1
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Amudhavalli SM, Paolillo V, Lawson C, Patterson M, Kussmann J, Nopper AJ, Lypka M, Saunders C. Novel blended SNRPE-related spliceosomopathy phenotype characterized by microcephaly and congenital atrichia. Am J Med Genet A 2023; 191:1425-1429. [PMID: 36814386 DOI: 10.1002/ajmg.a.63149] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/14/2023] [Accepted: 01/20/2023] [Indexed: 02/24/2023]
Abstract
Variants in genes encoding core components of the spliceosomes are associated with craniofacial syndromes, collectively called craniofacial spliceosomopathies. SNRPE encodes a core component of pre-mRNA processing U-rich small nuclear ribonuclear proteins (UsnRNPs). Heterozygous variants in SNRPE have been reported in six families with isolated hypotrichosis simplex in addition to one case of isolated non syndromic congenital microcephaly. Here, we report a patient with a novel blended phenotype of microcephaly and congenital atrichia with multiple congenital anomalies due to a de novo intronic SNRPE deletion, c.82-28_82-16del, which results in exon skipping. As discussed within, this phenotype, which we propose be named SNRPE-related syndromic microcephaly and hypotrichosis, overlaps other craniofacial splicesosomopathies.
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Affiliation(s)
- Shivarajan M Amudhavalli
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - V Paolillo
- Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Caitlin Lawson
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Melanie Patterson
- Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - J Kussmann
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - A J Nopper
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Division of Dermatology, Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - M Lypka
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Carol Saunders
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Clinical Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
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2
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Laqua H, Dietschreit JCB, Kussmann J, Ochsenfeld C. Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units. J Chem Theory Comput 2022; 18:6010-6020. [PMID: 36136665 DOI: 10.1021/acs.jctc.2c00509] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The computationally very demanding evaluation of the 4-center-2-electron (4c2e) integrals and their respective integral derivatives typically represents the major bottleneck within hybrid Kohn-Sham density functional theory molecular dynamics simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardware─especially when combined with graphics processing unit acceleration─improving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine-thymine and guanine-cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems.
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Affiliation(s)
- Henryk Laqua
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Johannes C B Dietschreit
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany.,Max Planck Institute for Solid State Research, 70569 Stuttgart, Germany
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3
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Sacchetta F, Graf D, Laqua H, Ambroise MA, Kussmann J, Dreuw A, Ochsenfeld C. An effective sub-quadratic scaling atomic-orbital reformulation of the scaled opposite-spin RI-CC2 ground-state model using Cholesky-decomposed densities and an attenuated Coulomb metric. J Chem Phys 2022; 157:104104. [DOI: 10.1063/5.0098719] [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: 11/14/2022] Open
Abstract
An atomic-orbital reformulation of the Laplace-transformed scaled opposite-spin (SOS) coupled cluster singles and doubles (CC2) model within the resolution of the identity (RI) approximation (SOS-RI-CC2) is presented that extends its applicability to molecules with several hundreds of atoms and triple-zeta basis sets. We exploit sparse linear algebra and an attenuated Coulomb metric to decrease the disk space demands and the computational efforts. In this way, an effective sub-quadratic computational scaling is achieved with our ω-SOS-CDD-RI-CC2 model. Moreover, Cholesky decomposition of the ground-state one-electron density matrix reduces the prefactor, allowing for an early crossover with the molecular orbital formulation. The accuracy and performance of the presented method are investigated for various molecular systems.
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Affiliation(s)
- F. Sacchetta
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - D. Graf
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - H. Laqua
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - M. A. Ambroise
- Chair of Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - A. Dreuw
- Chair of Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
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4
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Lemke Y, Graf D, Kussmann J, Ochsenfeld C. An assessment of orbital energy corrections for the direct random phase approximation and explicit σ-functionals. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2098862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Yannick Lemke
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - Daniel Graf
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
- Max Planck Institute for Solid State Research, Stuttgart, Germany
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5
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Lemke Y, Kussmann J, Ochsenfeld C. Efficient Integral-Direct Methods for Self-Consistent Reduced Density Matrix Functional Theory Calculations on Central and Graphics Processing Units. J Chem Theory Comput 2022; 18:4229-4244. [DOI: 10.1021/acs.jctc.2c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 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)
- Y. Lemke
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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6
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Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
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Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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7
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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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8
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Laqua H, Kussmann J, Ochsenfeld C. Accelerating seminumerical Fock-exchange calculations using mixed single- and double-precision arithmethic. J Chem Phys 2021; 154:214116. [PMID: 34240990 DOI: 10.1063/5.0045084] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the applicability of single-precision (fp32) floating point operations within our linear-scaling, seminumerical exchange method sn-LinK [Laqua et al., J. Chem. Theory Comput. 16, 1456 (2020)] and find that the vast majority of the three-center-one-electron (3c1e) integrals can be computed with reduced numerical precision with virtually no loss in overall accuracy. This leads to a near doubling in performance on central processing units (CPUs) compared to pure fp64 evaluation. Since the cost of evaluating the 3c1e integrals is less significant on graphic processing units (GPUs) compared to CPU, the performance gains from accelerating 3c1e integrals alone is less impressive on GPUs. Therefore, we also investigate the possibility of employing only fp32 operations to evaluate the exchange matrix within the self-consistent-field (SCF) followed by an accurate one-shot evaluation of the exchange energy using mixed fp32/fp64 precision. This still provides very accurate (1.8 µEh maximal error) results while providing a sevenfold speedup on a typical "gaming" GPU (GTX 1080Ti). We also propose the use of incremental exchange-builds to further reduce these errors. The proposed SCF scheme (i-sn-LinK) requires only one mixed-precision exchange matrix calculation, while all other exchange-matrix builds are performed with only fp32 operations. Compared to pure fp64 evaluation, this leads to 4-7× speedups for the whole SCF procedure without any significant deterioration of the results or the convergence behavior.
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Affiliation(s)
- Henryk Laqua
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
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9
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Kussmann J, Laqua H, Ochsenfeld C. Highly Efficient Resolution-of-Identity Density Functional Theory Calculations on Central and Graphics Processing Units. J Chem Theory Comput 2021; 17:1512-1521. [DOI: 10.1021/acs.jctc.0c01252] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Henryk Laqua
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
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10
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Peters LDM, Kussmann J, Ochsenfeld C. A Fermi smearing variant of the Tamm–Dancoff approximation for nonadiabatic dynamics involving S 1–S 0 transitions: Validation and application to azobenzene. J Chem Phys 2020; 153:094104. [DOI: 10.1063/5.0016487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laurens D. M. Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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11
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Peters LM, Kussmann J, Ochsenfeld C. Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics. J Phys Chem Lett 2020; 11:3955-3961. [PMID: 32374606 PMCID: PMC7304892 DOI: 10.1021/acs.jpclett.0c00320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Starting from our recently published implementation of nonadiabatic molecular dynamics (NAMD) on graphics processing units (GPUs), we explore further approaches to accelerate ab initio NAMD calculations at the time-dependent density functional theory (TDDFT) level of theory. We employ (1) the simplified TDDFT schemes of Grimme et al. and (2) the Hammes-Schiffer-Tully approach to obtain nonadiabatic couplings from finite-difference calculations. The resulting scheme delivers an accurate physical picture while virtually eliminating the two computationally most demanding steps of the algorithm. Combined with our GPU-based integral routines for SCF, TDDFT, and TDDFT derivative calculations, NAMD simulations of systems of a few hundreds of atoms at a reasonable time scale become accessible on a single compute node. To demonstrate this and to present a first, illustrative example, we perform TDDFT/MM-NAMD simulations of the rhodopsin protein.
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Affiliation(s)
- Laurens
D. M. Peters
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Jörg Kussmann
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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12
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Laqua H, Thompson TH, Kussmann J, Ochsenfeld C. Highly Efficient, Linear-Scaling Seminumerical Exact-Exchange Method for Graphic Processing Units. J Chem Theory Comput 2020; 16:1456-1468. [DOI: 10.1021/acs.jctc.9b00860] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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)
- Henryk Laqua
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Travis H. Thompson
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, Chair of Theoretical Chemistry, University of Munich (LMU), D-81377 München, Germany
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13
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Peters LM, Kussmann J, Ochsenfeld C. Nonadiabatic Molecular Dynamics on Graphics Processing Units: Performance and Application to Rotary Molecular Motors. J Chem Theory Comput 2019; 15:6647-6659. [PMID: 31763834 PMCID: PMC6909237 DOI: 10.1021/acs.jctc.9b00859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 11/29/2022]
Abstract
Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S1 lifetimes. Although all four rotors show different S1 excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies.
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Affiliation(s)
- Laurens
D. M. Peters
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Jörg Kussmann
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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14
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Musholt TJ, Bockisch A, Clerici T, Dotzenrath C, Dralle H, Goretzki PE, Hermann M, Holzer K, Karges W, Krude H, Kussmann J, Lorenz K, Luster M, Niederle B, Nies C, Riss P, Schabram J, Schabram P, Schmid KW, Simon D, Spitzweg C, Steinmüller T, Trupka A, Vorländer C, Weber T, Bartsch DK. [Update of the S2k guidelines : Surgical treatment of benign thyroid diseases]. Chirurg 2019; 89:699-709. [PMID: 29876616 DOI: 10.1007/s00104-018-0653-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 12/31/2022]
Abstract
Thyroid resections represent one of the most common operations with 76,140 interventions in the year 2016 in Germany (source Destatis). These are predominantly benign thyroid gland diseases. Recommendations for the operative treatment of benign thyroid diseases were last published by the CAEK in 2010 as S2k guidelines (Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften e.V. [AWMF] 003/002) against the background of increasingly more radical resection procedures. Hemithyroidectomy and thyroidectomy are routinely performed for benign thyroid disease in practice. The operation-specific risks show a clear increase with the extent of the resection. Therefore, weighing-up of the risk-indications ratio between unilateral lobectomy or thyroidectomy necessitates an independent evaluation of the indications for both sides. This principle in particular has been used to update the guidelines. In addition, the previously published recommendations of the CAEK for correct execution and consequences of intraoperative neuromonitoring were included into the guidelines, which in particular serve the aim to avoid bilateral recurrent laryngeal nerve paralysis. Moreover, the recommendations for the treatment of postoperative complications, such as hypoparathyroidism and postoperative infections were revised. The updated guidelines therefore represent the current state of the science as well as the resulting surgical practice.
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Affiliation(s)
- T J Musholt
- Sektion Endokrine Chirurgie der Klinik für Allgemein‑, Viszeral- und Transplantationschirurgie, Universitätsmedizin der Johannes Gutenberg Universität Mainz, Langenbeckstr. 1, 55101, Mainz, Deutschland.
| | - A Bockisch
- Klinik für Nuklearmedizin, Universitätsklinikum Essen, Hufelandstr. 55, 45147, Essen, Deutschland
| | - T Clerici
- Klinik für Chirurgie, Kantonsspital St. Gallen, 9007, St. Gallen, Schweiz
| | - C Dotzenrath
- Klinik für endokrine Chirurgie, Helios Universitätsklinikum Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Deutschland
| | - H Dralle
- Sektion Endokrine Chirurgie, Klinik für Allgemein‑, Viszeral- und Transplantationschirurgie, Universitätsklinikum Essen, Hufelandstr. 55, 45147, Essen, Deutschland
| | - P E Goretzki
- Chirurgische Klinik, Campus Charite Mitte/Campus Virchow Klinikum, Endokrine Chirurgie, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Deutschland
| | - M Hermann
- 2. Chirurgische Abteilung, Krankenanstalt Rudolfstiftung, Märzstr. 80, 1150, Wien, Österreich
| | - K Holzer
- Sektion Endokrine Chirurgie der Viszeral‑, Thorax- u. Gefäßchirurgie, Universitätsklinikum Marburg, Baldingerstr., 35043, Marburg, Deutschland
| | - W Karges
- Sektion Endokrinologie und Diabetologie - Medizinische Klinik III, Universitätsklinikum Aachen, RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - H Krude
- Klinik für Pädiatrie mit Schwerpunkt Endokrinologie und Diabetologie, Charité Berlin, Augustenburger Platz 1, 13353, Berlin, Deutschland
| | - J Kussmann
- Klinik für Endokrine Chirurgie, Schön Klinik Hamburg-Eilbeck, Dehnhaide 120, 22081, Hamburg, Deutschland
| | - K Lorenz
- Klinik u. Poliklinik f. Allgem.-, Viszeral- u. Gefäßchirurgie, Universitätsklinikum Halle, Ernst-Grube-Str. 40, 06120, Halle, Deutschland
| | - M Luster
- Nuklearmedizin, Universitätsklinikum Gießen und Marburg, GmbH, Standort Marburg, Baldingerstrass, 35041, Marburg, Deutschland
| | - B Niederle
- Sektion Endokrine Chirurgie, Franziskus Spital, Nikolsdorfergasse 32, 1050, Wien, Österreich
| | - C Nies
- Klinik für Allg.- u. Viszeralchirurgie, Marienhospital Osnabrück, Bischofsstr. 1, 49074, Osnabrück, Deutschland
| | - P Riss
- Chirurgische Universitätsklinik, Währinger Gürtel 18-20, 1090, Wien, Österreich
| | - J Schabram
- Klinik für Endokrine Chirurgie, Asklepios Klinik Lich, Goethestr. 4, 35423, Lich, Deutschland
| | - P Schabram
- Anwaltskanzlei Ratajczak & Partner, Heinrich-von-Stephan-Str. 25, 79100, Freiburg im Breisgau, Deutschland
| | - K W Schmid
- Pathologie, Universitätsklinikum Essen, Hufelandstr. 55, 45147, Essen, Deutschland
| | - D Simon
- Klinik f. Allg.- u. Viszeralchirurgie, Ev. Bethesda Krankenhaus Duisburg GmbH, Heerstr. 219, 47053, Duisburg, Deutschland
| | - Ch Spitzweg
- Medizinische Klinik und Poliklinik II, LMU Klinikum der Universität München - Campus Großhadern, Marchioninistr. 15, 81377, München, Deutschland
| | - Th Steinmüller
- Chirurgische Abteilung, Zentrum f. Allg.- u. Viszeralchirurgie, DRK-Kliniken Westend, Spandauer Damm 130, 14050, Berlin, Deutschland
| | - A Trupka
- Chirurgische Klinik, Klinikum Starnberg GmbH, Oßwaldstr. 1, 82319, Starnberg, Deutschland
| | - C Vorländer
- Endokrine Chirurgie, Bürgerhospital Frankfurt am Main, Nibelungenallee 37-41, 60318, Frankfurt am Main, Deutschland
| | - T Weber
- Klinik für Endokrine Chirurgie, Katholisches Klinikum Mainz, An der Goldgrube 11, 55131, Mainz, Deutschland
| | - D K Bartsch
- Klinik für Visceral‑, Thorax- und Gefäßchirurgie, Universitätsklinikum Gießen und Marburg, GmbH, Standort Marburg, Baldingerstrass, 35041, Marburg, Deutschland
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15
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Peters LDM, Dietschreit JCB, Kussmann J, Ochsenfeld C. Calculating free energies from the vibrational density of states function: Validation and critical assessment. J Chem Phys 2019; 150:194111. [DOI: 10.1063/1.5079643] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laurens D. M. Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Johannes C. B. Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
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16
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Affiliation(s)
- Johannes C. B. Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 München, Germany
| | - Laurens D. M. Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 München, Germany
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Laqua H, Kussmann J, Ochsenfeld C. An improved molecular partitioning scheme for numerical quadratures in density functional theory. J Chem Phys 2018; 149:204111. [DOI: 10.1063/1.5049435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Henryk Laqua
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
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18
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Laqua H, Kussmann J, Ochsenfeld C. Efficient and Linear-Scaling Seminumerical Method for Local Hybrid Density Functionals. J Chem Theory Comput 2018; 14:3451-3458. [DOI: 10.1021/acs.jctc.8b00062] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henryk Laqua
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
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Laqua H, Kussmann J, Ochsenfeld C. Communication: Density functional theory model for multi-reference systems based on the exact-exchange hole normalization. J Chem Phys 2018; 148:121101. [DOI: 10.1063/1.5025334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Henryk Laqua
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Jörg Kussmann
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry and Center for Integrated Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
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20
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Encke A, Haas S, Krauspe R, Riess H, Stürmer KM, Kopp I, Lorenz W, Beckmann MW, Breddin HK, Gams E, Gerhardus A, Gogarten W, Joppich I, Kujath P, Kussmann J, Mittelkötter U, Mittelkötter U, Partsch H, Pauschert R, Rabe E, Rohde U, Schellong S, Steudel I, Swoboda L, Ulsenheimer K, Vogt PM, Walz P, Weber H. Stationäre und ambulante Thromboembolieprophylaxe in der Chirurgie und der perioperativen Medizin. Phlebologie 2018. [DOI: 10.1055/s-0038-1639002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Präambel: Alle aufgeführten medizinischen Fachgesellschaften haben sich zusammengefunden, um die früheren verschiedenen Empfehlungen zur Thromboembolieprophylaxe zu aktualisieren und in einer gemeinsamen »Leitlinie zur stationären und ambulanten Thromboembolieprophylaxe in der perioperativen Medizin« zusammenzufassen. Dazu wurden in einem ersten Schritt durch eine Konsensuskonferenz mit nominalem Gruppenprozess die früheren Empfehlungen (Fassung vom Juni 2000) überarbeitet (S2-Leitlinie). Dies erschien notwendig, um neue Therapieprinzipien und neu zugelassene Medikamente zu berücksichtigen. Als nächster Schritt erfolgt die Weiterentwicklung der vorliegenden Leitlinie nach der Vorgaben der 3. Stufe der Leitlinienentwicklung der AWMF (S3-Leitlinie).
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Abstract
ZusammenfassungDer Wert einer präoperativen gerinnungsanalytischen Screening-Untersuchung zur Erhöhung der Patientensicherheit wird kontrovers diskutiert. In einer prospektiven Beobachtungsstudie mit dem Endpunkt Blutungskomplikation wurde bei 638 Patienten aus der elektiven Viszeralchirurgie die Bedeutung der präoperativen Bestimmung von Quick-Wert, APTT und Thrombozytenzahl untersucht. Zusätzlich wurde bei allen Patienten eine standardisierte Anamnese bezüglich einer möglichen Hämostasestörung erhoben. Postoperative Blutungskomplikationen wurden bei 3,1% der Patienten beobachtet. Die Gerinnungsanalytik zeigte bei 5,8% der Patienten Auffälligkeiten. Die Inzidenz von Blutungskomplikationen bei Patienten mit normaler bzw. auffälliger Gerinnungsuntersuchung unterschied sich nicht (p = 0,4141). Da sich 90% der Blutungskomplikationen bei Patienten mit normalem Gerinnungsstatus ereigneten, war die Sensitivität der Gerinnungsanalytik für das Auftreten einer Blutungskomplikation mit 10% ausgesprochen gering. Durch die standardisierte Anamnese und eine sich daran anschließende Spezialdiagnostik wurden 3 Patienten mit einem v.-Willebrand-Typ I identifiziert. Bei diesen Patienten war der Gerinnungsstatus normal.
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Abstract
An efficient scheme for the calculation of Born-Oppenheimer molecular dynamics (BOMD) simulations is introduced. It combines the corrected small basis set Hartree-Fock (HF-3c) method by Sure and Grimme [J. Comput. Chem. 2013, 43, 1672], extended Lagrangian BOMD (XL-BOMD) by Niklasson et al. [J. Chem. Phys. 2009, 130, 214109], and the calculation of the two electron integrals on graphics processing units (GPUs) [J. Chem. Phys. 2013, 138, 134114; J. Chem. Theory Comput. 2015, 11, 918]. To explore the parallel performance of our strong scaling implementation of the method, we present timings and extract, as its validation and first illustrative application, high-quality vibrational spectra from simulated trajectories of β-carotene, paclitaxel, and liquid water (up to 500 atoms). We conclude that the presented BOMD scheme may be used as a cost-efficient and reliable tool for computing vibrational spectra and thermodynamics of large molecular systems including explicit solvent molecules containing 500 atoms and more. Simulating 50 ps of maitotoxin (nearly 500 atoms) employing time steps of 0.5 fs requires ∼3 weeks on 12 CPUs (Intel Xeon E5 2620 v3) with 24 GPUs (AMD FirePro 3D W8100).
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Affiliation(s)
- Laurens D M Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 München, Germany.,Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 München, Germany
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Affiliation(s)
- Jörg Kussmann
- Department
of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany
- Center
for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Department
of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany
- Center
for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
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24
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Affiliation(s)
- Jörg Kussmann
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstraße
7, D-81377 München, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstraße
7, D-81377 München, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, D-81377 München, Germany
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25
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Beuerle M, Kussmann J, Ochsenfeld C. Screening methods for linear-scaling short-range hybrid calculations on CPU and GPU architectures. J Chem Phys 2017; 146:144108. [DOI: 10.1063/1.4978476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthias Beuerle
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 7, D-81377 München, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5-13, D-81377 München, Germany
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26
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Sundholm D, Rauhalahti M, Özcan N, Mera-Adasme R, Kussmann J, Luenser A, Ochsenfeld C. Nuclear Magnetic Shieldings of Stacked Aromatic and Antiaromatic Molecules. J Chem Theory Comput 2017; 13:1952-1962. [PMID: 28287722 DOI: 10.1021/acs.jctc.6b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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)
- Dage Sundholm
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Markus Rauhalahti
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Nergiz Özcan
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Raúl Mera-Adasme
- Departamento
de Ciencias del Ambiente, Universidad de Santiago de Chile (USACH), Av. Libertador Bernardo O’Higgins 3363, 9170022 Estación Central, Chile
| | - Jörg Kussmann
- Department
of Chemistry, University of Munich (LMU), München D-81377, Germany
| | - Arne Luenser
- Department
of Chemistry, University of Munich (LMU), München D-81377, Germany
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Luenser A, Kussmann J, Ochsenfeld C. Computation of indirect nuclear spin–spin couplings with reduced complexity in pure and hybrid density functional approximations. J Chem Phys 2016; 145:124103. [DOI: 10.1063/1.4962260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arne Luenser
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) and Center for Integrated Protein Science Munich (CIPSM, LMU Munich), Butenandtstr. 5–13, D-81377 Munich, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) and Center for Integrated Protein Science Munich (CIPSM, LMU Munich), Butenandtstr. 5–13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) and Center for Integrated Protein Science Munich (CIPSM, LMU Munich), Butenandtstr. 5–13, D-81377 Munich, Germany
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28
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Kussmann J, Luenser A, Beer M, Ochsenfeld C. A reduced-scaling density matrix-based method for the computation of the vibrational Hessian matrix at the self-consistent field level. J Chem Phys 2015; 142:094101. [DOI: 10.1063/1.4908131] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Arne Luenser
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Matthias Beer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
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Kussmann J, Ochsenfeld C. Preselective Screening for Linear-Scaling Exact Exchange-Gradient Calculations for Graphics Processing Units and General Strong-Scaling Massively Parallel Calculations. J Chem Theory Comput 2015; 11:918-22. [DOI: 10.1021/ct501189u] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [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)
- Jörg Kussmann
- Department of Chemistry and Center for Integrated
Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
| | - Christian Ochsenfeld
- Department of Chemistry and Center for Integrated
Protein Science (CIPSM), University of Munich (LMU), D-81377 München, Germany
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Maurer SA, Kussmann J, Ochsenfeld C. Communication: A reduced scaling J-engine based reformulation of SOS-MP2 using graphics processing units. J Chem Phys 2014; 141:051106. [DOI: 10.1063/1.4891797] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S. A. Maurer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
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31
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Kussmann J, Ochsenfeld C. Pre-selective screening for matrix elements in linear-scaling exact exchange calculations. J Chem Phys 2013; 138:134114. [DOI: 10.1063/1.4796441] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Maurer SA, Lambrecht DS, Kussmann J, Ochsenfeld C. Efficient distance-including integral screening in linear-scaling Møller-Plesset perturbation theory. J Chem Phys 2013; 138:014101. [DOI: 10.1063/1.4770502] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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34
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Beer M, Kussmann J, Ochsenfeld C. Nuclei-selected NMR shielding calculations: A sublinear-scaling quantum-chemical method. J Chem Phys 2011; 134:074102. [DOI: 10.1063/1.3526315] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Anderson JB, Anderson LE, Kussmann J. Monte Carlo simulations of single- and multistep enzyme-catalyzed reaction sequences: effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation. J Chem Phys 2010; 133:034104. [PMID: 20649305 DOI: 10.1063/1.3459111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Following the discovery of slow fluctuations in the catalytic activity of an enzyme in single-molecule experiments, it has been shown that the classical Michaelis-Menten (MM) equation relating the average enzymatic velocity and the substrate concentration may hold even for slowly fluctuating enzymes. In many cases, the average velocity is that given by the MM equation with time-averaged values of the fluctuating rate constants and the effect of enzyme fluctuations is simply averaged out. The situation is quite different for a sequence of reactions. For colocalization of a pair of enzymes in a sequence to be effective in promoting reaction, the second must be active when the first is active or soon after. If the enzymes are slowly varying and only rarely active, the product of the first reaction may diffuse away before the second enzyme is active, and colocalization may have little value. Even for single-step reactions the interplay of reaction and diffusion with enzyme fluctuations leads to added complexities, but for multistep reactions the interplay of reaction and diffusion, cell size, compartmentalization, enzyme fluctuations, colocalization, and segregation is far more complex than for single-step reactions. In this paper, we report the use of stochastic simulations at the level of whole cells to explore, understand, and predict the behavior of single- and multistep enzyme-catalyzed reaction systems exhibiting some of these complexities. Results for single-step reactions confirm several earlier observations by others. The MM relationship, with altered constants, is found to hold for single-step reactions slowed by diffusion. For single-step reactions, the distribution of enzymes in a regular grid is slightly more effective than a random distribution. Fluctuations of enzyme activity, with average activity fixed, have no observed effects for simple single-step reactions slowed by diffusion. Two-step sequential reactions are seen to be slowed by segregation of the enzymes for each step, and results of the calculations suggest limits for cell size. Colocalization of enzymes for a two-step sequence is seen to promote reaction, and rates fall rapidly with increasing distance between enzymes. Low frequency fluctuations of the activities of colocalized enzymes, with average activities fixed, can greatly reduce reaction rates for sequential reactions.
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Affiliation(s)
- James B Anderson
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Zienau J, Kussmann J, Ochsenfeld C. Quantum-chemical simulation of solid-state NMR spectra: the example of a molecular tweezer host–guest complex. Mol Phys 2010. [DOI: 10.1080/00268970903476647] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Doser B, Lambrecht DS, Kussmann J, Ochsenfeld C. Linear-scaling atomic orbital-based second-order Møller–Plesset perturbation theory by rigorous integral screening criteria. J Chem Phys 2009; 130:064107. [DOI: 10.1063/1.3072903] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Kussmann J, Ochsenfeld C. Linear-scaling fixed-node diffusion quantum Monte Carlo: Accounting for the nodal information in a density matrix-based scheme. J Chem Phys 2008; 128:134104. [DOI: 10.1063/1.2884920] [Citation(s) in RCA: 4] [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: 11/14/2022] Open
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39
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Kussmann J, Ochsenfeld C. A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels. J Chem Phys 2007; 127:204103. [DOI: 10.1063/1.2794033] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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41
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Kussmann J, Ochsenfeld C. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory. J Chem Phys 2007; 127:054103. [PMID: 17688330 DOI: 10.1063/1.2749509] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [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: 11/14/2022] Open
Abstract
Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.
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Affiliation(s)
- Jörg Kussmann
- Theoretische Chemie, Universität Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
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Pisula W, Tomović Z, Watson MD, Müllen K, Kussmann J, Ochsenfeld C, Metzroth T, Gauss J. Helical Packing of Discotic Hexaphenyl Hexa-peri-hexabenzocoronenes: Theory and Experiment. J Phys Chem B 2007; 111:7481-7. [PMID: 17555344 DOI: 10.1021/jp071167i] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [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: 11/30/2022]
Abstract
The arrangement of discotic hexa-peri-hexabenzocoronenes (HBCs) into columnar helical superstructures has been investigated in relation to their molecular architecture. The supramolecular structure of two hexaphenyl-substituted HBC derivatives, differing only in the chiral/achiral nature of the attached alkyl side chains, was studied by circular dichroism and temperature-dependent wide-angle X-ray diffraction on oriented filaments. A structural model in agreement with the experimental observations was developed on the basis of accompanying quantum-chemical calculations. The helical organization along the self-assembled columnar structures was induced by the steric requirements of the bulky phenyl rings near the aromatic core, i.e., by their rotation out-of-plane with respect to the aromatic core. On the other hand, a uniform handedness of the twist was generated by chiral alkyl substituents. At higher temperatures the degree of helical organization decreases due to lateral and longitudinal dynamics of the discotic molecules. Annealing at ambient conditions improved the long-range arrangement of the discs along the columnar structures. This reorganization indicated a self-healing of the plastic material which is desirable for application of discotics as active layers in electronic devices. The helical packing resulted in a considerable stability of the mesophase up to 500 degrees C, which has not been reported for a discotic so far.
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Affiliation(s)
- Wojciech Pisula
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
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Schaller T, Büchele UP, Klärner FG, Bläser D, Boese R, Brown SP, Spiess HW, Koziol F, Kussmann J, Ochsenfeld C. Structure of Molecular Tweezer Complexes in the Solid State: NMR Experiments, X-ray Investigations, and Quantum Chemical Calculations. J Am Chem Soc 2007; 129:1293-303. [PMID: 17263413 DOI: 10.1021/ja0666351] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [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
The structure of supramolecular complexes formed by a naphthalene-spaced tweezer molecule as host and 1,4-dicyanobenzene (DCNB), 1,2,4,5-tetracyanobenzene (TCNB), and 7,7,8,8-tetracyano-p-quinodimethane (TCNQ) as aromatic, electron-deficient guests is investigated by solid-state NMR and X-ray diffraction measurements. Quantum chemical calculations using linear scaling methods are applied to predict and to assign the 1H NMR chemical shifts of the complexes. By combining experiment and theory, insights into intra- and intermolecular effects influencing the proton chemical shifts of the host-guest system are provided in the solid state.
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Affiliation(s)
- Torsten Schaller
- Universität Duisburg-Essen, Institut für Organische Chemie, D-45117 Essen, Germany.
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Zienau J, Kussmann J, Koziol F, Ochsenfeld C. Molecular recognition in molecular tweezers systems: quantum-chemical calculation of NMR chemical shifts. Phys Chem Chem Phys 2007; 9:4552-62. [PMID: 17690781 DOI: 10.1039/b706045a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [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
Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.
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Affiliation(s)
- Jan Zienau
- Institut für Physikalische und Theoretische Chemie, Auf der Morgenstelle 8, Universität Tübingen, D-72076, Tübingen, Germany
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Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert ATB, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJO, Besley NA, Herbert JM, Lin CY, Van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EFC, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett AC, Subotnik JE, Woodcock HL, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF, Kong J, Krylov AI, Gill PMW, Head-Gordon M. Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys 2006; 8:3172-91. [PMID: 16902710 DOI: 10.1039/b517914a] [Citation(s) in RCA: 2118] [Impact Index Per Article: 117.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
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Affiliation(s)
- Yihan Shao
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Ochsenfeld C, Kussmann J, Koziol F. Cover Picture: Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear-Scaling Method (Angew. Chem. Int. Ed. 34/2004). Angew Chem Int Ed Engl 2004. [DOI: 10.1002/anie.200490114] [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] [Indexed: 11/08/2022]
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Ochsenfeld C, Kussmann J, Koziol F. Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear-Scaling Method. Angew Chem Int Ed Engl 2004; 43:4485-9. [PMID: 15317006 DOI: 10.1002/anie.200460336] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Ochsenfeld
- Institut für Physikalische und Theoretische Chemie, Abteilung für Theoretische Chemie, Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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Ochsenfeld C, Kussmann J, Koziol F. Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear-Scaling Method. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460336] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ochsenfeld C, Kussmann J, Koziol F. Titelbild: Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear-Scaling Method (Angew. Chem. 34/2004). Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200490113] [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] [Indexed: 11/12/2022]
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