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.

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.

Biomarkers of Inflammation and Redox Imbalance in Umbilical Cord in Pregnancies with and without Preeclampsia and Consequent Perinatal Outcomes.

OBJECTIVE: To compare redox imbalance and inflammation biomarkers in umbilical cords from pregnancies with and without preeclampsia (PE) and to analyse their relationships with perinatal outcomes. METHODS: A controlled cross-sectional study was conducted in Maceió, Alagoas, Brazil, that involved pregnant women with PE and a group of women without the disease, through the application of a standardized questionnaire. After delivery, umbilical cord samples were collected to measure antioxidant defense, products from oxidative damage, and inflammation biomarkers such as myeloperoxidase (MPO), interleukin- (IL-) 6, IL-8, IL-10, and tumor necrosis factor-alpha (TNF-α). Statistical analyses were performed using Stata version 13.0 software and IBM Statistical Package for the Social Sciences (SPSS) 20.0, adopting a 95% confidence level (α = 0.05), with the chi-square test, the Wilcoxon-Mann-Whitney test, and the multinomial and Poisson regression tests. RESULTS: One hundred PE pregnant women and 50 women without the disease were studied. The umbilical cords from PE pregnancies showed higher levels of reduced glutathione (GSH) (p ≤ 0.001), glutathione peroxidase (GPx) (p = 0.016), and malondialdehyde (MDA) (p = 0.028) and lower levels of IL-6 (p = 0.030) and TNF-α (p ≤ 0.001) than the other group, with some associations among these biomarkers with perinatal outcomes. CONCLUSION: The higher levels of GSH and GPx, in addition to the lower levels of IL-6 and TNF-α, found in the PE umbilical cord, may result from adaptive mechanisms to maintain the oxidative and inflammatory balance; however, despite these changes, the damage to the cell membranes was not minimized, as the MDA level was higher in women with PE than in women without the disease. This implies that a redox imbalance is present, confirming that other physiological and adaptive mechanisms are being activated to preserve foetal health. Therefore, the present work unveils an important role of the umbilical cord in controlling redox imbalance and inflammation in PE pregnancies. Our results reinforce the necessity for continuous research on GSH as a protective compound for the perinatal outcome, especially in PE women.

Colonic and Hepatic Modulation by Lipoic Acid and/or N-Acetylcysteine Supplementation in Mild Ulcerative Colitis Induced by Dextran Sodium Sulfate in Rats.

Lipoic acid (LA) and N-acetylcysteine (NAC) are antioxidant and anti-inflammatory agents that have not yet been tested on mild ulcerative colitis (UC). This study aims to evaluate the action of LA and/or NAC, on oxidative stress and inflammation markers in colonic and hepatic rat tissues with mild UC, induced by dextran sodium sulfate (DSS) (2% w/v). LA and/or NAC (100 mg·kg·day-1, each) were given, once a day, in the diet, in a pretreatment phase (7 days) and during UC induction (5 days). Colitis induction was confirmed by histological and biochemical analyses (high performance liquid chromatography, spectrophotometry, and Multiplex®). A redox imbalance occurred before an immunological disruption in the colon. NAC led to a decrease in hydrogen peroxide (H2O2), malondialdehyde (MDA) levels, and myeloperoxidase activity. In the liver, DSS did not cause damage but treatments with both antioxidants were potentially harmful, with LA increasing MDA and LA + NAC increasing H2O2, tumor necrosis factor alpha, interferon gamma, and transaminases. In summary, NAC exhibited the highest colonic antioxidant and anti-inflammatory activity, while LA + NAC caused hepatic damage.

Assessment of Different Quantum Mechanical Methods for the Prediction of Structure and Cohesive Energy of Molecular Crystals.

A comparative assessment of the accuracy of different quantum mechanical methods for evaluating the structure and the cohesive energy of molecular crystals is presented. In particular, we evaluate the performance of the semiempirical HF-3c method in comparison with the B3LYP-D* and the Local MP2 (LMP2) methods by means of a fully periodic approach. Three benchmark sets have been investigated: X23, G60, and the new K7; for a total of 82 molecular crystals. The original HF-3c method performs well but shows a tendency at overbinding molecular crystals, in particular for weakly bounded systems. For the X23 set, the mean absolute error for the cohesive energies computed with the HF-3c method is comparable to the LMP2 one. A refinement of the HF-3c has been attempted by tuning the dispersion term in the HF-3c energy. While the performance on cohesive energy prediction slightly worsens, optimized unit cell volumes are in excellent agreement with experiment. Overall, the B3LYP-D* method combined with a TZP basis set gives the best results. For cost-effective calculations on molecular crystals, we propose to compute cohesive energies at the B3LYP-D*/TZP level of theory on the dispersion-scaled HF-3c optimized geometries (i.e., B3LYP-D*/TZP//HF-3c(0.27) also dubbed as SP-B3LYP-D*). Besides, for further benchmarking on molecular crystals, we propose to combine the three test sets in a new one denoted as MC82.

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.

Elucidating the fundamental forces in protein crystal formation: the case of crambin.

Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H2O per cell). The agreement with the experiment is good for both protein geometry and protein-water interactions. The energetics was computed to predict crystal formation energies, protein-water and protein-protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H2O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

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.

Antioxidant therapy for treatment of inflammatory bowel disease: Does it work?

Oxidative stress (OS) is considered as one of the etiologic factors involved in several signals and symptoms of inflammatory bowel diseases (IBD) that include diarrhea, toxic megacolon and abdominal pain. This systematic review discusses approaches, challenges and perspectives into the use of nontraditional antioxidant therapy on IBD, including natural and synthetic compounds in both human and animal models. One hundred and thirty four papers were identified, of which only four were evaluated in humans. Some of the challenges identified in this review can shed light on this fact: lack of standardization of OS biomarkers, absence of safety data and clinical trials for the chemicals and biological molecules, as well as the fact that most of the compounds were not repeatedly tested in several situations, including acute and chronic colitis. This review hopes to stimulate researchers to become more involved in this fruitful area, to warrant investigation of novel, alternative and efficacious antioxidant-based therapies.

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.

Ab Initio Calculation of the Ultraviolet-Visible (UV-vis) Absorption Spectrum, Electron-Loss Function, and Reflectivity of Solids.

The field frequency has recently been taken into account in the coupled-perturbed Hartree-Fock or Kohn-Sham method implemented in the CRYSTAL code for calculating the high-frequency dielectric constant of semiconductors up to the first electronic transitions. In this work, we document how the code has been generalized and improved in order to compute the full ultraviolet-visible (UV-vis) absorption spectrum, the electron loss function, and the reflectivity from the real and imaginary parts of the electric response property. We show how spectra are modified when the crystalline orbital relaxation due to the dynamic electric field is taken into account, and how this modification increases with the percentage of Hartree-Fock exchange in the unperturbed hybrid Hamiltonian.

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.

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.

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.

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.

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.

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.

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.