Repository of works by Caltech published authors.
Type = Conference or Workshop Item
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Droplet Breakup in High-Speed Gas Flows - Meng, Jomela C.; Colonius, Tim
Numerical simulations are performed to study the breakup of water cylinders in the flow behind normal shocks. The computational setup is similar to previous experiments (Igra and Takayama, 2001, 2003). We examine the qualitative features of the so-called stripping breakup observed in the numerical results. Two interesting flow features are discussed: the existence of recirculation regions and an upstream jet in the wake. Various integral quantities associated with the cylinder’s deformation and acceleration are computed and compared with the experimental results, with generally good agreement. Furthermore, calculations of the velocity and acceleration of the cylinder’s center of mass provide an...
Natural and non-canonical mutagenesis studies of receptor gating in 5-HT3A receptors - Mosesso, Richard; Lummis, Sarah C. R.; Dougherty, Dennis A.
The 5-HT_(3A) receptor is a homopentameric ligand-gated ion channel belonging to the Cys-loop family of receptors, members
of which have many functions and are important targets for a variety of diseases. Previously, our lab has elucidated key
binding interactions between these receptors and their ligands. However, the "gating" events that link binding of ligand to
receptor activation are less well characterized. While obtaining high-resoln. crystal structures of transmembrane proteins can
be difficult, a recent crystal structure of the mouse 5-HT_(3A) receptor has guided our search for intramol. interactions involved in
gating. Focusing on regions identified to be important for gating in homologous receptors, we have...
Evidence for in situ catalyst modification in atom transfer radical reactions with ruthenium benzylidene complexes - Lee, Juneyoung; Grandner, Jessica M.; Engle, Keary; Houk, Kendall N.; Grubbs, Robert H.
Since the first report of ruthenium- based catalysts in atom transfer radical addn. (ATRA, also called Kharasch addn.) and
atom transfer radical polymn. (ATRP) , this area of research has attracted widespread interest. Well- defined ruthenium
benzylidene complexes, commonly used as olefin metathesis catalysts, have also been reported to catalyze ATRA and ATRP.
The ability of ruthenium benzylidene complexes to promote two reactions with such markedly different mechanisms has
been utilized in various tandem reactions in which olefin metathesis and atom transfer radical (ATR) reactions take place
in one pot. While the mechanism by which ruthenium benzylidenes initiate and catalyze olefin metathesis has been studied...
Mechanistic investigation of proton reduction by cobaloximes: Insight from H2 oxidation kinetics - Del Ciello, Sarah A.; Winkler, Jay R.; Peters, Jonas C.; Gray, Harry B.
Cobaloximes are a class of earth- abundant proton redn. catalysts that have been known since the 1980's. Previous studies
have come to conflicting conclusions about the mechanism of proton redn. by these catalysts, with evidence existing for both a
homolytic and heterolytic mechanism. In this work, kinetic anal. of the reverse reaction is used to gain further insight.
Cation-π interactions: Computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation of cys-loop receptors and related structures - Davis, Matthew R.; Dougherty, Dennis A.
Cation-π interactions are common in biol. systems, in particular ligand- gated ion channels (LGICs). Our own studies, in addn.
to more recent structural studies, have revealed the arom. box as a common motif for binding cationic ligands. With the aim
of understanding the nature of the arom. box, several computational methods were evaluated for their ability to reproduce
exptl. cation-π binding energies. We find the DFT method M06 with the 6-31G(d, p) basis set performs best of several methods
tested. The binding of benzene to a no. of different cations (sodium, potassium, ammonium, tetramethylammonium, and
guanidinium) was studied. In addn., the binding of the org....
Chemically specific dynamic bond percolation model for computational screening of polymer electrolytes - Webb, Michael; Savoie, Brett; Wang, Zhen-Gang; Miller, Thomas
Polymer electrolytes have significant promise for many lithium-ion battery applications because they are non-flammable,
electrochem. stable, and easily manufd. However, significant improvements in the ionic cond. of even state- of-the-art polymer
electrolytes is needed for technol. viability. The computationally- guided design of more conductive polymer electrolytes
would save significant time and monetary resources, but these efforts require both a better understanding of ion- transport
mechanisms in polymers and the development of tools for screening candidate polymers prior to synthesis and
characterization. Using atomistic mol. dynamics (MD) simulations, we provide new insights into the mechanisms of lithium-ion
diffusion in polymer electrolyte materials, including that the spatial distribution...
Reduction of CO2 on Cu and Au/W electrode surfaces: A study by differential electrochemical mass spectrometry - Javier, Alnald; Baricuatro, Jack; Kim, Youn-Geun; Soriaga, Manuel
This work describes results from an attempt to employ differential electrochem. mass spectrometry (DEMS) of selectively pre-adsorbed reactants and (postulated) intermediates as a supplementary exptl. approach in the study of the reaction
mechanism of the Cu-catalyzed electrochem. redn. of CO2. The results prompt the following empirical inferences: (i) CO is the
first product of CO2 redn., as well as the first intermediate in more advanced reactions that include formation of pure and
oxygenated hydrocarbons; this is in conformity with the (almost) unanimously held view. (ii) HCHO is not a precursor for C=C
double-bond formation. (iii) HCHO is an intermediate for the prodn. of methane...
Observation and reactivity studies of an unusual RhI intermediate in H2 evolution catalysis - Aguirre Quintana, Luis; Gray, Harry; Winkler, Jay; Blakemore, James
Understanding mechanisms of hydrogen evolution is important for improving catalysts that generate clean fuels. Catalysts
often operate via unknown mechanism(s) due to the difficulty of observing or isolating key intermediates in the 2e-/2H+ redn.
process. For our study, we prepd. a family of RhI complexes bearing the pentamethylcyclopentadienyl (η5-Cp*) ligand in
addn. to derivs. of 4,4'- bipyridyl or 1,10- phenanthroline (bound in the κ2 mode). Under carefully chosen conditions, these
compds. formed intermediate species that suggest a previously unknown mechanism of H2 evolution involving protonhydride
tautomerism driven by the Cp* ligand. This intermediate complex could be isolated in a MeCN soln., and even as a
Effects of the μ4-bridging atom in a tetranuclear iron cluster on the activation of nitric oxide - Reed, Christopher; Agapie, Theodor
A series of tetrairon μ_4-fluoride clusters, [LFe_3F(PhPz)_3Fe][OTf]_n (n=1-3), was synthesized using the previously reported 1,3,5-
triarylbenzene framework, a multinucleating ligand contg. pyridine and alkoxide donors, which bind three of the four metal
centers. These three metal sites contain six-coordinate iron atoms. 3-phenyl-pyrazolate ligands (PhPz) bridge the triiron core
to a four-coordinate, site-differentiated iron center. These clusters have notably different redox properties than the closely
related μ_4-oxo analogs, [LFe_3O(PhPz)_3Fe][OTf]_n (n=0-3). While for [LFe_3O(PhPz)_3Fe][OTf]_2 three reversible redox events are
obsd. at -1.73 V (vs. Fc /Fc+), -0.72 V, and +0.02 V (Fe^(II)_4 Fe^(II)Fe^(III)_3), only two redox events are obsd. for the fluoride-bridged
cluster, [LFe_3F(PhPz)_3Fe][OTf], at -0.52 V (Fe^(II)_4...
Scalable models of ion transport for electrolyte materials discovery - Savoie, Brett M.; Miller, Thomas F.
Solid polymeric electrolytes have the potential to greatly improve battery efficiency and stability, but ions like Li simply diffuse
too slowly in current materials for them to be viable. The challenge for computationally designing new polymers lies in
accurately modeling both the long- timescale of ion transport and the chem. specific ion- polymer couplings that govern ion
motion. In this talk, I will show how short atomistic simulations can be combined with a generalizable mesoscopic ion
transport model to reliably predict ion diffusivity across many chem. classes of polymers. This model has now been used to
characterize several hundred new materials and the talk will...
Probing binding interactions of agonists at a nicotinic acetylcholine receptor subtype important to addiction and Parkinson's disease - Post, Michael R.; Lester, Henry; Dougherty, Dennis A.
Nicotine addiction is still a major problem in American society. Sixteen percent of adults report smoking regularly, resulting in
96 billion dollars in healthcare costs per yr. Parkinson's disease is incurable, with 6,000 new diagnoses each year - it is the 14th
leading cause of death in the US. Parkinson's disease and nicotine addiction are disorders of the dopamine pathway, making
α6β2- contg. subtypes of the nicotinic acetylcholine receptor (nAChR) , which are ligand gated ion channels localized to
dopaminergic neurons, an attractive target. Advanced knowledge of the binding site, which sits at the interface of α6 and β2,
could lead to design of agonists...
Electrochemical CO2 reduction catalyzed by Mn catalysts: DFT investigations point to strategies for overpotential reduction and activity improvement - Lam, Yan Choi; Nielsen, Robert J.; Goddard, William A.; Gray, Harry B.
Exptl., [(L) Mn(CO)_3]- (where L = bis alkyl- substituted bipyridine) has been obsd. to catalyze the electrochem. redn. of CO_2 to
CO in the presence of trifluoroethanol (TFEH). Our DFT calcns. (B3LYP- d3 with continuum solvation) of the free energies of
reaction and activation show that the highly exergonic hydrogen bonding between TFEH and TFE (homoconjugation) plays a
crit. role in reaction thermodn. and kinetics. The analgous 2,2'- bipyrimidine complex is predicted to have a lower (by ca. 0.5 V)
onset overpotential, but at the expense of max. catalytic activity. As a strategy to improve catalytic activity and onset
overpotential, a series of 2,2'- and...
Variable binding modes of pyridine in molybdenum complexes supported by novel P-pyridine-P ligands - Wan, Ruomeng; Horak, Kyle; Buss, Joshua A.; Agapie, Theodor
Low oxidn. state molybdenum complexes bind N_2 and in some cases reduce it to NH_3. We have previously demonstrated
that molybdenum complexes supported by terphenyl diphosphine ligand platforms bind and activate small mols. We
report herein the synthesis and characterization of mononuclear Mo complexes supported by two isomers of a novel ligand
framework: 3,5-bis(2-(diisopropylphosphino)phenyl)pyridine (PNP^(3,5)) and 2, 6-bis(2-(diisopropylphosphino) phenyl) pyridine
(PNP^(2,6)). Metalation of the phosphines with Mo(CO)_3 (MeCN)_3 results in the formation of MoPNP(CO)_3 complexes. The PNP^(3,5)
isomer shows binding via the pyridine π system, while the PNP^(2,6) via the nitrogen lone pair. Oxidn. results in Mo species.
Upon photolysis, CO ligand substitution occurs to give...
Multi-layer anode for saline wastewater treatment: Manipulating oxidant generation pathway by TiO_2 thin film deposition - Yang, Yang; Hoffmann, Michael R.
Nowadays, both developed and developing countries are suffering from water scarcity due to the rapid urbanization and global
climate change. The on-site reuse of water is a possible soln., which calls for the development of various decentralized
wastewater treatment techniques. Electrochem. oxidn. is a promising candidate due to its modular design, convenient
operation, and small carbon footprint. In the past decades, the IrO_x based DSA electrode showed excellent performance on
saline wastewater treatment. However, the high cost and low energy efficiency impede the widespread application. In this
study, uniform TiO_2 thin film was deposited onto the IrO_x electrode by novel spray- pyrolysis process. Instead of...
Selective two-electron reduction of carbon monoxide mediated by molybdenum complexes supported on an asymmetric phenol phosphine ligand - Riduan, Siti Nurhanna; Buss, Joshua A.; Agapie, Theodor
Our group has recently reported a monometallic Molybdenum complex supported by a terphenyl diphosphine ligand capable
of undergoing multielectron reductive processes. Various oxidn. states of the metal center are stabilized by the ability of the
ligand to accommodate different binding modes. For example, the arene π-system displays η^2, η^4, η^6 binding while one of the
phosphine arms reversibly dissocs. To further study the significance of the hemilability of the ligand donor arms, a
monometallic Mo dicarbonyl complex supported by an asym. terphenyl phosphine- phenol ligand (POH) framework has been
isolated. Deprotonation and treatment of the (PMo(CO)_2OH) complex with KC_8 or K(C_(10)H_8) yields a reduced Mo...
Rolling revolution in analytical isotope geochemistry - Eiler, John
The many subjects of isotope geochem. have two things in common: they generally require anal. of isotope ratios at low
natural abundances (∼10^(-2)-10^(-6)) and high precision (∼10^(-3)-10(-6)). For the first 50 years of this field (ca. 1950-2000), these
requirements were met by a narrow range of technologies - mostly low mass resoln. (M/ΔM of a few hundred) TIMS and gas
source IRMS - that limited the field to a few simple mols. and elements. Over the last 15 years this field has been transformed
by the emergence of a wide range of new instruments and methods: plasma-source, high-resoln. MC-ICPMS has dramatically
expanded the list of...
Towards an energy landscape of G protein-coupled receptor (GPCR) activation using hybrid methods - Dong, Sijia S.; Abrol, Ravinder; Goddard, William A.
The prediction of various GPCR conformations along their activation pathways has been a challenge for computational
biophysicists. The shortage of exptl. active structures has impaired the study of GPCR activation mechanisms. We have
developed a hybrid computational method that predicts multiple GPCR conformations systematically, including the active ones.
This is one of the very few methods that can predict the high-energy active conformations, capable of coupling to the G
protein, starting from an inactive conformation. We are also able to generate, to the best of our knowledge, the first quant.
energy profile of GPCR activation consistent with the qual. energy landscape from expts. Our hybrid...
Homogeneous Ta/Ir tandem catalytic alkane/alkene coupling - Bercaw, John E.; Labinger, Jay A.; Leitch, David; Steelman, Keith
Light alkanes and alkenes are abundant but under-utilized energy carriers due to their high volatility and low energy d. A
tandem catalytic approach for the coupling of alkanes and alkenes has been developed in order to upgrade these light
hydrocarbons into heavier fuel mols. This process involves alkane dehydrogenation by pincer- ligated iridium complexes, and
alkene dimerization by a Cp*TaCl_2(alkene) catalyst. These two homogeneous catalysts operate with up to 60 /30
cooperative turnovers (Ir/Ta) in the dimerization of 1- hexene /n- heptane, giving C_(13)/C_(14) products in 40 % yield. Because there is
no kinetically relevant interaction between the two catalysts, the tandem mechanism can be...
Small molecule activation with metal complexes supported by ligands with pendant arene moieties - Agapie, Theodor
Multidentate ligands connected by terphenyl linkers have been employed to support mono and multimetallic complexes. The
central arene of the terphenyl unit acts as a labile donor and coordinates in a variety of modes as a function of metal and
oxidn. state. This arene can be non- innocent with respect to redox and H-transfer chem. Variants with catechol and
hydroquinone moieties show multi- proton, multi- electron transfer chem. Addnl., pendant phosphine arms can reversibly
dissoc., facilitating reactivity. The reactivity of these complexes for the activation of small mols. such as H_2, N_2, CO_2, O_2,
and CO will be discussed.