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From molecular dynamics (MD) simulations of melt-quenching and thermal aging procedures in pure Ag, Cu, Ag-Cu binary alloys, and Cu-Zr binary alloys, we have identified two distinct amorphous phases for a metastable undercooled liquid: the homogeneous L-phase with low shear rigidity and the heterogenous G-phase with much higher shear rigidity and a heterogeneity length scale Λ. Here, we examine two-phase equilibration studies showing that the G-phase melts to form the L-phase above ~1,000 K, which then transforms to form the crystal (X) phase; however, below the melting point of the G-Phase (~990 K), the X-and G-phases do not transform into each other. We suggest the presence of a G-phase is likely responsible for embrittlement often observed in metallic glasses. We also consider how mechanical milling or irradiation-induced defect accumulation in the crystalline metallic alloy triggers a crystal-to-glass transition. We use the Cu2Zr system as a model to investigate random interchange of Zr and Cu atoms at room temperature leading to a transition from a crystalline Laves-phase to an L-glass through formation and growth of amorphous regions and destabilization of the crystal. During relaxation of the nonequilibrium structures by annealing, the configurations either reverted to the crystalline phase or evolve to a heterogeneous G-phase equivalent to the G-phase formed during thermal quenching and aging of the melt. Athermal defect accumulation in the G-phase at low temperature led to a transition back to the L-phase. Our findings show how athermal disordering drives transitions among the X-, L-, and G-phases. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) regulate multiple cellular responses and represent highly successful therapeutic targets. The mechanisms by which agonists activate the G protein are unclear for many GPCR families, including the bitter taste receptors (TAS2Rs). We ascertained TAS2R5 properties by live cell-based functional assays, direct binding affinity measurements using optical resonators, and atomistic molecular dynamics simulations. We focus on three agonists that exhibit a wide range of signal transduction in cells despite comparable ligand–receptor binding energies derived from direct experiment and computation. Metadynamics simulations revealed that the critical barrier to activation is ligand-induced opening of the G protein between the α-helical (AH) and Ras-like domains of Gα subunit from a precoupled TAS2R5-G protein state to the fully activated state. A moderate agonist opens the AH-Ras cleft from 22 Å to 31 Å with an energy gain of −4.8 kcal mol−1, making GDP water-exposed for signaling. A high-potency agonist had an energy gain of −11.1 kcal mol−1. The low-potency agonist is also exothermic for Gα opening, but with an energy gain of only −1.4 kcal mol−1. This demonstrates that TAS2R5 agonist-bound functional potencies are derived from energy gains in the transition from a precoupled complex at the level of Gα opening. Our experimental and computational study provides insights into the activation mechanism of signal transduction that provide a basis for rational design of new drugs. [ABSTRACT FROM AUTHOR]

The intrinsically disordered C-terminal peptide region of severe acute respiratory syndrome Coronavirus 2 nonstructural protein-1 (Nspl-CT) inhibits host protein synthesis by blocking messenger RNA (mRNA) access to the 40S ribosome entrance tunnel. Aqueous copper(II) ions bind to the disordered peptide with micromolar affinity, creating a possible strategy to restore protein synthesis during host infection. Electron paramagnetic resonance (EPR) and tryptophan fluorescence measurements on a 10-residue model of the disordered protein region (Nsp1-CT10), combined with advanced quantum mechanics calculations, suggest that the peptide binds to copper(II) as a multidentate ligand. Two optimized computational models of the copper(II)-peptide complexes were derived: One corresponding to pH 6.5 and the other describing the complex at pH 7.5 to 8.5. Simulated EPR spectra based on the calculated model structures are in good agreement with experimental spectra. [ABSTRACT FROM AUTHOR]

Smoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein-coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein-coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R4516.32 and W5357.55, a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position. [ABSTRACT FROM AUTHOR]

G protein–coupled receptors (GPCRs) activate cellular responses ranging from odorants to neurotransmitters. Binding an agonist leads to activation of a heterotrimeric G protein (GP) that stimulates external signaling. Unfortunately, the mechanism remains unknown. We show for 15 class A GPCRs, including opioids, adrenergics, adenosines, chemokines, muscarinics, cannabinoids, serotonins, and dopamines, that interaction of an inactive GP, including Gs, Gi, Go, G11, and Gq, to the inactive GPCR, containing the intracellular ionic lock between transmembrane (TM) helices 3 and 6, evolves exothermically to form a precoupled GPCR-GP complex with an opened TM3-TM6 and the GP-α5 helix partially inserted into the GPCR but not activated. We show that binding of agonist to this precoupled GPCR-GP complex causes the Gα protein to open into its active form, with the guanosine diphosphate exposed for signaling. This GP-first paradigm provides a strategy for developing selective agonists for GPCRs since it is the pharmacophore for the precoupled GPCR-GP complex that should be used to design drugs. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors display multifunctional signaling, offering the potential for agonist structures to promote conformational selectivity for biased outputs. For β2-adrenergic receptors (β2AR), unbiased agonists stabilize conformation(s) that evoke coupling to Gαs (cyclic adenosine monophosphate [cAMP] production/human airway smooth muscle [HASM] cell relaxation) and β-arrestin engagement, the latter acting to quench Gαs signaling, contributing to receptor desensitization/tachyphylaxis. We screened a 40-million-compound scaffold ranking library, revealing unanticipated agonists with dihydroimidazolyl-butylcyclic urea scaffolds. The S-stereoisomer of compound C1 shows no detectable β-arrestin engagement/signaling by four methods. However, C1-S retained Gαs signaling--a divergence of the outputs favorable for treating asthma. Functional studies with two models confirmed the biasing: β2AR-mediated cAMP signaling underwent desensitization to the unbiased agonist albuterol but not to C1-S, and desensitization of HASM cell relaxation was observed with albuterol but not with C1-S. These HASM results indicate biologically pertinent biasing of C1-S, in the context of the relevant physiologic response, in the human cell type of interest. Thus, C1-S was apparently strongly biased away from β-arrestin, in contrast to albuterol and C5-S. C1-S structural modeling and simulations revealed binding differences compared with unbiased epinephrine at transmembrane (TM) segments 3,5,6,7 and ECL2. C1-S (R2 = cyclohexane) was repositioned in the pocket such that it lost a TM6 interaction and gained a TM7 interaction compared with the analogous unbiased C5-S (R2 = benzene group), which appears to contribute to C1-S biasing away from β-arrestin. Thus, an agnostic large chemical-space library identified agonists with receptor interactions that resulted in relevant signal splitting of β2AR actions favorable for treating obstructive lung disease. [ABSTRACT FROM AUTHOR]

This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over -10-nm spatial scales for -1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of -10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF-based reaction kinetics. [ABSTRACT FROM AUTHOR]

Interfacial mixing and transport are nonequilibrium processes coupling kinetic to macroscopic scales. They occur in fluids, plasmas, and materials over celestial events to atoms. Grasping their fundamentals can advance a broad range of disciplines in science, mathematics, and engineering. This paper focuses on the long-standing classic problem of stability of a phase boundary-a fluid interface that has a mass flow across it. We briefly review the recent advances in theoretical and experimental studies, develop the general theoretical framework directly linking the microscopic interfacial transport to the macroscopic flow fields, discover mechanisms of interface stabilization and destabilization that have not been discussed before for both inertial and accelerated dynamics, and chart perspectives for future research. [ABSTRACT FROM AUTHOR]

This issue of PNAS features "nonequilibrium transport and mixing across interfaces," with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in terms of the density and equations of state rather than specific atomic structures and chemical processes. It is at interfacial boundaries where such atomistic information is most relevant. However, there is not yet a practical way to couple these phenomena with the atomistic description of chemistry. The starting point for including such information is the quantum mechanics (QM). However, practical QM calculations are limited to a hundred atoms for dozens of picoseconds, far from the scales required to inform the continuum level with the proper atomistic description. To bridge this enormous gap, we need to develop practical methods to extend the scale of the atomistic simulation by several orders of magnitude while retaining the level of QM accuracy in describing the chemical process. These developments would enable continuum modeling of turbulent transport at interfaces to incorporate the relevant chemistry. In this perspective, we will focus on recent progress in accomplishing these extensions in first principles-based atomistic simulations and the strategies being pursued to increase the accuracy of very large scales while dramatically decreasing the computational effort. [ABSTRACT FROM AUTHOR]

Electrocatalysis provides a powerful means to selectively transform molecules, but a serious impediment in making rapid progress is the lack of a molecular-based understanding of the reactive mechanisms or intermediates at the electrode-electrolyte interface (EEI). Recent experimental techniques have been developed for operando identification of reaction intermediates using surface infrared (IR) and Raman spectroscopy. However, large noises in the experimental spectrum pose great challenges in resolving the atomistic structures of reactive intermediates. To provide an interpretation of these experimental studies and target for additional studies, we report the results from quantum mechanics molecular dynamics (QM-MD) with explicit consideration of solvent, electrode-electrolyte interface, and applied potential at 298 K, which conceptually resemble the operando experimental condition, leading to a prototype of operandoQM-MD(o-QM-MD). With o-QM-MD, we characterize 22 possible reactive intermediates in carbon dioxide reduction reactions (CO2RRs). Furthermore, we report the vibrational density of states (v-DoSs) of these intermediates from two-phase thermodynamic (2PT) analysis. Accordingly, we identify important intermediates such as chemisorbed CO2 (b-CO2), *HOC-COH, *C-CH, and *C-COH in our o-QM-MD likely to explain the experimental spectrum. Indeed, weassign the experimentalpeakat 1,191cm-1 to themodeofC-Ostretch in*HOC-COH predicted at 1,189 cm-1 and the experimental peak at 1,584 cm-1 to the mode of C-C stretch in *C-COD predicted at 1,581 cm-1. Interestingly, we find that surface ketene (*C=C=O), arising from *HOC-COH dehydration, also shows signals at around 1,584 cm-1, which indicates a nonelectrochemical pathway of hydrocarbon formation at low overpotential and high pH conditions. [ABSTRACT FROM AUTHOR]

We developed the RexPoN force field for water based entirely on quantum mechanics. It predicts the properties of water extremely accurately, with Tmelt = 273.3 K (273.15 K) and properties at 298 K: ΔHvap = 10.36 kcal/mol (10.52), density = 0.9965 g/cm3 (0.9965), entropy = 68.4 J/mol/K (69.9), and dielectric constant = 76.1 (78.4), where experimental values are in parentheses. Upon heating from 0.0 K (ice) to 273.0 K (still ice), the average number of strong hydrogen bonds (SHBs, rOO = 2.93 Å) decreases from 4.0 to 3.3, but upon melting at 273.5 K, the number of SHBs drops suddenly to 2.3, decreasing slowly to 2.1 at 298 K and 1.6 at 400 K. The lifetime of the SHBs is 90.3 fs at 298 K, increasing monotonically for lower temperature. These SHBs connect to form multibranched polymer chains (151 H2O per chain at 298 K), where branch points have 3 SHBs and termination points have 1 SHB. This dynamic fluctuating branched polymer view of water provides a dramatically modified paradigm for understanding the properties of water. It may explain the 20-nm angular correlation lengths at 298 K and the critical point at 227 K in supercooled water. Indeed, the 15% jump in the SHB lifetime at 227 K suggests that the supercooled critical point may correspond to a phase transition temperature of the dynamic polymer structure. This paradigm for water could have a significant impact on the properties for protein, DNA, and other materials in aqueous media. [ABSTRACT FROM AUTHOR]

The oxygen evolution reaction (OER) is critical to solar production of fuels, but the reaction mechanism underlying the performance for a best OER catalyst, Fe-doped NiOOH [(Ni,Fe)OOH], remains highly controversial. We used grand canonical quantum mechanics to predict the OER mechanisms including kinetics and thus overpotentials as a function of Fe content in (Ni,Fe)OOH catalysts. We find that density functional theory (DFT) without exact exchange predicts that addition of Fe does not reduce the overpotential much. However, DFT with exact exchange predicts dramatic improvement in performance for (Ni,Fe)OOH, leading to an overpotential of 0.42 V and a Tafel slope of 23 mV/decade (dec), in good agreement with experiments, 0.3-0.4 V and 30 mV/dec. We reveal that the high spin d4 Fe(IV) leads to efficient formation of an active O radical intermediate, while the closed shell d6 Ni(IV) catalyzes the subsequent O--O coupling, and thus it is the synergy between Fe and Ni that delivers the optimal performance for OER. [ABSTRACT FROM AUTHOR]

Cell-surface carbohydrates play important roles in numerous biological processes through their interactions with various proteinbinding partners. These interactions are made possible by the vast structural diversity of carbohydrates and the diverse array of carbohydrate presentations on the cell surface. Among the most complex and important carbohydrates are glycosaminoglycans (GAGs), which display varied stereochemistry, chain lengths, and patterns of sulfation. GAG--protein interactions participate in neuronal development, angiogenesis, spinal cord injury, viral invasion, and immune response. Unfortunately, little structural information is available for these complexes; indeed, for the highly sulfated chondroitin sulfate motifs, CS-E and CS-D, there are no structural data. We describe here the development and validation of the GAG-Dock computational method to predict accurately the binding poses of protein-bound GAGs. We validate that GAG-Dock reproduces accurately (<1-Å rmsd) the crystal structure poses for four known heparin--protein structures. Further, we predict the pose of heparin and chondroitin sulfate derivatives bound to the axon guidance proteins, protein tyrosine phosphatase σ (RPTPσ), and Nogo receptors 1-3 (NgR1-3). Such predictions should be useful in understanding and interpreting the role of GAGs in neural development and axonal regeneration after CNS injury. [ABSTRACT FROM AUTHOR]

We propose and validate with quantum mechanics methods a unique catalyst for electrochemical reduction of CO2 (CO2RR) in which selectivity and activity of CO and C2 products are both enhanced at the borders of oxidized and metallic surface regions. This Cu metal embedded in oxidized matrix (MEOM) catalyst is consistent with observations that Cu2O-based electrodes improve performance. However, we show that a fully oxidized matrix (FOM) model would not explain the experimentally observed performance boost, and we show that the FOM is not stable under CO2 reduction conditions. This electrostatic tension between the Cu+ and Cu0 surface sites responsible for the MEOM mechanism suggests a unique strategy for designing more efficient and selective electrocatalysts for CO2RR to valuable chemicals (HCOx), a critical need for practical environmental and energy applications. [ABSTRACT FROM AUTHOR]

A national priority is to convert CO2 into high-value chemical products such as liquid fuels. Because current electrocatalysts are not adequate, we aim to discover new catalysts by obtaining a detailed understanding of the initial steps of CO2 electroreduction on copper surfaces, the best current catalysts. Using ambient pressure X-ray photoelectron spectroscopy interpreted with quantum mechanical prediction of the structures and free energies, we show that the presence of a thin suboxide structure below the copper surface is essential to bind the CO2 in the physisorbed configuration at 298 K, and we show that this suboxide is essential for converting to the chemisorbed CO2 in the presence of water as the first step toward CO2 reduction products such as formate and CO. This optimum suboxide leads to both neutral and charged Cu surface sites, providing fresh insights into how to design improved carbon dioxide reduction catalysts. [ABSTRACT FROM AUTHOR]

We propose and validate with quantum mechanics methods a unique catalyst for electrochemical reduction of CO2 (CO2RR) in which selectivity and activity of CO and C2 products are both enhanced at the borders of oxidized and metallic surface regions. This Cu metal embedded in oxidized matrix (MEOM) catalyst is consistent with observations that Cu2O-based electrodes improve performance. However, we show that a fully oxidized matrix (FOM) model would not explain the experimentally observed performance boost, and we show that the FOM is not stable under CO2 reduction conditions. This electrostatic tension between the Cu+ and Cu0 surface sites responsible for the MEOM mechanism suggests a unique strategy for designing more efficient and selective electrocatalysts for CO2RR to valuable chemicals (HCOx), a critical need for practical environmental and energy applications. [ABSTRACT FROM AUTHOR]

The sweet taste in humans is mediated by the TAS1R2/TAS1R3 G protein-coupled receptor (GPCR), which belongs to the class C family that also includes the metabotropic glutamate and γ-aminobutyric acid receptors. We report here the predicted 3D structure of the fulllength TAS1R2/TAS1R3 heterodimer, including the Venus Flytrap Domains (VFDs) [in the closed–open (co) active conformation], the cysteine-rich domains (CRDs), and the transmembrane domains (TMDs) at the TM56/TM56 interface. We observe that binding of agonists to VFD2 of TAS1R2 leads to major conformational changes to form a TM6/TM6 interface between TMDs of TAS1R2 and TAS1R3, which is consistent with the activation process observed biophysically on the metabotropic glutamate receptor 2 homodimer. We find that the initial effect of the agonist is to pull the bottom part of VFD3/TAS1R3 toward the bottom part of VFD2/ TAS1R2 by ~6 Å and that these changes get transmitted from VFD2 of TAS1R2 (where agonists bind) through the VFD3 and the CRD3 to the TMD3 of TAS1R3 (which couples to the G protein). These structural transformations provide a detailed atomistic mechanism for the activation process in GPCR, providing insights and structural details that can now be validated through mutation experiments. [ABSTRACT FROM AUTHOR]

A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMµD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of -0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than -0.6 V (RHE) ethylene, the major product, is produced via the Eley-Rideal (ER) mechanism using H2O + e-. The rate-determining step (RDS) is C-C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than -0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than -0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4. These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface. [ABSTRACT FROM AUTHOR]

Findings of laser-assisted atom probe tomography experiments on boron carbide elucidate an approach for characterizing the atomic structure and interatomic bonding of molecules associated with extraordinary structural stability. The discovery of crystallographic planes in these boron carbide datasets substantiates that crystallinity is maintained to the point of field evaporation, and characterization of individual ionization events gives unexpected evidence of the destruction of individual icosahedra. Statistical analyses of the ions created during the field evaporation process have been used to deduce relative atomic bond strengths and show that the icosahedra in boron carbide are not as stable as anticipated. Combined with quantum mechanics simulations, this result provides insight into the structural instability and amorphization of boron carbide. The temporal, spatial, and compositional information provided by atom probe tomography makes it a unique platform for elucidating the relative stability and interactions of primary building blocks in hierarchically crystalline materials. [ABSTRACT FROM AUTHOR]

To gain insight into the large toughness variability observed between metallic glasses (MGs), we examine the origin of fracture toughness through bending experiments and molecular dynamics (MD) simulations for two binary MGs: Pd82Si18 and Cu46Zr54. The bending experiments show that Pd82Si18 is considerably tougher than Cu46Zr54, and the higher toughness of Pd82Si18 is attributed to an ability to deform plastically in the absence of crack nucleation through cavitation. The MD simulations study the initial stages of cavitation in both materials and extract the critical factors controlling cavitation. We find that for the tougher Pd82Si18, cavitation is governed by chemical inhomogeneity in addition to topological structures. In contrast, no such chemical correlations are observed in the more brittle Cu46Zr54, where topological low coordination number polyhedra are still observed around the critical cavity. As such, chemical inhomogeneity leads to more difficult cavitation initiation in Pd82Si18 than in Cu46Zr54, leading to a higher toughness. The absence of chemical separation during cavitation initiation in Cu46Zr54 decreases the energy barrier for a cavitation event, leading to lower toughness. [ABSTRACT FROM AUTHOR]

The remarkable adaptive strategies of insects to extreme environments are linked to the biochemical compounds in their body fluids. Trehalose, a versatile sugar molecule, can accumulate to high levels in freeze-tolerant and freeze-avoiding insects, functioning as a cryoprotectant and a supercooling agent. Antifreeze proteins (AFPs), known to protect organisms from freezing by lowering the freezing temperature and deferring the growth of ice, are present at high levels in some freeze-avoiding insects in winter, and yet, paradoxically are found in some freeze-tolerant insects. Here, we report a previously unidentified role for AFPs in effectively inhibiting trehalose precipitation in the hemolymph (or blood) of overwintering beetle larvae. We determine the trehalose level (29.6 ± 0.6 mg/mL) in the larval hemolymph of a beetle, Dendroides canadensis, and demonstrate that the hemolymph AFPs are crucial for inhibiting trehalose crystallization, whereas the presence of trehalose also enhances the antifreeze activity of AFPs. To dissect the molecular mechanism, we examine the molecular recognition between AFP and trehalose crystal interfaces using molecular dynamics simulations. The theory corroborates the experiments and shows preferential strong binding of the AFP to the fast growing surfaces of the sugar crystal. This newly uncovered role for AFPs may help explain the long-speculated role of AFPs in freeze-tolerant species. We propose that the presence of high levels of molecules important for survival but prone to precipitation in poikilotherms (their body temperature can vary considerably) needs a companion mechanism to prevent the precipitation and here present, to our knowledge, the first example. Such a combination of trehalose and AFPs also provides a novel approach for cold protection and for trehalose crystallization inhibition in industrial applications. [ABSTRACT FROM AUTHOR]

Efficient generation of hydrogen from renewable resources requires development of catalysts that avoid deep wells and high barriers. Information about the energy landscape for H2 production can be obtained by chemical characterization of catalytic intermediates, but few have been observed to date. We have isolated and characterized a key intermediate in 2e- + 2H+ → H2 catalysis. This intermediate, obtained by treatment of Cp*Rh(bpy) (Cp*, η5-pentamethylcyclopentadienyl; bpy, κ2-2,2'-bipyridyl) with acid, is not a hydride species but rather, bears [η4-Cp*H] as a ligand. Delivery of a second proton to this species leads to evolution of H2 and reformation of η5-Cp* bound to rhodium(III). With suitable choices of acids and bases, the Cp*Rh(bpy) complex catalyzes facile and reversible interconversion of H+ and H2. [ABSTRACT FROM AUTHOR]

It is well known that graphite has a low capacity for Na but a high capacity for other alkali metals. The growing interest in alternative cation batteries beyond Li makes it particularly important to elucidate the origin of this behavior, which is not well understood. In examining this question, we find a quite general phenomenon: among the alkali and alkaline earth metals, Na and Mg generally have the weakest chemical binding to a given substrate, compared with the other elements in the same column of the periodic table. We demonstrate this with quantum mechanics calculations for a wide range of substrate materials (not limited to C) covering a variety of structures and chemical compositions. The phenomenon arises from the competition between trends in the ionization energy and the ion-substrate coupling, down the columns of the periodic table. Consequently, the cathodic voltage for Na and Mg is expected to be lower than those for other metals in the same column. This generality provides a basis for analyzing the binding of alkali and alkaline earth metal atoms over a broad range of systems. [ABSTRACT FROM AUTHOR]

Nanocrystals are promising structures, but they are too large for achieving maximum energy storage performance. We show that rescaling 3-nm particles through lithiation followed by delithiation leads to high-performance energy storage by realizing high capacitance close to the theoretical capacitance available via ion-to-atom redox reactions. Reactive force-field (ReaxFF) molecular dynamics simulations support the conclusion that Li atoms react with nickel oxide nanocrystals (NiO-n) to form lithiated core-shell structures (Ni:Li2O), whereas subsequent delithiation causes Ni:Li2O to form atomic clusters of NiO-a. This is consistent with in situ X-ray photoelectron and optical spectroscopy results showing that Ni2+ of the nanocrystal changes during lithiation-delithiation through Ni0 and back to Ni2+. These processes are also demonstrated to provide a generic route to rescale another metal oxide. Furthermore, assembling NiO-a into the positive electrode of an asymmetric device enables extraction of full capacitance for a counter negative electrode, giving high energy density in addition to robust capacitance retention over 100,000 cycles. [ABSTRACT FROM AUTHOR]

We predicted the structural basis for pleiotropic signaling of the C-C chemokine type 5 (CCR5) G protein-coupled receptor (GPCR) by predicting the binding of several ligands to the lower-energy conformations of the CCR5 receptor and 11 mutants. For each case, we predicted the ~20 most stable conformations for the receptor along with the binding sites for four anti-HIV ligands. We found that none of the ligands bind to the lowest-energy apo-receptor conformation. The three ligands with a similar pharmacophore (Maraviroc, PF-232798, and Aplaviroc) bind to a specific higher-energy receptor conformation whereas TAK-779 (with a different pharmacophore) binds to a different high-energy conformation. This result is in agreement with the very different binding-site profiles for these ligands obtained by us and others. The predicted Maraviroc binding site agrees with the recent structure of CCR5 receptor cocrystallized with Maraviroc. We performed 11 site-directed mutagenesis experiments to validate the predicted binding sites. Here, we independently predicted the lowest 10 mutant protein conformations for each of the 11 mutants and then docked the ligands to these lowest conformations. We found the predicted binding energies to be in excellent agreement with our mutagenesis experiments. These results show that, for GPCRs, each ligand can stabilize a different protein conformation, complicating the use of cocrystallized structures for ligand screening. Moreover, these results show that a single-point mutation in a GPCR can dramatically alter the available low-energy conformations, which in turn alters the binding site, potentially altering downstream signaling events. These studies validate the conformational selection paradigm for the pleiotropic function and structural plasticity of GPCRs. [ABSTRACT FROM AUTHOR]

Sodium ion batteries offer promising opportunities in emerging utility grid applications because of the low cost of raw materials. yet low energy density and limited cycle life remain critical drawbacks in their electrochemical operations. Herein, we report a vanadium-based ortho-diphosphate, Na7V4(P2O7)4PO4, or VODP, that significantly reduces all these drawbacks. Indeed, VODP exhibits single-valued voltage plateaus at 3.88 V vs. Na/Na+ while retaining substantial capacity (>78%) over 1,000 cycles. Electronic structure calculations reveal that the remarkable single plateau and cycle life originate from an intermediate phase (a very shallow voltage step) that is similar both in the energy level and lattice parameters to those of fully intercalated and deintercalated states. We propose a theoretical scheme in which the reaction barrier that arises from lattice mismatches can be evaluated by using a simple energetic consideration, suggesting that the presence of intermediate phases is beneficial for cell kinetics by buffering the differences in lattice parameters between initial and final phases. We expect these insights into the role of intermediate phases found for VODP hold in general and thus provide a helpful guideline in the further understanding and design of battery materials. [ABSTRACT FROM AUTHOR]

A number of exotic structures have been formed through high-pressure chemistry, but applications have been hindered by difficulties in recovering the high-pressure phase to ambient conditions (i.e., one atmosphere and 300 K). Here we use dispersion-corrected density functional theory [PBE-ulg (Perdew-Burke-Ernzerhof flavor of DFT with the universal low gradient correction for long range London dispersion)] to predict that above 60 gigapascal (GPa) the most stable form of N2O (the laughing gas in its molecular form) is a one-dimensional polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03∼0.10 eV/ molecular unit less stable. Upon relaxation to ambient conditions, both polymers relax below 14 GPa to the same stable nonplanar trans-polymer. The predicted phonon spectrum and dissociation kinetics validates the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a type of conducting nonlinear optical polymer with all-nitrogen chains and as a highenergy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions (very high pressure or temperature). [ABSTRACT FROM AUTHOR]

The glucagon-like peptide 1 receptor (GLP1R) isa G protein-coupled receptor (GPCR) involved in insulin synthesis and regulation; therefore, it is an important drug target for treatment of diabetes. However, GLP1R is a member of the class Bi family of GPCRs for which there are no experimental structures. To provide a structural basis for drug design and to probe class B GPCR activation, we predicted the transmembrane (TM) bundle structure of GLP1R bound to the peptide Exendin-4 (Exe4; a GLP1R agonist on the market for treating diabetes) using the MembStruk method for scanning TM bundle conformations. We used protein-protein docking methods to combine the TM bundle with the X-ray crystal structure of the 143-aa N terminus coupled to the Exe4 peptide. This complex was subjected to 28 ns of full-solvent, full-lipid molecular dynamics. We find 14 strong polar interactions of Exe4 with GLP1R, of which 8 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions involve the N terminus (3 interactions found in the crystal structure). We also find 10 important hydrophobic interactions, of which 4 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions are in the N terminus (6 interactions present in the crystal structure). Thus, our predicted structure agrees with available mutagenesis studies. We suggest a number of mutation experiments to further validate our predicted structure. The structure should be useful for guiding drug design and can provide a structural basis for understanding ligand binding and receptor activation of GLP1R and other class B1 GPCRs. [ABSTRACT FROM AUTHOR]

Differences in the extent of protonation of functional groups lying on either side of water-hydrophobe interfaces are deemed essential to enzymatic catalysis, molecular recognition, bioenergetic transduction, and atmospheric aerosol-gas exchanges. The sign and range of such differences, however, remain conjectural. Herein we report experiments showing that gaseous carboxylic acids RCOOH(g) begin to deprotonate on the surface of water significantly more acidic than that supporting the dissociation of dissolved acids RCOOH(aq). Thermodynamic analysis indicates that> 6 H2O molecules must participate in the deprotonation of RCOOH(g) on water, but quantum mechanical calculations on a model air-water interface predict that such event is hindered by a significant kinetic barrier unless OH ions are present therein. Thus, by detecting RCOO we demonstrate the presence of OH on the aerial side of on pH > 2 water exposed to RCOOH(g). Furthermore, because in similar experiments the base (Me)3N(g) is protonated only on pH < 4 water, we infer that the outer surface of water is Brønsted neutral at pH ~3 (rather than at pH 7 as bulk water), a value that matches the isoelectric point of bubbles and oil droplets in independent electrophoretic experiments. The OH densities sensed by RCOOH(g) on the aerial surface of water, however, are considerably smaller than those at the (>1 nm) deeper shear planes probed in electrophoresis, thereby implying the existence of OHgradients in the interfacial region. This fact could account for the weak OH signals detected by surface-specific spectroscopies. [ABSTRACT FROM AUTHOR]

Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury. Their diverse biological activities are derived from an ability to regulate a remarkable number of proteins. However. few methods exist for the rapid identification of glycosaminoglycan-protein interactions and for studying the potential of glycosaminoglycans to assemble multimeric protein complexes. Here, we report a multidisciplinary approach that combines new carbohydrate microarray and computational modeling methodologies to elucidate glycosaminoglycan-protein interactions. The approach was validated through the study of know&protein partners for heparan and chondroitin sulfate, including fibroblast growth factor 2 (FGF2) and its receptor FGFR1, the malarial protein VAR2CSA, and tumor necrosis factor-α (TNF-α). We also applied the approach to identify previously undescribed interactions between a specific sulfated epitope on chondroitin sulfate, CS-E, and the neurotrophins, a critical family of growth factors involved in the development, maintenance, and survival of the vertebrate nervous system. Our studies show for the first time that CS is capable of assembling multimeric signaling complexes and modulating neurotrophin signaling pathways. In addition, we identify a contiguous CS-E-binding site by computational modeling that suggests a potential mechanism to explain how CS may promote neurotrophin-tyrosine receptor kinase (Trk) complex formation and neurotrophin signaling. Together, our combined microarray and computational modeling methodologies provide a general, facile means to identify new glycosaminoglycan-protein-protein interactions, as well as a molecular-level understanding of those complexes. [ABSTRACT FROM AUTHOR]

We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling-Levy coupling- constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn- Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size. [ABSTRACT FROM AUTHOR]

To understand how core ionization and subsequent Auger decay lead to bond breaking in large systems, we simulate the wave packet dynamics of electrons in the hydrogenated diamond nanoparticle C197H112. We find that surface core ionizations cause emission of carbon fragments and protons through a direct Auger mechanism, whereas deeper core ionizations cause hydrides to be emitted from the surface via remote heating, consistent with results from photon-stimulated desorption experiments [Hoffman A, Laikhtman A, (2006) J Phys Condens Mater 18:S1517-S1546]. This demonstrates that it is feasible to study the chemistry of highly excited large-scale systems using simulation and analysis tools comparable in simplicity to those used for classical molecular dynamics. [ABSTRACT FROM AUTHOR]

Using quantum mechanics (QM, Density Functional Theory) we show that all four phases of barium titanate (BaTiO3) have local Ti distortions toward 〈111〉 (an octahedral face). The stable rhombohedral phase has all distortions in phase (ferroelectric, FE), whereas higher temperature phases have antiferroelectric coupling (AFE) in one, two, or three dimensions (orthorhombic, tetragonal, cubic). This FE-AFE model from QM explains such puzzling aspects of these systems as the allowed Raman excitation observed for the cubic phase, the distortions toward 〈111〉 observed in the cubic phase using x-ray fine structure, the small transition entropies, the heavily damped soft phonon modes, and the strong diffuse x-ray scattering in all but the rhombohedral phase. In addition, we expect to see additional weak Bragg peaks at the face centers of the reciprocal lattice for the cubic phase. Similar FE-AFE descriptions are expected to occur for other FE materials. Accounting for this FE-AFE nature of these phases is expected to be important in accurately simulating the domain wall structures, energetics, and dynamics, which in turn may lead to the design of improved materials. [ABSTRACT FROM AUTHOR]

Recently we predicted the 3D structure of the human β2-adrenergic receptor (β2AR) and of the binding site of several agonists and antagonists to β2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H2O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-β2AR, epinephrine-bound β2AR, and butoxamine-bound β2AR (epinephrine is an endogenous agonist, and butoxamine is a β2AR selective antagonist). The predicted structures for apo-β2AR and butoxamine-β2AR are stable in MD, but in epinephrine-β2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-β2AR structure shows dynamic flexibility with small, piston-like movements of helices 3 and 6 and transient interhelical hydrogen bonding between Ser-165 on transmembrane 4 and Ser-207 on transmembrane 5. These couplings and motions may play a role in protein activation. The apo-β2AR shows less dynamic flexibility, whereas the antagonist-β2AR structure is quite rigid. This MD validation of the structure predictions for G protein-coupled receptors in explicit lipid and water suggests that these methods can be trusted for studying the mechanism of activation and the design of subtype-specific agonists and antagonists. [ABSTRACT FROM AUTHOR]

We derive the form for an exact exchange energy density for a density decaying with Gaussian-like behavior at long range. Based on this, we develop the X3LYP (extended hybrid functional combined with Lee-Yang-Parr correlation functional) extended functional for density functional theory to significantly improve the accuracy for hydrogen-bonded and van der Waals complexes while also improving the accuracy in heats of formation, ionization potentials, electron affinities, and total atomic energies [over the most popular and accurate method, B3LYP (Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional)]. X3LYP also leads to a good description of dipole moments, polarizabilities, and accurate excitation energies from s to d orbitals for transition metal atoms and ions. We suggest that X3LYP will be useful for predicting ligand binding in proteins and DNA. [ABSTRACT FROM AUTHOR]

We report the 3D structure of human β2 adrenergic receptor (AR) predicted by using the MembStruk first principles method. To validate this structure, we use the HierDock first principles method to predict the ligand-binding sites for epinephrine and norepinephrine and for eight other ligands, including agonists and antagonists to β2 AR and ligands not observed to bind to β2 AR. The binding sites agree well with available mutagenesis data, and the calculated relative binding energies correlate reasonably with measured binding affinities. In addition, we find characteristic differences in the predicted binding sites of known agonists and antagonists that allow us to infer the likely activity of other ligands. The predicted ligand-binding properties validate the methods used to predict the 3D structure and function. This validation is a successful step toward applying these procedures to predict the 3D structures and function of the other eight subtypes of ARs, which should enable the development of subtype-specific antagonists and agonists with reduced side effects. [ABSTRACT FROM AUTHOR]

Although numerous quantum calculations have been made over the years of the stabilities of the fluxional isomers of C[sub 4]H[sup +, sub 7], none have been reported for other than the gas phase (which is unrealistic for these ionic species) that exhibit exceptional fluxional properties in solution. To be sure, quantum-mechanical calculations for solutions are subject to substantial uncertainties, but nonetheless it is important to see whether the trends seen for the gas-phase C[sub 4]H[sup +, sub 7] species are also found in calculations for polar solutions. Of the C[sub 4]H[sup +, sub 7] species, commonly designated bisectedcyclopropylcarbinyl 1, unsym-bicyciobutonium 2, sym-bicyclobutonium 3, allylcarbinyl 4, and pyramidal structure 6, the most advanced gas-phase calculations available thus far suggest that the order of stability is I ≥ 2 ≥ 3 » 4 » 6 with barriers of only ≈1 kcal/mol for interconversions among 1, 2, and 3. We report here that, when account is taken of solvation, 2 turns out to be slightly more stable than 1 or 3 in polar solvents. The pattern of the overall results is unexpected, in that despite substantial differences in structures and charge distributions between the primary players in the C[sub 4]H[sup +, sub 7] equilibria and the large differences in solvation energies calculated for the solvents considered, the differential solvent effects from species to species are rather small. [ABSTRACT FROM AUTHOR]

The recent observation [Wentworth, P., Jones, L. H., Wentworth, A. D., Zhu, X. Y., Larsen, N. A., Wilson, I. A., Xu, X., Goddard, W. A., Janda, K. D., Eschenmoser, A. & Lerner, R. A. (2001) Science 293, 1806-1811] that antibodies form H[sub 2]O[sub 2] from ¹O[sub 2] plus H[sub 2]O was explained in terms of the formation of the H[sub 2]O[sub 3] species that in the antibody reacts with a second H[sub 2]O[sub 3] to form H[sub 2]O[sub 2]. There have been few reports of the chemistry for forming H[sub 2]O[sub 3], but recently Engdahl and Nelander [Engdahl, A. & Nelander, B. (2002) Science 295, 482-483] reported that photolysis of the ozone-hydrogen peroxide complex in argon matrices leads to significant concentrations of H[sub 2]O[sub 3]. We report here the chemical mechanism for this process, determined by using first-principles quantum mechanics. We show that in an argon matrix it is favorable (3.5 kcal/mol barrier) for H[sub 2]O[sub 2] and O[sub 3] to form a [(HO[sub 2])(HO[sub 3])] hydrogen-bonded complex [head-to-tail sevenmembered ring (7r)]. In this complex, the barrier for forming H[sub 2]O[sub 3] plus ³O[sub 2] is only 4.8 kcal/mol, which should be observable by means of thermal processes (not yet reported). Irradiation of the [(HO[sub 2])(HO[sub 3])-7r] complex should break the HO-OO bond of the HO[sub 3] moiety, eliminating ³O[sub 2] and leading to [(HO[sub 2])(HO)]. This [(HO[sub 2])(HO)] confined in the matrix cage is expected to rearrange to also form H[sub 2]O[sub 3] (observed experimentally). We show that these two processes can be distinguished isotopically. These results (including the predicted vibrational frequencies) suggest strategies for synthesizing H[sub 2]O[sub 3] and characterizing its chemistry. We suggest that the [(HO[sub 2])(HO[sub 3])-Tr] complex and H[sub 2]O[sub 3] are involved in biological, atmospheric, and environmental oxidative processes. [ABSTRACT FROM AUTHOR]

Investigates the prediction of structure and function of G protein-coupled receptors (GPCR). Role of GPCR in sensation; Identification of ligand binding sites and affinities; Use of HierDock ligand screening protocol.

Examines the structure-based design of Methanococcus jannaschii tyrosyl (Tyr)-transfer RNA synthetase (RS). Incorporation of amino acid into proteins by RS; Use of clash opportunity progressive method for designing a mutant aminoacyl RS; Molecular dynamics of M. jannaschii-TyrRS.

Investigates the chemical reaction mechanisms of the oxidation of water by singlet molecular oxygen to generate hydrogen peroxide (HOOH). Use of quantum chemical methods; Types of pathways in converting water to HOOH; Summary of the HOOOH dimer mechanism pathway.

Tests the Pentamer Channel Stiffening Model by examining the changes in strain energy associated with opening the pentamer channel through which the RNA is released. Use of molecular dynamics methods; RMS variations in coordinates; Helium balloon string measurement of pentamer stiffness.

The article offers an overview on a study by Jenelle K. Bray and colleagues regarding the SuperBiHelix method, which is aimed at determining the low-energy structures that might play a role in binding and signaling G-protein-coupled receptors.

A national priority is to convert CO2 into high-value chemical products such as liquid fuels. Because current electrocatalysts are not adequate, we aim to discover new catalysts by obtaining a detailed understanding of the initial steps of CO2 electroreduction on copper surfaces, the best current catalysts. Using ambient pressure X-ray photoelectron spectroscopy interpreted with quantum mechanical prediction of the structures and free energies, we show that the presence of a thin suboxide structure below the copper surface is essential to bind the CO2 in the physisorbed configuration at 298 K, and we show that this suboxide is essential for converting to the chemisorbed CO2 in the presence of water as the first step toward CO2 reduction products such as formate and CO. This optimum suboxide leads to both neutral and charged Cu surface sites, providing fresh insights into how to design improved carbon dioxide reduction catalysts. [ABSTRACT FROM AUTHOR]