50 results on '"Eva Zurek"'
Search Results
2. A Computational Experiment Introducing Undergraduates to Geometry Optimizations, Vibrational Frequencies, and Potential Energy Surfaces
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Matthew D. Hanson, Daniel P. Miller, Cholavardhan Kondeti, Adam Brown, Eva Zurek, and Scott Simpson
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General Chemistry ,Education - Published
- 2023
3. Applying Density Functional Theory to Common Organic Mechanisms: A Computational Exercise
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Jonathan P. Antle, Masashi W. Kimura, Stefano Racioppi, Corey Damon, Meredith Lang, Caitlyn Gatley-Montross, Laura S. Sánchez B., Daniel P. Miller, Eva Zurek, Adam M. Brown, Kellie Gast, and Scott M. Simpson
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General Chemistry ,Education - Published
- 2022
4. Intercalating Helium into A-Site Vacant Perovskites
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Stefano Racioppi, Maosheng Miao, and Eva Zurek
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Condensed Matter - Materials Science ,General Chemical Engineering ,Materials Chemistry ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,General Chemistry - Abstract
Evolutionary searches were employed to predict the most stable structures of perovskites with helium atoms on their A-sites up to pressures of 10 GPa. The thermodynamics associated with helium intercalation into [CaZr]F6, structure that [He]2[CaZr]F6 adopts under pressure, and the mechanical properties of the parent perovskite and helium-bearing phase were studied via density functional theory (DFT) calculations. The pressure-temperature conditions where the formation of HeAlF3, HeGaF3, HeInF3, HeScF3 and HeReO3 from elemental helium and the vacant A-site perovskites is favored were found. Our DFT calculations show that entropy can stabilize the helium-filled perovskites provided that the volume that the noble gas atom occupies within their pores is larger than within the elemental solid at that pressure. We find that helium incorporation will increase the bulk modulus of AlF3 from a value characteristic of tin to one characteristic of steel, and hinders rotations of its octahedra that occur under pressure.
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- 2023
5. Corrigendum: Ultra‐Tight Host‐Guest Binding with Exceptionally Strong Positive Cooperativity
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Thomas A. Sobiech, Yulong Zhong, Daniel P. Miller, Jillian K. McGrath, Christina T. Scalzo, Morgan C. Redington, Eva Zurek, and Bing Gong
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General Chemistry ,Catalysis - Published
- 2023
6. Reliable folding of hybrid tetrapeptides into short β-hairpins
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Quan Tang, Yao-Hua Li, Yulong Zhong, Rui Liu, Yukun Zhang, Daniel P. Miller, Bing Gong, Eva Zurek, Sagar Buttan, Hongwei Tan, Jin Zhu, Xue-Yi Sun, Xiang-Xiang Wu, and Zhong-Lin Lu
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Dipeptide ,Stereochemistry ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Turn (biochemistry) ,Folding (chemistry) ,chemistry.chemical_compound ,chemistry ,Side chain ,0210 nano-technology - Abstract
Five hybrid tetrapeptides, each consisting a central dipeptide segment of α-amino acid residues flanked by two aromatic γ-amino acid residues, are found to fold into well-defined β-hairpin conformations as shown by NMR, computational study, and X-ray structures. The turn loop of this β-hairpin motif accommodates different two-residue α-amino acid sequences from the highly flexible Gly-Gly, to the more restricted d -Pro-Gly. The presence of α-amino acid side chains enhances the stabilities of the β-hairpins with the exception of d -Pro-Gly-which results in destabilization. Based on this hairpin/turn motif, a variety of different dipeptide sequences of α-amino acids which rarely occur in β-turns can be introduced and presented as two-residue loops.
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- 2022
7. Conventional High-Temperature Superconductivity in Metallic, Covalently Bonded, Binary-Guest C-B Clathrates
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Nisha Geng, Katerina P. Hilleke, Li Zhu, Xiaoyu Wang, Timothy A. Strobel, and Eva Zurek
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Superconductivity (cond-mat.supr-con) ,Colloid and Surface Chemistry ,Condensed Matter - Superconductivity ,FOS: Physical sciences ,General Chemistry ,Biochemistry ,Catalysis - Abstract
Inspired by the synthesis of XB3C3 (X= Sr, La) compounds in the bipartite sodalite clathrate structure, density functional theory (DFT) calculations are performed on members of this family containing up to two different metal atoms. A DFT-chemical pressure analysis on systems with X= Mg, Ca, Sr, Ba reveals that the size of the metal cation, which can be tuned to stabilize the B-C framework, is key for their ambient-pressure dynamic stability. High-throughput density functional theory calculations on 105 Pm-3 symmetry XYB6C6 binary-guest compounds (where X, Y are electropositive metal atoms) find 22 that are dynamically stable at 1 atmosphere, expanding the number of potentially synthesizable phases by 19 (18 metals and 1 insulator). The density of states at the Fermi level and superconducting critical temperature, Tc, can be tuned by changing the average oxidation state of the metal atoms, with Tc being highest for an average valence of +1.5. KPbB6C6, with an ambient-pressure Eliashberg Tc of 88 K, is predicted to possess the highest-Tc among the studied Pm-3n XB3C3 or Pm-3 XY B6C6 phases, and calculations suggest it may be synthesized using high-pressure high-temperature techniques then quenched to ambient conditions.
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- 2023
8. Superfast Tetrazole–BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells
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Gangam Srikanth Kumar, Stefano Racioppi, Eva Zurek, and Qing Lin
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Colloid and Surface Chemistry ,Cycloaddition Reaction ,General Chemistry ,Biochemistry ,Article ,Catalysis - Abstract
Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principle computations provide vital insights into the origin of the tetrazole-BCN cycloaddition’s superior kinetics compared to the tetrazole–spirohexene cycloaddition. The tetrazole–BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 seconds.
- Published
- 2021
9. Electronic Structure and Superconductivity of Compressed Metal Tetrahydrides
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Tiange Bi and Eva Zurek
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Superconductivity ,Valence (chemistry) ,Hydride ,Phonon ,Chemistry ,Organic Chemistry ,Fermi level ,General Chemistry ,Electronic structure ,Catalysis ,Electron transfer ,symbols.namesake ,Chemical physics ,Atom ,symbols ,Condensed Matter::Strongly Correlated Electrons - Abstract
Tetrahydrides crystallizing in the ThCr2 Si2 structure type have been predicted to become stable for a plethora of metals under pressure, and some have recently been synthesized. Through detailed first-principles investigations we show that the metal atoms within these I4/mmm symmetry MH4 compounds may be divalent, trivalent or tetravalent. The valence of the metal atom and its radius govern the bonding and electronic structure of these phases, and their evolution under pressure. The factors important for enhancing superconductivity include a large number of hydrogenic states at the Fermi level, and the presence of quasi-molecular H 2δ- units whose bonds have been stretched and weakened (but not broken) via electron transfer from the electropositive metal, and via a Kubas-like interaction with the metal. Analysis of the microscopic mechanism of superconductivity in MgH4 , ScH4 and ZrH4 reveals that phonon modes involving a coupled libration and stretch of the H 2δ- units leading to the formation of more complex hydrogenic motifs are important contributors towards the electron phonon coupling mechanism. In the divalent hydride MgH4 , modes associated with motions of the hydridic hydrogen atoms are also key contributors, and soften substantially at lower pressures.
- Published
- 2021
10. Rational Design of Superconducting Metal Hydrides via Chemical Pressure Tuning**
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Eva Zurek and Katerina Hilleke
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Superconductivity (cond-mat.supr-con) ,Condensed Matter - Superconductivity ,Physics::Atomic and Molecular Clusters ,FOS: Physical sciences ,General Chemistry ,General Medicine ,Catalysis - Abstract
The high critical superconducting temperatures ($T_c$s) of metal hydride phases with clathrate-like hydrogen networks have generated great interest. Herein, we employ the Density Functional Theory-Chemical Pressure (DFT-CP) method to explain why certain electropositive elements adopt these structure types, whereas others distort the hydrogenic lattice, thereby decreasing the $T_c$. The progressive opening of the H$_{24}$ polyhedra in MH$_6$ phases is shown to arise from internal pressures exerted by large metal atoms, some of which may favor an even higher hydrogen content that loosens the metal atom coordination environments. The stability of the LaH$_{10}$ and LaBH$_8$ phases is tied to stuffing of their shared hydrogen network with either additional hydrogen or boron atoms. The predictive capabilities of DFT-CP are finally applied to the Y-X-H system to identify possible ternary additions yielding a superconducting phase stable to low pressures., 13 pages, 3 figures
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- 2022
11. Correction to 'Conventional High-Temperature Superconductivity in Metallic, Covalently Bonded, Binary-Guest C–B Clathrates'
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Nisha Geng, Katerina P. Hilleke, Li Zhu, Xiaoyu Wang, Timothy A. Strobel, and Eva Zurek
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Colloid and Surface Chemistry ,General Chemistry ,Biochemistry ,Catalysis - Published
- 2023
12. Copper-catalyzed enantioselective alkene carboetherification for the synthesis of saturated six-membered cyclic ethers
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Jonathan J. Kennedy-Ellis, Eva Zurek, Ameya S. Burde, Sherry R. Chemler, and Ilyas A. Berhane
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chemistry.chemical_classification ,Base (chemistry) ,Chemistry ,Alkene ,Ligand ,Metals and Alloys ,Enantioselective synthesis ,General Chemistry ,σ1 receptor ,Medicinal chemistry ,Article ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Solvent ,Materials Chemistry ,Ceramics and Composites ,Copper catalyzed ,Oxidative coupling of methane - Abstract
The enantioselective copper-catalyzed oxidative coupling of alkenols with styrenes for the construction of dihydropyrans, isochromans, pyrans and morpholines is reported. A concise formal synthesis of a σ(1) receptor ligand using this alkene carboetherification methodology was demonstrated. Ligand, solvent and base all impact reaction efficiency. DFT transition state calculations are presented.
- Published
- 2021
13. The Microscopic Diamond Anvil Cell: Stabilization of Superhard, Superconducting Carbon Allotropes at Ambient Pressure
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Xiaoyu Wang, Davide M. Proserpio, Corey Oses, Cormac Toher, Stefano Curtarolo, and Eva Zurek
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Carbon Allotropes ,Settore CHIM/03 - Chimica Generale e Inorganica ,Condensed Matter - Materials Science ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,Density Functional Calculations ,General Medicine ,General Chemistry ,Catalysis ,Superhard Materials ,Condensed Matter::Materials Science ,Electronic Structure ,Condensed Matter::Superconductivity ,Superconductors - Abstract
A metallic covalently bonded carbon allotrope is predicted via first principles calculations. It is composed of an $sp^3$ carbon framework that acts as a diamond anvil cell by constraining the distance between parallel cis-polyacetylene chains. The distance between these $sp^2$ carbon atoms renders the phase metallic, and yields two well-nested nearly parallel bands that span the Fermi level. Calculations show that this phase is a conventional superconductor, with the motions of the $sp^2$ carbons being key contributors to the electron phonon coupling. The $sp^3$ carbon atoms impart superior mechanical properties, with a predicted Vickers hardness of 48~GPa. This phase, metastable at ambient conditions, could be made via cold compression of graphite to 40~GPa. A family of multifunctional materials with tunable superconducting and mechanical properties could be derived from this phase by varying the $sp^2$ versus $sp^3$ carbon content and by doping.
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- 2022
14. Chemistry under high pressure
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Hai-qing Lin, Yuanhui Sun, Maosheng Miao, and Eva Zurek
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Chemical species ,Chemical bond ,Atomic orbital ,Core electron ,Chemistry ,Chemical physics ,General Chemical Engineering ,Interstitial defect ,General Chemistry ,Electron ,Quantum ,Homonuclear molecule - Abstract
Thanks to the development of experimental high-pressure techniques and methods for crystal-structure prediction based on quantum mechanics, in the past decade, numerous new compounds, mostly binary, with atypical compositions have been predicted, and some have been synthesized. Differing from conventional solid-state materials, many of these new compounds are comprised of various homonuclear chemical species, such as dimers, trimers, pentagonal and heptagonal rings, polymeric chains, atomic layers and 3D networks. Strikingly, it has been shown that pressure can alter the chemistry of an element by activating its (semi)core electrons, unoccupied orbitals and even the non-atom-centred quantum orbitals located on the interstitial sites, leading to many new surprising phenomena. This Review provides a summary of atypical compounds that result from the effects of high pressure on either the chemical bonds or the local orbitals. We describe various unusual chemical species and motifs, show how the chemical properties of the elements are altered under pressure and illustrate how compound formation is favoured even in situations in which chemical bonds are not formed. An extraordinary new picture of chemistry emerges as we piece together these unexpected high-pressure phenomena. In marked contrast to the previously held beliefs regarding the behaviour of solids under pressure, we are learning that the quantum-mechanical features of electrons, such as those that lead to the formation of directional bonds, inhomogeneous distributions of electrons and atoms, as well as variations in symmetry, might be magnified under pressure. We discuss the influence of these phenomena on future studies that will probe chemistry at higher pressures and explore more complex chemical compositions than those that have been studied to date. High pressure leads to striking new chemistry. Many new compounds with atypical compositions and a plethora of novel chemical species can be stabilized by the formation of homonuclear bonds and the activation of core electrons, non-valence and non-atomic orbitals.
- Published
- 2020
15. Pressure-Induced Superconductivity in the Wide-Band-Gap Semiconductor Cu2Br2Se6 with a Robust Framework
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Jared Coles, Duck Young Chung, Jin-Ke Bao, Eva Zurek, Dongzhou Zhang, Katerina P. Hilleke, Yan Yan, Weizhao Cai, Jingui Xu, Mercouri G. Kanatzidis, Shanti Deemyad, and Wenwen Lin
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Superconductivity ,Materials science ,Quantitative Biology::Neurons and Cognition ,Condensed matter physics ,Band gap ,business.industry ,General Chemical Engineering ,Wide-bandgap semiconductor ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Condensed Matter::Materials Science ,Semiconductor ,Condensed Matter::Superconductivity ,Materials Chemistry ,Wide band ,0210 nano-technology ,business ,Ternary operation - Abstract
We report pressure-induced superconductivity in a ternary and nonmagnetic Cu-containing semiconductor, Cu2Br2Se6, with a wide band gap of 1.89 eV, in which the Cu and Br atoms generate infinite 21 ...
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- 2020
16. Self-Assembly and Molecular Recognition in Water: Tubular Stacking and Guest-Templated Discrete Assembly of Water-Soluble, Shape-Persistent Macrocycles
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Daniel P. Miller, Xiaoxing Lu, Bing Gong, Quan Tang, Yulong Zhong, Rui Liu, Zhong-Lin Lu, Eva Zurek, and Qiuhua Wang
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chemistry.chemical_classification ,Aqueous medium ,technology, industry, and agriculture ,Stacking ,Supramolecular chemistry ,macromolecular substances ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,0104 chemical sciences ,Colloid and Surface Chemistry ,Molecular recognition ,Water soluble ,chemistry ,Chemical engineering ,Non-covalent interactions ,Self-assembly - Abstract
Supramolecular chemistry in aqueous media is an area with great fundamental and practical significance. To examine the role of multiple noncovalent interactions in controlled assembling and binding behavior in water, the self-association of five water-soluble hexakis(
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- 2020
17. aflow++: a C++ framework for autonomous materials design
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Corey Oses, Marco Esters, David Hicks, Simon Divilov, Hagen Eckert, Rico Friedrich, Michael J. Mehl, Andriy Smolyanyuk, Xiomara Campilongo, Axel van de Walle, Jan Schroers, A. Gilad Kusne, Ichiro Takeuchi, Eva Zurek, Marco Buongiorno Nardelli, Marco Fornari, Yoav Lederer, Ohad Levy, Cormac Toher, and Stefano Curtarolo
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Condensed Matter - Materials Science ,Computational Mathematics ,General Computer Science ,Mechanics of Materials ,General Physics and Astronomy ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,General Materials Science ,General Chemistry - Abstract
The realization of novel technological opportunities given by computational and autonomous materials design requires efficient and effective frameworks. For more than two decades, aflow++ (Automatic-Flow Framework for Materials Discovery) has provided an interconnected collection of algorithms and workflows to address this challenge. This article contains an overview of the software and some of its most heavily-used functionalities, including algorithmic details, standards, and examples. Key thrusts are highlighted: the calculation of structural, electronic, thermodynamic, and thermomechanical properties in addition to the modeling of complex materials, such as high-entropy ceramics and bulk metallic glasses. The aflow++ software prioritizes interoperability, minimizing the number of independent parameters and tolerances. It ensures consistency of results across property sets - facilitating machine learning studies. The software also features various validation schemes, offering real-time quality assurance for data generated in a high-throughput fashion. Altogether, these considerations contribute to the development of large and reliable materials databases that can ultimately deliver future materials systems, Comment: 47 pages, 14 figures
- Published
- 2022
- Full Text
- View/download PDF
18. The Computational Design of Two-Dimensional Materials
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Eva Zurek, Sarah Swihart, Jochen Autschbach, Herbert D. Ludowieg, Adam B. Phillips, and Daniel P. Miller
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Molecular model ,010405 organic chemistry ,Band gap ,Interface (Java) ,Computation ,05 social sciences ,050301 education ,General Chemistry ,01 natural sciences ,Quantum chemistry ,0104 chemical sciences ,Education ,symbols.namesake ,Chemical physics ,Avogadro constant ,symbols ,Molecule ,Density functional theory ,0503 education - Abstract
A computational laboratory experiment investigating molecular models for hexagonal boron–carbon–nitrogen sheets (h-BCN) was developed and employed in an upper-level undergraduate chemistry course. Students used the Avogadro user interface for molecular editing and the WebMO interface for the quantum computational workflow. Density functional theory calculations were carried out to compare the electronic structures, relative energies, and other properties of mono-, di-, and tetrameric h-BCN molecular models. Experimental precursor molecules and other analogous single-layer two-dimensional (2D) materials were studied as well. These computations exemplified how electronic properties such as the band gaps of potentially useful 2D materials can be finely tuned by varying chemical structure.
- Published
- 2019
19. Superalkali-alkalide interactions and ion pairing in low-polarity solvents
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Daniel Malko, René Riedel, Peter P. Edwards, Anthony G. M. Barrett, Daniel P. Miller, Heungjae Choi, Thomas F. Headen, Eva Zurek, Adrian Porch, N.C. Pyper, Andrew G. Seel, Brendan T. Sperling, Anthony Kucernak, and Commission of the European Communities
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Science & Technology ,Polarity (physics) ,Alkalide ,Ion pairing ,Chemistry, Multidisciplinary ,General Chemistry ,Neutron scattering ,010402 general chemistry ,Alkali metal ,01 natural sciences ,Biochemistry ,Catalysis ,Article ,0104 chemical sciences ,Dielectric spectroscopy ,Ion ,chemistry.chemical_compound ,Chemistry ,Colloid and Surface Chemistry ,chemistry ,Chemical physics ,Physical Sciences ,Ionic conductivity ,03 Chemical Sciences - Abstract
The nature of anionic alkali metals in solution is traditionally thought to be “gaslike” and unperturbed. In contrast to this noninteracting picture, we present experimental and computational data herein that support ion pairing in alkalide solutions. Concentration dependent ionic conductivity, dielectric spectroscopy, and neutron scattering results are consistent with the presence of superalkali–alkalide ion pairs in solution, whose stability and properties have been further investigated by DFT calculations. Our temperature dependent alkali metal NMR measurements reveal that the dynamics of the alkalide species is both reversible and thermally activated suggesting a complicated exchange process for the ion paired species. The results of this study go beyond a picture of alkalides being a “gaslike” anion in solution and highlight the significance of the interaction of the alkalide with its complex countercation (superalkali).
- Published
- 2021
20. Fluorides of Silver Under Large Compression*
- Author
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Eva Zurek, Mariana Derzsi, Wojciech Grochala, and Dominik Kurzydłowski
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Phase transition ,Band gap ,Thermodynamics ,FOS: Physical sciences ,010402 general chemistry ,7. Clean energy ,01 natural sciences ,Catalysis ,Condensed Matter - Strongly Correlated Electrons ,symbols.namesake ,Paramagnetism ,Condensed Matter::Materials Science ,Phase diagram ,Condensed Matter - Materials Science ,Strongly Correlated Electrons (cond-mat.str-el) ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Fermi level ,Materials Science (cond-mat.mtrl-sci) ,General Chemistry ,Magnetic semiconductor ,0104 chemical sciences ,symbols ,Chemical stability ,Condensed Matter::Strongly Correlated Electrons ,Ambient pressure - Abstract
The silver-fluorine phase diagram has been scrutinized as a function of external pressure using theoretical methods. Our results indicate that two novel stoichiometries containing Ag+ and Ag2+ cations (Ag3 F4 and Ag2 F3 ) are thermodynamically stable at ambient and low pressure. Both are computed to be magnetic semiconductors under ambient pressure conditions. For Ag2 F5 , containing both Ag2+ and Ag3+ , we find that strong 1D antiferromagnetic coupling is retained throughout the pressure-induced phase transition sequence up to 65 GPa. Our calculations show that throughout the entire pressure range of their stability the mixed-valence fluorides preserve a finite band gap at the Fermi level. We also confirm the possibility of synthesizing AgF4 as a paramagnetic compound at high pressure. Our results indicate that this compound is metallic in its thermodynamic stability region. Finally, we present general considerations on the thermodynamic stability of mixed-valence compounds of silver at high pressure.
- Published
- 2021
21. Materials under high pressure: A chemical perspective
- Author
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Katerina P. Hilleke, Tiange Bi, and Eva Zurek
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Condensed Matter - Materials Science ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,General Materials Science ,General Chemistry - Abstract
At high pressure, the typical behavior of elements dictated by the periodic table - including oxidation numbers, stoichiometries in compounds, and reactivity, to name but a few - is altered dramatically. As pressure is applied, the energetic ordering of atomic orbitals shifts, allowing core orbitals to become chemically active, atypical electron configurations to occur, and in some cases, non-atom-centered orbitals to form in the interstices of solid structures. Strange stoichiometries, structures, and bonding motifs result. Crystal structure prediction tools, not burdened by preconceived notions about structural chemistry learned at atmospheric pressure, have been applied to great success to explore phase diagrams at high pressure, identifying novel structures in diverse chemical systems. Several of these have been subsequently observed by experimental investigations, whose access to high-pressure regimes is bolstered by advances in diamond anvil cell and dynamic compression techniques. The joint efforts of experiment and theory have led to particular success in the realm of high-temperature superconductors, identifying many novel phases whose superconducting transition approaches room temperature., Comment: 17 pages (35 with references), 6 figures
- Published
- 2021
- Full Text
- View/download PDF
22. Major Factors for the Persistent Folding of Hybrid α, β, γ-Hybrid Peptides Into Hairpins
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Yulong Zhong, Rui Liu, Eva Zurek, Daniel P. Miller, Quan Tang, Bing Gong, and Zhong-Lin Lu
- Subjects
Stereochemistry ,Peptide ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,lcsh:Chemistry ,hybrid peptide ,β-turn ,chemistry.chemical_compound ,foldamer ,unnatural amino acid ,β-hairpin ,Original Research ,chemistry.chemical_classification ,hydrogen bond ,Oligopeptide ,Dipeptide ,Tetrapeptide ,Hydrogen bond ,Foldamer ,General Chemistry ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Chemistry ,lcsh:QD1-999 ,chemistry ,0210 nano-technology - Abstract
Factors responsible for the persistent adoption of hairpin conformations by hybrid oligopeptides, each having a central β/α dipeptide segment flanked by aromatic γ-amino acid (γAr) residues, are probed. Our recent studies revealed that tetrapeptide 1 and 2, having central dipeptide segments consisting of β-alanine (β-Ala) and glycine (Gly), and L-β-homophenylalanine (L-β-homoPhe) and Gly residues, respectively, that are flanked by γAr residues, fold into well-defined, expanded β-turns with doubly H-bonded γAr residues. Replacing the γAr residues of 1 and 2 with L-Val and L-Leu residues results in tetrapetides 1′ and 2′ that fail to fold into defined conformations, which confirms the decisive role played by the H-bonded γAr residues in the promoting folding of 1 and 2. Attaching L-Val and L-Leu residues to the termini of 1 affords hexapeptide 1a. With an additional H-bond between its L-Val and L-Leu residues, peptide 1a folds into a hairpin with higher stability than that of 1, indicating that the expanded β-turn can nucleate and stabilize β-hairpin with longer β-strands. Attaching L-Val and L-Leu residues to the termini of 2 affords hexapeptide 2a. Substituting the L-β-homoPhe residue of 2a with a D-β-homoPhe residue gives hexapeptide 2b. Surprisingly, hexapeptide 2a fold into a hairpin showing the similar stability as those of tetrapeptides 1 and 2. Hexapeptide 2b, with its combination of a D-β-homoPhe residue and the L-Val/L-Leu pair, fold into a hairpin that is significantly more stable than the other hybrid peptides, demonstrating that a combination of hetero-chirality between the β-amino acid residue of the dipeptide loop and the α-amino acid residues of the β-strands enhances the stability of the resultant β-hairpin.
- Published
- 2020
23. Cover Feature: Electronic Structure and Superconductivity of Compressed Metal Tetrahydrides (Chem. Eur. J. 60/2021)
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Eva Zurek and Tiange Bi
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Superconductivity ,Metal ,Condensed matter physics ,Feature (computer vision) ,Chemistry ,visual_art ,Organic Chemistry ,visual_art.visual_art_medium ,Cover (algebra) ,General Chemistry ,Electronic structure ,Catalysis - Published
- 2021
24. Extended Hückel Calculations on Solids Using the Avogadro Molecular Editor and Visualizer
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Herbert D. Ludowieg, Patrick Avery, Jochen Autschbach, and Eva Zurek
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Physics ,Computation ,Molecular orbital theory ,02 engineering and technology ,General Chemistry ,Orbital overlap ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Education ,Crystal ,symbols.namesake ,Avogadro constant ,symbols ,Density of states ,Physical chemistry ,Molecule ,Molecular orbital ,Atomic physics ,0210 nano-technology - Abstract
The “Yet Another extended Huckel Molecular Orbital Package” (YAeHMOP) has been merged with theAvogadro open-source molecular editor and visualizer. It is now possible to perform YAeHMOP calculations directly from the Avogadro graphical user interface for materials that are periodic in one, two, or three dimensions, and to visualize band structures, total and projected density of states, and crystal orbital overlap/Hamilton populations (COOPs/COHPs). Calculations on graphite, silicon, sodium, and a one-dimensional hydrogen chain are provided to illustrate the functionality. Similar exercises have been carried out in an upper-level undergraduate quantum theory course.
- Published
- 2017
25. Folding and Assembly of Short α, β, γ-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures
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Surya V.S.R.K. Pulavarti, Eva Zurek, Bing Gong, Yulong Zhong, Rui Liu, Yukun Zhang, Huaqiang Zeng, Thomas Szyperski, Richard D. Smith, Ruikai Cao, Xiaopeng Li, Jin Zhu, Jie Shen, Zhong-Lin Lu, Bo Song, Erin S. Baker, Alan L. Connor, Quan Tang, Qiwei Wang, and Daniel P. Miller
- Subjects
Models, Molecular ,Protein Folding ,Dipeptide ,Stereochemistry ,Chemistry ,Sequence (biology) ,Hydrogen Bonding ,General Chemistry ,010402 general chemistry ,Crystallography, X-Ray ,01 natural sciences ,Biochemistry ,Oligomer ,Catalysis ,Protein Structure, Secondary ,0104 chemical sciences ,Turn (biochemistry) ,Folding (chemistry) ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Protein structure ,Helix ,Protein folding ,Peptides - Abstract
Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible, and peptides 2a and 2b adopt a noncanonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. The revealed systems offer ample opportunity for further structural optimization and applications.
- Published
- 2019
26. Electron Counting and a Large Family of Two-Dimensional Semiconductors
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Maosheng Miao, Eva Zurek, Jing-yao Liu, Jorge Botana, Tao Hu, and Wen Yang
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Fabrication ,Materials science ,Condensed matter physics ,Band gap ,business.industry ,General Chemical Engineering ,Structure (category theory) ,Heterojunction ,Nanotechnology ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Lattice constant ,Semiconductor ,Materials Chemistry ,Density functional theory ,0210 nano-technology ,Electron counting ,business - Abstract
In comparison with conventional semiconductors, most two-dimensional semiconductor (2DSC) materials are dissimilar in structure and composition. Herein, we use electron-counting rules to propose a large family of 2DSCs, which all adopt the same structure and are composed of solely main group elements. Advanced density functional theory calculations are used to predict a number of novel 2DSCs, and we show that they span a large range of lattice constants, band gaps, and band edge states. As a result, they are good candidate materials for heterojunctions. This family of two-dimensional materials may be instrumental in the fabrication of 2DSC devices that may rival the currently employed 3D semiconductors.
- Published
- 2016
27. M-graphene: a metastable two-dimensional carbon allotrope
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Ketao Yin, Lili Gao, Eva Zurek, Yuanye Tian, Wensheng Yang, Mingchun Lu, Yan Yan, Xin Qu, Miao Zhang, Xiaoyu Wang, and Chunlei Kou
- Subjects
Materials science ,Mechanics of Materials ,Carbon allotrope ,Graphene ,law ,Chemical physics ,Mechanical Engineering ,Metastability ,General Materials Science ,General Chemistry ,Condensed Matter Physics ,law.invention - Published
- 2020
28. Reactivity of He with ionic compounds under high pressure
- Author
-
Hai-Qing Lin, Maosheng Miao, Jorge Botana, Zhen Liu, Steven Valdez, Dadong Yan, Andreas Hermann, and Eva Zurek
- Subjects
inorganic chemicals ,Work (thermodynamics) ,genetic structures ,Science ,General Physics and Astronomy ,Ionic bonding ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,Coulomb ,Physics::Atomic and Molecular Clusters ,Reactivity (chemistry) ,Physics::Atomic Physics ,lcsh:Science ,Helium ,Range (particle radiation) ,Multidisciplinary ,General Chemistry ,respiratory system ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,respiratory tract diseases ,chemistry ,Chemical bond ,Chemical physics ,lcsh:Q ,0210 nano-technology ,Earth (classical element) ,circulatory and respiratory physiology - Abstract
Until very recently, helium had remained the last naturally occurring element that was known not to form stable solid compounds. Here we propose and demonstrate that there is a general driving force for helium to react with ionic compounds that contain an unequal number of cations and anions. The corresponding reaction products are stabilized not by local chemical bonds but by long-range Coulomb interactions that are significantly modified by the insertion of helium atoms, especially under high pressure. This mechanism also explains the recently discovered reactivity of He and Na under pressure. Our work reveals that helium has the propensity to react with a broad range of ionic compounds at pressures as low as 30 GPa. Since most of the Earth’s minerals contain unequal numbers of positively and negatively charged atoms, our work suggests that large quantities of He might be stored in the Earth’s lower mantle., Helium was long thought to be unable to form stable solid compounds, until a recent discovery that helium reacts with sodium at high pressure. Here, the authors demonstrate the driving force for helium reactivity, showing that it can form new compounds under pressure without forming any local chemical bonds.
- Published
- 2018
29. DFT-D Investigation of Active and Dormant Methylaluminoxane (MAO) Species Grafted onto a Magnesium Dichloride Cluster: A Model Study of Supported MAO
- Author
-
Nina Tymińska and Eva Zurek
- Subjects
Magnesium ,Model study ,Methylaluminoxane ,chemistry.chemical_element ,General Chemistry ,Heterogeneous catalysis ,Catalysis ,chemistry.chemical_compound ,Polymerization ,chemistry ,Polymer chemistry ,Cluster (physics) ,Density functional theory - Abstract
Density functional theory calculations were carried out to study the interaction of various models for methylaluminoxane and the active and dormant species in polymerization with the (110) MgCl2 surface. MAO species may bind to the surface via Al–Cl, Mg–O, and Al−μ-CH3–Mg bonds. Our results suggest that the activity of supported MAO may be higher than of homogeneous MAO because the support stabilizes (AlOMe)n·(AlMe3)m, precursors to the active species in polymerization. Moreover, the support lowers the free energy of formation of species that are active in polymerization relative to those that are dormant. Finally, it may be that the support decreases the energy associated with the cation–anion separation in [Cp2ZrMe]+[Me(AlOMe)n]−, a species that is likely dormant in homogeneous processes, hinting that the support has the possibility of increasing the number of potentially active sites.
- Published
- 2015
30. Epitaxial growth of aligned atomically precise chevron graphene nanoribbons on Cu(111)
- Author
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Paulo S. Costa, Alexander Sinitskii, Mohammad Mehdi Pour, Axel Enders, Eva Zurek, Daniel P. Miller, and Jacob D. Teeter
- Subjects
Materials science ,Nanotechnology ,02 engineering and technology ,Substrate (electronics) ,010402 general chemistry ,Epitaxy ,01 natural sciences ,Catalysis ,Materials Chemistry ,Chevron (geology) ,Coupling (piping) ,chemistry.chemical_classification ,business.industry ,Metals and Alloys ,General Chemistry ,Polymer ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry ,Ceramics and Composites ,Optoelectronics ,0210 nano-technology ,business ,Graphene nanoribbons - Abstract
Atomically precise chevron graphene nanoribbons (GNRs) have been synthesized on Cu(111) substrates by the surface-assisted coupling of 6,11-dibromo-1,2,3,4-tetraphenyltriphenylene (C42Br2H26) and thermal cyclodehydrogenation of the resulting polymer. The GNRs form on Cu(111) epitaxially along the 〈112〉 crystallographic directions, which was found to be in agreement with the computational results, and at lower temperatures than on Au(111). This work demonstrates that the substrate plays an important role in the on-surface synthesis of GNRs and can result in new assembly modes of GNR structures.
- Published
- 2017
31. Superconducting Phases of Phosphorus Hydride Under Pressure: Stabilization by Mobile Molecular Hydrogen
- Author
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Daniel P. Miller, Tiange Bi, Andrew Shamp, and Eva Zurek
- Subjects
Condensed Matter::Quantum Gases ,Hydrogen ,010405 organic chemistry ,Hydride ,Inorganic chemistry ,chemistry.chemical_element ,General Medicine ,General Chemistry ,Electronic structure ,010402 general chemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Condensed Matter::Materials Science ,chemistry.chemical_compound ,chemistry ,Chemical physics ,Phase (matter) ,Physics::Atomic and Molecular Clusters ,Molecule ,Physics::Atomic Physics ,Stoichiometry ,Phosphine ,Diborane - Abstract
At 80 GPa, phases with the PH2 stoichiometry, which are composed of simple cubic like phosphorus layers capped with hydrogen atoms and layers of H2 molecules, are predicted to be important species contributing to the recently observed superconductivity in compressed phosphine. The electron–phonon coupling in these phases results from the motions of the phosphorus atoms and the hydrogen atoms bound to them. The role of the mobile H2 layers is to decrease the Coulomb repulsion between the negatively charged hydrogen atoms capping the phosphorus layers. An insulating PH5 phase, the structure and bonding of which is reminiscent of diborane, is also predicted to be metastable at this pressure.
- Published
- 2017
32. Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum
- Author
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Eva Zurek, Scott Simpson, Benjamin Pritchard, and Jochen Autschbach
- Subjects
Physics ,Chemical shift ,General Chemistry ,Electronic structure ,Vanadocene ,Education ,Paramagnetism ,chemistry.chemical_compound ,Unpaired electron ,chemistry ,Chemical physics ,Molecule ,Density functional theory ,Open shell - Abstract
A computational experiment investigating the 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The chemical shift range for paramagnetic systems differs substantially from the well-known range of diamagnetic compounds. Students carried out density functional theory calculations of the chemical shifts of an organic radical and a related closed-shell system. This simple exercise illustrated that a single unpaired electron may result in dramatically different chemical shifts. Organometallic systems were also considered. The chemical shifts of the closed shell molecule ferrocene were compared to those of vanadocene and nickelocene, which afford three and two unpaired electrons, respectively. A natural bonding orbital (NBO) analysis was employed to study the electronic structure of NiCp2.
- Published
- 2014
33. Enantioselective Copper‐Catalyzed Carboetherification of Unactivated Alkenes
- Author
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Eva Zurek, Nicole E. Kendel, Sherry R. Chemler, Timothy W. Liwosz, Michael T. Bovino, Nina Tymińska, and Yan Miller
- Subjects
chemistry.chemical_classification ,Molecular Structure ,Chemistry ,Alkene ,Intermolecular force ,Enantioselective synthesis ,chemistry.chemical_element ,Stereoisomerism ,General Medicine ,General Chemistry ,Alkenes ,Crystallography, X-Ray ,Copper ,Article ,Catalysis ,Cyclization ,Copper catalyzed ,Organic chemistry ,Molecule ,Ethers - Abstract
Chiral saturated oxygen heterocycles are important components of bioactive compounds. Cyclization of alcohols onto pendant alkenes is a direct route to their synthesis, but few catalytic enantioselective methods enabling cyclization onto unactivated alkenes exist. Herein reported is a highly efficient copper-catalyzed cyclization of γ-unsaturated pentenols which terminates in C-C bond formation, a net alkene carboetherification. Both intra- and intermolecular C-C bond formations are demonstrated, thus yielding functionalized chiral tetrahydrofurans as well as fused-ring and bridged-ring oxabicyclic products. Transition-state calculations support a cis-oxycupration stereochemistry-determining step.
- Published
- 2014
34. Kagome-like lattice of π–π stacked 3-hydroxyphenalenone on Cu(111)
- Author
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Xiao Cheng Zeng, Sumit Beniwal, Donna A. Kunkel, Shuang Chen, Scott Simpson, Axel Enders, Eva Zurek, and James Hooper
- Subjects
Crystallography ,Chemistry ,Lattice (order) ,Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,Perpendicular ,Molecule ,General Chemistry ,Lattice symmetry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
We have identified a structurally complex double-layer of 3-hydroxyphenalenone on Cu(111), which exhibits Kagome lattice symmetry. A key feature is the perpendicular attachment of π-π stacked molecular dimers on top of molecules that are flat-lying on the substrate, representing a rare example of a three-dimensional arrangement of molecules on a two-dimensional surface.
- Published
- 2014
35. A Computational Investigation of a Molecular Switch
- Author
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Scott Simpson, Eva Zurek, and Alex Van Fleet
- Subjects
Molecular switch ,Physics ,Chemical species ,Chemical physics ,Computational chemistry ,Catenane ,Molecule ,Molecular orbital ,General Chemistry ,Ground state ,Quantum chemistry ,Molecular machine ,Education - Abstract
We have developed and implemented a computational experiment that explores the behavior of a [2]catenane as a molecular switch. The experiment introduces mechanically interlocked molecules and discusses their potential as artificial molecular machines. The relaxation rate and lifetime, as well as the ratio of the ground state and the metastable state configurations, are calculated in the gas phase as well as solvents of varying polarity using semiempirical quantum chemical calculations. The π–π donor–acceptor interactions between the two macrocycles comprising the catenane are probed via Hartree–Fock calculations of the frontier molecular orbitals. It is shown that NMR calculations may be employed to aid in the identification of various chemical species. The graphical user interface of the open-source molecular editor Avogadro was employed to visualize the crystal structure of the catenane, followed by quantum chemical calculations using the WebMO graphical interface.
- Published
- 2013
36. A Computational Experiment on Single-Walled Carbon Nanotubes
- Author
-
David Lonie, Eva Zurek, Scott Simpson, and Jiechen Chen
- Subjects
Physics ,Nanotube ,Computation ,Nanotechnology ,General Chemistry ,Electronic structure ,Carbon nanotube ,Condensed Matter::Mesoscopic Systems and Quantum Hall Effect ,Quantum chemistry ,Education ,Computational physics ,law.invention ,Condensed Matter::Materials Science ,symbols.namesake ,law ,Avogadro constant ,symbols ,Molecule ,Molecular orbital - Abstract
A computational experiment that investigates single-walled carbon nanotubes (SWNTs) has been developed and employed in an upper-level undergraduate physical chemistry laboratory course. Computations were carried out to determine the electronic structure, radial breathing modes, and the influence of the nanotube’s diameter on the curvature-induced strain. The students used a new graphical user interface to the TubeGen nanotube builder, which we have implemented as an extension to the open-source molecular editor Avogadro, to build and visualize SWNTs. Geometry optimizations, molecular orbital calculations, and frequencies were computed by an external quantum chemical program.
- Published
- 2013
37. Computational Modeling of the Optical Rotation of Amino Acids: An ‘in Silico’ Experiment for Physical Chemistry
- Author
-
Jochen Autschbach, Scott Simpson, and Eva Zurek
- Subjects
Physics ,chemistry.chemical_classification ,Quantitative Biology::Biomolecules ,Molecular model ,General Chemistry ,Quantitative Biology::Genomics ,Quantum chemistry ,Force field (chemistry) ,Education ,Amino acid ,chemistry ,Computational chemistry ,Physical chemistry ,Molecule ,Density functional theory ,Optical rotation ,Conformational isomerism - Abstract
A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l configuration renders the optical rotation more positive. Correspondingly, if the optical rotation becomes more negative, the amino acid is of the d configuration. The students employed the open-source molecular editor Avogadro to build the molecules, conduct conformer searches, and calculate the energies of the conformers with a molecular mechanics force field. Subsequent geometry optimizations and optical rotation calculations were performed with a quantum chemistry program, using the WebMO graphical interface. The role of the solvent in stabilizing the zwitterionic form of an amino acid was investigated.
- Published
- 2013
38. Decomposition Products of Phosphine Under Pressure: PH2 Stable and Superconducting?
- Author
-
Tyson Terpstra, Zackary Falls, Tiange Bi, Eva Zurek, Patrick Avery, and Andrew Shamp
- Subjects
Superconductivity ,Hydrogen ,Condensed matter physics ,chemistry.chemical_element ,Primitive cell ,02 engineering and technology ,General Chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Biochemistry ,Decomposition ,Catalysis ,Metal ,Pseudopotential ,Crystallography ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,chemistry ,visual_art ,0103 physical sciences ,visual_art.visual_art_medium ,Density functional theory ,010306 general physics ,0210 nano-technology ,Phosphine - Abstract
Evolutionary algorithms (EAs) coupled with density functional theory (DFT) calculations have been used to predict the most stable hydrides of phosphorus (PHn, n = 1-6) at 100, 150, and 200 GPa. At these pressures phosphine is unstable with respect to decomposition into the elemental phases, as well as PH2 and H2. Three metallic PH2 phases were found to be dynamically stable and superconducting between 100 and 200 GPa. One of these contains five formula units in the primitive cell and has C2/m symmetry (5FU-C2/m). It comprises 1D periodic PH3-PH-PH2-PH-PH3 oligomers. Two structurally related phases consisting of phosphorus atoms that are octahedrally coordinated by four phosphorus atoms in the equatorial positions and two hydrogen atoms in the axial positions (I4/mmm and 2FU-C2/m) were the most stable phases between ∼160-200 GPa. Their superconducting critical temperatures (Tc) were computed as 70 and 76 K, respectively, via the Allen-Dynes modified McMillan formula and using a value of 0.1 for the Coulomb pseudopotential, μ*. Our results suggest that the superconductivity recently observed by Drozdov, Eremets, and Troyan when phosphine was subject to pressures of 207 GPa in a diamond anvil cell may result from these, and other, decomposition products of phosphine.
- Published
- 2016
39. First principles investigation on how site preference and entropy affect the stability of $(Eu_xM_{1-x})_2Ge_2Pb$ (M = Ca, Sr, Ba) polar intermetallics
- Author
-
Eva Zurek, Tyson Terpstra, and James Hooper
- Subjects
Chemistry ,Organic Chemistry ,Configuration entropy ,Intermetallic ,chemistry.chemical_element ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Catalysis ,Calculation methods ,0104 chemical sciences ,Gibbs free energy ,Ion ,symbols.namesake ,Crystallography ,symbols ,Polar ,Density functional theory ,0210 nano-technology ,Europium - Abstract
Density functional theory calculations have been carried out to analyze the factors contributing to the stabilities of a set of recently synthesized quaternary polar intermetallic compounds, (EuxM1–x)2Ge2Pb with M = Ca, Sr, and Ba. Experiments showed that these preferentially crystallized with Pbam (M = Ca) or Cmmm (M = Sr, Ba) symmetry. We systematically explored how the electronic energies of these structures depended on how they were “colored” by the europium/M ions for a wide composition range. It was found that whereas there was very little site preference in the Cmmm structure, the “B” site in the Pbam structure strongly preferred smaller cations. The configurational entropy was also found to play a role in determining which structures might be preferred. However, the experimentally obtained product ratios could only be fully rationalized by the Gibbs free energies of structures containing M:Eu ratios resembling those that were synthesized experimentally. Our results highlight the importance of calculating vibrational contributions to the entropy for realistic structure models (in terms of coloring and composition) to explain product ratios for syntheses carried out at high temperatures.
- Published
- 2016
40. (Barely) Solid Li(NH3)4: The Electronics of an Expanded Metal
- Author
-
Eva Zurek, Roald Hoffmann, and Xiaodong Wen
- Subjects
Electron density ,Valence (chemistry) ,Enthalpy ,General Chemistry ,Electronic structure ,Biochemistry ,Catalysis ,Metal ,Crystallography ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,chemistry ,Computational chemistry ,visual_art ,Tetrahedron ,visual_art.visual_art_medium ,Electride ,Electronic band structure - Abstract
The highly expanded metal, lithium(0)tetraamine, and its electronic structure is as full of complexity and surprises as the lithium solutions in anhydrous ammonia from which it crystallizes at 90 K. Our theoretical studies of the Phase II, Z = 8, I43d structure of this material reveal that the molecular building block is an almost ideal tetrahedron, in agreement with recent experiments. Close in enthalpy at P = 1 atm, and consistent with the low melting point, are bcc and Cs-IV configurations. Under pressure, the I43d structure emerges as more stable than its alternatives. In this phase six relatively narrow bands, four of them occupied, separate from the conduction and valence bands. We trace these bands to pockets of electron density arising between sterically encumbered ammonias, six such pockets in the Z = 8 unit cell. The observed band structure can be explained by considering a Jortner-type model, where pseudoatoms are placed in these holes. The electride Li(NH(3))(4), while not a very good metal, is a unique material, by virtue of its low melting point.
- Published
- 2011
41. Low energy structural dynamics and constrained libration of Li(NH3)4, the lowest melting point metal
- Author
-
Andrew G. Seel, Kate R. Ryan, Eva Zurek, Peter P. Edwards, Matthew T. J. Lodge, and Anibal J. Ramirez-Cuesta
- Subjects
Chemistry ,Metals and Alloys ,General Chemistry ,Catalysis ,Inelastic neutron scattering ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Metal ,Molecular dynamics ,Low energy ,Lattice (order) ,visual_art ,Materials Chemistry ,Ceramics and Composites ,Melting point ,visual_art.visual_art_medium ,Solid phases ,Density functional theory ,Astrophysics::Earth and Planetary Astrophysics ,Atomic physics ,Astrophysics::Galaxy Astrophysics - Abstract
The lattice and molecular dynamics for the solid phases of the lowest melting-point metal, Li(NH3)4, are determined by incoherent inelastic neutron scattering. Measurements of internal molecular displacements and distortions of the Li(NH3)4 units have been modelled and assigned using density functional theory calculations for the solid and molecular system. Inelastic neutron scattering measurement allow for the first determination of NH3 librational transitions.
- Published
- 2014
42. Rubidium Polyhydrides Under Pressure: Emergence of the Linear H3- Anion
- Author
-
Eva Zurek and James Hooper
- Subjects
Condensed Matter - Materials Science ,Materials science ,Organic Chemistry ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,chemistry.chemical_element ,02 engineering and technology ,General Chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Catalysis ,3. Good health ,Rubidium ,Ion ,Crystallography ,chemistry ,Phase (matter) ,0103 physical sciences ,Molecule ,Symmetrization ,Density functional theory ,010306 general physics ,0210 nano-technology - Abstract
The structures of compressed rubidium polyhydrides, RbHn with n>1, and their evolution under pressure are studied using density functional theory calculations. These phases, which start to stabilize at only P=2 GPa, consist of Rb+ cations and one or more of the following species: H- anions, H2 molecules, and H3- units. The latter motif, the simplest example of a three-center four-electron bond, is found in the most stable structures, RbH5 and RbH3. Pressure induces the symmetrization of H3-. The thermodynamically most stable polyhydrides metallize above 200 GPa. At the highest pressures studied, our evolutionary searches find an RbH6 phase which contains polymeric (H3-)$_\infty$ chains that show signs of one-dimensional liquid-like behavior.
- Published
- 2012
43. Lithium Subhydrides Under Pressure and their Superatom-Like Building Blocks
- Author
-
James Hooper and Eva Zurek
- Subjects
Condensed Matter - Materials Science ,Materials science ,Hydrogen ,Superatom ,chemistry.chemical_element ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Alkali metal ,Block (periodic table) ,01 natural sciences ,0104 chemical sciences ,chemistry ,Ab initio quantum chemistry methods ,Chemical physics ,Cluster (physics) ,Lithium ,0210 nano-technology ,Phase diagram - Abstract
Evolutionary structure searches are used to predict a new class of compounds in the lithium--rich region of the lithium/hydrogen phase diagram under pressure. First principles computations show that LimH, 4, Comment: ChemPlusChem, accepted
- Published
- 2012
- Full Text
- View/download PDF
44. Alkali metals in ethylenediamine: a computational study of the optical absorption spectra and NMR parameters of [M(en)3(δ+)·M(δ-)] ion pairs
- Author
-
Eva Zurek
- Subjects
Magnetic Resonance Spectroscopy ,Metals, Alkali ,Inorganic chemistry ,chemistry.chemical_element ,Ethylenediamine ,General Chemistry ,Alkali metal ,Solvated electron ,Ethylenediamines ,Biochemistry ,Catalysis ,Ion ,Metal ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,chemistry ,visual_art ,visual_art.visual_art_medium ,Organometallic Compounds ,Physical chemistry ,Quantum Theory ,Lithium ,Density functional theory ,Spectrophotometry, Ultraviolet ,Valence electron - Abstract
The optical absorption spectra of alkali metals in ethylenediamine have provided evidence for a third oxidation state, -1, of all of the alkali metals heavier than lithium. Experimentally determined NMR parameters have supported this interpretation, further indicating that whereas Na(-) is a genuine metal anion, the interaction of the alkali anion with the medium becomes progressively stronger for the larger metals. Herein, first-principles computations based upon density functional theory are carried out on various species which may be present in solutions composed of alkali metals and ethylenediamine. The energies of a number of hypothetical reactions computed with a continuum solvation model indicate that neither free metal anions, M(-), nor solvated electrons are the most stable species. Instead, [Li(en)(3)](2) and [M(en)(3)(δ+)·M(δ-)] (M = Na, K, Rb, Cs) are predicted to have enhanced stability. The M(en)(3) complexes can be viewed as superalkalis or expanded alkalis, ones in which the valence electron density is pulled out to a greater extent than in the alkali metals alone. The computed optical absorption spectra and NMR parameters of the [Li(en)(3)](2) superalkali dimer and the [M(en)(3)(δ+)·M(δ-)] superalkali-alkali mixed dimers are in good agreement with the aforementioned experimental results, providing further evidence that these may be the dominant species in solution. The latter can also be thought of as an ion pair formed from an alkali metal anion (M(-)) and solvated cation (M(en)(3)(+)).
- Published
- 2011
45. A molecular perspective on lithium-ammonia solutions
- Author
-
Peter P. Edwards, Roald Hoffmann, and Eva Zurek
- Subjects
Free Radicals ,Chemistry ,Hydrogen bond ,chemistry.chemical_element ,Electrons ,Hydrogen Bonding ,General Chemistry ,Electron ,Lithium ,Solvated electron ,Molecular physics ,Catalysis ,Ammonia ,Computational chemistry ,Solvents ,Quantum Theory ,Thermodynamics ,Molecule ,Molecular orbital ,Singlet state ,Absorption (chemistry) - Abstract
A detailed molecular orbital (MO) analysis of the structure and electronic properties of the great variety of species in lithium-ammonia solutions is provided. In the odd-electron, doublet states we have considered: e-@(NH3)n (the solvated electron, likely to be a dynamic ensemble of molecules), the Li(NH3)4 monomer, and the [Li(NH3)4+.e-@(NH3)n] ion-pairs, the Li 2s electron enters a diffuse orbital built up largely from the lowest unoccupied MOs of the ammonia molecules. The singly occupied MOs are bonding between the hydrogen atoms; we call this stabilizing interaction H-->H bonding. In e-@(NH3)n the odd electron is not located in the center of the cavities formed by the ammonia molecules. Possible species with two or more weakly interacting electrons also exhibit H-->H bonding. For these, we find that the singlet (S=0) states are slightly lower in energy than those with unpaired (S=1, 2...) spins. TD-DFT calculations on various ion-pairs show that the three most intense electronic excitations arise from the transition between the SOMO (of s pseudosymmetry) into the lowest lying p-like levels. The optical absorption spectra are relatively metal-independent, and account for the absorption tail which extends into the visible. This is the source of Sir Humphry Davy's "fine blue colour" first observed just over 200 years ago.
- Published
- 2009
46. A density functional study of the 13C NMR chemical shifts in functionalized single-walled carbon nanotubes
- Author
-
Eva Zurek, Jochen Autschbach, and Chris J. Pickard
- Subjects
Carbon Isotopes ,Magnetic Resonance Spectroscopy ,Molecular Structure ,Chemistry ,Nanotubes, Carbon ,Chemical shift ,Substituent ,General Chemistry ,Nuclear magnetic resonance spectroscopy ,Carbon-13 NMR ,Biochemistry ,Catalysis ,Crystallography ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Covalent bond ,Computational chemistry ,Proton NMR ,Molecule ,Density functional theory - Abstract
The 13C NMR chemical shifts for functionalized (7,0), (8,0), (9,0), and (10,0) single-walled carbon nanotubes (SWNTs) have been studied computationally using gauge-including projector-augmented plane-wave (GIPAW) density functional theory (DFT). The functional groups NH, NCH3, NCH2OH, and CH2NHCH2 have been considered, and different sites where covalent addition or substitution may occur have been examined. The shifts of the carbons directly attached to the group are sensitive to the bond which has been functionalized and may, therefore, be used to identify whether the group has reacted with a parallel or a diagonal C-C bond. The addition of NH to a parallel bond renders the functionalized carbons formally sp3-hybridized, yielding shifts of around 44 ppm, independent of the SWNT radius. Reaction with a diagonal bond retains the formal sp2 hybridization of the substituted carbons, and their shifts are slightly lower or higher than those of the unsubstituted carbon atoms. The calculated 1H NMR shifts of protons in the functional groups are also dependent upon the SWNT-group interaction. Upon decreasing the degree of functionalization for the systems where the group is added to a parallel bond, the average chemical shift of the unfunctionalized carbons approaches that of the pristine tube. At the same time, the shifts of the functionalized carbons remain independent upon the degree of functionalization. For the SWNTs where N-R attaches to a parallel bond, the average shift of the sp2 carbons was found to be insensitive to the substituent R. Moreover, the shifts of the functionalized sp3 carbons, as well as of the carbons within the group itself, are independent of the SWNT radius. The results indicate that a wealth of knowledge may be obtained from the 13C NMR of functionalized SWNTs.
- Published
- 2007
47. Cover Picture: Lithium Subhydrides under Pressure and Their Superatom-like Building Blocks (ChemPlusChem 11/2012)
- Author
-
James Hooper and Eva Zurek
- Subjects
Bond theory ,Ab initio quantum chemistry methods ,Chemistry ,Computational chemistry ,Superatom ,chemistry.chemical_element ,Lithium ,Cover (algebra) ,General Chemistry ,Alkali metal - Published
- 2012
48. Dipole driven bonding schemes of quinonoid zwitterions on surfaces
- Author
-
Pierre Braunstein, Peter A. Dowben, Donna A. Kunkel, Lucie Routaboul, Axel Enders, Geoffrey Rojas, Eva Zurek, Justin Nitz, Bernard Doudin, and Scott Simpson
- Subjects
Electron density ,Chemistry ,Metals and Alloys ,Charge (physics) ,General Chemistry ,Antiparallel (biochemistry) ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Dipole ,Adsorption ,Chemical physics ,Computational chemistry ,Materials Chemistry ,Ceramics and Composites ,Molecule ,HOMO/LUMO ,Electrostatic interaction - Abstract
The permanent dipole of quinonoid zwitterions changes significantly when the molecules adsorb on Ag(111) and Cu(111) surfaces. STM reveals that sub-monolayers of adsorbed molecules can exhibit parallel dipole alignment on Ag(111), in strong contrast with the antiparallel ordering prevailing in the crystalline state and retrieved on Cu(111) surfaces, which minimizes the dipoles electrostatic interaction energy. DFT shows that the rearrangement of electron density upon adsorption is a result of donation from the molecular HOMO to the surface, and back donation to the LUMO with a concomitant charge transfer that effectively reduces the overall charge dipole.
- Published
- 2012
49. On the Nature of Ge-Pb Bonding in the Solid State. Synthesis, Structural Characterization, and Electronic Structures of Two Unprecedented Germanide-Plumbides
- Author
-
James Hooper, Nian-Tzu Suen, Svilen Bobev, and Eva Zurek
- Subjects
Germanide ,chemistry.chemical_compound ,Crystallography ,Colloid and Surface Chemistry ,chemistry ,Group (periodic table) ,Solid-state ,General Chemistry ,Space (mathematics) ,Biochemistry ,Catalysis ,Characterization (materials science) - Abstract
Reported are the syntheses and the crystallographic characterization of two structurally related solid-state compounds: (Eu(1-x)Ca(x))(2)Ge(2)Pb (space group Pbam) and (Sr(x)Eu(1-x))(2)Ge(2)Pb (space group Cmmm). Both structures boast anionic sublattices with fully ordered Ge and Pb at the atomic level, which is unusual for elements of the same group. Despite the nearly identical formulas and the similar chemical makeup, the nature of the chemical bonding in the two compounds is subtly different; in the (Eu(1-x)Ca(x))(2)Ge(2)Pb structure, Ge and Pb are positioned at a relatively shorter distance from one another (3.0 Å). The close proximity of the atoms leads to interactions, which are seen for the first time in an extended structure and can be suggested to have a covalent character. This conjecture is supported by extensive electronic band-structure calculations using first principles. Magnetic susceptibility measurements reveal Eu(2+) ground state ([Xe]4f(7) configuration) and the presence of an antiferromagnetic ordering at cryogenic temperatures.
50. Density Functional Calculations of the $^13$C NMR Chemical Shifts in (9,0) Single-Walled Carbon Nanotubes
- Author
-
Jochen Autschbach and Eva Zurek
- Subjects
Models, Molecular ,Nanotube ,Magnetic Resonance Spectroscopy ,Carbon nanotube ,Electronic structure ,Biochemistry ,Molecular physics ,Catalysis ,law.invention ,Metal ,Colloid and Surface Chemistry ,Computational chemistry ,law ,Molecule ,HOMO/LUMO ,Nanotubes, Carbon ,Chemistry ,business.industry ,Chemical shift ,Carbon-13 ,General Chemistry ,Nuclear magnetic resonance spectroscopy ,General Medicine ,Carbon-13 NMR ,Semiconductor ,visual_art ,visual_art.visual_art_medium ,Thermodynamics ,business - Abstract
The electronic structure and (13)C NMR chemical shift of (9,0) single-walled carbon nanotubes (SWNTs) are investigated theoretically. Shielding tensor components are also reported. Density functional calculations were carried out for C(30)-capped and H-capped fragments which serve as model systems for the infinite (9,0) SWNT. Based on the vanishing HOMO-LUMO gap, H-capped nanotube fragments are predicted to exhibit "metallic" behavior. The (13)C chemical shift approaches a value of approximately 133 ppm for the longest fragment studied here. The C(30)-capped SWNT fragments of D(3d)/D(3h) symmetry, on the other hand, are predicted to be small-gap semiconductors just like the infinite (9,0) SWNT. The differences in successive HOMO-LUMO gaps and HOMO and LUMO energies, as well as the (13)C NMR chemical shifts, converge slightly faster with the fragment's length than for the H-capped tubes. The difference between the H-capped and C(30)-capped fragments is analyzed in some detail. The results indicate that (at least at lengths currently accessible to quantum chemical computations) the H-capped systems represent less suitable models for the (9,0) SWNT because of pronounced artifacts due to their finite length. From our calculations for the C(30)-capped fragments, the chemical shift of a carbon atom in the (9,0) SWNT is predicted to be about 130 ppm. This value is in reasonably good agreement with experimental estimates for the (13)C chemical shift in SWNTs.
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