systems. The electron charge and momentum densities of the system, the electrostatic potential, X-ray structure factors, directional Compton profiles can be effectively evaluated at low computational cost along with a full topological analysis of the electron charge density (ECD) of the system according to Bader's quantum theory of atoms in molecules. The speedup of the parallelization of the different algorithms is presented. The search of all symmetry-irreducible critical points of the ECD of the crystallized crambin protein and the evaluation of all the corresponding bond paths, for instance, would require about 32 days if run in serial mode and reduces to less than 2 days when run in parallel mode over 32 processors.

Origins of contrasting copper coordination geometries in crystalline copper sulfate pentahydrate.

Metal-aqua ion ([M(H2O)n](X+)) formation is a fundamental step in mechanisms that are central to enzymatic and industrial catalysis. Past investigations of such ions have yielded a wealth of information regarding their properties, however questions still exist involving the exact structures of these complexes. A prominent example of this is hexaaqua copper(II) ([Cu(H2O)6](2+)), with the solution versus gas-phase configurations under debate. The differences are often attributed to the intermolecular interactions between the bulk solvent and the aquated complex, resulting in structures stabilized by extended hydrogen-bonding networks. Yet solution phase systems are difficult to study due to the lack of atomic-level positional details. Crystalline solids are ideal models for comparative study, as they contain fixed structures that can be fully characterized using diffraction techniques. Here, crystalline copper sulfate pentahydrate (CuSO4·5H2O), which contains two unique copper-water geometries, was studied in order to elucidate the origin of these contrasting hydrated metal envrionments. A combination of solid-state density functional theory and low-temperature X-ray diffraction was used to probe the electronic origins of this phenomenon. This was accomplished through implementation of crystal orbital overlap population and crystal orbital Hamiltonian population analyses into a developmental version of the CRYSTAL14 software. These new computational methods help highlight the delicate interplay between electronic structure and metal-water geometries.

Oxidative Stress and Inflammation in Hepatic Diseases: Therapeutic Possibilities of N-Acetylcysteine.

Liver disease is highly prevalent in the world. Oxidative stress (OS) and inflammation are the most important pathogenetic events in liver diseases, regardless the different etiology and natural course. N-acetyl-l-cysteine (the active form) (NAC) is being studied in diseases characterized by increased OS or decreased glutathione (GSH) level. NAC acts mainly on the supply of cysteine for GSH synthesis. The objective of this review is to examine experimental and clinical studies that evaluate the antioxidant and anti-inflammatory roles of NAC in attenuating markers of inflammation and OS in hepatic damage. The results related to the supplementation of NAC in any form of administration and type of study are satisfactory in 85.5% (n = 59) of the cases evaluated (n = 69, 100%). Within this percentage, the dosage of NAC utilized in studies in vivo varied from 0.204 up to 2 g/kg/day. A standard experimental design of protection and treatment as well as the choice of the route of administration, with a broader evaluation of OS and inflammation markers in the serum or other biological matrixes, in animal models, are necessary. Clinical studies are urgently required, to have a clear view, so that, the professionals can be sure about the effectiveness and safety of NAC prescription.

Structural, electronic and energetic properties of giant icosahedral fullerenes up to C6000: insights from an ab initio hybrid DFT study.

The properties of the (n,n) icosahedral family of carbon fullerenes up to n = 10 (6000 atoms) have been investigated through ab initio quantum-mechanical simulation by using a Gaussian type basis set of double zeta quality with polarization functions (84,000 atomic orbitals for the largest case), the hybrid B3LYP functional and the CRYSTAL14 code featuring generalization of symmetry treatment. The geometry of giant fullerenes shows hybrid features, between a polyhedron and a sphere; as n increases, it approaches the former. Hexagon rings at face centres take a planar, graphene-like configuration; the 12 pentagon rings at vertices impose, however, a severe structural constraint to which hexagon rings at the edges must adapt smoothly, adopting a bent (rather than sharp) transversal profile and an inward longitudinal curvature. The HOMO and LUMO electronic levels, as well as the band gap, are well described using power laws. The gap is predicted to become zero for n ≥ 34 (69,360 atoms). The atomic excess energy with respect to the ideal graphene sheet goes to zero following the log(Nat)/Nat law, which is well described through the continuum elastic theory applied to graphene; the limits for the adopted model are briefly outlined. Compared to larger fullerenes of the series, C60 shows unique features with respect to all the considered properties; C240 presents minor structural and energetic peculiarities, too.

On the full exploitation of symmetry in periodic (as well as molecular) self-consistent-field ab initio calculations.

Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.

The Raman spectrum of CaCO3 polymorphs calcite and aragonite: a combined experimental and computational study.

Powder and single crystal Raman spectra of the two most common phases of calcium carbonate are calculated with ab initio techniques (using a "hybrid" functional and a Gaussian-type basis set) and measured both at 80 K and room temperature. Frequencies of the Raman modes are in very good agreement between calculations and experiments: the mean absolute deviation at 80 K is 4 and 8 cm(-1) for calcite and aragonite, respectively. As regards intensities, the agreement is in general good, although the computed values overestimate the measured ones in many cases. The combined analysis permits to identify almost all the fundamental experimental Raman peaks of the two compounds, with the exception of either modes with zero computed intensity or modes overlapping with more intense peaks. Additional peaks have been identified in both calcite and aragonite, which have been assigned to (18)O satellite modes or overtones. The agreement between the computed and measured spectra is quite satisfactory; in particular, simulation permits to clearly distinguish between calcite and aragonite in the case of powder spectra, and among different polarization directions of each compound in the case of single crystal spectra.

Accurate dynamical structure factors from ab initio lattice dynamics: the case of crystalline silicon.

A fully ab initio technique is discussed for the determination of dynamical X-ray structure factors (XSFs) of crystalline materials, which is based on a standard Debye-Waller (DW) harmonic lattice dynamical approach with all-electron atom-centered basis sets, periodic boundary conditions, and one-electron Hamiltonians. This technique requires an accurate description of the lattice dynamics and the electron charge distribution of the system. The main theoretical parameters involved and final accuracy of the technique are discussed with respect to the experimental determinations of the XSFs at 298 K of crystalline silicon. An overall agreement factor of 0.47% between the ab initio predicted values and the experimental determinations is found. The best theoretical determination of the anisotropic displacement parameter, of silicon is here 60.55 × 10(-4) Å(2), corresponding to a DW factor B = 0.4781 Å(2).

Use of ab initio methods for the interpretation of the experimental IR reflectance spectra of crystalline compounds.

It is shown that ab initio simulation can be used as a powerful complementary tool in the interpretation of the experimental reflectance spectra R(ν) of crystalline compounds. Experimental frequencies and intensities are obtained from a best fit of R(ν) with a set of damped harmonic oscillators, whose number and initial position in frequency can dramatically influence the final results, as the parameters are strongly correlated. Computed ab initio values for frequencies and intensities are accurate enough to represent an excellent starting point for the best fit process. Moreover, at variance with respect to experiment, simulation permits to identify all the symmetry allowed modes, also when characterized by low intensity or when close to a very intense peak. Overall, simulation-aided analysis of experimental spectra prevents from classifying combination modes as fundamental modes and permits to discard artifacts due to superposition of bands, background, and noise. Finally, it allows to (almost) completely characterize the set of fundamental modes.

Raman spectrum of pyrope garnet. A quantum mechanical simulation of frequencies, intensities, and isotope shifts.

The Raman spectrum of pyrope garnet is simulated in ab initio quantum mechanical calculations, using an all-electron Gaussian-type basis set and the hybrid B3LYP functional. Frequencies calculated for the 25 Raman-active modes are in excellent agreement with the several sets of experimental data, with the mean absolute difference ranging from 4 to 8 cm(-1). Comparison of the computed and experimental spectrum shows excellent agreement for most of the intensities as well. Modes missing from experiment are shown to be characterized by low (computed) intensity. Spurious peaks in the experimental spectra are also identified. The isotopic effect has been simulated for (24)Mg → (26)Mg substitution and shows excellent agreement with shifts reported in one of the experiments. Agreement is excellent for all but one mode, which turns out to be attributed to the wrong symmetry in the experiment.

Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. I. Theory.

We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.

Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. II. Validation and comparison with experiments.

In this work, we validate a new, fully analytical method for calculating Raman intensities of periodic systems, developed and presented in Paper I [L. Maschio, B. Kirtman, M. Rérat, R. Orlando, and R. Dovesi, J. Chem. Phys. 139, 164101 (2013)]. Our validation of this method and its implementation in the CRYSTAL code is done through several internal checks as well as comparison with experiment. The internal checks include consistency of results when increasing the number of periodic directions (from 0D to 1D, 2D, 3D), comparison with numerical differentiation, and a test of the sum rule for derivatives of the polarizability tensor. The choice of basis set as well as the Hamiltonian is also studied. Simulated Raman spectra of α-quartz and of the UiO-66 Metal-Organic Framework are compared with the experimental data.

Extraintestinal Manifestations in Induced Colitis: Controversial Effects of N-Acetylcysteine on Colon, Liver, and Kidney.

Ulcerative colitis (UC) is a chronic and recurrent inflammatory bowel disease (IBD) characterized by continuous inflammation in the colonic mucosa. Extraintestinal manifestations (EIM) occur due to the disruption of the intestinal barrier and increased permeability caused by redox imbalance, dysbiosis, and inflammation originating from the intestine and contribute to morbidity and mortality. The aim of this study is to investigate the effects of oral N-acetylcysteine (NAC) on colonic, hepatic, and renal tissues in mice with colitis induced by dextran sulfate sodium (DSS). Male Swiss mice received NAC (150 mg/kg/day) in the drinking water for 30 days before and during (DSS 5% v/v; for 7 days) colitis induction. On the 38th day, colon, liver, and kidney were collected and adequately prepared for the analysis of oxidative stress (superoxide dismutase (SOD), catalase (CAT), glutathione reduced (GSH), glutathione oxidized (GSSG), malondialdehyde (MDA), and hydrogen peroxide (H2O2)) and inflammatory biomarkers (myeloperoxidase (MPO) -, tumor necrosis factor alpha - (TNF-α, and interleukin-10 (IL-10)). In colon, NAC protected the histological architecture. However, NAC did not level up SOD, in contrast, it increased MDA and pro-inflammatory effect (increased of TNF-α and decreased of IL-10). In liver, colitis caused both oxidative (MDA, SOD, and GSH) and inflammatory damage (IL-10). NAC was able only to increase GSH and GSH/GSSG ratio. Kidney was not affected by colitis; however, NAC despite increasing CAT, GSH, and GSH/GSSG ratio promoted lipid peroxidation (increased MDA) and pro-inflammatory action (decreased IL-10). Despite some beneficial antioxidant effects of NAC, the negative outcomes concerning irreversible oxidative and inflammatory damage in the colon, liver, and kidney confirm the nonsafety of the prophylactic use of this antioxidant in models of induced colitis, suggesting that additional studies are needed, and its use in humans not yet recommended for the therapeutic routine of this disease.

Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations.

Large-scale periodic quantum mechanical calculations (509 atoms, 7852 atomic orbitals) based on the hybrid B3LYP functional focused on the peptide folding induced by the adsorption on the (001) and (010) hydroxyapatite (HA) surfaces give interesting insights on the role of specific interactions between surface sites and the peptide, which stabilize the helix conformation over the "native" random coil ones for in silico designed model peptides. The two peptides were derived from the 12-Gly oligomer, with one (P1, C-tGGKGGGGGGEGGN-t) and two (P2, C-tGGKGGKEGGEGGN-t) glutamic acid (E) and lysine (K) residue mutations. The most stable gas-phase "native" conformation for both peptides resulted in a random coil (RC) structure, with the helix (H) conformation being ≈100 kJ mol(-1) higher in free energy. The two peptide conformations interact with the HA (001) and (010) surfaces by C═O groups via Ca(2+) ions, by hydrogen bond between NH(2) groups and the basic PO(4)(3-) groups and by a relevant fraction due to dispersion forces. Peptide adsorption was studied on the dry (001) surface, the wet one envisaging 2 H(2)O per surface Ca(2+) and, on the latter, also considering the adsorption of microsolvated peptides with 4 H(2)O molecules located at sites responsible of the interaction with the surface. The P1 mutant does prefer to be adsorbed as a random coil by ≈160 kJ/mol, whereas the reverse is computed for P2, preferring the helix conformation by ≈50 kJ/mol. Adsorption as helix of both P1 and P2 mutants brings about proton transfer toward the HA surfaces with a large charge transfer component to the interaction energy.

A new massively parallel version of CRYSTAL for large systems on high performance computing architectures.

Fully ab initio treatment of complex solid systems needs computational software which is able to efficiently take advantage of the growing power of high performance computing (HPC) architectures. Recent improvements in CRYSTAL, a periodic ab initio code that uses a Gaussian basis set, allows treatment of very large unit cells for crystalline systems on HPC architectures with high parallel efficiency in terms of running time and memory requirements. The latter is a crucial point, due to the trend toward architectures relying on a very high number of cores with associated relatively low memory availability. An exhaustive performance analysis shows that density functional calculations, based on a hybrid functional, of low-symmetry systems containing up to 100,000 atomic orbitals and 8000 atoms are feasible on the most advanced HPC architectures available to European researchers today, using thousands of processors.

Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

Ab initio analytical infrared intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method.

A fully analytical method for calculating Born charges and, hence, infrared intensities of periodic systems, is formulated and implemented in the CRYSTAL program, which uses a local gaussian type basis set. Our efficient formalism combines integral gradients with first-order coupled perturbed Hartree-Fock/Kohn Sham electronic response to an electric field. It avoids numerical differentiation with respect to wave vectors, as in some Berry phase approaches, and with respect to atomic coordinates. No perturbation equations for the atomic displacements need to be solved. Several tests are carried out to verify numerical stability, consistency in one, two, and three dimensions, and applicability to large unit cells. Future extensions to piezoelectricity and Raman intensities are noted.

Calculation of longitudinal polarizability and second hyperpolarizability of polyacetylene with the coupled perturbed Hartree-Fock/Kohn-Sham scheme: where it is shown how finite oligomer chains tend to the infinite periodic polymer.

The longitudinal polarizability, α(xx), and second hyperpolarizability, γ(xxxx), of polyacetylene are evaluated by using the coupled perturbed Hartree-Fock/Kohn-Sham (HF/KS) scheme as implemented in the periodic CRYSTAL code and a split valence type basis set. Four different density functionals, namely local density approximation (LDA) (pure local), Perdew-Becke-Ernzerhof (PBE) (gradient corrected), PBE0, and B3LYP (hybrid), and the Hartree-Fock Hamiltonian are compared. It is shown that very tight computational conditions must be used to obtain well converged results, especially for γ(xxxx), that is, very sensitive to the number of k(->) points in reciprocal space when the band gap is small (as for LDA and PBE), and to the extension of summations of the exact exchange series (HF and hybrids). The band gap in LDA is only 0.01 eV: at least 300 k(->) points are required to obtain well converged total energy and equilibrium geometry, and 1200 for well converged optical properties. Also, the exchange series convergence is related to the band gap. The PBE0 band gap is as small as 1.4 eV and the exchange summation must extend to about 130 Å from the origin cell. Total energy, band gap, equilibrium geometry, polarizability, and second hyperpolarizability of oligomers -(C(2)H(2))(m)-, with m up to 50 (202 atoms), and of the polymer have been compared. It turns out that oligomers of that length provide an extremely poor representation of the infinite chain polarizability and hyperpolarizability when the gap is smaller than 0.2 eV (that is, for LDA and PBE). Huge differences are observed on α(xx) and γ(xxxx) of the polymer when different functionals are used, that is in connection to the well-known density functional theory (DFT) overshoot, reported in the literature about short oligomers: for the infinite model the ratio between LDA (or PBE) and HF becomes even more dramatic (about 500 for α(xx) and 10(10) for γ(xxxx)). On the basis of previous systematic comparisons of results obtained with various approaches including DFT, HF, Moller-Plesset (MP2) and coupled cluster for finite chains, we can argue that, for the infinite chain, the present HF results are the most reliable.

Static and dynamic coupled perturbed Hartree-Fock vibrational (hyper)polarizabilities of polyacetylene calculated by the finite field nuclear relaxation method.

The vibrational contribution to static and dynamic (hyper)polarizability tensors of polyacetylene are theoretically investigated. Calculations were carried out by the finite field nuclear relaxation (FF-NR) method for periodic systems, newly implemented in the CRYSTAL code, using the coupled perturbed Hartree-Fock scheme for the required electronic properties. The effect of the basis set is also explored, being particularly important for the non-periodic direction perpendicular to the polymer plane. Components requiring a finite (static) field in the longitudinal direction for evaluation by the FF-NR method were not evaluated. The extension to that case is currently being pursued. Whereas the effect on polarizabilities is relatively small, in most cases the vibrational hyperpolarizability tensor component is comparable to, or larger than the corresponding static electronic contribution.