Bypassing the Kohn-Sham equations with machine learning.

Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields. Machine learning holds the promise of learning the energy functional via examples, bypassing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing larger systems and/or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction.

A nociceptive stress model of adolescent physical abuse induces contextual fear and cingulate nociceptive neuroplasticities.

Adolescent physical abuse impairs emotional development and evokes cingulate pathologies, but its neuronal and circuit substrates are unknown. Conditioning adolescent rabbits with noxious colorectal distension for only 2 h over 3 weeks simulated the human child abuse in amplitude, frequency, and duration. Thermal withdrawal thresholds were unchanged suggesting that sensitized spinal mechanisms may not be operable.

Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics.

Prediction and exploration of possible polymorphism in organic crystal compounds are of great importance for industries ranging from organic electronics to pharmaceuticals to high-energy materials. Here we apply our crystal structure prediction procedure and the enhanced molecular dynamics based sampling approach called the Crystal-Adiabatic Free Energy Dynamics (Crystal-AFED) method to benzene and naphthalene. Crystal-AFED allows the free energy landscape of structures to be explored efficiently at any desired temperature and pressure.

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations.

Oxygen-evolving complex of Photosystem II: an analysis of second-shell residues and hydrogen-bonding networks.

The oxygen-evolving complex (OEC) is a Mn4O5Ca cluster embedded in the Photosystem II (PSII) protein complex. As the site of water oxidation, the OEC is connected to the lumen by channels that conduct water, oxygen, and/or protons during the catalytic cycle. The hydrogen-bond networks found in these channels also serve to stabilize the oxidized intermediates, known as the S states.

Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II.

The oxygen-evolving complex (OEC) of photosystem II (PSII) is a unique Mn4O5Ca cluster that catalyzes water oxidation via four photoactivated electron transfer steps. As the protein influence on the redox and protonation chemistry of the OEC remains an open question, we present a classical valence model of the OEC that allows the redox state of each Mn and the protonation state of bridging μ-oxos and terminal waters to remain in equilibrium with the PSII protein throughout the redox cycle. We find that the last bridging oxygen loses its proton during the transition from S0 to S1.

Computational insights on crystal structures of the oxygen-evolving complex of photosystem II with either Ca(2+) or Ca(2+) substituted by Sr(2+).

The oxygen-evolving complex of photosystem II can function with either Ca(2+) or Sr(2+) as the heterocation, but the reason for different turnover rates remains unresolved despite reported X-ray crystal structures for both forms. Using quantum mechanics/molecular mechanics (QM/MM) calculations, we optimize structures with each cation in both the resting state (S1) and in a series of reduced states (S0, S-1, and S-2). Through comparison with experimental data, we determine that the X-ray crystal structures with either Ca(2+) or Sr(2+) are most consistent with the S-2 state (i.

Single Molecule Rectification Induced by the Asymmetry of a Single Frontier Orbital.

A mechanism for electronic rectification under low bias potentials is elucidated for the prototype molecule HS-phenyl-amide-phenyl-SH. We apply density functional theory (DFT) combined with the nonequilibrium Green's function formalism (NEGF), as implemented in the TranSIESTA computational code to calculate transport properties. We find that a single frontier orbital, the closest to the Fermi level, provides the dominant contribution to the overall transmission and determines the current.

S0-State model of the oxygen-evolving complex of photosystem II.

The S0 → S1 transition of the oxygen-evolving complex (OEC) of photosystem II is one of the least understood steps in the Kok cycle of water splitting. We introduce a quantum mechanics/molecular mechanics (QM/MM) model of the S0 state that is consistent with extended X-ray absorption fine structure spectroscopy and X-ray diffraction data. In conjunction with the QM/MM model of the S1 state, we address the proton-coupled electron-transfer (PCET) process that occurs during the S0 → S1 transition, where oxidation of a Mn center and deprotonation of a μ-oxo bridge lead to a significant rearrangement in the OEC.

Cingulate area 32 homologies in mouse, rat, macaque and human: cytoarchitecture and receptor architecture.

Homologizing between human and nonhuman area 32 has been impaired since Brodmann said he could not homologize with certainty human area 32 to a specific cortical domain in other species. Human area 32 has four divisions, however, and two can be structurally homologized to nonhuman species with cytoarchitecture and receptor architecture: pregenual (p32) and subgenual (s32) in human and macaque monkey and areas d32 and v32 in rat and mouse. Cytoarchitecture showed that areas d32/p32 have a dysgranular layer IV in all species and that areas v32/s32 have large and dense neurons in layer V, whereas a layer IV is not present in area v32.

Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II.

The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the oxygen-evolving complex (OEC) of photosystem II (PSII) are investigated. The reported study introduces an enhanced multiconformer continuum electrostatics (MCCE) model, parametrized at the density functional theory (DFT) level with a classical valence model for the oxomanganese core. The calculated pKa's and oxidation midpoint potentials (E(m)'s) match experimental values for eight complexes, indicating that purely electrostatic contributions account for most of the observed couplings between deprotonation and oxidation state transitions.

Nociceptive processing by anterior cingulate pyramidal neurons.

Although the cingulate cortex is frequently activated in acute human pain studies, postsynaptic responses are not known nor are links between nociceptive afferents, neuronal responses, and outputs to other structures. Intracellular potentials were recorded from neurobiotin-injected, pyramidal neurons in anterior cingulate area 24b following noxious stimulation of the sciatic nerve in anesthetized rabbits. Layer IIIc pyramids had extensive and horizontally oriented basal dendrites in layer IIIc where nociceptive afferents terminate.

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library.

Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general black-box approach for the efficient GPU acceleration of matrix-matrix multiplications where the matrix size is too large for the whole computation to be held in the GPU's onboard memory. Second, we show how to improve the accuracy of matrix multiplications when using only single-precision GPU devices by proposing a heterogeneous computing model, whereby single- and double-precision operations are evaluated in a mixed fashion on the GPU and central processing unit, respectively.

Norepinephrinergic afferents and cytology of the macaque monkey midline, mediodorsal, and intralaminar thalamic nuclei.

The midline and intralaminar thalamic nuclei (MITN), locus coeruleus (LC) and cingulate cortex contain nociceptive neurons. The MITN that project to cingulate cortex have a prominent innervation by norepinephrinergic axons primarily originating from the LC. The hypothesis explored in this study is that MITN neurons that project to cingulate cortex receive a disproportionately high LC input that may modulate nociceptive afferent flow into the forebrain.

Accelerating resolution-of-the-identity second-order Møller-Plesset quantum chemistry calculations with graphical processing units.

The modification of a general purpose code for quantum mechanical calculations of molecular properties (Q-Chem) to use a graphical processing unit (GPU) is reported. A 4.3x speedup of the resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) execution time is observed in single point energy calculations of linear alkanes.

Using computer modeling to predict and optimize separations for comprehensive two-dimensional gas chromatography.

In order to fully realize the separation power of comprehensive two-dimensional gas chromatography (GC x GC), a means of predicting and optimizing separations based on operating variables was developed. This approach initially calculates the enthalpy (DeltaH) and entropy (DeltaS) for the target compounds from experimental input data, and then uses this information to simultaneously optimize all column and runtime variables, including stationary phase composition, by comparing the performance of large numbers of simulated separations. This use of computer simulation has been shown to be a useful aid in conventional separations.

Distribution and properties of visceral nociceptive neurons in rabbit cingulate cortex.

Human imaging localizes most visceral nociceptive responses to anterior cingulate cortex (ACC), however, imaging in conscious subjects cannot completely control anticipatory and reflexive activity or resolve neuron activity. This study overcame these shortcomings by recording individual neuron responses in 12 anesthetized and paralyzed rabbits to define the visceronociceptive response pattern by region and layer. Balloon distension was applied to the colon at innocuous (15 mmHg) or noxious (60 mmHg) intensities, and innocuous and noxious mechanical, thermal and electrical stimuli were applied to the skin.

Automated compound classification for ambient aerosol sample separations using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

Comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GCxGC-TOF-MS) is useful in analyzing complex samples, such as the semi-volatile organic compounds (SVOC) in daily aerosol samples collected in Augsburg, Germany. For efficient routine analysis, a partial classification system based on mass spectra has been proposed to group compounds into substance classes. Classifiers based on fragmentation patterns, retention time, and spectral transformations are incorporated into software scripts for automated classification.

Cytology and functionally correlated circuits of human posterior cingulate areas.

Human posterior cingulate cortex (PCC) and retrosplenial cortex (RSC) form the posterior cingulate gyrus, however, monkey connection and human imaging studies suggest that PCC area 23 is not uniform and atlases mislocate RSC. We histologically assessed these regions in 6 postmortem cases, plotted a flat map, and characterized differences in dorsal (d) and ventral (v) area 23. Subsequently, functional connectivity of histologically guided regions of interest (ROI) were assessed in 163 [(18)F]fluorodeoxyglucose human cases with PET.

Architecture and neurocytology of monkey cingulate gyrus.

Human functional imaging and neurocytology have produced important revisions to the organization of the cingulate gyrus and demonstrate four structure/function regions: anterior, midcingulate (MCC), posterior (PCC), and retrosplenial. This study evaluates the brain of a rhesus and 11 cynomolgus monkeys with Nissl staining and immunohistochemistry for neuron-specific nuclear binding protein, intermediate neurofilament proteins, and parvalbumin. The MCC region was identified along with its two subdivisions (a24' and p24').

Cytology of human dorsal midcingulate and supplementary motor cortices.

Human dorsal midcingulate cortex (MCC) is activated during many cognitive tasks and its role in skeletomotor functions is reflected in the size, density, and neurofilament proteins (NFP) expressed by neurons in this region. The present study used antibodies for neuron-specific nuclear binding protein and NFP in three postmortem cases to assess the cytology of the dorsal midcingulate areas 24c', 24d, and 32' and supplementary motor cortex. Area 24c' has a thin layer Va and a Vb with large and NFP+ neurons not present on the gyral surface.

Distribution of ORL-1 receptor binding and receptor-activated G-proteins in rat forebrain and their experimental localization in anterior cingulate cortex.

Opioid receptor-like (ORL-1) receptors and ORL-1-activated G-proteins are found in high levels in the forebrain, particularly cingulate cortex, an area involved in processing of nociceptive stimuli. [(3)H]nociceptin/orphanin FQ (N/OFQ) and N/OFQ-stimulated [(35)S]GTPgammaS autoradiography in rat brain were used to localize ORL-1 receptors and activated G-proteins, respectively. N/OFQ binding and activated G-proteins were highest in anterior cingulate, agranular insula, piriform, perirhinal and entorhinal cortices; midline and intralaminar thalamic nuclei; and subnuclei of the amygdala and hippocampus.

Cellular localization of cannabinoid receptors and activated G-proteins in rat anterior cingulate cortex.

Cannabinoid receptors are found in moderate density throughout the cerebral cortex. The anterior cingulate cortex (ACC) is of particular interest due its high level of cannabinoid receptors and role in behaviors known to be modulated by cannabinoids. These studies were conducted to determine the cellular localization of cannabinoid receptors and to compare the level of cannabinoid receptor binding with receptor-mediated G-protein activity in the rat ACC.

Effect of ethanol self-administration on mu- and delta-opioid receptor-mediated G-protein activity.

Background: This study examined the effects of ethanol self-administration on mu- and delta-opioid receptor-mediated G-protein activity in specific brain regions of male Long Evans rats.

Methods: Rats were trained to self-administer ethanol by using a home-cage modification of the sucrose substitution paradigm. After 30 to 40 days of sucrose or sucrose/15% ethanol self-administration (20 min sessions, Monday-Friday), rats were killed for autoradiographic assays.