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Sterling AJ, Levine DS, Aldossary A, Head-Gordon M. Chemical Bonding and the Role of Node-Induced Electron Confinement. J Am Chem Soc 2024; 146:9532-9543. [PMID: 38532619 DOI: 10.1021/jacs.3c10633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The chemical bond is the cornerstone of chemistry, providing a conceptual framework to understand and predict the behavior of molecules in complex systems. However, the fundamental origin of chemical bonding remains controversial and has been responsible for fierce debate over the past century. Here, we present a unified theory of bonding, using a separation of electron delocalization effects from orbital relaxation to identify three mechanisms [node-induced confinement (typically associated with Pauli repulsion, though more general), orbital contraction, and polarization] that each modulate kinetic energy during bond formation. Through analysis of a series of archetypal bonds, we show that an exquisite balance of energy-lowering delocalizing and localizing effects are dictated simply by atomic electron configurations, nodal structure, and electronegativities. The utility of this unified bonding theory is demonstrated by its application to explain observed trends in bond strengths throughout the periodic table, including main group and transition metal elements.
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Affiliation(s)
- Alistair J Sterling
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel S Levine
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Levine DS, Jacobson LD, Bochevarov AD. Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase. J Chem Theory Comput 2023; 19:9302-9317. [PMID: 38085599 DOI: 10.1021/acs.jctc.3c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.
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Affiliation(s)
- Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
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Patel PH, Tunariu N, Levine DS, de Bono JS, Eeles RA, Khoo V, Murray J, Parker CC, Pathmanathan A, Reid A, van As N, Tree AC. Oligoprogression in Metastatic, Castrate-Resistant Prostate Cancer-Prevalence and Current Clinical Practice. Front Oncol 2022; 12:862995. [PMID: 35656509 PMCID: PMC9152030 DOI: 10.3389/fonc.2022.862995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Aims Oligoprogression is poorly defined in current literature. Little is known about the natural history and significance of oligoprogression in patients with hormone-resistant prostate cancer on abiraterone or enzalutamide treatment [termed androgen receptor-targeted therapy (ARTT)]. The aim of this study was to determine the prevalence of oligoprogression, describe the characteristics of oligoprogression in a cohort of patients from a single center, and identify the number of patients potentially treatable with stereotactic body radiotherapy (SBRT). Methods Castration-resistant prostate cancer (CRPC) patients who radiologically progressed while on ARTT were included. Patients with oligoprogressive disease (OPD) (≤3 lesions) on any imaging were identified in a retrospective analysis of electronic patient records. Kaplan-Meier method and log-rank test were used to calculate progression-free and overall survival. Results A total of 102 patients with metastatic CRPC on ARTT were included. Thirty (29%) patients presented with oligoprogression (46 lesions in total); 21 (21% of total) patients had lesions suitable for SBRT. The majority of lesions were in the bone (21, 46%) or lymph nodes (15, 33%). Patients with oligoprogression while on ARTT had a significantly better prostate-specific antigen (PSA) response on commencing ARTT as compared to patients who later developed polyprogression. However, PSA doubling time immediately prior to progression did not predict OPD. Median progression-free survival to oligoprogression versus polyprogression was 16.8 vs. 11.7 months. Time to further progression after oligoprogression was 13.6 months in those treated with radiotherapy (RT) for oligoprogression vs. 5.7 months in those treated with the continuation of ARTT alone. Conclusions In this study, nearly a third of patients on ARTT for CRPC were found to have OPD. OPD patients had a better PSA response on ART and a longer duration on ARTT before developing OPD as compared to those developing polyprogressive disease (Poly-PD). The majority of patients (70%) with OPD had lesions suitable for SBRT treatment. Prospective randomized control trials are needed to establish if there is a survival benefit of SBRT in oligoprogressive prostate cancer and to determine predictive indicators.
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Affiliation(s)
- Priyanka H. Patel
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
- *Correspondence: Priyanka H. Patel,
| | - Nina Tunariu
- Radiology and Imaging, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Daniel S. Levine
- Radiology and Imaging, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Johann S. de Bono
- Drug Development Unit, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Rosalind A. Eeles
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Vincent Khoo
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Julia Murray
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Christopher C. Parker
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Angela Pathmanathan
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Alison Reid
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Nicholas van As
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
| | - Alison C. Tree
- Department of Radiotherapy, Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, United Kingdom
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 412] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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5
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Doerfler SM, Tajmirriyahi M, Dhaliwal A, Bradetich AJ, Ickes W, Levine DS. The Dark Triad trait of psychopathy and message framing predict risky decision‐making during the
COVID
‐19 pandemic. Int J Psychol 2021; 56:623-631. [PMID: 33851414 PMCID: PMC8250605 DOI: 10.1002/ijop.12766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/28/2021] [Indexed: 12/19/2022]
Abstract
The effects of framing on risky decision‐making have been studied extensively in research using Kahneman and Tversky's (1981) hypothetical scenario about a contagious Asian disease. The COVID‐19 pandemic offers a unique opportunity to test how message framing affects risky decision‐making when millions of real lives are at stake worldwide. In a sample of US adults (N = 294), we investigated the effects of message framing and personality (Dark Triad traits) in relation to risky decision‐making during the COVID‐19 crisis. We found that both gain‐ and loss‐framing influenced risk choice in response to COVID‐19. People were more risk‐averse in the loss condition of the current study compared to the benchmark established by Tversky and Kahneman (1981). Among the Dark Triad traits, psychopathy emerged as the significant predictor of risk taking, suggesting that people who score high in psychopathy are more likely to gamble with other people's lives during the COVID‐19 crisis. We suggest that both voters and pandemic‐related public awareness campaigns should consider the possibility that decision‐makers with psychopathic tendencies may take greater risks with other people's lives during a pandemic. In addition, the framing of public‐health messages should be tailored to increase the chances of compliance with government restrictions.
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6
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Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Prasad Veccham S, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annu Rev Phys Chem 2021; 72:641-666. [PMID: 33636998 DOI: 10.1146/annurev-physchem-090419-115149] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.
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Affiliation(s)
- Yuezhi Mao
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Matthias Loipersberger
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Paul R Horn
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Akshaya Das
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Omar Demerdash
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Daniel S Levine
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Srimukh Prasad Veccham
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
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7
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Dombrowski JP, Ziegler MS, Phadke NM, Mansoor E, Levine DS, Witzke RJ, Head-Gordon M, Bell AT, Tilley TD. Siloxyaluminate and Siloxygallate Complexes as Models for Framework and Partially Hydrolyzed Framework Sites in Zeolites and Zeotypes. Chemistry 2021; 27:307-315. [PMID: 32926472 DOI: 10.1002/chem.202002926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Indexed: 11/07/2022]
Abstract
Anionic molecular models for nonhydrolyzed and partially hydrolyzed aluminum and gallium framework sites on silica, M[OSi(OtBu)3 ]4 - and HOM[OSi(OtBu)3 ]3 - (where M=Al or Ga), were synthesized from anionic chlorides Li{M[OSi(OtBu)3 ]3 Cl} in salt metathesis reactions. Sequestration of lithium cations with [12]crown-4 afforded charge-separated ion pairs composed of monomeric anions M[OSi(OtBu)3 ]4 - with outer-sphere [([12]crown-4)2 Li]+ cations, and hydroxides {HOM[OSi(OtBu)3 ]3 } with pendant [([12]crown-4)Li]+ cations. These molecular models were characterized by single-crystal X-ray diffraction, vibrational spectroscopy, mass spectrometry and NMR spectroscopy. Upon treatment of monomeric [([12]crown-4)Li]{HOM[OSi(OtBu)3 ]3 } complexes with benzyl alcohol, benzyloxide complexes were formed, modeling a possible pathway for the formation of active sites for Meerwin-Ponndorf-Verley (MPV) transfer hydrogenations with Al/Ga-doped silica catalysts.
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Affiliation(s)
- James P Dombrowski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Micah S Ziegler
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Neelay M Phadke
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Erum Mansoor
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.,Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Daniel S Levine
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ryan J Witzke
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Martin Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Alexis T Bell
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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8
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Eriksen JJ, Anderson TA, Deustua JE, Ghanem K, Hait D, Hoffmann MR, Lee S, Levine DS, Magoulas I, Shen J, Tubman NM, Whaley KB, Xu E, Yao Y, Zhang N, Alavi A, Chan GKL, Head-Gordon M, Liu W, Piecuch P, Sharma S, Ten-No SL, Umrigar CJ, Gauss J. The Ground State Electronic Energy of Benzene. J Phys Chem Lett 2020; 11:8922-8929. [PMID: 33022176 DOI: 10.1021/acs.jpclett.0c02621] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report on the findings of a blind challenge devoted to determining the frozen-core, full configuration interaction (FCI) ground-state energy of the benzene molecule in a standard correlation-consistent basis set of double-ζ quality. As a broad international endeavor, our suite of wave function-based correlation methods collectively represents a diverse view of the high-accuracy repertoire offered by modern electronic structure theory. In our assessment, the evaluated high-level methods are all found to qualitatively agree on a final correlation energy, with most methods yielding an estimate of the FCI value around -863 mEH. However, we find the root-mean-square deviation of the energies from the studied methods to be considerable (1.3 mEH), which in light of the acclaimed performance of each of the methods for smaller molecular systems clearly displays the challenges faced in extending reliable, near-exact correlation methods to larger systems. While the discrepancies exposed by our study thus emphasize the fact that the current state-of-the-art approaches leave room for improvement, we still expect the present assessment to provide a valuable community resource for benchmark and calibration purposes going forward.
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Affiliation(s)
- Janus J Eriksen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Tyler A Anderson
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - J Emiliano Deustua
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Khaldoon Ghanem
- Max-Planck-Institut für Festkörperforschung, 70569 Stuttgart, Germany
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Mark R Hoffmann
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ilias Magoulas
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jun Shen
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Norm M Tubman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - K Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Enhua Xu
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Yuan Yao
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ali Alavi
- Max-Planck-Institut für Festkörperforschung, 70569 Stuttgart, Germany
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Sandeep Sharma
- Department of Chemistry, The University of Colorado at Boulder, Boulder, Colorado 80302, United States
| | - Seiichiro L Ten-No
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - C J Umrigar
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, United States
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz,Duesbergweg 10-14, 55128 Mainz, Germany
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9
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Levine DS, Watson MA, Jacobson LD, Dickerson CE, Yu HS, Bochevarov AD. Pattern-free generation and quantum mechanical scoring of ring-chain tautomers. J Comput Aided Mol Des 2020; 35:417-431. [PMID: 32830300 DOI: 10.1007/s10822-020-00334-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 07/21/2020] [Indexed: 11/24/2022]
Abstract
In contrast to the computational generation of conventional tautomers, the analogous operation that would produce ring-chain tautomers is rarely available in cheminformatics codes. This is partly due to the perceived unimportance of ring-chain tautomerism and partly because specialized algorithms are required to realize the non-local proton transfers that occur during ring-chain rearrangement. Nevertheless, for some types of organic compounds, including sugars, warfarin analogs, fluorescein dyes and some drug-like compounds, ring-chain tautomerism cannot be ignored. In this work, a novel ring-chain tautomer generation algorithm is presented. It differs from previously proposed solutions in that it does not rely on hard-coded patterns of proton migrations and bond rearrangements, and should therefore be more general and maintainable. We deploy this algorithm as part of a workflow which provides an automated solution for tautomer generation and scoring. The workflow identifies protonatable and deprotonatable sites in the molecule using a previously described approach based on rapid micro-pKa prediction. These data are used to distribute the active protons among the protonatable sites exhaustively, at which point alternate resonance structures are considered to obtain pairs of atoms with opposite formal charge. These pairs are connected with a single bond and a 3D undistorted geometry is generated. The scoring of the generated tautomers is performed with a subsequent density functional theory calculation employing an implicit solvent model. We demonstrate the performance of our workflow on several types of organic molecules known to exist in ring-chain tautomeric equilibria in solution. In particular, we show that some ring-chain tautomers not found using previously published algorithms are successfully located by ours.
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Affiliation(s)
- Daniel S Levine
- Schrödinger, Inc., 120 West 45th St, New York, NY, 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 120 West 45th St, New York, NY, 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 120 West 45th St, New York, NY, 10036, USA.,Schrödinger, Inc., Suite 1300, 101 SW Main Street, Portland, OR, 97204, USA
| | - Claire E Dickerson
- Schrödinger, Inc., 120 West 45th St, New York, NY, 10036, USA.,College of Chemistry & Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Haoyu S Yu
- Schrödinger, Inc., 120 West 45th St, New York, NY, 10036, USA
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10
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Mao Y, Levine DS, Loipersberger M, Horn PR, Head-Gordon M. Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals. Phys Chem Chem Phys 2020; 22:12867-12885. [PMID: 32510096 DOI: 10.1039/d0cp01933j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H2O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H2O) and ˙OH(H2O)2), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH3CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
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11
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Levine DS, Hait D, Tubman NM, Lehtola S, Whaley KB, Head-Gordon M. CASSCF with Extremely Large Active Spaces Using the Adaptive Sampling Configuration Interaction Method. J Chem Theory Comput 2020; 16:2340-2354. [PMID: 32109055 DOI: 10.1021/acs.jctc.9b01255] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complete active space self-consistent field (CASSCF) method is the principal approach employed for studying strongly correlated systems. However, exact CASSCF can only be performed on small active spaces of ∼20 electrons in ∼20 orbitals due to exponential growth in the computational cost. We show that employing the Adaptive Sampling Configuration Interaction (ASCI) method as an approximate Full CI solver in the active space allows CASSCF-like calculations within chemical accuracy (<1 kcal/mol for relative energies) in active spaces with more than ∼50 active electrons in ∼50 active orbitals, significantly increasing the sizes of systems amenable to accurate multiconfigurational treatment. The main challenge with using any selected CI-based approximate CASSCF is the orbital optimization problem; they tend to exhibit large numbers of local minima in orbital space due to their lack of invariance to active-active rotations (in addition to the local minima that exist in exact CASSCF). We highlight methods that can avoid spurious local extrema as a practical solution to the orbital optimization problem. We employ ASCI-SCF to demonstrate a lack of polyradical character in moderately sized periacenes with up to 52 correlated electrons and compare against heat-bath CI on an iron porphyrin system with more than 40 correlated electrons.
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Affiliation(s)
- Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Norm M Tubman
- Quantum Artificial Intelligence Lab (QuAIL), Exploration Technology Directorate, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Susi Lehtola
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - K Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
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12
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Tubman NM, Freeman CD, Levine DS, Hait D, Head-Gordon M, Whaley KB. Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method. J Chem Theory Comput 2020; 16:2139-2159. [DOI: 10.1021/acs.jctc.8b00536] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norm M. Tubman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - C. Daniel Freeman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - Daniel S. Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - K. Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
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13
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Levine DS. One or two minds? Neural network modeling of decision making by the unified self. Neural Netw 2019; 120:74-85. [DOI: 10.1016/j.neunet.2019.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/14/2019] [Accepted: 08/09/2019] [Indexed: 11/28/2022]
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14
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Hait D, Tubman NM, Levine DS, Whaley KB, Head-Gordon M. What Levels of Coupled Cluster Theory Are Appropriate for Transition Metal Systems? A Study Using Near-Exact Quantum Chemical Values for 3d Transition Metal Binary Compounds. J Chem Theory Comput 2019; 15:5370-5385. [PMID: 31465217 DOI: 10.1021/acs.jctc.9b00674] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition metal compounds are traditionally considered to be challenging for standard quantum chemistry approximations like coupled cluster (CC) theory, which are usually employed to validate lower level methods like density functional theory (DFT). To explore this issue, we present a database of bond dissociation energies (BDEs) for 74 spin states of 69 diatomic species containing a 3d transition metal atom and a main group element, in the moderately sized def2-SVP basis. The presented BDEs appear to have an (estimated) 3σ error less than 1 kJ/mol relative to the exact solutions to the nonrelativistic Born-Oppenheimer Hamiltonian. These benchmark values were used to assess the performance of a wide range of standard single reference CC models, as the results should be beneficial for understanding the limitations of these models for transition metal systems. We find that interactions between metals and monovalent ligands like hydride and fluoride are well described by CCSDT. Similarly, CCSDTQ appears to be adequate for bonds between metals and nominally divalent ligands like oxide and sulfide. However, interactions with polyvalent ligands like nitride and carbide are more challenging, with even CCSDTQ(P)Λ yielding errors on the scale of a few kJ/mol. We also find that many perturbative and iterative approximations to higher order terms either yield disappointing results or actually worsen the performance relative to the baseline low level CC method, indicating that complexity does not always guarantee accuracy.
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Affiliation(s)
- Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Norman M Tubman
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Quantum Artificial Intelligence Lab. (QuAIL), Exploration Technology Directorate , NASA Ames Research Center , Moffett Field , California 94035 , United States
| | - Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - K Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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15
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Cai IC, Ziegler MS, Bunting PC, Nicolay A, Levine DS, Kalendra V, Smith PW, Lakshmi KV, Tilley TD. Monomeric, Divalent Vanadium Bis(arylamido) Complexes: Linkage Isomerism and Reactivity. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Irene C. Cai
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Micah S. Ziegler
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Philip C. Bunting
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Amélie Nicolay
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Vidmantas Kalendra
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Patrick W. Smith
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - T. Don Tilley
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Affiliation(s)
- Micah S. Ziegler
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nicole A. Torquato
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Amélie Nicolay
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hasan Celik
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - T. Don Tilley
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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17
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Levine DS, Tilley TD, Andersen RA. Efficient and selective catalysis for hydrogenation and hydrosilation of alkenes and alkynes with PNP complexes of scandium and yttrium. Chem Commun (Camb) 2018; 53:11881-11884. [PMID: 29043320 DOI: 10.1039/c7cc06417a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scandium and yttrium congeneric complexes, supported by a monoanionic PNP ligand, were studied as catalysts for alkene hydrogenation and hydrosilation, and alkyne semihydrogenation and semihydrosilation. The yttrium congener was found to be much more active in all cases, but this greater activity is accompanied by more rapid catalyst decomposition and therefore higher total yields for some of the reactions with the scandium catalyst. Calculations indicate that the reactions may proceed via σ-bond metathesis of the alkyl complexes to form metal hydride intermediates into which alkenes/alkynes insert.
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Affiliation(s)
- Daniel S Levine
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA.
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18
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Kiel GR, Patel SC, Smith PW, Levine DS, Tilley TD. Expanded Helicenes: A General Synthetic Strategy and Remarkable Supramolecular and Solid-State Behavior. J Am Chem Soc 2017; 139:18456-18459. [PMID: 29215272 DOI: 10.1021/jacs.7b10902] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A divergent synthetic strategy allowed access to several members of a new class of helicenes, the "expanded helicenes", which are composed of alternating linearly and angularly fused rings. The strategy is based on a three-fold, partially intermolecular [2+2+n] (n = 1 or 2) cycloaddition with substrates containing three diyne units. Investigation of aggregation behavior, both in solution and in the solid state, revealed that one of these compounds forms an unusual homochiral, π-stacked dimer via an equilibrium that is slow on the NMR time scale. The versatility of the method was harnessed to access a selenophene-annulated expanded helicene that, in contrast to its benzannulated analogue, exhibits long-range π-stacking in the solid state. The new helicenes possess low racemization barriers, as demonstrated by dynamic 1H NMR spectroscopy.
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Affiliation(s)
- Gavin R Kiel
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Sajan C Patel
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Patrick W Smith
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Daniel S Levine
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
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19
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Guerra-García P, Hirsch S, Levine DS, Taj MM. Preliminary experience on the use of PET/CT in the management of pediatric post-transplant lymphoproliferative disorder. Pediatr Blood Cancer 2017; 64. [PMID: 28612477 DOI: 10.1002/pbc.26685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/11/2017] [Accepted: 05/24/2017] [Indexed: 11/11/2022]
Abstract
INTRODUCTION Post-transplant lymphoproliferative disorder (PTLD) is a well-known complication following prolonged immunosuppression. Contrary to other lymphomas, there is no standardized imaging approach to assess PTLD either at staging or for response to therapy. Positron emission tomography/computed tomography (PET/CT) is an imaging modality that has proven to be useful in lymphoma. However, there is still limited data concerning its use in pediatric PTLD. Our study evaluates the use of PET/CT in pediatric PTLD at our institution. METHODS To assess the role of PET/CT in pediatric PTLD, we reviewed the pediatric patients with PTLD who had undergone PET/CT at our institution between 2000 and 2016. RESULTS Nine patients were identified. Six had PET/CT at diagnosis. All lesions seen on CT were identified with PET/CT. Fourteen PET/CTs were done during treatment. Eight PET/CTs were negative, including three where CT showed areas of uncertain significance. In these cases, PET/CT helped us to stop treatment and the patients remain in remission after a long follow-up (mean 74.3 months; range 12.4-180.9 months). PET/CT revealed additional disease in two cases, therefore treatment was intensified. Six biopsies and close follow-up was done to confirm PET/CT results. In one case, PET/CT did not identify central nervous system involvement demonstrated on magnetic resonance imaging. CONCLUSION PET/CT may have an important role in the staging and follow-up of pediatric PTLD. In our cohort, PET/CT was helpful in staging and assessing treatment response and in clarifying equivocal findings on other imaging modalities.
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Affiliation(s)
- Pilar Guerra-García
- Pediatric Oncology, The Royal Marsden Hospital, Sutton, UK.,Pediatric Hematology and Oncology, University Hospital 12 de Octubre, Madrid, Spain
| | - Steffen Hirsch
- Pediatric Oncology, The Royal Marsden Hospital, Sutton, UK.,Pediatric Hematology and Oncology, University Hospital Cologne, Cologne, Germany
| | - Daniel S Levine
- Department of Nuclear Medicine & PET/CT, The Royal Marsden Hospital, Sutton, UK
| | - Mary M Taj
- Pediatric Oncology, The Royal Marsden Hospital, Sutton, UK
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20
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Abstract
An energy decomposition analysis (EDA) for single chemical bonds is presented within the framework of Kohn-Sham density functional theory based on spin projection equations that are exact within wave function theory. Chemical bond energies can then be understood in terms of stabilization caused by spin-coupling augmented by dispersion, polarization, and charge transfer in competition with destabilizing Pauli repulsions. The EDA reveals distinguishing features of chemical bonds ranging across nonpolar, polar, ionic, and charge-shift bonds. The effect of electron correlation is assessed by comparison with Hartree-Fock results. Substituent effects are illustrated by comparing the C-C bond in ethane against that in bis(diamantane), and dispersion stabilization in the latter is quantified. Finally, three metal-metal bonds in experimentally characterized compounds are examined: a [Formula: see text]-[Formula: see text] dimer, the [Formula: see text]-[Formula: see text] bond in dizincocene, and the Mn-Mn bond in dimanganese decacarbonyl.
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Affiliation(s)
- Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA 94720;
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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21
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22
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Nguyen AI, Wang J, Levine DS, Ziegler MS, Tilley TD. Synthetic control and empirical prediction of redox potentials for Co 4O 4 cubanes over a 1.4 V range: implications for catalyst design and evaluation of high-valent intermediates in water oxidation. Chem Sci 2017; 8:4274-4284. [PMID: 29081963 PMCID: PMC5635813 DOI: 10.1039/c7sc00627f] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/03/2017] [Indexed: 01/12/2023] Open
Abstract
The oxo-cobalt cubane unit [Co4O4] is of interest as a homogeneous oxygen-evolution reaction (OER) catalyst, and as a functional mimic of heterogeneous cobalt oxide OER catalysts. The synthesis of several new cubanes allows evaluation of redox potentials for the [Co4O4] cluster, which are highly sensitive to the ligand environment and span a remarkable range of 1.42 V. The [CoIII4O4]4+/[CoIII3CoIVO4]5+ and [CoIII3CoIVO4]5+/[CoIII2CoIV2O4]6+ redox potentials are reliably predicted by the pKas of the ligands. Hydrogen bonding is also shown to significantly raise the redox potentials, by ∼500 mV. The potential-pKa correlation is used to evaluate the feasibility of various proposed OER catalytic intermediates, including high-valent Co-oxo species. The synthetic methods and structure-reactivity relationships developed by these studies should better guide the design of new cubane-based OER catalysts.
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Affiliation(s)
- Andy I Nguyen
- Department of Chemistry , University of California , Berkeley , California 94720-1460 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - Jianing Wang
- Department of Chemistry , University of California , Berkeley , California 94720-1460 , USA .
| | - Daniel S Levine
- Department of Chemistry , University of California , Berkeley , California 94720-1460 , USA .
| | - Micah S Ziegler
- Department of Chemistry , University of California , Berkeley , California 94720-1460 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
| | - T Don Tilley
- Department of Chemistry , University of California , Berkeley , California 94720-1460 , USA .
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , USA
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23
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Abstract
This work reports an approach to variationally quantify orbital contraction in chemical bonds by an extension of an energy decomposition analysis (EDA). The orbital contraction energy is defined as the energy lowering due to optimization of the isolated fragments (that combine to form the bond) with a specially constructed virtual set of contraction/expansion functions. This set contains one function per occupied orbital, obtained as the linear response to scaling the nuclear charges. EDA results for a variety of single bonds show substantial changes in the importance of orbital contraction; it plays a critical role for bonds to H but only a very minor role in the bonds between heavier elements. Additionally, energetic stabilization due to rehybridization is separated from inductive polarization by the fact that no mixing with virtual orbitals is involved and is shown to be significant in fragments such as NH2, OH, and F.
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Affiliation(s)
- Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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24
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Nguyen AI, Suess DLM, Darago LE, Oyala PH, Levine DS, Ziegler MS, Britt RD, Tilley TD. Manganese-Cobalt Oxido Cubanes Relevant to Manganese-Doped Water Oxidation Catalysts. J Am Chem Soc 2017; 139:5579-5587. [PMID: 28347135 DOI: 10.1021/jacs.7b01792] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Incorporation of Mn into an established water oxidation catalyst based on a Co(III)4O4 cubane was achieved by a simple and efficient assembly of permanganate, cobalt(II) acetate, and pyridine to form the cubane oxo cluster MnCo3O4(OAc)5py3 (OAc = acetate, py = pyridine) (1-OAc) in good yield. This allows characterization of electronic and chemical properties for a manganese center in a cobalt oxide environment, and provides a molecular model for Mn-doped cobalt oxides. The electronic properties of the cubane are readily tuned by exchange of the OAc- ligand for Cl- (1-Cl), NO3- (1-NO3), and pyridine ([1-py]+). EPR spectroscopy, SQUID magnetometry, and DFT calculations thoroughly characterized the valence assignment of the cubane as [MnIVCoIII3]. These cubanes are redox-active, and calculations reveal that the Co ions behave as the reservoir for electrons, but their redox potentials are tuned by the choice of ligand at Mn. This MnCo3O4 cubane system represents a new class of easily prepared, versatile, and redox-active oxido clusters that should contribute to an understanding of mixed-metal, Mn-containing oxides.
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Affiliation(s)
- Andy I Nguyen
- Department of Chemistry, University of California at Berkeley , Berkeley, California 94720-1460, United States
| | - Daniel L M Suess
- Department of Chemistry, University of California at Davis , Davis, California 95616, United States
| | - Lucy E Darago
- Department of Chemistry, University of California at Berkeley , Berkeley, California 94720-1460, United States
| | - Paul H Oyala
- Department of Chemistry, University of California at Davis , Davis, California 95616, United States
| | - Daniel S Levine
- Department of Chemistry, University of California at Berkeley , Berkeley, California 94720-1460, United States
| | - Micah S Ziegler
- Department of Chemistry, University of California at Berkeley , Berkeley, California 94720-1460, United States
| | - R David Britt
- Department of Chemistry, University of California at Davis , Davis, California 95616, United States
| | - T Don Tilley
- Department of Chemistry, University of California at Berkeley , Berkeley, California 94720-1460, United States
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25
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Levine DS, Horn PR, Mao Y, Head-Gordon M. Variational Energy Decomposition Analysis of Chemical Bonding. 1. Spin-Pure Analysis of Single Bonds. J Chem Theory Comput 2016; 12:4812-4820. [DOI: 10.1021/acs.jctc.6b00571] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel S. Levine
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Paul R. Horn
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yuezhi Mao
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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26
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Affiliation(s)
- Daniel S. Levine
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - T. Don Tilley
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Richard A. Andersen
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
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27
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Ziegler MS, Levine DS, Lakshmi KV, Tilley TD. Aryl Group Transfer from Tetraarylborato Anions to an Electrophilic Dicopper(I) Center and Mixed-Valence μ-Aryl Dicopper(I,II) Complexes. J Am Chem Soc 2016; 138:6484-91. [PMID: 27176131 DOI: 10.1021/jacs.6b00802] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of discrete, cationic binuclear μ-aryl dicopper complexes [Cu2(μ-η(1):η(1)-Ar)DPFN]X (Ar = C6H5, 3,5-(CF3)2C6H3, and C6F5; DPFN = 2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine; X = BAr4(-) and NTf2(-); Tf = SO2CF3) was achieved by treatment of a dicopper complex [Cu2(μ-η(1):η(1)-NCCH3)DPFN]X2 (X = PF6(-) and NTf2(-)) with tetraarylborates. Structural characterization revealed symmetrically bridging aryl groups, and (1)H NMR spectroscopy evidenced the same structure in solution at 24 °C. Electrochemical investigation of the resulting arylcopper complexes uncovered reversible redox events that led to the synthesis and isolation of a rare mixed-valence organocopper complex [Cu2(μ-η(1):η(1)-Ph)DPFN](NTf2)2 in high yield. The solid-state structure of the mixed-valence μ-phenyl complex exhibits inequivalent copper centers, despite a short Cu···Cu distance. Electronic and variable-temperature electron paramagnetic resonance spectroscopy of the mixed-valence μ-phenyl complex suggest that the degree of spin localization is temperature-dependent, with a high degree of spin localization observed at lower temperatures. Electronic structure calculations agree with the experimental results and suggest that the spin is localized almost entirely on one metal center.
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Affiliation(s)
- Micah S Ziegler
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Daniel S Levine
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - T Don Tilley
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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28
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Liberman-Martin AL, Levine DS, Liu W, Bergman RG, Tilley TD. Biaryl Reductive Elimination Is Dramatically Accelerated by Remote Lewis Acid Binding to a 2,2′-Bipyrimidyl–Platinum Complex: Evidence for a Bidentate Ligand Dissociation Mechanism. Organometallics 2016. [DOI: 10.1021/acs.organomet.5b01003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Daniel S. Levine
- Department
of Chemistry, University of California−Berkeley, Berkeley, California 94720, United States
| | - Wenjun Liu
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert G. Bergman
- Department
of Chemistry, University of California−Berkeley, Berkeley, California 94720, United States
| | - T. Don Tilley
- Department
of Chemistry, University of California−Berkeley, Berkeley, California 94720, United States
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29
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Liberman-Martin AL, Levine DS, Ziegler MS, Bergman RG, Tilley TD. Lewis acid–base interactions between platinum(ii) diaryl complexes and bis(perfluorophenyl)zinc: strongly accelerated reductive elimination induced by a Z-type ligand. Chem Commun (Camb) 2016; 52:7039-42. [DOI: 10.1039/c6cc02433e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Z-type interactions between bis(perfluorophenyl)zinc and platinum(ii) diaryl complexes supported by 1,10-phenanthroline (phen), 2,2′-bipyridine (bpy), and bis(dimethylphosphino)ethane (dmpe) ligands are reported.
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Affiliation(s)
| | | | | | | | - T. Don Tilley
- Department of Chemistry
- University of California
- Berkeley
- USA
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30
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31
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Affiliation(s)
- Daniel S. Levine
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - T. Don Tilley
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Richard A. Andersen
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
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32
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Kiumarsi B, Lewis FL, Levine DS. Optimal control of nonlinear discrete time-varying systems using a new neural network approximation structure. Neurocomputing 2015. [DOI: 10.1016/j.neucom.2014.12.067] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Weichman ML, Kim JB, DeVine JA, Levine DS, Neumark DM. Vibrational and Electronic Structure of the α- and β-Naphthyl Radicals via Slow Photoelectron Velocity-Map Imaging. J Am Chem Soc 2015; 137:1420-3. [DOI: 10.1021/ja5124896] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marissa L. Weichman
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jongjin B. Kim
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jessalyn A. DeVine
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel S. Levine
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel M. Neumark
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Oakton E, Vilé G, S. Levine D, Zocher E, Baudouin D, Pérez-Ramírez J, Copéret C. Silver nanoparticles supported on passivated silica: preparation and catalytic performance in alkyne semi-hydrogenation. Dalton Trans 2014; 43:15138-42. [DOI: 10.1039/c4dt01320d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When X = SiMe3, small (2.1 ± 0.5 nm) densely packed silica-supported Ag particles can be prepared, which show an improved catalytic activity (per gram) whilst maintaining high alkene selectivity.
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Affiliation(s)
- Emma Oakton
- Laboratory of Inorganic Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
| | - Gianvito Vilé
- Institute for Chemical and Bioengineering
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
| | - Daniel S. Levine
- Université de Lyon
- Institut de Chimie de Lyon
- UMR C2P2 CNRS-UCBL-ESCPE Lyon
- 69616 Villeurbanne, France
- Department of Chemistry
| | - Eva Zocher
- Laboratory of Inorganic Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
- Université de Lyon
| | - David Baudouin
- Laboratory of Inorganic Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
| | - Javier Pérez-Ramírez
- Institute for Chemical and Bioengineering
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
| | - Christophe Copéret
- Laboratory of Inorganic Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zürich
- Zürich, Switzerland
- Université de Lyon
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Tee MC, Chan SK, Nguyen V, Strugnell SS, Yang J, Jones S, Tiwari P, Levine DS, Wiseman SM. Incremental value and clinical impact of neck sonography for primary hyperparathyroidism: a risk-adjusted analysis. Can J Surg 2013; 56:325-31. [PMID: 24067517 DOI: 10.1503/cjs.015612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Despite the different preoperative imaging modalities available for parathyroid adenoma localization, there is currently no uniform consensus on the most appropriate preoperative imaging algorithm that should be routinely followed prior to the surgical management of primary hyperparathyroidism (PHPT). We sought to determine the incremental value of adding neck ultrasonography to scintigraphy-based imaging tests. METHODS In a single institution, surgically naive patients with PHPT underwent the following localization studies before parathyroidectomy: 1) Tc-99m sestamibi imaging with single photon emission computed tomography/computed tomography (SPECT/CT) or Tc-99m sestamibi imaging with SPECT alone, or 2) ultrasonography in addition to those tests. We retrospectively collected data and performed a multivariate analysis comparing group I (single study) to group II (addition of ultrasonography) and risk of bilateral (BNE) compared with unilateral (UNE) neck exploration. RESULTS Our study included 208 patients. Group II had 0.45 times the odds of BNE versus UNE compared with group I (unadjusted odds ratio [OR] 0.45, 95% confidence interval [CI] 0.25-0.81, p = 0.008). When adjusting for patient age, sex, preoperative calcium level, use of intraoperative PTH monitoring, preoperative PTH level, adenoma size, and number of abnormal parathyroid glands, Group II had 0.48 times the odds of BNE versus UNE compared with group I (adjusted OR 0.48, 95% CI 0.23-1.03, p = 0.06). In a subgroup analysis, only the addition of ultrasonography to SPECT decreased the risk of undergoing BNE compared with SPECT alone (unadjusted OR 0.40, 95% CI 0.19-0.84, p = 0.015; adjusted OR 0.38, 95% CI 0.15-0.96, p = 0.043). CONCLUSION The addition of ultrasonography to SPECT, but not to SPECT/CT, has incremental value in decreasing the extent of surgery during parathyroidectomy, even after adjusting for multiple confounding factors.
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Affiliation(s)
- May C Tee
- From St. Paul's Hospital, Department of Surgery and University of British Columbia, Vancouver, BC
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Marinescu SC, Levine DS, Zhao Y, Schrock RR, Hoveyda AH. Isolation of pure disubstituted E olefins through Mo-catalyzed Z-selective ethenolysis of stereoisomeric mixtures. J Am Chem Soc 2011; 133:11512-4. [PMID: 21718001 DOI: 10.1021/ja205002v] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoaryloxide-pyrrolide (MAP) complexes of molybdenum were employed for the selective ethenolysis of 1,2-disubstituted Z olefins in the presence of the corresponding E olefins. Reactions were performed in the presence of 0.02-3.0 mol % catalyst at 22 °C under 20 atm ethylene. We have demonstrated that the Z isomer of an easily accessible E:Z mixture can be destroyed through ethenolysis and the E alkene thereby isolated readily in high yield and exceptional stereoisomeric purity.
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Affiliation(s)
- Smaranda C Marinescu
- Department of Chemistry 6-331, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Paulus PB, Levine DS, Brown V, Minai AA, Doboli S. Modeling Ideational Creativity in Groups: Connecting Cognitive, Neural, and Computational Approaches. Small Group Research 2010. [DOI: 10.1177/1046496410369561] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Many creative activities take place in a group context, whether in short-term meetings, work teams, or by means of electronic interaction. The group creative process necessarily involves the exchange of ideas or information. Recent models of group creativity have focused on the cognitive underpinnings of this type of group creative process, primarily based on the group brainstorming literature. The authors describe an elaborated computational version of their cognitive model of group creativity and related computational models, and highlight some plausible neural bases for various involved processes. The major findings and theoretical perspectives in this literature are summarized and some potentially fruitful empirical and theoretical directions are highlighted. It is hoped that this comprehensive treatment can be a basis for integrating the present literature and providing useful predictions for further research on this topic.
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Abstract
Theories of cognitive processes, such as decision making and creative problem solving, for a long time neglected the contributions of emotion or affect in favor of analysis based on use of deliberative rules to optimize performance. Since the 1990s, emotion has increasingly been incorporated into theories of these cognitive processes. Some theorists have in fact posited a “dual-systems approach” to understanding decision making and high-level cognition. One system is fast, emotional, and intuitive, while the other is slow, rational, and deliberative. However, one’s understanding of the relevant brain regions indicate that emotional and rational processes are deeply intertwined, with each exerting major influences on the functioning of the other. Also presented in this paper are neural network modeling principles that may capture the interrelationships of emotion and cognition. The authors also review evidence that humans, and possibly other mammals, possess a “knowledge instinct,” which acts as a drive to make sense of the environment. This drive typically incorporates a strong affective component in the form of aesthetic fulfillment or dissatisfaction.
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Levine DS. Evolution or culture, but music may soothe the savage breast. Phys Life Rev 2010; 7:39-40; discussion 49-54. [DOI: 10.1016/j.plrev.2010.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 10/20/2022]
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Parks RW, Long DL, Levine DS, Crockett DJ, McGeer EG, McGeer PL, Dalton IE, Zec RF, Becker RE, Coburn KL, Siler G, Nelson ME, Bower JM. Parallel Distributed Processing and Neural Networks: Origins, Methodology and Cognitive Functions. Int J Neurosci 2009. [DOI: 10.3109/00207459109080640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Iyer LR, Doboli S, Minai AA, Brown VR, Levine DS, Paulus PB. Neural dynamics of idea generation and the effects of priming. Neural Netw 2009; 22:674-86. [DOI: 10.1016/j.neunet.2009.06.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 05/31/2009] [Accepted: 06/25/2009] [Indexed: 11/28/2022]
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Levine DS. Brain pathways for cognitive-emotional decision making in the human animal. Neural Netw 2009; 22:286-93. [DOI: 10.1016/j.neunet.2009.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 03/07/2009] [Accepted: 03/13/2009] [Indexed: 11/26/2022]
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Abstract
Bone marrow transplantation is frequently performed to restore hematologic and immunologic competence after chemotherapy and radiation therapy for a range of childhood malignancies, as well as to treat various congenital conditions in which hematologic and immunologic functions are depressed or absent. Potentially devastating complications may occur during the pre-engraftment period after bone marrow transplantation, when marrow aplasia may supervene for several weeks until engraftment occurs, as well as during the post-engraftment period (the 3 months after engraftment) and in subsequent months and years. Complications of bone marrow transplantation may be classified either according to the time interval between transplantation and the occurrence of the complication or according to the organ system affected. The range of complications that may affect the central nervous system and the rest of the body may be detected with ultrasonography, computed tomography, and magnetic resonance imaging. Neurologic, paranasal sinus, pulmonary, and abdominopelvic complications all may be seen after bone marrow transplantation. Graft-versus-host disease and lymphoproliferative disorders also may occur. The increasing use of bone marrow transplantation mandates that the radiologist be familiar with the full range of potential complications and their imaging appearances.
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Affiliation(s)
- Daniel S Levine
- Department of Diagnostic Imaging, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
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Parks RW, Thiyagesh SN, Levine DS, Lee KH, Bhaker R, Mysore A, Ingram L, Young C, Birkett P, Pegg E, Woodruff PWR. Executive dysfunction screening test for neuropsychiatric disorders. Int J Neurosci 2007; 117:507-18. [PMID: 17365131 DOI: 10.1080/00207450600773525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Analogies Understanding Test (AUT) was developed as a brief cognitive screening task of executive problem solving. A few of the test items at the beginning are "facilitated" as a means of engaging patients. Individuals with schizophrenia and mild Alzheimer's Disease (AD) made significantly less correct responses than their control groups. The schizophrenia patients, but not AD patients, made significantly more perseverations than controls on the AUT. As expected, AUT performance in schizophrenia patients correlated with the Wisconsin Card Sorting test measures. Preliminary findings suggest that the AUT test may be useful as a measure of executive dysfunction in neuropsychiatric patients.
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Affiliation(s)
- Randolph W Parks
- University of Sheffield School of Medicine, Sheffield, United Kingdom.
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Chaudry G, Navarro OM, Levine DS, Oudjhane K. Abdominal manifestations of cystic fibrosis in children. Pediatr Radiol 2006; 36:233-40. [PMID: 16391928 DOI: 10.1007/s00247-005-0049-2] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2005] [Revised: 09/29/2005] [Accepted: 10/10/2005] [Indexed: 10/25/2022]
Abstract
Pulmonary complications remain the main cause of mortality in cystic fibrosis, but the presenting symptoms in children are often related to gastrointestinal or pancreaticobiliary disease. Furthermore, abdominal manifestations are now seen throughout childhood, from infancy to adolescence. The child might present in the neonatal period with meconium ileus or its attendant complications. The older child might present with distal intestinal obstruction syndrome or colonic stricture secondary to high doses of pancreatic enzyme replacement. Less-common gastrointestinal manifestations include intussusception, duodenitis and fecal impaction of the appendix. Most children also show evidence of exocrine pancreatic deficiency. Radiologically, the combination of fat deposition and pancreatic fibrosis leads to varying CT and MR appearances. A higher than normal incidence of pancreatic cysts and calcification is also seen. Decreased transport of water and chloride also increases the viscosity of bile, with subsequent obstruction of the biliary ductules. If extensive, this can progress to obstructive cirrhosis, portal hypertension and esophageal varices. Diffuse fatty infiltration, hypersplenism and gallstones are also commonly seen in these patients. We present a pictorial review of the radiological appearance of these abdominal manifestations. The conditions are dealt with individually, together with typical appearances in various imaging modalities.
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Affiliation(s)
- Gulraiz Chaudry
- Department of Diagnostic Imaging, The Hospital for Sick Children, University of Toronto, 555 University Ave., Toronto, Ontario M5G 1X8, Canada.
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Coleman SL, Brown VR, Levine DS, Mellgren RL. A neural network model of foraging decisions made under predation risk. Cognitive, Affective, & Behavioral Neuroscience 2005; 5:434-51. [PMID: 16541813 DOI: 10.3758/cabn.5.4.434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This article develops the cognitive-emotional forager (CEF) model, a novel application of a neural network to dynamical processes in foraging behavior. The CEF is based on a neural network known as the gated dipole, introduced by Grossberg, which is capable of representing short-term affective reactions in a manner similar to Solomon and Corbit's (1974) opponent process theory. The model incorporates a trade-off between approach toward food and avoidance of predation under varying levels of motivation induced by hunger. The results of simulations in a simple patch selection paradigm, using a lifetime fitness criterion for comparison, indicate that the CEF model is capable of nearly optimal foraging and outperforms a run-of-luck rule-of-thumb model. Models such as the one presented here can illuminate the underlying cognitive and motivational components of animal decision making.
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Affiliation(s)
- Scott L Coleman
- University of North Texas Health Science Center, Fort Worth, Texas, USA
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