Moderate blood alcohol and brain neurovulnerability: Selective depletion of calcium-independent phospholipase A2, omega-3 docosahexaenoic acid, and its synaptamide derivative as a potential harbinger of deficits in anti-inflammatory reserve.

BACKGROUND: Repetitive, highly elevated blood alcohol (ethanol) concentrations (BACs) of 350 to 450 mg/dl over several days cause brain neurodegeneration and coincident neuroinflammation in adult rats localized in the hippocampus (HC), temporal cortex (especially the entorhinal cortex; ECX), and olfactory bulb (OB). The profuse neuroinflammation involves microgliosis, increased proinflammatory cytokines, and elevations of Ca+2 -dependent phospholipase A2 (cPLA2) and secretory PLA2 (sPLA2), which both mobilize proinflammatory ω-6 arachidonic acid (ARA). In contrast, Ca+2 -independent PLA2 (iPLA2) and anti-inflammatory ω-3 docosahexaenoic acid (DHA), a polyunsaturated fatty acid regulated primarily by iPLA2, are diminished. Furthermore, supplemented DHA exerts neuroprotection. Given uncertainties about the possible effects of lower circulating BACs that are common occurring during short- term binges, we examined how moderate BACs affected the above inflammatory events, and the impact of supplemented DHA. METHODS AND RESULTS: Young adult male rats sustaining upper-moderate BACs (~150 mg/dl) from once-daily alcohol intubations were sacrificed with appropriate controls after 1 week. The HC, ECX and OB were quantitatively examined using immunoblotting, neurodegeneration staining, and lipidomics assays. Whereas neurodegeneration, increases in cPLA2 IVA, sPLA2 IIA, and ARA, and microglial activation were not detected, the HC and ECX regions demonstrated significantly reduced iPLA2 levels. Levels of DHA and synaptamide, its anti-inflammatory N-docosahexaenoylethanolamide derivative, also were lower in HC, and DHA supplementation prevented the iPLA2 decrements in HC. Additionally, adult mice maintaining upper-moderate BACs from limited alcohol binges had reduced midbrain iPLA2 levels. CONCLUSIONS: The apparently selective depletion by moderate BACs of the metabolically linked anti-inflammatory triad of hippocampal iPLA2, DHA, and synaptamide, and of iPLA2 in the ECX, potentially indicates an unappreciated deficit in brain anti-inflammatory reserve that may be a harbinger of regional neurovulnerability.

Accelerating the Calculation of Solute-Solvent Interaction Energies through Systematic Molecular Fragmentation.

The method of systematic molecular fragmentation by annihilation (SMFA) is modified to apply to the interaction energy between a solute and solvent, where the solute is a pair of reacting molecules. For NH3 + CH3Cl as the solute, it is shown that SMFA can estimate (to chemical accuracy) the average binding energy of the solute in large water clusters containing up to 160 water molecules, at an appropriate level of electronic structure theory. The SMFA calculation can be carried out in a computation time that makes it feasible to estimate the solvation contribution to free energies of activation and reaction by ensemble averaging.

PARP Inhibition Prevents Ethanol-Induced Neuroinflammatory Signaling and Neurodegeneration in Rat Adult-Age Brain Slice Cultures.

Using rat adult-age hippocampal-entorhinal cortical (HEC) slice cultures, we examined the role of poly [ADP-ribose] polymerase (PARP) in binge ethanol's brain inflammatory and neurodegenerative mechanisms. Activated by DNA strand breaks, PARP (principally PARP1 in the brain) promotes DNA repair via poly [ADP-ribose] (PAR) products, but PARP overactivation triggers regulated neuronal necrosis (e.g., parthanatos). Previously, we found that brain PARP1 levels were upregulated by neurotoxic ethanol binges in adult rats and HEC slices, and PARP inhibitor PJ34 abrogated slice neurodegeneration. Binged HEC slices also exhibited increased Ca+2-dependent phospholipase A2 (PLA2) isoenzymes (cPLA2 IVA and sPLA2 IIA) that mobilize proinflammatory ω6 arachidonic acid (ARA). We now find in 4-day-binged HEC slice cultures (100 mM ethanol) that PARP1 elevations after two overnight binges precede PAR, cPLA2, and sPLA2 enhancements by 1 day and high-mobility group box-1 (HMGB1), an ethanol-responsive alarmin that augments proinflammatory cytokines via toll-like receptor-4 (TLR4), by 2 days. After verifying that PJ34 effectively blocks PARP activity (↑PAR), we demonstrated that, like PJ34, three other PARP inhibitors-olaparib, veliparib, and 4-aminobenzamide-provided neuroprotection from ethanol. Importantly, PJ34 and olaparib also prevented ethanol's amplification of the PLA2 isoenzymes, and two PLA2 inhibitors were neuroprotective-thus coupling PARP to PLA2, with PLA2 activity promoting neurodegeneration. Also, PJ34 and olaparib blocked ethanol-induced HMGB1 elevations, linking brain PARP induction to TLR4 activation. The results provide evidence in adult brains that induction of PARP1 may mediate dual neuroinflammatory pathways (PLA2→phospholipid→ARA and HMGB1→TLR4→proinflammatory cytokines) that are complicit in binge ethanol-induced neurodegeneration.

Application of the Systematic Molecular Fragmentation by Annihilation Method to ab Initio NMR Chemical Shift Calculations.

NMR is a powerful tool for obtaining information on the structural characterization and dynamics of proteins, and nucleic acids, and their complexes. The complexity of the spectra is such that elucidation through computational simulation is a much desired thing. However, the size of most structures of interest is such that they remain out of reach of accurate quantum chemical techniques. Fragmentation methods have been shown to be a viable means of reducing the cost of ab initio calculations to enable the prediction of molecular properties of large systems to chemical accuracy. We look at the systematic molecular fragmentation by annihilation method for a model peptide system and show that this procedure reproduces the shielding constants of a full calculation at only a fraction of the cost. Discussion of the considerations needed in applying this method is discussed and comparison made with the results of the similar fragment molecular orbital and ONIOM methods.

Microsolvation within the Systematic Molecular Fragmentation by Annihilation Approach.

We have applied the systematic molecular fragmentation by annihilation (SMFA) fragmentation technique to glycine and DNA base pairs in water clusters, systems for which explicit solvation is believed to be important. The SMFA method was found to be capable of describing the structures, especially in handling the complexity of hydrogen bonding, with energies produced being comparable with those from full molecule results. Thus, the ability to break down large calculations into a manageable time without loss of accuracy shows promise for application to real biological systems for which these effects are relevant.

Can Systematic Molecular Fragmentation Be Applied to Direct Ab Initio Molecular Dynamics?

This paper demonstrates that systematic molecular fragmentation can be applied to direct ab initio molecular dynamics of solvated molecules under periodic boundary conditions. A method for rapidly updating the fragmentation of water at each time step in a simulation is presented and tested. This approach reduces the time required for implementation of systematic molecular fragmentation at each time step, in a highly connected system like water, from an excessively long time to a feasible value.

The combined fragmentation and systematic molecular fragmentation methods.

Conspectus Chemistry, particularly organic chemistry, is mostly concerned with functional groups: amines, amides, alcohols, ketones, and so forth. This is because the reactivity of molecules can be categorized in terms of the reactions of these functional groups, and by the influence of other adjacent groups in the molecule. These simple truths ought to be reflected in the electronic structure and electronic energy of molecules, as reactivity is determined by electronic structure. However, sophisticated ab initio quantum calculations of the molecular electronic energy usually do not make these truths apparent. In recent years, several computational chemistry groups have discovered methods for estimating the electronic energy as a sum of the energies of small molecular fragments, or small sets of groups. By decomposing molecules into such fragments of adjacent functional groups, researchers can estimate the electronic energy to chemical accuracy; not just qualitative trends, but accurate enough to understand reactivity. In addition, this has the benefit of cutting down on both computational time and cost, as the necessary calculation time increases rapidly with an increasing number of electrons. Even with steady advances in computer technology, progress in the study of large molecules is slow. In this Account, we describe two related "fragmentation" methods for treating molecules, the combined fragmentation method (CFM) and systematic molecular fragmentation (SMF). In addition, we show how we can use the SMF approach to estimate the energy and properties of nonconducting crystals, by fragmenting the periodic crystal structure into relatively small pieces. A large part of this Account is devoted to simple overviews of how the methods work. We also discuss the application of these approaches to calculating reactivity and other useful properties, such as the NMR and vibrational spectra of molecules and crystals. These applications rely on the ability of these fragmentation methods to accurately estimate derivatives of the molecular and crystal energies. Finally, to provide some common applications of CFM and SMF, we present some specific examples of energy calculations for moderately large molecules. For computational chemists, this fragmentation approach represents an important practical advance. It reduces the computer time required to estimate the energies of molecules so dramatically, that accurate calculations of the energies and reactivity of very large organic and biological molecules become feasible.

Calculating nuclear magnetic resonance shieldings using systematic molecular fragmentation by annihilation.

SMFA was used to calculate NMR shieldings in a test set of 15 molecules. Level 4 fragments were found to yield satisfactory results when hydrogen bonding was included in the calculations. The utility of additional long range corrections was also investigated. It was found that with hydrogen bonding already included, ab initio long range corrections were not necessary. Instead, inclusion of the McConnell correction for fragments was found to be sufficient. With these parameters the algorithm produces MADs of 0.046, 0.26, 0.24 and 1.04 ppm for hydrogens, carbons, nitrogens and oxygens respectively.

H2 Adsorption in a Porous Crystal: Accurate First-Principles Quantum Simulation.

A general method is presented for constructing, from ab initio quantum chemistry calculations, the potential energy surface (PES) for H2 absorbed in a porous crystalline material. The method is illustrated for the metal-organic framework material MOF-5. Rigid body quantum diffusion Monte Carlo simulations are used in the construction of the PES and to evaluate the quantum ground state of H2 in MOF-5, the zero-point energy, and the enthalpy of adsorption at 0 K.

Phospholipase A2, oxidative stress, and neurodegeneration in binge ethanol-treated organotypic slice cultures of developing rat brain.

BACKGROUND: Brain neurodamage from chronic binge ethanol (EtOH) exposure is linked to neuroinflammation and associated oxidative stress. Using rat organotypic hippocampal-entorhinal cortical (HEC) slice cultures of developing brain age, we reported that binge EtOH promotes release of a neuroinflammatory instigator, arachidonic acid (AA), concomitant with neurodegeneration, and that mepacrine, a global inhibitor of phospholipase A2 (PLA2) enzymes mobilizing AA from phospholipids, is neuroprotective. Here, we sought with binge EtOH-treated HEC cultures to establish that PLA2 activity is responsible in part for significant oxidative stress and to ascertain the PLA2 families responsible for AA release and neurodegeneration. METHODS: HEC slices, prepared from 1-week-old rats and cultured 2 to 2.5 weeks, were exposed to 100 mM EtOH over 6 successive days, with 4 daytime "withdrawals" (no EtOH). Brain 3-nitrotyrosinated (3-NT)- and 4-hydroxy-2-nonenal (4-HNE)-adducted proteins, oxidative stress footprints, were immunoassayed on days 3 through 6, and mepacrine's effect was determined on day 6. The effects of specific PLA2 inhibitors on neurodegeneration (propidium iodide staining) and AA release (ELISA levels in media) in the cultures were then determined. Also, the effect of JZL184, an inhibitor of monoacylglycerol lipase (MAGL) which is reported to mobilize AA from endocannabinoids during neuroinflammatory insults, was examined. RESULTS: 3-NT- and 4-HNE-adducted proteins were significantly increased by the binge EtOH exposure, consistent with oxidative stress, and mepacrine prevented the increases. The PLA2 inhibitor results implicated secretory PLA2 (group II sPLA2) and to some extent Ca(2+) -independent cytosolic PLA2 (group VI iPLA2) in binge EtOH-induced neurotoxicity and in AA release, but surprisingly, Ca(2+) -dependent cytosolic PLA2 (group IV cPLA2) did not appear important. Furthermore, unlike PLA2 inhibition, MAGL inhibition failed to prevent the neurodegeneration. CONCLUSIONS: In these developing HEC slice cultures, pro-oxidative signaling via sPLA2 and iPLA2, but not necessarily cPLA2 or MAGL, is involved in EtOH neurotoxicity. This study provides further insights into neuroinflammatory phospholipase signaling and oxidative stress underlying binge EtOH-induced neurodegeneration in developing (adolescent age) brain in vitro.

Molecular forces, geometries, and frequencies by systematic molecular fragmentation including embedded charges.

The accuracy of energies, energy gradients, and hessians evaluated by systematic molecular fragmentation is examined for a wide range of neutral molecules, zwitterions, and ions. A protocol is established that may employ embedded charges in conjunction with fragmentation to provide accurate evaluation of minimum energy geometries and vibrational frequencies in an automated procedure.

Molecular electrostatic potentials by systematic molecular fragmentation.

A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.

Depression of reactivity by the collision energy in the single barrier H + CD4 -> HD + CD3 reaction.

Crossed molecular beam experiments and accurate quantum scattering calculations have been carried out for the polyatomic H + CD(4) --> HD + CD(3) reaction. Unprecedented agreement has been achieved between theory and experiments on the energy dependence of the integral cross section in a wide collision energy region that first rises and then falls considerably as the collision energy increases far over the reaction barrier for this simple hydrogen abstraction reaction. Detailed theoretical analysis shows that at collision energies far above the barrier the incoming H-atom moves so quickly that the heavier D-atom on CD(4) cannot concertedly follow it to form the HD product, resulting in the decline of reactivity with the increase of collision energy. We propose that this is also the very mechanism, operating in many abstraction reactions, which causes the differential cross section in the backward direction to decrease substantially or even vanish at collision energies far above the barrier height.

Systematic fragmentation of large molecules by annihilation.

A new version of systematic molecular fragmentation is presented which provides a hierarchy of estimates for the energy, and other properties, of large molecules with a computation time that scales linearly with the size of the molecule. This method is combined with an algorithm which ensures that the evaluation of the fragment compositions is efficient for very large molecules. The method is illustrated using protein structures derived from NMR spectroscopy.

The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters.

Two electronic structure methods, the fragment molecular orbital (FMO) and systematic molecular fragmentation (SMF) methods, that are based on fragmenting a large molecular system into smaller, more computationally tractable components (fragments), are presented and compared with fully ab initio results for the predicted binding energies of water clusters. It is demonstrated that, even when explicit three-body effects are included (especially necessary for water clusters due to their complex hydrogen-bonded networks) both methods present viable, computationally efficient alternatives to fully ab initio quantum chemistry.

Modified Shepard interpolation of gas-surface potential energy surfaces with strict plane group symmetry and translational periodicity.

A new formulation of modified Shepard interpolation of potential energy surface data for gas-surface reactions has been developed. The approach has been formulated for monoatomic or polyatomic adsorbates interacting with crystalline solid surfaces of any plane group symmetry. The interpolation obeys the two dimensional translational periodicity and plane group symmetry of the solid surface by construction. The interpolation remains continuous and smooth everywhere. The interpolation developed here is suitable for constructing potential energy surfaces by sampling classical trajectories using the Grow procedure. A model function has been used to demonstrate the method, showing the convergence of the classical gas-surface reaction probability.

Risk assessment for consumer exposure to toluene diisocyanate (TDI) derived from polyurethane flexible foam.

Polyurethanes (PU) are polymers made from diisocyanates and polyols for a variety of consumer products. It has been suggested that PU foam may contain trace amounts of residual toluene diisocyanate (TDI) monomers and present a health risk. To address this concern, the exposure scenario and health risks posed by sleeping on a PU foam mattress were evaluated. Toxicity benchmarks for key non-cancer endpoints (i.e., irritation, sensitization, respiratory tract effects) were determined by dividing points of departure by uncertainty factors. The cancer benchmark was derived using the USEPA Benchmark Dose Software. Results of previous migration and emission data of TDI from PU foam were combined with conservative exposure factors to calculate upper-bound dermal and inhalation exposures to TDI as well as a lifetime average daily dose to TDI from dermal exposure. For each non-cancer endpoint, the toxicity benchmark was divided by the calculated exposure to determine the margin of safety (MOS), which ranged from 200 (respiratory tract) to 3×10(6) (irritation). Although available data indicate TDI is not carcinogenic, a theoretical excess cancer risk (1×10(-7)) was calculated. We conclude from this assessment that sleeping on a PU foam mattress does not pose TDI-related health risks to consumers.

Potential energy surfaces for gas-surface reactions.

A method for constructing the potential energy surface for reactions of a molecule with the surface of cleaved non-conducting crystals is reported. The method uses systematic fragmentation to express the total potential in terms of potential energy surfaces which describe reactions of relatively small molecules in the gas phase. The approach is illustrated by an application to the reaction of hydrogen atoms with a hydrogen-terminated silicon(111) surface.

Ab initio lattice dynamics of nonconducting crystals by systematic fragmentation.

A systematic method for approximating the ab initio electronic energy of crystal lattices has been improved by the incorporation of long range electrostatic and dispersion interactions. The effect of these long range interactions on the optimization of the crystal structure is reported. The harmonic lattice dynamics have been evaluated to give phonon frequencies and neutron scattering intensities. Exemplary results are reported for diamond, silicon, and α-quartz using Hartree-Fock, Möller-Plesset perturbation, and coupled-cluster levels of ab initio theory.