Publications by authors named "William A Goddard"

519 Publications

Hedgehog proteins create a dynamic cholesterol interface.

PLoS One 2021 25;16(2):e0246814. Epub 2021 Feb 25.

Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America.

During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR ("Hog") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246814PLOS
February 2021

Spatiotemporal Temperature and Pressure in Thermoplasmonic Gold Nanosphere-Water Systems.

ACS Nano 2021 Feb 23. Epub 2021 Feb 23.

Chemical Sciences Division, Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.

We offer a detailed investigation of the photophysical properties of plasmonic solid and hollow gold nanospheres suspended in water by combining ultrafast transient absorption (TA) spectroscopy with molecular dynamics (MD) simulations. TA reveals that hollow gold nanospheres (HGNs) exhibit faster excited state relaxation and larger amplitude acoustic phonon modes than solid gold nanoparticles of the same outer diameter. MD simulation carried out on full scale nanoparticle-water models (over 10 million atoms) to simulate the temporal evolution (0-100 ps) of the thermally excited particles (1000 or 1250 K) provides atomic-scale resolution of the spatiotemporal temperature and pressure maps, as well as visualization of the lattice vibrational modes. For the 1000 K HGN, temperatures upward of 500 K in the vicinity of the shell surface were observed, along with pressures up to several hundred MPa in the inner cavity, revealing potential use as a photoinduced nanoreactor. Our approach of combining TA and MD provides a path to better understanding how thermal-structural properties (such as expansion and contraction) and thermal-optical properties (such as modulated dielectrics) manifest themselves as TA signatures. The detailed picture of heat transfer at interfaces should help guide nanoparticle design for a wide range of applications that rely on photothermal conversion, including photothermal coupling agents for nanoparticle-mediated photothermal therapy and photocatalysts for light-driven chemical reactions.
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http://dx.doi.org/10.1021/acsnano.0c09804DOI Listing
February 2021

Reduction of N to Ammonia by Phosphate Molten Salt and Li Electrode: Proof of Concept Using Quantum Mechanics.

J Phys Chem Lett 2021 Feb 9;12(6):1696-1701. Epub 2021 Feb 9.

Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States.

Electrochemical routes provide an attractive alternative to the Haber-Bosch process for cheaper and more efficient ammonia (NH) synthesis from N while avoiding the onerous environmental impact of the Haber-Bosch process. We prototype a strategy based on a eutectic mixture of phosphate molten salt. Using quantum-mechanics (QM)-based reactive molecular dynamics, we demonstrate that lithium nitride (LiN) produced from the reduction of nitrogen gas (N) by a lithium electrode can react with the phosphate molten salt to form ammonia. We extract reaction kinetics of the various steps from QM to identify conditions with favorable reaction rates for N reduction by a porous lithium electrode to form LiN followed by protonation from phosphate molten salt (LiHPO-LiHPO mixture) to selectively form NH.
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http://dx.doi.org/10.1021/acs.jpclett.0c03467DOI Listing
February 2021

The DFT-ReaxFF Hybrid Reactive Dynamics Method with Application to the Reductive Decomposition Reaction of the TFSI and DOL Electrolyte at a Lithium-Metal Anode Surface.

J Phys Chem Lett 2021 Feb 27;12(4):1300-1306. Epub 2021 Jan 27.

Institute of Functional Nano and Soft Materials, Soochow University, Suzhou 215123, China.

The high energy density and suitable operating voltage make rechargeable lithium ion batteries (LIBs) promising candidates to replace such conventional energy storage devices as nonrechargeable batteries. However, the large-scale commercialization of LIBs is impeded significantly by the degradation of the electrolyte, which reacts with the highly reactive lithium metal anode. Future improvement of the battery performance requires a knowledge of the reaction mechanism that is responsible for the degradation and formation of the solid-electrolyte interphase (SEI). In this work, we develop a hybrid computational scheme, , denoted , to accelerate Quantum Mechanics-based reaction dynamics (QM-MD or AIMD, for ab initio RD) simulations. The HAIR scheme extends the time scale accessible to AIMD by a factor of 10 times through interspersing reactive force field (ReaxFF) simulations between the AIMD parts. This enables simulations of the initial chemical reactions of SEI formation, which may take 1 ns, far too long for AIMD. We apply the HAIR method to the bis(trifluoromethanesulfonyl)imide (TFSI) electrolyte in 1,3-dioxolane (DOL) solvent at the Li metal electrode, demonstrating that HAIR reproduces the initial reactions of the electrolyte (decomposition of TFSI) previously observed in AIMD simulation while also capturing solvent reactions (DOL) that initiate by ring-opening to form such stable products as CO, CHO, and CH, as observed experimentally. These results demonstrate that the HAIR scheme can significantly increase the time scale for reactive MD simulations while retaining the accuracy of AIMD simulations. This enables a full atomistic description of the formation and evolution of SEI.
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http://dx.doi.org/10.1021/acs.jpclett.0c03720DOI Listing
February 2021

Controlling the Shapes of Nanoparticles by Dopant-Induced Enhancement of Chemisorption and Catalytic Activity: Application to Fe-Based Ammonia Synthesis.

ACS Nano 2021 Jan 23;15(1):1675-1684. Epub 2020 Dec 23.

Materials and Process Simulation Center (MSC), California Institute of Technology, Pasadena, California 91125, United States.

We showed recently that the catalytic efficiency of ammonia synthesis on Fe-based nanoparticles (NP) for Haber-Bosch (HB) reduction of N to ammonia depends very dramatically on the crystal surface exposed and on the doping. In turn, the stability of each surface depends on the stable intermediates present during the catalysis. Thus, under reaction conditions, the shape of the NP is expected to evolve to optimize surface energies. In this paper, we propose to manipulate the shape of the nanoparticles through doping combined with chemisorption and catalysis. To do this, we consider the relationships between the catalyst composition (adding dopant elements) and on how the distribution of the dopant atoms on the bulk and facet sites affects the shape of the particles and therefore the number of active sites on the catalyst surfaces. We use our hierarchical, high-throughput catalyst screening (HHTCS) approach but extend the scope of HHTCS to select dopants that can increase the catalytically active surface orientations, such as Fe-bcc(111), at the expense of catalytically inactive facets, such as Fe-bcc(100). Then, for the most promising dopants, we predict the resulting shape and activity of doped Fe-based nanoparticles under reaction conditions. We examined 34 possible dopants across the periodic table and found 16 dopants that can potentially increase the fraction of active Fe-bcc(111) inactive Fe-bcc(100) facets. Combining this reshaping criterion with our HHTCS estimate of the resulting catalytic performance, we show that Si and Ni are the most promising elements for improving the rates of catalysis by optimizing the shape to decrease reaction barriers. Then, using Si dopant as a working example, we build a steady-state dynamical Wulff construction of Si-doped Fe bcc nanoparticles. We use nanoparticles with a diameter of ∼10 nm, typical of industrial catalysts. We predict that doping Si into such Fe nanoparticles at the optimal atomic content of ∼0.3% leads to rate enhancements by a factor of 56 per nanoparticle under target HB conditions.
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http://dx.doi.org/10.1021/acsnano.0c09346DOI Listing
January 2021

London Dispersion Corrections to Density Functional Theory for Transition Metals Based on Fitting to Experimental Temperature-Programmed Desorption of Benzene Monolayers.

J Phys Chem Lett 2021 Jan 11;12(1):73-79. Epub 2020 Dec 11.

Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States.

Standard implementations of generalized gradient approximation (GGA)-based density functional theory (DFT) describe well strongly bound molecules and solids but fail to describe long-range London dispersion or van der Waals (vdW) attraction interactions that are important in molecular crystals and two-dimensional solids. To provide accurate values for the vdW distance and energies for the metals Cu, Ag, Au, Ni, Pd, and Pt, we determined empirical vdW corrections to Perdew, Burke, and Ernzerhof (PBE) DFT by fitting the experimental adsorption enthalpies measured by temperature-programmed desorption (TPD) from benzene monolayers by Campbell and co-workers ( 2016, 120, 25161-25172). Benzene physisorbed to these metals without chemical reaction; therefore, we consider the bonding to be vdW. We use the low gradient form for the vdW corrections, = -/[ + ] with just two parameters per atom ( and ). This LG form leads to negligible changes in bond distances and angles, so adjusting the parameters should not sacrifice accuracy for the bonding interactions. We demonstrate that the parameters fitted to benzene also describe well the physisorption enthalpies for other hydrocarbons (naphthalene, cyclohexane, methane, ethane, and propane) on Pt. We also report low gradient vdW correction parameters for the noble gases that fit the equilibrium lattice parameter and heat of vaporization of the crystals.
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http://dx.doi.org/10.1021/acs.jpclett.0c03126DOI Listing
January 2021

The Transition Metal Catalyzed [π2s + π2s + σ2s + σ2s] Pericyclic Reaction: Woodward-Hoffmann Rules, Aromaticity, and Electron Flow.

J Am Chem Soc 2020 11 27;142(45):19033-19039. Epub 2020 Oct 27.

The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.

We have shown that the fundamental step responsible for enantioinduction in the inner-sphere asymmetric Tsuji allylic alkylation is C-C bond formation through a seven-membered pericyclic transition state. We employ an extensive series of quantum mechanics (QM) calculations to delineate how the electronic structure of the Pd-catalyzed C-C bond forming process controls the reaction. Phase inversion introduced by d orbitals renders the Pd-catalyzed [π2s + π2s + σ2s + σ2s] reaction symmetry-allowed in the ground state, proceeding through a transition state with Craig-Möbius-like σ-aromaticity. Lastly, we connect QM to fundamental valence bonding concepts by deriving an ab initio "arrow-pushing" mechanism that describes the flow of electron density through the reaction.
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http://dx.doi.org/10.1021/jacs.0c09575DOI Listing
November 2020

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(ε-caprolactone) (PEG-b-PCL) micelles.

Phys Chem Chem Phys 2020 Nov 20;22(41):24028-24040. Epub 2020 Oct 20.

Materials and Process Simulation Center (MSC), California Institute of Technology, Pasadena, California 91125, USA.

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer-air and polymer-water interfaces, indicating the accuracy of the NB interactions. The structural properties (density, radius of gyration (R), and end-to-end distance (h)) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG-b-PCL diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).
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http://dx.doi.org/10.1039/d0cp04364hDOI Listing
November 2020

Sulfated glycans engage the Ang-Tie pathway to regulate vascular development.

Nat Chem Biol 2021 02 5;17(2):178-186. Epub 2020 Oct 5.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.

The angiopoietin (Ang)-Tie pathway is essential for the proper maturation and remodeling of the vasculature. Despite its importance in disease, the mechanisms that control signal transduction through this pathway are poorly understood. Here, we demonstrate that heparan sulfate glycosaminoglycans (HS GAGs) regulate Ang-Tie signaling through direct interactions with both Ang ligands and Tie1 receptors. HS GAGs formed ternary complexes with Ang1 or Ang4 and Tie2 receptors, resulting in potentiation of endothelial survival signaling. In addition, HS GAGs served as ligands for the orphan receptor Tie1. The HS-Tie1 interaction promoted Tie1-Tie2 heterodimerization and enhanced Tie1 stability within the mature vasculature. Loss of HS-Tie1 binding using CRISPR-Cas9-mediated mutagenesis in vivo led to decreased Tie protein levels, pathway suppression and aberrant retinal vascularization. Together, these results reveal that sulfated glycans use dual mechanisms to regulate Ang-Tie signaling and are important for the development and maintenance of the vasculature.
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http://dx.doi.org/10.1038/s41589-020-00657-7DOI Listing
February 2021

Oxygen induced promotion of electrochemical reduction of CO via co-electrolysis.

Nat Commun 2020 Jul 31;11(1):3844. Epub 2020 Jul 31.

State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.

Harnessing renewable electricity to drive the electrochemical reduction of CO is being intensely studied for sustainable fuel production and as a means for energy storage. Copper is the only monometallic electrocatalyst capable of converting CO to value-added products, e.g., hydrocarbons and oxygenates, but suffers from poor selectivity and mediocre activity. Multiple oxidative treatments have shown improvements in the performance of copper catalysts. However, the fundamental underpinning for such enhancement remains controversial. Here, we combine reactivity, in-situ surface-enhanced Raman spectroscopy, and computational investigations to demonstrate that the presence of surface hydroxyl species by co-electrolysis of CO with low concentrations of O can dramatically enhance the activity of copper catalyzed CO electroreduction. Our results indicate that co-electrolysis of CO with an oxidant is a promising strategy to introduce catalytically active species in electrocatalysis.
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http://dx.doi.org/10.1038/s41467-020-17690-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7395777PMC
July 2020

Highly Selective Electrocatalytic Reduction of CO into Methane on Cu-Bi Nanoalloys.

J Phys Chem Lett 2020 Sep 20;11(17):7261-7266. Epub 2020 Aug 20.

Materials and Process Simulation Center (MSC) and Joint Center for Artificial Photosynthesis (JCAP), California Institute of Technology, Pasadena, California 91125, United States.

Methane (CH), the main component of natural gas, is one of the most valuable products facilitating energy storage via electricity conversion. However, the poor selectivity and high overpotential for CH formation with metallic Cu catalysts prevent realistic applications. Introducing a second element to tune the electronic state of Cu has been widely used as an effective method to improve catalytic performance, but achieving high selectivity and activity toward CH remains challenging. Here, we successfully synthesized Cu-Bi NPs, which exhibit a CH Faradaic efficiency (FE) as high as 70.6% at -1.2 V versus reversible hydrogen electrode (RHE). The FE of Cu-Bi NPs has increased by approximately 25-fold compared with that of Cu NPs. DFT calculations showed that alloying Cu with Bi significantly decreases the formation energy of *COH formation, the rate-determining step, which explains the improved performance. Further analysis showed that Cu that has been partially oxidized because of electron withdrawal by Bi is the most possible active site.
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http://dx.doi.org/10.1021/acs.jpclett.0c01261DOI Listing
September 2020

Reaction Mechanism, Origins of Enantioselectivity, and Reactivity Trends in Asymmetric Allylic Alkylation: A Comprehensive Quantum Mechanics Investigation of a C(sp)-C(sp) Cross-Coupling.

J Am Chem Soc 2020 08 30;142(32):13917-13933. Epub 2020 Jul 30.

Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States.

We utilize quantum mechanics to evaluate a variety of plausible mechanistic pathways for the entirety of the catalytic cycle for asymmetric decarboxylative allylic alkylation of allyl β-ketoesters. We present a mechanistic picture that unites all current experimental observations, including enantioinduction, reaction rate, catalyst resting state, enolate crossover experiments, water tolerance, and the effects of solvation on inner- and outer-sphere mechanisms. Experiments designed to evaluate the fidelity and predictive power of the computational models reveal the methods employed herein to be highly effective in elucidating the reactivity of the catalytic system. On the basis of these findings, we highlight a computational framework from which chemically accurate results are obtained and address the current limitations of the decarboxylative asymmetric allylic alkylation reaction.
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http://dx.doi.org/10.1021/jacs.0c06243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7802888PMC
August 2020

Mechanism of β-arrestin recruitment by the μ-opioid G protein-coupled receptor.

Proc Natl Acad Sci U S A 2020 07 29;117(28):16346-16355. Epub 2020 Jun 29.

Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA 91125

Agonists to the μ-opioid G protein-coupled receptor (μOR) can alleviate pain through activation of G protein signaling, but they can also induce β-arrestin activation, leading to such side effects as respiratory depression. Biased ligands to μOR that induce G protein signaling without inducing β-arrestin signaling can alleviate pain while reducing side effects. However, the mechanism for stimulating β-arrestin signaling is not known, making it difficult to design optimum biased ligands. We use extensive molecular dynamics simulations to determine three-dimensional (3D) structures of activated β-arrestin2 stabilized by phosphorylated μOR bound to the morphine and D-Ala, -MePhe, Gly-ol]-enkephalin (DAMGO) nonbiased agonists and to the TRV130 biased agonist. For nonbiased agonists, we find that the β-arrestin2 couples to the phosphorylated μOR by forming strong polar interactions with intracellular loop 2 (ICL2) and either the ICL3 or cytoplasmic region of transmembrane (TM6). Strikingly, Gi protein makes identical strong bonds with these same ICLs. Thus, the Gi protein and β-arrestin2 compete for the same binding site even though their recruitment leads to much different outcomes. On the other hand, we find that TRV130 has a greater tendency to bind the extracellular portion of TM2 and TM3, which repositions TM6 in the cytoplasmic region of μOR, hindering β-arrestin2 from making polar anchors to the ICL3 or to the cytosolic end of TM6. This dramatically reduces the affinity between μOR and β-arrestin2.
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http://dx.doi.org/10.1073/pnas.1918264117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368253PMC
July 2020

Electrochemical Switching of a Fluorescent Molecular Rotor Embedded within a Bistable Rotaxane.

J Am Chem Soc 2020 07 25;142(27):11835-11846. Epub 2020 Jun 25.

Institute for Molecular Design and Synthesis, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China.

We report how the nanoconfined environment, introduced by the mechanical bonds within an electrochemically switchable bistable [2]rotaxane, controls the rotation of a fluorescent molecular rotor, namely, an 8-phenyl-substituted boron dipyrromethene (BODIPY). The electrochemical switching of the bistable [2]rotaxane induces changes in the ground-state coconformation and in the corresponding excited-state properties of the BODIPY rotor. In the starting redox state, when no external potential is applied, the cyclobis(paraquat--phenylene) (CBPQT) ring component encircles the tetrathiafulvalene (TTF) unit on the dumbbell component, leaving the BODIPY rotor unhindered and exhibiting low fluorescence. Upon oxidation of the TTF unit to a TTF dication, the CBPQT ring is forced toward the molecular rotor, leading to an increased energy barrier for the excited state to rotate the rotor into the state with a high nonradiative rate constant, resulting in an overall 3.4-fold fluorescence enhancement. On the other hand, when the solvent polarity is high enough to stabilize the excited charge-transfer state between the BODIPY rotor and the CBPQT ring, movement of the ring toward the BODIPY rotor produces an unexpectedly strong fluorescence signal decrease as the result of photoinduced electron transfer from the BODIPY rotor to the CBPQT ring. The nanoconfinement effect introduced by mechanical bonding can effectively lead to modulation of the physicochemical properties as observed in this bistable [2]rotaxane. On account of the straightforward synthetic strategy and the facile modulation of switchable electrochromic behavior, our approach could pave the way for the development of new stimuli-responsive materials based on mechanically interlocked molecules for future electro-optical applications, such as sensors, molecular memories, and molecular logic gates.
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http://dx.doi.org/10.1021/jacs.0c03701DOI Listing
July 2020

Synergy between a Silver-Copper Surface Alloy Composition and Carbon Dioxide Adsorption and Activation.

ACS Appl Mater Interfaces 2020 Jun 21;12(22):25374-25382. Epub 2020 May 21.

Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.

Bimetallic electrocatalysts provide a promising strategy for improving performance, especially in the enhancement of selectivity of CO reduction reactions. However, the first step of CO activation on bimetallic materials remains obscure. Considering bimetallic silver-copper (AgCu) as an example, we coupled ambient pressure X-ray photoelectron spectroscopy (APXPS) and quantum mechanics (QM) to examine CO adsorption and activation on AgCu exposed to CO with and without HO at 298 K. The interplay between adsorbed species and the surface alloy composition of Cu and Ag is studied in atomic details. The APXPS experiment and density functional theory (DFT) calculations indicate that the clean sample has a Ag-rich surface layer. Upon adsorption of CO and surface O, we found that it is thermodynamically more favorable to induce subsurface Cu atoms substitution for some surface Ag atoms, modifying the stability and activation of CO-related chemisorbed species. We further characterized this substitution effect by correlating the new adsorption species with the observed binding energy (BE) shift and intensity change in APXPS.
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http://dx.doi.org/10.1021/acsami.0c02057DOI Listing
June 2020

Si-Doped Fe Catalyst for Ammonia Synthesis at Dramatically Decreased Pressures and Temperatures.

J Am Chem Soc 2020 05 21;142(18):8223-8232. Epub 2020 Apr 21.

Materials and Process Simulation Center (MSC), California Institute of Technology, Pasadena, California 91125, United States.

The Haber-Bosch (HB) process combining nitrogen (N) and hydrogen (H) into ammonia (NH) gas plays an essential role in the synthesis of fertilizers for food production and many other commodities. However, HB requires enormous energy resources (2% of world energy production), and the high pressures and temperatures make NH production facilities very expensive. Recent advances in improving HB catalysts have been incremental and slow. To accelerate the development of improved HB catalysts, we developed a hierarchical high-throughput catalyst screening (HHTCS) approach based on the recently developed complete reaction mechanism to identify non-transition-metal (NTM) elements from a total set of 18 candidates that can significantly improve the efficiency of the most active Fe surface, Fe-bcc(111), through surface and subsurface doping. Surprisingly, we found a very promising subsurface dopant, Si, that had not been identified or suggested previously, showing the importance of the subsurface Fe atoms in N reduction reactions. Then we derived the full reaction path of the HB process for the Si doped Fe-bcc(111) from QM simulations, which we combined with kinetic Monte Carlo (kMC) simulations to predict a ∼13-fold increase in turnover frequency (TOF) under typical extreme HB conditions (200 atm reactant pressure and 500 °C) and a ∼43-fold increase in TOF under ideal HB conditions (20 atm reactant pressure and 400 °C) for the Si-doped Fe catalyst, in comparison to pure Fe catalyst. Importantly, the Si-doped Fe catalyst can achieve the same TOF of pure Fe at 200 atm/500 °C under much milder conditions, e.g. at a much decreased reactant pressure of 20 atm at 500 °C, or alternatively at temperature and reactant pressure decreased to 400 °C and 60 atm, respectively. Production plants using the new catalysts that operate under such milder conditions could be much less expensive, allowing production at local sites needing fertilizer.
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http://dx.doi.org/10.1021/jacs.9b13996DOI Listing
May 2020

Highly Stable Organic Bisradicals Protected by Mechanical Bonds.

J Am Chem Soc 2020 04 7;142(15):7190-7197. Epub 2020 Apr 7.

Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States.

Two new highly charged [2]catenanes-namely, ·6PF and ·6PF-were synthesized by exploiting radical host-guest templation between derivatives containing BIPY radical cations and the meta analogue of cyclobis(paraquat--phenylene). In contrast to related [2]catenanes that have been isolated as air-stable monoradicals, both ·6PF and ·6PF exist as air-stable singlet bisradicals, as evidenced by both X-ray crystallography in the solid state and EPR spectroscopy in solution. Electrochemical studies indicate that the first two reduction peaks of these two [2]catenanes are shifted significantly to more positive potentials, a feature which is responsible for their extraordinary stability in air. The mixed-valence nature of the mono- and bisradical states endows them with unique NIR absorption properties, e.g., NIR absorption bands for the mono- and bisradical states observed at ∼1800 and ∼1450 nm, respectively. These [2]catenanes are potentially useful in applications that include NIR photothermal conversion, UV-vis-NIR multiple-state electrochromic materials, and multiple-state memory devices. Our findings highlight the principle of "mechanical-bond-induced stabilization" as an efficient strategy for designing persistent organic radicals.
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http://dx.doi.org/10.1021/jacs.0c01989DOI Listing
April 2020

Design of a Graphene Nitrene Two-Dimensional Catalyst Heterostructure Providing a Well-Defined Site Accommodating One to Three Metals, with Application to CO Reduction Electrocatalysis for the Two-Metal Case.

J Phys Chem Lett 2020 Apr 17;11(7):2541-2549. Epub 2020 Mar 17.

Materials and Process Simulation Center (MSC), California Institute of Technology (Caltech), Pasadena, California 91125, United States.

Recently, the reduction of CO to fuels has been the subject of numerous studies, but the selectivity and activity remain inadequate. Progress has been made on single-site two-dimensional catalysts based on graphene coupled to a metal and nitrogen for the CO reduction reaction (CORR); however, the product is usually CO, and the metal-N environment remains ambiguous. We report a novel two-dimensional graphene nitrene heterostructure (grafiN) providing well-defined active sites (N) that can bind one to three metals for the CORR. We find that homobimetallic FeFe-grafiN could reduce CO to CH at -0.61 V and to CHCHOH at -0.68 V versus reversible hydrogen electrode, with high product selectivity. Moreover, the heteronuclear FeCu-grafiN system may be significantly less affected by hydrogen evolution reaction, while maintaining a low limiting potential (-0.68 V) for C1 and C2 mechanisms. Binding metals to one N site but not the other could promote efficient electron transport facilitating some reaction steps. This framework for single or multiple metal sites might also provide unique catalytic sites for other catalytic processes.
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http://dx.doi.org/10.1021/acs.jpclett.0c00642DOI Listing
April 2020

The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist.

Proc Natl Acad Sci U S A 2020 03 3;117(11):5836-5843. Epub 2020 Mar 3.

Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125

The kappa opioid receptor (κOR) is an important target for pain therapeutics to reduce depression and other harmful side effects of existing medications. The analgesic activity is mediated by κOR signaling through the adenylyl cyclase-inhibitory family of Gi protein. Here, we report the three-dimensional (3D) structure for the active state of human κOR complexed with both heterotrimeric Gi protein and MP1104 agonist. This structure resulted from long molecular dynamics (MD) and metadynamics (metaMD) simulations starting from the 3.1-Å X-ray structure of κOR-MP1104 after replacing the nanobody with the activated Gi protein and from the 3.5-Å cryo-EM structure of μOR-Gi complex after replacing the 168 missing residues. Using MD and metaMD we discovered interactions to the Gi protein with strong anchors to two intracellular loops and transmembrane helix 6 of the κOR. These anchors strengthen the binding, contributing to a contraction in the binding pocket but an expansion in the cytoplasmic region of κOR to accommodate G protein. These remarkable changes in κOR structure reveal that the anchors are essential for activation.
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http://dx.doi.org/10.1073/pnas.1910006117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084096PMC
March 2020

Li-diffusion at the interface between Li-metal and [Pyr][TFSI]-ionic liquid: Ab initio molecular dynamics simulations.

J Chem Phys 2020 Jan;152(3):031101

Battery R&D, LG Chem, Yuseong-Gu, Daejeon 34122, South Korea.

We previously reported comprehensive density functional theory-molecular dynamics (DFT-MD) at 400 K to determine the composition and structure of the solid electrolyte interface (SEI) between a Li anode and [Pyr][TFSI] ionic liquid. In this paper, we examined diffusion rates in both the Li-electrode region and SEI compact layer in smaller 83Li/2[TFSI] and larger 164Li/4[TFSI] systems. At 400 K, the Li-diffusion constant in the Li-region is 1.35 × 10 m/s for 83Li/2[TFSI] and 5.64 × 10 m/s for 164Li/4[TFSI], while for the SEI it is 0.33 × 10 m/s and 0.22 × 10 m/s, thus about one order slower in the SEI compared to the Li-region. This Li-diffusion is dominated by hopping from the neighbor shell of one F or O to the neighbor shell of another. Comparing the Li-diffusion at different temperatures, we find that the activation energy is 0.03 and 0.11 eV for the Li-region in the smaller and larger systems, respectively, while for the SEI it is 0.09 and 0.06 eV.
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http://dx.doi.org/10.1063/1.5132566DOI Listing
January 2020

Predicted Optimal Bifunctional Electrocatalysts for the Hydrogen Evolution Reaction and the Oxygen Evolution Reaction Using Chalcogenide Heterostructures Based on Machine Learning Analysis of in Silico Quantum Mechanics Based High Throughput Screening.

J Phys Chem Lett 2020 Feb 22;11(3):869-876. Epub 2020 Jan 22.

Materials and Process Simulation Center (MSC) and Joint Center for Artificial Photosynthesis (JCAP) , California Institute of Technology , Pasadena , California 91125 , United States.

Two-dimensional van der Waals heterostructure materials, particularly transition metal dichalcogenides (TMDC), have proved to be excellent photoabsorbers for solar radiation, but performance for such electrocatalysis processes as water splitting to form H and O is not adequate. We propose that dramatically improved performance may be achieved by combining two independent TMDC while optimizing such descriptors as rotational angle, bond length, distance between layers, and the ratio of the bandgaps of two component materials. In this paper we apply the least absolute shrinkage and selection operator (LASSO) process of artificial intelligence incorporating these descriptors together with quantum mechanics (density functional theory) to predict novel structures with predicted superior performance. Our predicted best system is MoTe/WTe with a rotation of 300°, which is predicted to have an overpotential of 0.03 V for HER and 0.17 V for OER, dramatically improved over current electrocatalysts for water splitting.
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http://dx.doi.org/10.1021/acs.jpclett.9b03875DOI Listing
February 2020

First-Order Phase Transition in Liquid Ag to the Heterogeneous G-Phase.

J Phys Chem Lett 2020 Feb 10;11(3):632-645. Epub 2020 Jan 10.

Materials and Process Simulation Center , California Institute of Technology , Pasadena , California 91125 , United States.

A molten metal is an atomic liquid that lacks directional bonding and is free from chemical ordering effects. Experimentally, liquid metals can be undercooled by up to ∼20% of their melting temperature but crystallize rapidly in subnanosecond time scales at deeper undercooling. To address this limited metastability with respect to crystallization, we employed molecular dynamics simulations to study the thermodynamics and kinetics of the glass transition and crystallization in deeply undercooled liquid Ag. We present direct evidence that undercooled liquid Ag undergoes a first-order configurational freezing transition from the high-temperature homogeneous disordered liquid phase (L) to a metastable, heterogeneous, configurationally ordered state that displays elastic rigidity with a persistent and finite shear modulus, μ. We designate this ordered state as the G-phase and conclude it is a metastable non-crystalline phase. We show that the L-G transition occurs by nucleation of the G-phase from the L-phase. Both the L- and G-phases are metastable because both ultimately crystallize. The observed first-order transition is reversible: the G-phase displays a first-order melting transition to the L-phase at a coexistence temperature, . We develop a thermodynamic description of the two phases and their coexistence boundary.
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http://dx.doi.org/10.1021/acs.jpclett.9b03699DOI Listing
February 2020

Reply to the 'Comment on "The chemical reactions in electrosprays of water do not always correspond to those at the pristine air-water interface"' by A. J. Colussi and S. Enami, , 2019, , DOI: 10.1039/c9sc00991d.

Chem Sci 2019 Sep 23;10(35):8256-8261. Epub 2019 Jul 23.

King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia . Email:

The air-water interface serves as a crucial site for numerous chemical and physical processes in environmental science and engineering, such as cloud chemistry, ocean-atmosphere exchange, and wastewater treatment. The development of "surface-selective" techniques for probing interfacial properties of water therefore lies at the forefront of research in chemical science. Recently, researchers have adapted electrospray ionization mass spectrometry (ESIMS) to generate microdroplets of water to investigate interfacial phenomena at thermodynamic equilibrium. In contrast, using a broad set of experimental and theoretical techniques, we found that electrosprays of water could facilitate partially hydrated (gas-phase) ions (, HO·(HO)) to drive/catalyze chemical reactions that are otherwise not possible to accomplish by purely interfacial effects (, enhanced water-hydrophobe surface area) (, 2019, , 2566). Thus, techniques exploiting electrosprays of water cannot be relied upon as generalized surface-selective platforms. Here, we respond to the comments raised by Colussi & Enami (, 2019, , DOI: ; 10.1039/c9sc00991d) on our paper.
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http://dx.doi.org/10.1039/c9sc02702eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6837019PMC
September 2019

Finite-pulse waves for efficient suppression of evolving mesoscale dendrites in rechargeable batteries.

Phys Rev E 2019 Oct;100(4-1):042801

California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.

The ramified and stochastic evolution of dendritic microstructures has been a major issue on the safety and longevity of rechargeable batteries, particularly for the utilization of high-energy metallic electrodes. We analytically develop criteria for the pulse characteristics leading to the effective halting of the ramified electrodeposits grown during extensive timescales beyond inter-ionic collisions. Our framework is based on the competitive interplay between diffusion and electromigration and tracks the gradient of ionic concentration throughout the entire cycle of pulse-rest as a critical measure for heterogeneous evolution. In particular, the framework incorporates the Brownian motion of the ions and investigates the role of the geometry of the electrodeposition interface. Our experimental observations verify the analytical developments, where the dimension-free developments allows the application to the electrochemical systems of various scales.
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http://dx.doi.org/10.1103/PhysRevE.100.042801DOI Listing
October 2019

Accurate non-bonded potentials based on periodic quantum mechanics calculations for use in molecular simulations of materials and systems.

J Chem Phys 2019 Oct;151(15):154111

Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA.

Molecular dynamics simulations require accurate force fields (FFs) to describe the physical and chemical properties of complex materials and systems. FF parameters for valence interactions can be determined from high-quality Quantum Mechanical (QM) calculations. However, it has been challenging to extract long-range nonbonded interaction potentials from QM calculations since there is no unambiguous method to separate the total QM energy into electrostatics (polarization), van der Waals (vdW), and other components. Here, we propose to use density functional theory with dispersion corrections to obtain the equation of state for single element solid systems (of H, C, N, O, F, Cl, Br, I, P, He, Ne, Ar, Kr, Xe, and Rn) from which we obtain the pure 2-body vdW nonbonded potentials. Recently, we developed the polarizable charge equilibration (PQEq) model based on QM polarization energy of electric probe dipoles with no contributions from vdW. Together, the vdW and PQEq interactions form the nonbonded potential of our new transferrable reactive FF (RexPoN). They may also be useful to replace the nonbonded parts of standard FFs, such as OPLS, Amber, UFF, and CHARMM. We find that the individual 2-body vdW potential curves can be scaled to a universal vdW potential using just three specific atomic parameters. This simplifies extension to the rest of the periodic table for atoms that do not exhibit molecular packing. We validate the accuracy of these nonbonded interactions for liquid water, energetic, and biological systems. In all cases, we find that our new nonbonded potentials provide good agreement with QM and experimental data.
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http://dx.doi.org/10.1063/1.5113811DOI Listing
October 2019

Design of a One-Dimensional Stacked Spin Peierls System with Room-Temperature Switching from Quantum Mechanical Predictions.

J Phys Chem Lett 2019 Nov 9;10(21):6432-6437. Epub 2019 Oct 9.

State Key Laboratory of Materials-Oriented Chemical Engineering and College of Chemistry and Molecular Engineering , Nanjing Tech University , Nanjing 211816 , People's Republic of China.

Planar bis-1,2-dithiolene complex anions of a transition metal (denoted as [M(dithiolato)] and M = Ni, Pd, or Pt ion) favor forming columnar stacks of anions in the crystal that feature S = 1/2 spin-chains, and such a spin-chain compound often undergoes a spin-Peierls-type transition, making this a promising material for conducting and magnetic switching. However, current examples show the transition temperatures are far too low for most applications. We use quantum mechanics to predict that changing the cation arrangement from the boat-type to the chair-type packing configuration in a spin-Peierls-type [Ni(dithiolato)] complex will substantially stabilize the antiferromagnetic coupling, dramatically increasing the transition temperature. We estimate that the [Ni(mnt)]-based complexes (mnt = maleonitriledithiolate) with chair-type packing of cations will lead to critical temperatures of ∼170, ∼252, and ∼310 K for S-, Se-, and Te-based mnt, respectively. We also suggest how to stabilize the chair-type configurations of these systems.
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http://dx.doi.org/10.1021/acs.jpclett.9b02219DOI Listing
November 2019

Anomalies in Supercooled Water at ∼230 K Arise from a 1D Polymer to 2D Network Topological Transformation.

J Phys Chem Lett 2019 Oct 3;10(20):6267-6273. Epub 2019 Oct 3.

Materials and Process Simulation Center (139-74) , California Institute of Technology , Pasadena , California 91125 , United States.

Puzzling anomalous properties of water are drastically enhanced in the supercooled region. However, the nature of these anomalies is not known. We report here molecular dynamics simulations using the RexPoN force field from 298 to 200 K along the 1 atm density curve. At 298 K, there are 2.1 strong hydrogen bonds (SHBs), leading to a dynamic branched one-dimensional (1D) polymer. Water remains 1D down to 240 K, but at and below 230 K, the number of SHBs becomes 3.0, leading to a two-dimensional (2D) network that persists to 200 K. We propose that this 1D-to-2D topological transition accounts for the anomalous properties of supercooled water. Near 230 K, the power spectra show dramatic increases in the angular vibrational frequency modes, while the diffusivity decreases dramatically, both arising from the 1D-to-2D transformation. This transition is not first order because free energy changes uniformly but fluctuations in the entropy near 230 K suggest a possible second-order transition.
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http://dx.doi.org/10.1021/acs.jpclett.9b02443DOI Listing
October 2019

Reply to Head-Gordon and Paesani: Liquid water, a branched polymer with ∼100-fs short-lived heterogeneous hydrogen bonds.

Proc Natl Acad Sci U S A 2019 10 10;116(41):20257-20258. Epub 2019 Sep 10.

Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125

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http://dx.doi.org/10.1073/pnas.1913076116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789962PMC
October 2019

Interfaces and mixing: Nonequilibrium transport across the scales.

Proc Natl Acad Sci U S A 2019 09;116(37):18171-18174

Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125.

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http://dx.doi.org/10.1073/pnas.1818855116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744842PMC
September 2019