[ { "id": "authors:5twmy-cbv13", "collection": "authors", "collection_id": "5twmy-cbv13", "cite_using_url": "https://authors.library.caltech.edu/records/5twmy-cbv13", "type": "monograph", "title": "Enantioselective Michael Spirocyclization of Palladium Enolates", "author": [ { "family_name": "Strong", "given_name": "Christian S.", "orcid": "0000-0003-1349-302X", "clpid": "Strong-Christian-S" }, { "family_name": "Chen", "given_name": "Peng-Jui", "clpid": "Chen-Peng-Jui" }, { "family_name": "Bissenali", "given_name": "Sanzhar", "orcid": "0009-0009-2568-393X", "clpid": "Bissenali-Sanzhar" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "abstract": "

We report an enantio- and diastereoselective Michael spirocyclization reaction of tetrasubstituted palladium enolates. This allows for the formation of adjacent all-carbon quaternary and tertiary stereocenters in good yield, dr, and ee. Various subsequent cyclization reactions enable access to a diverse range of tricyclic scaffolds. The mechanism of this trans-formation is evaluated via quantum mechanics calculations to elucidate the origins of stereoselectivity and the mechanism of catalyst turnover.

", "doi": "10.26434/chemrxiv-2025-59lfh", "publisher": "ChemRxiv", "publication_date": "2025-03-07" }, { "id": "authors:x6vtx-82q67", "collection": "authors", "collection_id": "x6vtx-82q67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-864199000.4", "type": "monograph", "title": "Hydrodynamics Determine Tafel Slopes in Electrochemical CO\u2082 Reduction on Copper", "author": [ { "family_name": "Watkins", "given_name": "Nicholas B.", "orcid": "0000-0001-7251-9387", "clpid": "Watkins-Nicholas-B" }, { "family_name": "Schiffer", "given_name": "Zachary J.", "orcid": "0000-0001-6069-8613", "clpid": "Schiffer-Zachary-J" }, { "family_name": "Lai", "given_name": "Yungchieh", "orcid": "0000-0001-9392-1447", "clpid": "Lai-Yungchieh" }, { "family_name": "Musgrave", "given_name": "Charles B., III", "orcid": "0000-0002-3432-0817", "clpid": "Musgrave-Charles-B-III" }, { "family_name": "Atwater", "given_name": "Harry A.", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "Peters", "given_name": "Jonas", "orcid": "0000-0002-6610-4414", "clpid": "Peters-J-C" }, { "family_name": "Gregoire", "given_name": "John M.", "orcid": "0000-0002-2863-5265", "clpid": "Gregoire-J-M" } ], "abstract": "The hydrodynamics of electrochemical CO\u2082 reduction (CO\u2082) systems is an insufficiently investigated area of research that has broad implications on catalyst activity and selectivity. While most previous reports are limited to laminar and CO\u2082-sparged systems, herein we address a wide range of hydrodynamics via electrolyte recirculation systems. We find that increased hydrodynamics at the electrode surface results directly in changes to the ethylene and methane Tafel slopes, demonstrating that mass transport is on equal footing with catalyst active sites in determining reaction mechanisms and the ensuing product distribution. Mass transport is traditionally considered to be in the purview of systems-level engineering, yet the present work shows that CO\u2082R mechanistic work must be considered in the context of the mass transport conditions. We extend our analysis to organic coatings, demonstrating that the films shield the active sites from variability in hydrodynamics and increase the residence time of CO so that it may be further reduced to desirable products.", "doi": "10.26434/chemrxiv-2023-npdmn", "publication_date": "2023-03-09" }, { "id": "authors:fddph-qkq10", "collection": "authors", "collection_id": "fddph-qkq10", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-284930000.4", "type": "monograph", "title": "Prediction and experimental validation of drug candidates that bind specifically to the SARS-CoV-2 receptor-binding domain to prevent entry via Angiotensin-converting enzyme 2 (ACE2)", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Suebka", "given_name": "Sartanee", "clpid": "Suebka-Sartanee" }, { "family_name": "Gin", "given_name": "Adley", "orcid": "0000-0002-4906-8781", "clpid": "Gin-Adley-N" }, { "family_name": "Nguyen", "given_name": "Phuong-Diem", "clpid": "Nguyen-Phuong-Diem" }, { "family_name": "Tang", "given_name": "Yisha", "clpid": "Tang-Yisha" }, { "family_name": "Su", "given_name": "Judith", "orcid": "0000-0002-1005-1755", "clpid": "Su-Judith" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 (SARS-CoV-2) virus has created enormous public health and economic crises. The SARS-CoV-2 spike protein binds to its host receptor, human angiotensin-converting enzyme 2 (hACE2), through its receptor binding domain (RBD) and is proteolytically activated by human protease TMPRSS2 to process the SARS-CoV-2 spike protein to facilitate host cell entry. To identify new candidate drugs to inhibit binding of the RBD to hACE2 (the first step of virus entry), we used in silico screening (Phase VS from Schr\u04e7dinger) to predict the RBD binding site and energetics for molecules in the ZINC FDA approved Drug Bank database (1,657 drugs), which includes clinical trial drugs approved by FDA. Using a pharmacophore (1 acceptor, 1 donor, 3 negatively charged, 1 positively charged) derived from the 2.5-\u00c5 X-ray structure SARS-CoV-2 RBD complexed with hACE2 (PDB ID: 6LZG), we found 29 unique hits. To refine the binding energies and bonding sites, we applied our DarwinDock complete sampling method, predicting that 4 of these 29 should bind strongly to the RBD site. Next, we tested 3 of these experimentally using FLOWER, a label-free optical whispering gallery mode sensing technique that can measure ligand-receptor binding affinities down to attomolar levels. We measure that methotrexate (MTX) and Diethylenetriamine pentaacetate (DTPA) bind with an inhibitory constant (Ki) of 0.2 pM in Tricine buffer, which is 1.832 million fold increase in binding strength compared to hACE2 (Kd: 366.4 nM). We then tested these ligands against common mutations: alpha, delta, and omicron. Our measured binding studies demonstrate that MTX provides inhibition against all four variants of SARS-coV-2. Indeed, the clinical and experimental data have shown that humans taking WT MTX are protected against infection by SARS-CoV-2.", "doi": "10.26434/chemrxiv-2022-nrhzz", "publication_date": "2022-12-21" }, { "id": "authors:5h0cv-hev08", "collection": "authors", "collection_id": "5h0cv-hev08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-457152000.11", "type": "monograph", "title": "Improving Molecular Catalyst Activity using Strain-Inducing Carbon Nanotube Supports", "author": [ { "family_name": "Su", "given_name": "Jianjun", "clpid": "Su-Jianjun" }, { "family_name": "Musgrave", "given_name": "Charles B., III", "orcid": "0000-0002-3432-0817", "clpid": "Musgrave-Charles-B-III" }, { "family_name": "Song", "given_name": "Yun", "clpid": "Song-Yun" }, { "family_name": "Huang", "given_name": "Libei", "clpid": "Huang-Libei" }, { "family_name": "Liu", "given_name": "Yong", "clpid": "Liu-Yong" }, { "family_name": "Li", "given_name": "Geng", "clpid": "Li-Geng" }, { "family_name": "Xin", "given_name": "Yinger", "clpid": "Xin-Yinger" }, { "family_name": "Xiong", "given_name": "Pei", "clpid": "Xiong-Pei" }, { "family_name": "Li", "given_name": "Molly Meng-Jung", "clpid": "Li-Molly-Meng-Jung" }, { "family_name": "Chen", "given_name": "Hao Ming", "clpid": "Chen-Hao-Ming" }, { "family_name": "Tang", "given_name": "Ben Zhong", "clpid": "Tang-Ben-Zhong" }, { "family_name": "Robert", "given_name": "Marc", "clpid": "Robert-Marc" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Ye", "given_name": "Ruquan", "orcid": "0000-0002-2543-9090", "clpid": "Ye-Ruquan" } ], "abstract": "Support-induced strain engineering is a powerful strategy to modulate the electronic structure of two-dimensional materials. However, controlling strain of planar molecules such as metallophthalocyanines and metalloporphyrins is technically challenging due to their sub\u20132 nm lateral size. In addition, the effect of strain on molecular properties remains poorly understood. Starting with cobalt phthalocyanine (CoPc), a model CO\u2082 reduction reaction (CO\u2082RR) catalyst, we show that carbon nanotubes (CNTs) are ideal substrates for inducing optimum properties through molecular curvature. Using a tandem-flow electrolyzer with monodispersed CoPc on single-walled CNTs (CoPc/SWCNT) as the catalyst, we achieve a methanol partial current density of >90 mA cm\u207b\u00b2 with a selectivity of >60%. CoPc on wide multi-walled CNTs (MWCNTs) leads to only 16.6% selectivity. We report X-ray spectroscopic characterizations to unravel the distinct local coordinations and electronic structures induced by the strong molecule-support interactions. These results agree with our Grand Canonical Density Functional Theory that calculates the energetics as a function of applied potential. We find that SWCNTs induce curvature in CoPc, which improves *CO binding to enable subsequent formation of methanol, while wide MWCNTs favor CO desorption. Thus, we demonstrate that the SWCNT-induced molecular strain increases methanol formation. We also show that induced strain can accelerate the oxygen reduction reaction and CO2RR for other catalysts. Our results show the important role of SWCNTs beyond catalyst dispersion and electron conduction.", "doi": "10.26434/chemrxiv-2022-r9r22", "publication_date": "2022-12-20" }, { "id": "authors:30z0h-9s741", "collection": "authors", "collection_id": "30z0h-9s741", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-7248000.5", "type": "monograph", "title": "Understanding pH within a nanoscopic water pool", "author": [ { "family_name": "Li", "given_name": "Sirui", "clpid": "Li-Sirui" }, { "family_name": "Kwon", "given_name": "Soonho", "orcid": "0000-0002-9225-3018", "clpid": "Kwon-Soonho" }, { "family_name": "Goddard", "given_name": "W. A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Houle", "given_name": "Frances A.", "orcid": "0000-0001-5571-2548", "clpid": "Houle-Frances-A" } ], "abstract": "The nature of pH within a water pool that is too small to have a constant population of ions formed by water dissociation is a long-standing question. The breakdown of the conventional pH definition is due to the rare and intermittent presence of ion pairs (H\u207a and OH\u207b) in these pools, leading to pH = -log\u2081\u2080 (0). To characterize water ion pair lifetimes and populations in such systems, we have performed a set of stochastic kinetics simulations of the water dissociation reaction in pools ranging from 10\u00b3 to 10\u00b9\u2070 waters. We extract a kinetically derived availability coefficient, \u03b1_(i>0), as a suitable parameter to quantify the intermittent presence of a number i of ion pairs during an observation period. In this way, pH in confinement is intrinsically connected with the transient ion pair lifetimes and the stochastics associated with their formation. We propose that \u03b1_(i>0) is equivalent to an activity coefficient, and use \u03b1_(i>0) along with the thermodynamic definition of pH to estimate an effective pH for a nanoscopic H\u2082 O pool. As the availability coefficient quickly converges to 1 for pool containing well over 5 \u00d7 10\u2079 waters, the effective pH converges to the pure water bulk pH of 7. The implications of the effective pH concept for confined aqueous environments are discussed.", "doi": "10.26434/chemrxiv-2022-bjdlh", "publication_date": "2022-09-27" }, { "id": "authors:qhrkw-mna52", "collection": "authors", "collection_id": "qhrkw-mna52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220805-540001000", "type": "monograph", "title": "Behavior of hydrogarnet-type defects in hydrous stishovite at various temperatures and pressures", "author": [ { "family_name": "Palfey", "given_name": "William R.", "orcid": "0000-0002-9555-7877", "clpid": "Palfrey-William-R" }, { "family_name": "Rossman", "given_name": "George R.", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Goddard III", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Dense polymorphs of silica have been demonstrated experimentally to incorporate from 1.5% to as much as 11.6% weight percent H\u2082O as OH groups, with implications for the hydrogen budgets of Earth and other planets. This OH is thought to enter the SiO\u2082 structure via a charge-balanced substitution in which silicon vacancies (V_(Si)) are compensated by protonating four of the surrounding six oxygen atoms, often referred to as a hydrogarnet-type defect. There are many possible configurations for this defect structure in dense silica, but the nature of these configurations and whether they can be distinguished experimentally is unknown. We present here density functional theory (DFT) calculations that systematically assess the possible configurations of a hydrogarnet-type defect in stishovite (rutile-type SiO\u2082), with direct comparisons to experimental vibrational spectroscopy data. We predict that stishovite synthesized at 450K and 10 GPa quenched to room temperature is dominated by a single defect type with tetrahedral geometry. This leads to OH stretching modes (2500-3000 cm\u207b\u00b9) and SiOH bending modes (~1400 to 1450 cm\u207b\u00b9) largely consistent with experimentally observed modes. One remaining issue is that our calculations produce results compatible with experimental data on H to D exchange, but do not explain why a considerable fraction of the 1420 cm\u207b\u00b9 mode shifts by only 40 cm\u207b\u00b9 in deuterated samples. At elevated pressures and temperatures, we find that a second square planar defect configuration also becomes favorable, leading to modes that should allow differentiation from the tetrahedral configuration.", "doi": "10.1002/essoar.10512070.1", "publication_date": "2022-08-05" }, { "id": "authors:g5ns4-9rc08", "collection": "authors", "collection_id": "g5ns4-9rc08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220707-204114065", "type": "monograph", "title": "Multivalent optical cycling centers in polyatomic molecules", "author": [ { "family_name": "Yu", "given_name": "Phelan", "orcid": "0000-0002-3715-9133", "clpid": "Yu-Phelan" }, { "family_name": "Lopez", "given_name": "Adrian", "clpid": "Lopez-Adrian-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hutzler", "given_name": "Nicholas R.", "orcid": "0000-0002-5203-3635", "clpid": "Hutzler-N-R" } ], "abstract": "Optical control of polyatomic molecules promises new opportunities in precision metrology, fundamental chemistry, quantum information, and many-body science. Contemporary experimental and theoretical efforts have mostly focused on cycling photons via excitation of a single electron localized to an alkaline earth (group 2)-like metal center. In this manuscript, we consider pathways towards optical cycling in polyatomic molecules with multi-electron degrees of freedom, which arise from two or more cycling electrons localized to p-block post-transition metal and metalloid (group 13, 14, and 15) centers. We characterize the electronic structure and rovibrational branching of several prototypical candidates using ab initio quantum chemical methods. Despite increased internal complexity and challenging design parameters, we find several molecules possessing quasi-closed photon cycling schemes with highly diagonal, visible and near-infrared transitions. Furthermore, we identify new heuristics for engineering optically controllable and laser-coolable polyatomic molecules with multi-electron cycling centers. Our results help elucidate the interplay between hybridization, repulsion, and ionicity in optically active species and provide a first step towards using polyatomic molecules with complex electronic structure as a resource for quantum science and measurement.", "doi": "10.48550/arXiv.arXiv.2205.11860", "publisher": "arXiv", "publication_date": "2022-05-24" }, { "id": "authors:92zn0-wek82", "collection": "authors", "collection_id": "92zn0-wek82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-503348000.1", "type": "monograph", "title": "Understanding hydrogen electrocatalysis by probing the hydrogen-bond network of water at the electrified Pt/solution interface", "author": [ { "family_name": "Sun", "given_name": "Qiang", "orcid": "0000-0002-4589-8040", "clpid": "Sun-Qiang" }, { "family_name": "Oliveira", "given_name": "Nicholas J.", "clpid": "Oliveira-Nicholas-J" }, { "family_name": "Kwon", "given_name": "Soonho", "orcid": "0000-0002-9225-3018", "clpid": "Kwon-Soonho" }, { "family_name": "Tyukhtenko", "given_name": "Sergiy", "orcid": "0000-0002-0446-9979", "clpid": "Tyukhtenko-Sergiy" }, { "family_name": "Guo", "given_name": "Jason J.", "clpid": "Guo-Jason J." }, { "family_name": "Myrthil", "given_name": "Nathalie", "clpid": "Myrthil-Nathalie" }, { "family_name": "Lopez", "given_name": "Steven A.", "orcid": "0000-0002-8418-3638", "clpid": "Lopez-Steven-A" }, { "family_name": "Kendrick", "given_name": "Ian", "clpid": "Kendrick-Ian" }, { "family_name": "Mukerjee", "given_name": "Sanjeev", "orcid": "0000-0002-2980-7655", "clpid": "Mukerjee-Sanjeev" }, { "family_name": "Ma", "given_name": "Lu", "orcid": "0000-0001-9646-0738", "clpid": "Ma-Lu" }, { "family_name": "Ehrlich", "given_name": "Steven N.", "orcid": "0000-0002-4570-8833", "clpid": "Ehrlich-Steven-N" }, { "family_name": "Li", "given_name": "Jingkun", "clpid": "Li-Jingkun" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Yan", "given_name": "Yushan", "orcid": "0000-0001-6616-4575", "clpid": "Yan-Yushan" }, { "family_name": "Jia", "given_name": "Qingying", "orcid": "0000-0002-4005-8894", "clpid": "Jia-Qingying" } ], "abstract": "A grand challenge in electrochemistry is to understand and promote electrochemical processes by exploring and exploiting the interface. Herein, we promoted the hydrogen evolution and oxidation reactions (HER/HOR) of platinum in base by employing N-methylimidazoles to reorientate interfacial water against the interfacial electric field as evidenced by in situ spectroscopic characterization of the interface. We accordingly established a unified mechanism by which the HER/HOR in acid and base proceeds via diffusion of proton and hydroxide, respectively, through interface via interfacial water by the Grotthuss mechanism. This mechanism accounts for the pH-dependent HER/HOR kinetics of platinum, a long-standing puzzle. Furthermore, we demonstrated 40% performance improvement of an anion exchange membrane electrolyzer by adding 1,2-dimethylimidazole into the alkaline solution fed into its Pt cathode.", "doi": "10.26434/chemrxiv-2021-gks2k", "publication_date": "2022-02-01" }, { "id": "authors:p1a52-w7j03", "collection": "authors", "collection_id": "p1a52-w7j03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211209-231124000", "type": "monograph", "title": "Stereochemical engineering of a peptide macrocycle allosteric inhibitor of phospho-Akt2 controls cell penetration by fine-tuning macrocycle-cell membrane interactions", "author": [ { "family_name": "Nag", "given_name": "Arundhati", "orcid": "0000-0002-1328-1695", "clpid": "Nag-Arundhati" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Das", "given_name": "Samir", "clpid": "Das-Samir" }, { "family_name": "Yu", "given_name": "Mary Beth", "clpid": "Yu-Mary-Beth" }, { "family_name": "Alvarez-Villalonga", "given_name": "Belen", "clpid": "Alvarez-Villalonga-Belen" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "We report the development of a cell-penetrant cyclic loop biligand that selectively binds, in vitro, to the phosphorylated Ser474 site of Protein Kinase B (p-Akt2) with high affinity (K_D = 10 nM). The cyclic loop biligand consists of a linear peptide joined to a macrocycle peptide through triazole linkage, and it was isolated through two iterative in situ screens. This biligand allosterically inhibited kinase activity of Akt2 but it was cell-impermeable, as isolated from the screening process. Since Akt2 is an oncoprotein hyperactivated via phosphorylation at Ser474 in cancers, we sought to visualize p-Akt2 in live cancer cells using the developed biligand. To this end, we matured this biligand into a cell-penetrant reagent through systematic iterations of its chemical structure to promote cell-penetrating properties, while retaining its binding and inhibition for p-Akt2. Two retro-inverso, N-methylated versions of the macrocyclic ligand were developed which were uptaken by live cancer cells, while retaining their high affinities for pAkt2. Interestingly, the stereochemistry of two amino acid residues in the cell-penetrant ligands exhibited strong influence on their extent of cell penetration. This phenomenon of difference in cell penetration was explored through metadynamics simulations of each ligand in the cell membrane. It was found that the ligand uptaken to a greater extent by cells had more intramolecular interactions with itself and had fewer cholesterol molecules associated with it, which aided in its cell-penetration.", "doi": "10.26434/chemrxiv-2021-kldh7", "publication_date": "2021-11-24" }, { "id": "authors:er2r3-g6p27", "collection": "authors", "collection_id": "er2r3-g6p27", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190522-205136353", "type": "monograph", "title": "Stability and flow fields structure for interfacial dynamics with interfacial mass flux", "author": [ { "family_name": "Ilyin", "given_name": "Daniil V.", "clpid": "Ilyin-D-V" }, { "family_name": "Fukumoto", "given_name": "Yasuhide", "clpid": "Fukumoto-Yasuhide" }, { "family_name": "Anisimov", "given_name": "Sergei I.", "clpid": "Anisimov-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Abarzhi", "given_name": "Snezhana I.", "clpid": "Abarzhi-S-I" } ], "abstract": "We analyze from a far field the evolution of an interface that separates ideal incompressible fluids of different densities and has an interfacial mass flux. We develop and apply the general matrix method to rigorously solve the boundary value problem involving the governing equations in the fluid bulk and the boundary conditions at the interface and at the outside boundaries of the domain. We find the fundamental solutions for the linearized system of equations, and analyze the interplay of interface stability with flow fields structure, by directly linking rigorous mathematical attributes to physical observables. New mechanisms are identified of the interface stabilization and destabilization. We find that interfacial dynamics is stable when it conserves the fluxes of mass, momentum and energy. The stabilization is due to inertial effects causing small oscillations of the interface velocity. In the classic Landau dynamics, the postulate of perfect constancy of the interface velocity leads to the development of the Landau-Darrieus instability. This destabilization is also associated with the imbalance of the perturbed energy at the interface, in full consistency with the classic results. We identify extreme sensitivity of the interface dynamics to the interfacial boundary conditions, including formal properties of fundamental solutions and qualitative and quantitative properties of the flow fields. This provides new opportunities for studies, diagnostics, and control of multiphase flows in a broad range of processes in nature and technology.", "doi": "10.48550/arXiv.1901.04575", "publication_date": "2019-01-14" }, { "id": "authors:40qt8-hh505", "collection": "authors", "collection_id": "40qt8-hh505", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-456755000.1", "type": "monograph", "title": "Effects of Solvent-Salt Charge-Transfer Complexes on Oxidative Stability of Li-Ion Battery Electrolytes", "author": [ { "family_name": "Fadel", "given_name": "Eric R.", "clpid": "Fadel-Eric-R" }, { "family_name": "Faglioni", "given_name": "Francesco", "orcid": "0000-0002-3327-8848", "clpid": "Faglioni-Francesco" }, { "family_name": "Samsonidze", "given_name": "Georgy", "orcid": "0000-0002-3759-1794", "clpid": "Samsonidze-Georgy-C" }, { "family_name": "Molinari", "given_name": "Nicola", "orcid": "0000-0002-2913-7030", "clpid": "Molinari-Nicola" }, { "family_name": "Merinov", "given_name": "Boris V.", "orcid": "0000-0002-2783-4262", "clpid": "Merinov-Boris-V" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grossman", "given_name": "Jeffrey C.", "orcid": "0000-0003-1281-2359", "clpid": "Grossman-Jeffrey-C" }, { "family_name": "Mailoa", "given_name": "Jonathan P.", "orcid": "0000-0003-2239-6192", "clpid": "Mailoa-Jonathan-P" }, { "family_name": "Kozinsky", "given_name": "Boris", "orcid": "0000-0002-0638-539X", "clpid": "Kozinsky-Boris" } ], "abstract": "Electrochemical stability windows of electrolytes largely determine the limitations of operating regimes and energy density of Li-ion batteries but the controlling degradation mechanisms are difficult to characterize and remain poorly understood. We investigate the oxidative decomposition mechanisms governing high voltage stability of multi-component organic electrolytes using computational techniques of quantum chemistry. The intrinsic oxidation potential is modeled using vertical ionization potentials (IP) of ensembles of anion-solvent clusters generated using molecular dynamics. In some cases, the IP of the solvent-anion complex is significantly lower than that of each individual component. This effect is found to originate from the oxidation-driven charge transfer complex formation between the anion and the solvent. We propose a simple model to quantitatively understand this phenomenon and validate it for 16 combinations of common anions (4,5-dicyano-2-(trifluoromethyl)imidazolium, bis-(trifluoromethane solfonimmide), tetrafluroborate, hexafluorophosphate) and solvents (dimethyl sulfoxide, dimethoxyethane, propylene carbonate, acetonitrile). This new understanding of the microscopic details of oxidation allows us to interpret trends in published experimental and computational results and to formulate design rules for rapidly assessing stability of electrolyte compositions.", "doi": "10.26434/chemrxiv.6889160.v1", "publication_date": "2018-08-21" }, { "id": "authors:kyrzx-29p78", "collection": "authors", "collection_id": "kyrzx-29p78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160705-130213482", "type": "monograph", "title": "Percolation structure in metallic glasses and liquids", "author": [ { "family_name": "Chen", "given_name": "David Z.", "clpid": "Chen-David-Z" }, { "family_name": "An", "given_name": "Qi", "orcid": "0000-0003-4838-6232", "clpid": "An-Qi" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" } ], "abstract": "The atomic-level structures of liquids and glasses are similar, obscuring any structural basis for the glass transition. To delineate structural differences between them, we characterized the atomic structures using the integrated radial distribution functions (RDF) from molecular dynamics (MD) simulations for several metallic liquids and glasses: Cu_(46)Zr_(54), Ni_(80)Al_(20),\nNi_(33.3)Zr_(66.7), and Pd_(82)Si_(18). We find that the integrated RDF leads to cumulative coordination numbers (CN) that are similar for all four metallic glasses and for all four liquids, but are consistently different between the liquid and glass phases. We find that metallic liquids have a fractal dimension of df = 2.54 \u00b1 0.06 from the center atom to the first coordination shell whereas the metallic glasses have d_f = 2.66 \u00b1 0.04, which suggests the development of weak ordering during the glass transition. Beyond the second coordination shell, the CN indicates a dimension of d = 3 as for a crystal. Crossovers in dimension from d_f~2.54-2.66 to d = 3 between the first and second coordination shells imply an underlying percolation structure in metallic liquids and glasses.", "doi": "10.48550/arXiv.1601.02057", "publication_date": "2016-01-09" }, { "id": "authors:94ajb-vxa28", "collection": "authors", "collection_id": "94ajb-vxa28", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190702-100203558", "type": "monograph", "title": "Equivalent electric circuit of a carbon nanotube based molecular conductor", "author": [ { "family_name": "Yam", "given_name": "ChiYung", "clpid": "Yam-ChiYung" }, { "family_name": "Mo", "given_name": "Yan", "clpid": "Mo-Yan" }, { "family_name": "Wang", "given_name": "Fan", "clpid": "Wang-Fan" }, { "family_name": "Li", "given_name": "Xiaobo", "clpid": "Li-Xiaobo" }, { "family_name": "Chen", "given_name": "Guanhua", "clpid": "Chen-Guanhua" }, { "family_name": "Zheng", "given_name": "Xiao", "clpid": "Zheng-Xiao" }, { "family_name": "Matsuda", "given_name": "Yuki", "clpid": "Matsuda-Yuki" }, { "family_name": "Tahir-Kheli", "given_name": "Jamil", "clpid": "Tahir-Kheli-J" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "We apply our first-principles method to simulate the transient electrical response through carbon nanotube based conductors under time-dependent bias voltages, and report the dynamic conductance for a specific system. We find that the electrical response of the carbon nanotube device can be mapped onto an equivalent classical electric circuit. This is confirmed by studying the electric response of a simple model system and its equivalent circuit.", "doi": "10.48550/arXiv.0801.3914", "publisher": "arXiv", "publication_date": "2008-01-25" }, { "id": "authors:zechb-q7g14", "collection": "authors", "collection_id": "zechb-q7g14", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190702-100852563", "type": "monograph", "title": "First Principles Force Field for Metallic Tantalum", "author": [ { "family_name": "Strachan", "given_name": "Alejandro", "orcid": "0000-0002-4174-9750", "clpid": "Strachan-Alejandro" }, { "family_name": "\u00c7a\u011fin", "given_name": "Tahir", "orcid": "0000-0002-3665-0932", "clpid": "\u00c7a\u011fin-T" }, { "family_name": "G\u00fclseren", "given_name": "O\u011fuz", "clpid": "G\u00fclseren-O\u011fuz" }, { "family_name": "Mukherjee", "given_name": "Sonali", "clpid": "Mukherjee-Sonali" }, { "family_name": "Cohen", "given_name": "Ronald E.", "orcid": "0000-0001-5871-2359", "clpid": "Cohen-R-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "We propose a general strategy to develop accurate Force Fields (FF) for metallic systems derived from ab initio quantum mechanical (QM) calculations; we illustrate this approach for tantalum. As input data to the FF we use the linearized augmented plane wave method (LAPW) with the generalized gradient approximation (GGA) to calculate: (i) the zero temperature equation of state (EOS) of Ta for bcc, fcc, and hcp crystal structures for pressures up to ~500 GPa. (ii) Elastic constants. (iii) We use a mixed-basis pseudopotential code to calculate volume relaxed vacancy formation energy also as a function of pressure. In developing the Ta FF we also use previous QM calculations of: (iv) the equation of state for the A15 structure. (v) the surface energy bcc (100). (vi) energetics for shear twinning of the bcc crystal. We find that withappropriate parameters an embedded atom model force field (denoted as qEAM FF) is able to reproduce all this QM data. Thus, the same FF describes with good accuracy the bcc, fcc, hcp and A15 phases of Ta for pressures from ~ -10 GPa to ~ 500 GPa, while also describing the vacancy, surface energy, and shear transformations. The ability of this single FF to describe such a range of systems with a variety of coordinations suggests that it would be accurate for describing defects such as dislocations, grain boundaries, etc. \nWe illustrate the use of the qEAM FF with molecular dynamics to calculate such finite temperature properties as the melting curve up to 300 GPa; we obtain a zero pressure melting temperature of T_(melt)=3150 +/- 50 K in good agreement with experiment (3213-3287 K). We also report on the thermal expansion of Ta in a wide temperature range; our calculated thermal expansivity agrees well with experimental data.", "doi": "10.48550/arXiv.0208027", "publication_date": "2002-08-01" }, { "id": "authors:m0p7y-jsw88", "collection": "authors", "collection_id": "m0p7y-jsw88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230210-354927000.2", "type": "monograph", "title": "A Multiscale Approach for Modeling Crystalline Solids", "author": [ { "family_name": "Cuiti\u00f1o", "given_name": "A. M.", "orcid": "0000-0002-5180-9147", "clpid": "Cuiti\u00f1o-Alberto-M" }, { "family_name": "Stainier", "given_name": "L.", "orcid": "0000-0001-6719-6616", "clpid": "Stainier-Laurent" }, { "family_name": "Wang", "given_name": "G.", "orcid": "0000-0001-8249-4101", "clpid": "Wang-Guofeng" }, { "family_name": "Strachan", "given_name": "A.", "orcid": "0000-0002-4174-9750", "clpid": "Strachan-Alejandro" }, { "family_name": "\u00c7a\u011fin", "given_name": "T.", "orcid": "0000-0002-3665-0932", "clpid": "\u00c7a\u011fin-Tahir" }, { "family_name": "Goddard", "given_name": "W. A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Ortiz", "given_name": "M.", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" } ], "abstract": "In this paper we present a modeling approach to bridge the atomistic with macroscopic scales in crystalline materials. The methodology combines identification and modeling of the controlling unit processes at microscopic level with the direct atomistic determination of fundamental material properties. These properties are computed using a many body Force Field derived from ab initio quantum-mechanical calculations. This approach is exercised to describe the mechanical response of high-purity Tantalum single crystals, including the effect of temperature and strain-rate on the hardening rate. The resulting atomistically informed model is found to capture salient features of the behavior of these crystals such as: the dependence of the initial yield point on temperature and strain rate; the presence of a marked stage I of easy glide, specially at low temperatures and high strain rates; the sharp onset of stage II hardening and its tendency to shift towards lower strains, and eventually disappear, as the temperature increases or the strain rate decreases; the parabolic stage II hardening at low strain rates or high temperatures; the stage II softening at high strain rates or low temperatures; the trend towards saturation at high strains; the temperature and strain-rate dependence of the saturation stress; and the orientation dependence of the hardening rate.", "publisher": "Caltech Library", "publication_date": "2001" }, { "id": "authors:rx3ef-rng15", "collection": "authors", "collection_id": "rx3ef-rng15", "cite_using_url": "https://resolver.caltech.edu/CaltechASCI:1999.033", "type": "monograph", "title": "The 1999 Center for Simulation of Dynamic Response in Materials Annual Technical Report", "author": [ { "family_name": "Aivazis", "given_name": "Michael", "clpid": "Aivazis-Michael-A-G" }, { "family_name": "Goddard", "given_name": "Bill", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Meiron", "given_name": "Dan", "orcid": "0000-0003-0397-3775", "clpid": "Meiron-D-I" }, { "family_name": "Ortiz", "given_name": "Michael", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Pool", "given_name": "James C. T.", "clpid": "Pool-James-C-T" }, { "family_name": "Shepherd", "given_name": "Joe", "orcid": "0000-0003-3181-9310", "clpid": "Shepherd-J-E" } ], "abstract": "Introduction: \nThis annual report describes research accomplishments for FY 99 of the Center\nfor Simulation of Dynamic Response of Materials. The Center is constructing a\nvirtual shock physics facility in which the full three dimensional response of a\nvariety of target materials can be computed for a wide range of compressive, ten-\nsional, and shear loadings, including those produced by detonation of energetic\nmaterials. The goals are to facilitate computation of a variety of experiments\nin which strong shock and detonation waves are made to impinge on targets\nconsisting of various combinations of materials, compute the subsequent dy-\nnamic response of the target materials, and validate these computations against\nexperimental data.", "publisher": "Caltech Library", "publication_date": "1999-01-01" }, { "id": "authors:sz75e-ve313", "collection": "authors", "collection_id": "sz75e-ve313", "cite_using_url": "https://resolver.caltech.edu/CaltechASCI:1998.032", "type": "monograph", "title": "The 1998 Center for Simulation of Dynamic Response in Materials Annual Technical Report", "author": [ { "family_name": "Goddard", "given_name": "W. A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Meiron", "given_name": "D. I.", "orcid": "0000-0003-0397-3775", "clpid": "Meiron-D-I" }, { "family_name": "Ortiz", "given_name": "M.", "orcid": "0000-0001-5877-4824", "clpid": "Ortiz-M" }, { "family_name": "Shepherd", "given_name": "J. E.", "orcid": "0000-0003-3181-9310", "clpid": "Shepherd-J-E" } ], "abstract": "Introduction: \nThis annual report describes research accomplishments for FY 98 of the Center for Simulation\nof Dynamic Response of Materials. The Center is constructing a virtual shock physics facility\nin which the full three dimensional response of a variety of target materials can be computed\nfor a wide range of compressive, tensional, and shear loadings, including those produced by\ndetonation of energetic materials. The goals are to facilitate computation of a variety of\nexperiments in which strong shock and detonation waves are made to impinge on targets\nconsisting of various combinations of materials, compute the subsequent dynamic response\nof the target materials, and validate these computations against experimental data.", "publisher": "Caltech Library", "publication_date": "1998-01-01" } ]