601
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A computational study for the antioxidant capacity increases in hydroxy-derivatives of paracetamol and salicylic acid. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1393-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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602
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Chan B, Goerigk L, Radom L. On the inclusion of post-MP2 contributions to double-Hybrid density functionals. J Comput Chem 2015; 37:183-93. [DOI: 10.1002/jcc.23972] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Bun Chan
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
| | - Lars Goerigk
- School of Chemistry; The University of Melbourne; Parkville Victoria 3010 Australia
| | - Leo Radom
- School of Chemistry; The University of Sydney and Centre of Excellence for Free Radical Chemistry and Biotechnology; Sydney New South Wales 2006 Australia
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603
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Kulik HJ. Perspective: Treating electron over-delocalization with the DFT+U method. J Chem Phys 2015; 142:240901. [DOI: 10.1063/1.4922693] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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604
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Vuckovic S, Wagner LO, Mirtschink A, Gori-Giorgi P. Hydrogen Molecule Dissociation Curve with Functionals Based on the Strictly Correlated Regime. J Chem Theory Comput 2015; 11:3153-62. [DOI: 10.1021/acs.jctc.5b00387] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Vuckovic
- Department of Theoretical
Chemistry and Amsterdam Center for Multiscale Modeling, FEW, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Lucas O. Wagner
- Department of Theoretical
Chemistry and Amsterdam Center for Multiscale Modeling, FEW, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - André Mirtschink
- Department of Theoretical
Chemistry and Amsterdam Center for Multiscale Modeling, FEW, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Paola Gori-Giorgi
- Department of Theoretical
Chemistry and Amsterdam Center for Multiscale Modeling, FEW, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
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605
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Gun’ko V, Goncharuk O, Goworek J. Evaporation of polar and nonpolar liquids from silica gels and fumed silica. Colloids Surf A Physicochem Eng Asp 2015. [DOI: 10.1016/j.colsurfa.2015.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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606
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Berland K, Cooper VR, Lee K, Schröder E, Thonhauser T, Hyldgaard P, Lundqvist BI. van der Waals forces in density functional theory: a review of the vdW-DF method. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:066501. [PMID: 25978530 DOI: 10.1088/0034-4885/78/6/066501] [Citation(s) in RCA: 309] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.
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Affiliation(s)
- Kristian Berland
- Centre for Materials Science and Nanotechnology, SMN, University of Oslo, NO-0318 Oslo, Norway. Microtechnology and Nanoscience, MC2, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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607
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Johnson ER, Clarkin OJ, Dale SG, DiLabio GA. Kinetics of the Addition of Olefins to Si-Centered Radicals: The Critical Role of Dispersion Interactions Revealed by Theory and Experiment. J Phys Chem A 2015; 119:5883-8. [DOI: 10.1021/acs.jpca.5b03251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
- Chemistry
and Chemical Biology, University of California, Merced, 5200 North Lake
Road, Merced, California 95343, United States
| | - Owen J. Clarkin
- University of Ottawa Heart Institute, 40 Ruskin
Street, Ottawa, Ontario, Canada K1Y 4W7
| | - Stephen G. Dale
- Chemistry
and Chemical Biology, University of California, Merced, 5200 North Lake
Road, Merced, California 95343, United States
| | - Gino A. DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2M9
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608
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Andrzejak M, Szczepanik DW, Orzeł Ł. The lowest triplet states of bridged cis-2,2'-bithiophenes - theory vs. experiment. Phys Chem Chem Phys 2015; 17:5328-37. [PMID: 25609244 DOI: 10.1039/c4cp03327b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical methods that were previously used to give a good quantitative description of the 3(1)Bu state of trans-2,2'-bithiophene are applied to characterize the lowest triplet states of three bridged cis-2,2'-bithiophenes: 3,3'-cyclopentadithiophene (CPDT), 3,3'-dithienylpyrrole (DTP), and 3,3'-dithienylthiophene (DTT). By obtaining highly accurate reproductions of the phosphorescence spectra of all three compounds, we rationalize the observed vibronic activity, further explore the performance of the applied theoretical methods, and address the quality of the reported experimental spectra. Over the course of this study we have, first, characterized the changes in the electronic structures between the ground state and the lowest triplet state and, second, expressed the related geometrical differences in terms of the Huang-Rhys factors. The Huang-Rhys factors have then been used to generate theoretical emission spectra with vibronic resolution. The applied procedure has yielded quantitative reproductions of the previously reported experimental phosphorescence spectra of DTT and DTP. The experimental spectrum of CPDT, on the other hand, turned out to be considerably narrower and intensity-deficient in its low energy region when compared with the theoretical results. Our experimental reinvestigation of the CPDT phosphorescence has given a refined spectrum that is significantly wider than the previously reported one, and is in nearly quantitative agreement with the theoretical prediction. This enabled us to attribute the observed discrepancy to an experimental artifact associated with the sensitivity characteristics of the commonly used photomultipliers.
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Affiliation(s)
- Marcin Andrzejak
- K. Gumiński Department of Theoretical Chemistry, Jagiellonian University, Poland.
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609
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Proenza YG, de Souza MAF, Ventura E, do Monte SA, Longo RL. Assessment of density-functionals for describing the X(-) + CH3ONO2 gas-phase reactions with X = F, OH, CH2CN. Phys Chem Chem Phys 2015; 16:26769-78. [PMID: 25372179 DOI: 10.1039/c4cp03674c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The energetics of the ECO2, SN2@C and SN2@N channels of X(-) + CH3ONO2 (X = F, OH, CH2CN) gas-phase reactions were computed using the CCSD(T)/CBS method. This benchmark extends a previous study with X = OH [M. A. F. de Souza et al., J. Am. Chem. Soc., 2012, 134, 19004] and was used to ascertain the accuracy and robustness of nineteen density-functionals for describing these potential energy profiles (PEP) as well as the kinetic product distributions obtained from RRKM calculations. Assessments were based on the mean unsigned error (MUE), the mean signed error (MSE), the #best : #worst (BW) criterion and the statistical confidence interval (CI) for the MSE. In general, double-hybrid (DH) functionals perform better than the range-separated ones, and both are better than the global-hybrid functionals. Based on the MUE and CI criteria the B2GPPLYP, B2PLYP, M08-SO, BMK, ωB97X-D, CAM-B3LYP, M06, M08-HX, ωB97X and B97-K functionals show the best performance in the description of these PEPs. Within this set, the B2GPPLYP functional is the most accurate and robust. The RRKM results indicate that the DHs are the best for describing the selectivities of these reactions. Compared to CCSD(T), the B2PLYP method has a relative error of only ca. 1% for the selectivity and the accuracy to provide the correct conclusion concerning the nonstatistical behavior of these reactions.
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Affiliation(s)
- Yaicel G Proenza
- Departamento de Química Fundamental, CCEN, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE 50.740-560, Brazil.
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610
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Santana JA, Krogel JT, Kim J, Kent PRC, Reboredo FA. Structural stability and defect energetics of ZnO from diffusion quantum Monte Carlo. J Chem Phys 2015; 142:164705. [DOI: 10.1063/1.4919242] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Juan A. Santana
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jaron T. Krogel
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jeongnim Kim
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Paul R. C. Kent
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Fernando A. Reboredo
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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611
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Grimme S, Hansen A. A Practicable Real-Space Measure and Visualization of Static Electron-Correlation Effects. Angew Chem Int Ed Engl 2015; 54:12308-13. [DOI: 10.1002/anie.201501887] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 11/10/2022]
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612
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Grimme S, Hansen A. Ein praktikables räumliches Maß für Effekte statischer Elektronenkorrelation und deren Visualisierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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613
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Abstract
This Special Topic Issue on the Advances in Density Functional Theory, published as a celebration of the fifty years of density functional theory, contains a retrospective article, a perspective article, and a collection of original research articles that showcase recent theoretical advances in the field. It provides a timely discussion reflecting a cross section of our understanding, and the theoretical and computational developments, which have significant implications in broad areas of sciences and engineering.
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Affiliation(s)
- Weitao Yang
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA
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614
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Valsson O, Filippi C, Casida ME. Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory. J Chem Phys 2015; 142:144104. [DOI: 10.1063/1.4916354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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615
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616
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Salazar JM, Weber G, Simon JM, Bezverkhyy I, Bellat JP. Characterization of adsorbed water in MIL-53(Al) by FTIR spectroscopy and ab-initio calculations. J Chem Phys 2015; 142:124702. [DOI: 10.1063/1.4914903] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- J. M. Salazar
- Laboratoire Interdisciplinaire Carnot de Bourgogne, Adsorption Sur Solides Poreux (ASP), UMR-6303 CNRS-Université de Bourgogne, 9, Av. Alain Savary B.P. 47870 F-21078 Dijon Cedex, France
| | - G. Weber
- Laboratoire Interdisciplinaire Carnot de Bourgogne, Adsorption Sur Solides Poreux (ASP), UMR-6303 CNRS-Université de Bourgogne, 9, Av. Alain Savary B.P. 47870 F-21078 Dijon Cedex, France
| | - J. M. Simon
- Laboratoire Interdisciplinaire Carnot de Bourgogne, Adsorption Sur Solides Poreux (ASP), UMR-6303 CNRS-Université de Bourgogne, 9, Av. Alain Savary B.P. 47870 F-21078 Dijon Cedex, France
| | - I. Bezverkhyy
- Laboratoire Interdisciplinaire Carnot de Bourgogne, Adsorption Sur Solides Poreux (ASP), UMR-6303 CNRS-Université de Bourgogne, 9, Av. Alain Savary B.P. 47870 F-21078 Dijon Cedex, France
| | - J. P. Bellat
- Laboratoire Interdisciplinaire Carnot de Bourgogne, Adsorption Sur Solides Poreux (ASP), UMR-6303 CNRS-Université de Bourgogne, 9, Av. Alain Savary B.P. 47870 F-21078 Dijon Cedex, France
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617
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Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method. J Chem Phys 2015; 142:124101. [DOI: 10.1063/1.4915068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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618
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Technical advances in molecular simulation since the 1980s. Arch Biochem Biophys 2015; 582:3-9. [PMID: 25772387 DOI: 10.1016/j.abb.2015.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 12/14/2022]
Abstract
This review describes how the theory and practice of molecular simulation have evolved since the beginning of the 1980s when the author started his career in this field. The account is of necessity brief and subjective and highlights the changes that the author considers have had significant impact on his research and mode of working.
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619
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Li Z. Density functional theory for field emission from carbon nano-structures. Ultramicroscopy 2015; 159 Pt 2:162-72. [PMID: 25747284 DOI: 10.1016/j.ultramic.2015.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 02/06/2015] [Accepted: 02/20/2015] [Indexed: 11/20/2022]
Abstract
Electron field emission is understood as a quantum mechanical many-body problem in which an electronic quasi-particle of the emitter is converted into an electron in vacuum. Fundamental concepts of field emission, such as the field enhancement factor, work-function, edge barrier and emission current density, will be investigated, using carbon nanotubes and graphene as examples. A multi-scale algorithm basing on density functional theory is introduced. We will argue that such a first principle approach is necessary and appropriate for field emission of nano-structures, not only for a more accurate quantitative description, but, more importantly, for deeper insight into field emission.
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Affiliation(s)
- Zhibing Li
- The State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China.
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620
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Sousa AM, Coutinho WS, Lima AF, Lalic MV. Structural, bonding, and electronic properties of the hexagonal ferroelectric and paraelectric phases of LuMnO3 compound: a density functional theory study. J Chem Phys 2015; 142:074703. [PMID: 25702020 DOI: 10.1063/1.4907787] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have investigated the structural, bonding, and electronic properties of both ferroelectric (FE) and paraelectric (PE) phases of the hexagonal LuMnO3 compound using calculations based on density functional theory. The structural properties have been determined by employing the generalized gradient approximation with Perdew-Burke-Ernzerhof and Wu-Cohen parameterization. The bonding and electronic properties have been treated by recently developed modified Becke-Johnson exchange potential, which succeeded to open a band gap for both PE and FE phases, in agreement with experimental predictions. The Bader's topological analysis of electronic density showed that the character of the Lu-O axial bonds changes when the crystal exhibits the PE → FE structural transition. This fact is in agreement with experimental findings. The covalent character of the Lu-O bond significantly increases due to orbital hybridization between the Lu 5dz(2) and O 2pz-states. This bonding mechanism causes the ferroelectricity in the hexagonal LuMnO3 compound.
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Affiliation(s)
- A M Sousa
- Physics Department, Federal University of Sergipe, São Cristóvão 49100-000, Brazil
| | - W S Coutinho
- Physics Department, Federal University of Sergipe, São Cristóvão 49100-000, Brazil
| | - A F Lima
- Physics Department, Federal University of Sergipe, São Cristóvão 49100-000, Brazil
| | - M V Lalic
- Physics Department, Federal University of Sergipe, São Cristóvão 49100-000, Brazil
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621
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Thompson LM, Hratchian HP. Second derivatives for approximate spin projection methods. J Chem Phys 2015; 142:054106. [DOI: 10.1063/1.4907269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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622
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Carmona-Espíndola J, Gázquez JL, Vela A, Trickey SB. Generalized gradient approximation exchange energy functional with correct asymptotic behavior of the corresponding potential. J Chem Phys 2015; 142:054105. [DOI: 10.1063/1.4906606] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Javier Carmona-Espíndola
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México D. F. 09340, México
| | - José L. Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México D. F. 09340, México
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, México D. F. 07360, México
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, México D. F. 07360, México
| | - S. B. Trickey
- Quantum Theory Project, Department of Physics and Department of Chemistry, University of Florida, P.O. Box 118435, Gainesville, Florida 32611-8435, USA
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623
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Wyrick J, Einstein TL, Bartels L. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals. J Chem Phys 2015; 142:101907. [PMID: 25770496 DOI: 10.1063/1.4906048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jonathan Wyrick
- Pierce Hall, University of California-Riverside, Riverside, California 92521, USA
| | - T. L. Einstein
- Department of Physics and Condensed Matter Theory Center, University of Maryland, College Park, Maryland 20742-4111, USA
| | - Ludwig Bartels
- Pierce Hall, University of California-Riverside, Riverside, California 92521, USA
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624
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625
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Cheng GJ, Zhang X, Chung LW, Xu L, Wu YD. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. J Am Chem Soc 2015; 137:1706-25. [PMID: 25568962 DOI: 10.1021/ja5112749] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.
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Affiliation(s)
- Gui-Juan Cheng
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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626
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Gun’ko VM, Nasiri R, Sazhin SS. Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes. J Chem Phys 2015; 142:034502. [DOI: 10.1063/1.4905496] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vladimir M. Gun’ko
- Chuiko Institute of Surface Chemistry, 17 General Naumov Street, Kiev 03164 Ukraine
- Sir Harry Ricardo Laboratories, School of Computing, Engineering and Mathematics, University of Brighton, Cockcroft Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
| | - Rasoul Nasiri
- Sir Harry Ricardo Laboratories, School of Computing, Engineering and Mathematics, University of Brighton, Cockcroft Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
| | - Sergei S. Sazhin
- Sir Harry Ricardo Laboratories, School of Computing, Engineering and Mathematics, University of Brighton, Cockcroft Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
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627
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Modelling and Rationalizing Organometallic Chemistry with Computation: Where Are We? STRUCTURE AND BONDING 2015. [DOI: 10.1007/430_2015_176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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628
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Zhao S, Liu Y, Chen X, Lu Y, Liu H, Hu Y. Unified Framework of Multiscale Density Functional Theories and Its Recent Applications. MESOSCALE MODELING IN CHEMICAL ENGINEERING PART II 2015. [DOI: 10.1016/bs.ache.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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629
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Realistic Simulation of Organometallic Reactivity in Solution by Means of First-Principles Molecular Dynamics. STRUCTURE AND BONDING 2015. [DOI: 10.1007/430_2015_183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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630
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Gaiduk AP, Ryabinkin IG, Staroverov VN. Modified Slater exchange potential with correct uniform electron gas limit. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bulat and Levy recently deduced an expansion for the exact-exchange potential whose leading term is Slater’s averaged exchange-charge potential modified through the inclusion of orbital eigenvalues. When used as a stand-alone approximation to the exact-exchange potential, this leading term is much more accurate than Slater’s original. We give an alternative derivation of this term and show that, unlike the Slater potential, it correctly reduces to the Dirac exchange potential (i.e., the local density approximation) for a uniform electron gas, provided that the zero-energy reference of orbital eigenvalues is chosen as the Fermi level of the system. The orbital-energy-modified Slater potential should also recover the Dirac exchange potential for neutral atoms in the limit of infinite nuclear charge, but in practice converges to this limit very slowly on account of extreme sensitivity to the choice of zero-energy reference around the Fermi level.
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Affiliation(s)
- Alex P. Gaiduk
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Ilya G. Ryabinkin
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Viktor N. Staroverov
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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631
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George J, Wang A, Deringer VL, Wang R, Dronskowski R, Englert U. Anisotropic displacement parameters from dispersion-corrected DFT methods and their experimental validation by temperature-dependent X-ray diffraction. CrystEngComm 2015. [DOI: 10.1039/c5ce01219h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How reliably can anisotropic displacement parameters be derived from theory? Experiments and computations on pentachloropyridine shed new light on this question.
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Affiliation(s)
- Janine George
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
| | - Ai Wang
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
| | - Volker L. Deringer
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
| | - Ruimin Wang
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
| | - Richard Dronskowski
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
- Jülich-Aachen Research Alliance (JARA-HPC)
- RWTH Aachen University
| | - Ulli Englert
- Institute of Inorganic Chemistry
- RWTH Aachen University
- Aachen 52074, Germany
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632
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Hybrid Functionals with Variationally Fitted Exact Exchange. ADVANCES IN QUANTUM CHEMISTRY 2015. [DOI: 10.1016/bs.aiq.2015.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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633
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Alipour M. In search of the appropriate theoretically justified mixing coefficient in parameter-free hybrid functionals for computing the NMR parameters. RSC Adv 2015. [DOI: 10.1039/c4ra13186j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The parameter-free hybrid density functionals, with theoretically justified mixing coefficients, are recommended to predict the NMR parameters.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
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634
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Feinblum DV, Kenison J, Burke K. Communication: Testing and using the Lewin-Lieb bounds in density functional theory. J Chem Phys 2014; 141:241105. [DOI: 10.1063/1.4904448] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David V. Feinblum
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - John Kenison
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Kieron Burke
- Department of Chemistry, University of California, Irvine, California 92697, USA
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
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635
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Wang LW. Divide-and-conquer quantum mechanical material simulations with exascale supercomputers. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwu060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Recent developments in large-scale materials science simulations, especially under the divide-and-conquer method, are reviewed. The pros and cons of the divide-and-conquer method are discussed. It is argued that the divide-and-conquer method, such as the linear-scaling 3D fragment method, is an ideal approach to take advantage of the heterogeneous architectures of modern-day supercomputers despite their relatively large prefactors among linear-scaling methods. Some developments in graphics processing unit (GPU) electronic structure calculations are also reviewed. The accelerators like GPU could be an essential part for the future exascale supercomputing.
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Affiliation(s)
- Lin-Wang Wang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 66, Berkeley, CA 94720, USA
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636
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Mezei PD, Csonka GI, Ruzsinszky A, Sun J. Accurate, Precise, and Efficient Theoretical Methods To Calculate Anion−π Interaction Energies in Model Structures. J Chem Theory Comput 2014; 11:360-71. [DOI: 10.1021/ct5008263] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pál D. Mezei
- Department
of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest, Hungary
| | - Gábor I. Csonka
- Department
of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest, Hungary
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Jianwei Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
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637
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Otero-de-la-Roza A, Johnson ER, DiLabio GA. Halogen Bonding from Dispersion-Corrected Density-Functional Theory: The Role of Delocalization Error. J Chem Theory Comput 2014; 10:5436-47. [DOI: 10.1021/ct500899h] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- A. Otero-de-la-Roza
- National Institute
for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G
2M9, Canada
| | - Erin R. Johnson
- Chemistry
and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, United States
| | - Gino A. DiLabio
- National Institute
for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G
2M9, Canada
- Department
of Chemistry, University of British Columbia, Okanagan, Fipke Center 357, 3247
University Way, Kelowna, British Columbia V1V 1V7, Canada
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638
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639
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Lehtola S, Jónsson H. Variational, Self-Consistent Implementation of the Perdew–Zunger Self-Interaction Correction with Complex Optimal Orbitals. J Chem Theory Comput 2014; 10:5324-37. [DOI: 10.1021/ct500637x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Susi Lehtola
- COMP
Centre of Excellence and Department of Applied Physics, P.O. Box 11100, FI-00076 Aalto University, Espoo, Finland
| | - Hannes Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, P.O. Box 11100, FI-00076 Aalto University, Espoo, Finland
- Faculty
of Physical Sciences, University of Iceland, Reykjavík, Iceland
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640
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Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J Phys Chem A 2014; 119:1511-23. [PMID: 25321186 PMCID: PMC4353191 DOI: 10.1021/jp5072296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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In
combined quantum mechanical/molecular mechanical (QM/MM) free
energy calculations, it is often advantageous to have a frozen geometry
for the quantum mechanical (QM) region. For such multiple-environment
single-system (MESS) cases, two schemes are proposed here for estimating
the polarization energy: the first scheme, termed MESS-E, involves
a Roothaan step extrapolation of the self-consistent field (SCF) energy;
whereas the other scheme, termed MESS-H, employs a Newton–Raphson
correction using an approximate inverse electronic Hessian of the
QM region (which is constructed only once). Both schemes are extremely
efficient, because the expensive Fock updates and SCF iterations in
standard QM/MM calculations are completely avoided at each configuration.
They produce reasonably accurate QM/MM polarization energies: MESS-E
can predict the polarization energy within 0.25 kcal/mol in terms
of the mean signed error for two of our test cases, solvated methanol
and solvated β-alanine, using the M06-2X or ωB97X-D functionals;
MESS-H can reproduce the polarization energy within 0.2 kcal/mol for
these two cases and for the oxyluciferin–luciferase complex,
if the approximate inverse electronic Hessians are constructed with
sufficient accuracy.
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Affiliation(s)
- Alexander J Sodt
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
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641
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Fabián JS, García de la Vega JM, San Fabián E. Improvements in DFT Calculations of Spin–Spin Coupling Constants. J Chem Theory Comput 2014; 10:4938-49. [DOI: 10.1021/ct500676m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- J. San Fabián
- Departamento
de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - J. M. García de la Vega
- Departamento
de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - E. San Fabián
- Departamento
de Química Física, Unidad Asociada del CSIC and Instituto
Universitario de Materiales, Universidad de Alicante, San Vicente
del Raspeig, 03690 Alicante, Spain
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642
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Affiliation(s)
- Benjamin G. Janesko
- Department of Chemistry, Texas Christian University Fort Worth, Texas 76129, USA
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40 , Wallingford, Connecticut 06492, USA
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac St., Bldg. 40 , Wallingford, Connecticut 06492, USA
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643
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Liu ZF, Wei S, Yoon H, Adak O, Ponce I, Jiang Y, Jang WD, Campos LM, Venkataraman L, Neaton JB. Control of single-molecule junction conductance of porphyrins via a transition-metal center. NANO LETTERS 2014; 14:5365-70. [PMID: 25111197 DOI: 10.1021/nl5025062] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Using scanning tunneling microscope break-junction experiments and a new first-principles approach to conductance calculations, we report and explain low-bias charge transport behavior of four types of metal-porphyrin-gold molecular junctions. A nonequilibrium Green's function approach based on self-energy corrected density functional theory and optimally tuned range-separated hybrid functionals is developed and used to understand experimental trends quantitatively. Importantly, due to the localized d states of the porphyrin molecules, hybrid functionals are essential for explaining measurements; standard semilocal functionals yield qualitatively incorrect results. Comparing directly with experiments, we show that the conductance can change by nearly a factor of 2 when different metal cations are used, counter to trends expected from gas-phase ionization energies which are relatively unchanged with the metal center. Our work explains the sensitivity of the porphyrin conductance with the metal center via a detailed and quantitative portrait of the interface electronic structure and provides a new framework for understanding transport quantitatively in complex junctions involving molecules with localized d states of relevance to light harvesting and energy conversion.
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Affiliation(s)
- Zhen-Fei Liu
- Molecular Foundry and Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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644
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Hoffmann A, Grunzke R, Herres-Pawlis S. Insights into the influence of dispersion correction in the theoretical treatment of guanidine-quinoline copper(I) complexes. J Comput Chem 2014; 35:1943-50. [DOI: 10.1002/jcc.23706] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Alexander Hoffmann
- Department of Chemistry; Ludwig-Maximilians-Universität München, Butenandtstr. 5 - 13; 81377 München Germany
| | - Richard Grunzke
- Zentrum für Informationsdienste und Hochleistungsrechnen; Technische Universität Dresden; Zellescher Weg 12-14 01062 Dresden Germany
| | - Sonja Herres-Pawlis
- Department of Chemistry; Ludwig-Maximilians-Universität München, Butenandtstr. 5 - 13; 81377 München Germany
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645
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Bulik IW, Chen W, Scuseria GE. Electron correlation in solids via density embedding theory. J Chem Phys 2014; 141:054113. [DOI: 10.1063/1.4891861] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
| | - Weibing Chen
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Gustavo E. Scuseria
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
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646
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Janesko BG, Scalmani G, Frisch MJ. Practical auxiliary basis implementation of Rung 3.5 functionals. J Chem Phys 2014; 141:034103. [DOI: 10.1063/1.4887085] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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647
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Abstract
Nitrosylcobalamin (NOCbl) is readily formed when Co(II)balamin reacts with nitric oxide (NO) gas. NOCbl has been implicated in the inhibition of various B12-dependent enzymes, as well as in the modulation of blood pressure and of the immunological response. Previous studies revealed that among the known biologically relevant cobalamin species, NOCbl possesses the longest bond between the Co ion and the axially bound 5,6-dimethylbenzimidazole base, which was postulated to result from a strong trans influence exerted by the NO ligand. In this study, various spectroscopic (electronic absorption, circular dichroism, magnetic circular dichroism, and resonance Raman) and computational (density functional theory (DFT) and time-dependent DFT) techniques were used to generate experimentally validated electronic structure descriptions for the "base-on" and "base-off" forms of NOCbl. Further insights into the principal Co-ligand bonding interactions were obtained by carrying out natural bond orbital analyses. Collectively, our results indicate that the formally unoccupied Co 3dz(2) orbital engages in a highly covalent bonding interaction with the filled NO π* orbital and that the Co-NO bond is strengthened further by sizable π-backbonding interactions that are not present in any other Co(III)Cbl characterized to date. Because of the substantial NO(-) to Co(III) charge donation, NOCbl is best described as a hybrid of Co(III)-NO(-) and Co(II)-NO(•) resonance structures. In contrast, our analogous computational characterization of a related species, superoxocobalamin, reveals that in this case a Co(III)-O2(-) description is adequate due to the larger oxidizing power of O2 versus NO. The implications of our results with respect to the unusual structural features and thermochromism of NOCbl and the proposed inhibition mechanisms of B12-dependent enzymes by NOCbl are discussed.
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Affiliation(s)
- Ivan G. Pallares
- Department of Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
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648
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Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
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649
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Liu Y, Wu J. A new exchange–correlation functional free of delocalization and static correlation errors. Phys Chem Chem Phys 2014; 16:16373-7. [DOI: 10.1039/c4cp01987c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A combination of weighted density approximation and classical mapping leads to a new exchange–correlation energy free of delocalization and static correlation errors in Kohn–Sham density functional theory.
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Affiliation(s)
- Yu Liu
- Department of Chemical and Environmental Engineering and Department of Mathematics
- University of California
- Riverside, USA
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering and Department of Mathematics
- University of California
- Riverside, USA
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650
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Barbatti M, Crespo-Otero R. Surface Hopping Dynamics with DFT Excited States. DENSITY-FUNCTIONAL METHODS FOR EXCITED STATES 2014; 368:415-44. [DOI: 10.1007/128_2014_605] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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