551
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Carmona-Espíndola J, Gázquez JL, Vela A, Trickey SB. Global hybrid exchange energy functional with correct asymptotic behavior of the corresponding potential. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1864-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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552
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Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds. CRYSTALS 2016. [DOI: 10.3390/cryst6040037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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553
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554
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Ramos-Cordoba E, Lopez X, Piris M, Matito E. H4: A challenging system for natural orbital functional approximations. J Chem Phys 2016; 143:164112. [PMID: 26520503 DOI: 10.1063/1.4934799] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The correct description of nondynamic correlation by electronic structure methods not belonging to the multireference family is a challenging issue. The transition of D(2h) to D(4h) symmetry in H4 molecule is among the most simple archetypal examples to illustrate the consequences of missing nondynamic correlation effects. The resurgence of interest in density matrix functional methods has brought several new methods including the family of Piris Natural Orbital Functionals (PNOF). In this work, we compare PNOF5 and PNOF6, which include nondynamic electron correlation effects to some extent, with other standard ab initio methods in the H4 D(4h)/D(2h) potential energy surface (PES). Thus far, the wrongful behavior of single-reference methods at the D(2h)-D(4h) transition of H4 has been attributed to wrong account of nondynamic correlation effects, whereas in geminal-based approaches, it has been assigned to a wrong coupling of spins and the localized nature of the orbitals. We will show that actually interpair nondynamic correlation is the key to a cusp-free qualitatively correct description of H4 PES. By introducing interpair nondynamic correlation, PNOF6 is shown to avoid cusps and provide the correct smooth PES features at distances close to the equilibrium, total and local spin properties along with the correct electron delocalization, as reflected by natural orbitals and multicenter delocalization indices.
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Affiliation(s)
- Eloy Ramos-Cordoba
- Faculty of Chemistry, University of the Basque Country UPV/EHU, and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Xabier Lopez
- Faculty of Chemistry, University of the Basque Country UPV/EHU, and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Mario Piris
- Faculty of Chemistry, University of the Basque Country UPV/EHU, and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Eduard Matito
- Faculty of Chemistry, University of the Basque Country UPV/EHU, and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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555
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Paier J. Hybrid Density Functionals Applied to Complex Solid Catalysts: Successes, Limitations, and Prospects. Catal Letters 2016. [DOI: 10.1007/s10562-016-1735-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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556
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Huang W, Xing DH, Lu JB, Long B, Schwarz WHE, Li J. How Much Can Density Functional Approximations (DFA) Fail? The Extreme Case of the FeO4 Species. J Chem Theory Comput 2016; 12:1525-33. [PMID: 26938575 DOI: 10.1021/acs.jctc.5b01040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A thorough theoretical study of the relative energies of various molecular Fe·4O isomers with different oxidation states of both Fe and O atoms is presented, comparing simple Hartree-Fock through many Kohn-Sham approximations up to extended coupled cluster and DMRG multiconfiguration benchmark methods. The ground state of Fe·4O is a singlet, hexavalent iron(VI) complex (1)C2v-[Fe(VI)O2](2+)(O2)(2-), with isomers of oxidation states Fe(II), Fe(III), Fe(IV), Fe(V), and Fe(VIII) all lying slightly higher within the range of 1 eV. The disputed existence of oxidation state Fe(VIII) is discussed for isolated FeO4 molecules. Density functional theory (DFT) at various DF approximation (DFA) levels of local and gradient approaches, Hartree-Fock exchange and meta hybrids, range dependent, DFT-D and DFT+U models do not perform better for the relative stabilities of the geometric and electronic Fe·4O isomers than within 1-5 eV. The Fe·4O isomeric species are an excellent testing and validation ground for the development of density functional and wave function methods for strongly correlated multireference states, which do not seem to always follow chemical intuition.
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Affiliation(s)
- Wei Huang
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Deng-Hui Xing
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Jun-Bo Lu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Bo Long
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - W H Eugen Schwarz
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
| | - Jun Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Tsinghua University , Beijing 100084, China
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557
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Blood-Forsythe MA, Markovich T, DiStasio RA, Car R, Aspuru-Guzik A. Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions. Chem Sci 2016; 7:1712-1728. [PMID: 29899903 PMCID: PMC5964951 DOI: 10.1039/c5sc03234b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022] Open
Abstract
An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al., J. Chem. Phys., 2014, 140, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C60@C60H28 buckyball catcher host-guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.
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Affiliation(s)
| | - Thomas Markovich
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
| | - Robert A DiStasio
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , NY , USA
| | - Roberto Car
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Princeton Institute for the Science and Technology of Materials , Princeton University , Princeton , NJ , USA
- Department of Physics , Princeton University , Princeton , NJ , USA
- Program in Applied and Computational Mathematics , Princeton University , Princeton , NJ , USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
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558
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Grimmel S, Schoendorff G, Wilson AK. Gauging the Performance of Density Functionals for Lanthanide-Containing Molecules. J Chem Theory Comput 2016; 12:1259-66. [DOI: 10.1021/acs.jctc.5b01193] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephanie Grimmel
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry and Biochemistry, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - George Schoendorff
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Angela K. Wilson
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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559
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Marks LD, Peng L. Nanoparticle shape, thermodynamics and kinetics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:053001. [PMID: 26792459 DOI: 10.1088/0953-8984/28/5/053001] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nanoparticles can be beautiful, as in stained glass windows, or they can be ugly as in wear and corrosion debris from implants. We estimate that there will be about 70,000 papers in 2015 with nanoparticles as a keyword, but only one in thirteen uses the nanoparticle shape as an additional keyword and research focus, and only one in two hundred has thermodynamics. Methods for synthesizing nanoparticles have exploded over the last decade, but our understanding of how and why they take their forms has not progressed as fast. This topical review attempts to take a critical snapshot of the current understanding, focusing more on methods to predict than a purely synthetic or descriptive approach. We look at models and themes which are largely independent of the exact synthetic method whether it is deposition, gas-phase condensation, solution based or hydrothermal synthesis. Elements are old dating back to the beginning of the 20th century-some of the pioneering models developed then are still relevant today. Others are newer, a merging of older concepts such as kinetic-Wulff constructions with methods to understand minimum energy shapes for particles with twins. Overall we find that while there are still many unknowns, the broad framework of understanding and predicting the structure of nanoparticles via diverse Wulff constructions, either thermodynamic, local minima or kinetic has been exceedingly successful. However, the field is still developing and there remain many unknowns and new avenues for research, a few of these being suggested towards the end of the review.
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Affiliation(s)
- L D Marks
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA
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560
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Theilacker K, Arbuznikov AV, Kaupp M. Gauge effects in local hybrid functionals evaluated for weak interactions and the GMTKN30 test set. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1139209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Kolja Theilacker
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
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561
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Jia X, Wang M, Shao Y, König G, Brooks BR, Zhang JZH, Mei Y. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics. J Chem Theory Comput 2016; 12:499-511. [DOI: 10.1021/acs.jctc.5b00920] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xiangyu Jia
- State
Key Laboratory of Precision Spectroscopy and Department of Physics
and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Meiting Wang
- State
Key Laboratory of Precision Spectroscopy and Department of Physics
and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite
105, Pleasanton, California 94588, United States
| | - Gerhard König
- Laboratory
of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - John Z. H. Zhang
- State
Key Laboratory of Precision Spectroscopy and Department of Physics
and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center
for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- State
Key Laboratory of Precision Spectroscopy and Department of Physics
and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center
for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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562
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Abstract
Constrained Subsystem Density Fucntional Theory (CSDFT) allows to compute diabatic states for charge transfer reactions using the machinery of the constrained DFT method, and at the same time is able to embed such diabatic states in a molecular environment via a subsystem DFT scheme.
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Affiliation(s)
- Pablo Ramos
- Department of Chemistry
- Rutgers University
- Newark
- USA
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563
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Mahmood A, Longo RL. Structural and relative energy assessments of DFT functionals and the MP2 method to describe the gas phase methylation of nitronates: [R1R2CNO2]− + CH3I. Phys Chem Chem Phys 2016; 18:17062-70. [DOI: 10.1039/c5cp07833d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures and energetics of CH3I + [R1R2CNO2]− gas phase C- and O-methylation reactions were computed with several functionals and ECP/basis sets and compared to CCSD(T)/CBS.
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Affiliation(s)
- Ayyaz Mahmood
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
- Recife
| | - Ricardo L. Longo
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
- Recife
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564
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Kroes GJ, Díaz C. Quantum and classical dynamics of reactive scattering of H2 from metal surfaces. Chem Soc Rev 2016; 45:3658-700. [DOI: 10.1039/c5cs00336a] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
State-of-the-art theoretical models allow nowadays an accurate description of H2/metal surface systems and phenomena relative to heterogeneous catalysis. Here we review the most relevant ones investigated during the last 10 years.
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Affiliation(s)
- Geert-Jan Kroes
- Leiden Institute of Chemistry
- Gorlaeus Laboratories
- Leiden University
- 2300 RA Leiden
- The Netherlands
| | - Cristina Díaz
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
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565
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Qi SC, Hayashi JI, Zhang L. Recent application of calculations of metal complexes based on density functional theory. RSC Adv 2016. [DOI: 10.1039/c6ra16168e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent application of density functional theory (DFT) for metal complexes is reviewed to show the achievements of DFT and the challenges for it, as well as the methods for selecting proper functionals.
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Affiliation(s)
- Shi-Chao Qi
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
| | - Jun-ichiro Hayashi
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
| | - Lu Zhang
- Institute for Materials Chemistry and Engineering
- Kyushu University
- Kasuga
- Japan
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566
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Ribeiro RAP, de Lazaro SR, Gatti C. The role of exchange–correlation functional on the description of multiferroic properties using density functional theory: the ATiO3 (A = Mn, Fe, Ni) case study. RSC Adv 2016. [DOI: 10.1039/c6ra21465g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In this study, ab initio density functional theory calculations were performed on ATiO3 (A = Mn, Fe, Ni) materials for multiferroic applications.
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Affiliation(s)
| | | | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari
- 20133 Milano
- Italy
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567
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Optimal Dopant Selection for Water Splitting with Cerium Oxides: Mining and Screening First Principles Data. INFORMATION SCIENCE FOR MATERIALS DISCOVERY AND DESIGN 2016. [DOI: 10.1007/978-3-319-23871-5_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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568
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Maier TM, Haasler M, Arbuznikov AV, Kaupp M. New approaches for the calibration of exchange-energy densities in local hybrid functionals. Phys Chem Chem Phys 2016; 18:21133-44. [DOI: 10.1039/c6cp00990e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new derivation of semi-local calibration functions is proposed, to ameliorate the gauge problem of exchange-energy densities in local hybrid functionals.
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Affiliation(s)
- Toni M. Maier
- Technische Universität Berlin
- Institut für Chemie
- Theoretische Chemie/Quantenchemie
- Berlin
- Germany
| | - Matthias Haasler
- Technische Universität Berlin
- Institut für Chemie
- Theoretische Chemie/Quantenchemie
- Berlin
- Germany
| | - Alexei V. Arbuznikov
- Technische Universität Berlin
- Institut für Chemie
- Theoretische Chemie/Quantenchemie
- Berlin
- Germany
| | - Martin Kaupp
- Technische Universität Berlin
- Institut für Chemie
- Theoretische Chemie/Quantenchemie
- Berlin
- Germany
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569
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Korabel’nikov DV, Zhuravlev YN. Positive and negative linear compressibility and electronic properties of energetic and porous hybrid crystals with nitrate anions. Phys Chem Chem Phys 2016; 18:33126-33133. [DOI: 10.1039/c6cp06902a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Within the framework of DFT-D calculations, the compressibility anisotropy of UN and DATN energetic nitrates and the Ag(en)N hybrid crystal is established.
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Affiliation(s)
- D. V. Korabel’nikov
- Institute of Fundamental Sciences
- Kemerovo State University
- Kemerovo 650043
- Russia
| | - Yu. N. Zhuravlev
- Institute of Fundamental Sciences
- Kemerovo State University
- Kemerovo 650043
- Russia
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570
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Wodtke AM. Electronically non-adiabatic influences in surface chemistry and dynamics. Chem Soc Rev 2016; 45:3641-57. [DOI: 10.1039/c6cs00078a] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronically nonadiabatic interactions between molecules and metal surfaces are now well known. But evidence that such interactions influence reaction rates is still scarce. This paper reviews research related to this topic and proposes pathways forward.
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Affiliation(s)
- Alec M. Wodtke
- Institute for Physical Chemistry
- Georg-August University of Göttingen
- Germany
- Max Planck Institute for Biophysical Chemistry
- Göttingen
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571
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Kong J, Proynov E. Density Functional Model for Nondynamic and Strong Correlation. J Chem Theory Comput 2015; 12:133-43. [DOI: 10.1021/acs.jctc.5b00801] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Kong
- Department of Chemistry and
Center for Computational Sciences, Middle Tennessee State University, 1301 Main Street, Murfreesboro, Tennessee 37130, United States
| | - Emil Proynov
- Department of Chemistry and
Center for Computational Sciences, Middle Tennessee State University, 1301 Main Street, Murfreesboro, Tennessee 37130, United States
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572
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Li C, Lu J, Yang W. Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals. J Chem Phys 2015; 143:224110. [PMID: 26671361 DOI: 10.1063/1.4936411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.
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Affiliation(s)
- Chen Li
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Jianfeng Lu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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573
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Ranasinghe DS, Frisch MJ, Petersson GA. A density functional for core-valence correlation energy. J Chem Phys 2015; 143:214111. [DOI: 10.1063/1.4935973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Duminda S. Ranasinghe
- Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459-0180, USA
| | - Michael J. Frisch
- Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459-0180, USA
| | - George A. Petersson
- Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459-0180, USA
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574
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Assessment of Density-Functional Tight-Binding Ionization Potentials and Electron Affinities of Molecules of Interest for Organic Solar Cells Against First-Principles GW Calculations. COMPUTATION 2015. [DOI: 10.3390/computation3040616] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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575
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Patrikeev L, Joubert L, Tognetti V. Atomic decomposition of Kohn–Sham molecular energies: the kinetic energy component. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1113314] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Leonid Patrikeev
- Normandie Université COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA Rouen, CNRS, Mont St Aignan, Cedex, France
| | - Laurent Joubert
- Normandie Université COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA Rouen, CNRS, Mont St Aignan, Cedex, France
| | - Vincent Tognetti
- Normandie Université COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA Rouen, CNRS, Mont St Aignan, Cedex, France
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576
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Ali AA, Hashim AM. Density Functional Theory Study of Atomic Layer Deposition of Zinc Oxide on Graphene. NANOSCALE RESEARCH LETTERS 2015. [PMID: 26198282 PMCID: PMC4510105 DOI: 10.1186/s11671-015-1008-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The dissociation of zinc ions (Zn(2+)) from vapor-phase zinc acetylacetonate, Zn(C5H7O2)2, or Zn(acac)2 and its adsorption onto graphene oxide via atomic layer deposition (ALD) were studied using a quantum mechanics approach. Density functional theory (DFT) was used to obtain an approximate solution to the Schrödinger equation. The graphene oxide cluster model was used to represent the surface of the graphene film after pre-oxidation. In this study, the geometries of reactants, transition states, and products were optimized using the B3LYB/6-31G** level of theory or higher. Furthermore, the relative energies of the various intermediates and products in the gas-phase radical mechanism were calculated at the B3LYP/6-311++G** and MP2/6-311 + G(2df,2p) levels of theory. Additionally, a molecular orbital (MO) analysis was performed for the products of the decomposition of the Zn(acac)2 complex to investigate the dissociation of Zn(2+) and the subsequent adsorption of H atoms on the C5H7O2 cluster to form acetylacetonate enol. The reaction energies were calculated, and the reaction mechanism was accordingly proposed. A simulation of infrared (IR) properties was performed using the same approach to support the proposed mechanism via a complete explanation of bond forming and breaking during each reaction step.
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Affiliation(s)
- Amgad Ahmed Ali
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Abdul Manaf Hashim
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
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577
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Soini TM, Rösch N. Size-dependent properties of transition metal clusters: from molecules to crystals and surfaces--computational studies with the program ParaGauss. Phys Chem Chem Phys 2015; 17:28463-83. [PMID: 26456800 DOI: 10.1039/c5cp04281j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the so-called scalable regime the size-dependent behavior of the physical and chemical properties of transition metal clusters is described by scaling relationships. For most quantities this scalable regime is reached for cluster sizes between a few tens and a few hundreds of atoms, hence for systems for which an accurate treatment by density functional theory is still feasible. Thus, by invoking scaling relations one is able to obtain properties of very large nanoparticles and even the bulk limit from the results of a series of smaller cluster models. In this invited review we illustrate this strategy by exploiting results from computational studies that mostly were carried out with the density functional theory software ParaGauss. We address mainly the size-dependent behavior of the properties of transition metal clusters. To this end, we first present benchmark studies probing various approximations that are used in such density functional calculations. Subsequently we show how physical insight may be gained by exploring less understood types of systems. These applications range from bare clusters to nanoislands and nanoalloys to adsorption complexes.
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Affiliation(s)
- Thomas M Soini
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany.
| | - Notker Rösch
- Department Chemie and Catalysis Research Center, Technische Universität München, 85747 Garching, Germany. and Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, Connexis #16-16, Singapore 138632, Singapore
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578
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Hagler AT. Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials. J Chem Theory Comput 2015; 11:5555-72. [DOI: 10.1021/acs.jctc.5b00666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A. T. Hagler
- Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
- Shifa Biopharm, Shifa Biomedical Corporation, Malvern, Pennsylvania 19355, United States
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579
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Scaling correction approaches for reducing delocalization error in density functional approximations. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5501-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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580
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Al-Hamdani YS, Alfè D, von Lilienfeld OA, Michaelides A. Water on BN doped benzene: a hard test for exchange-correlation functionals and the impact of exact exchange on weak binding. J Chem Phys 2015; 141:18C530. [PMID: 25399195 DOI: 10.1063/1.4898356] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B3N3H6) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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581
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582
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Pavlíková Přecechtělová J, Bahmann H, Kaupp M, Ernzerhof M. Design of exchange-correlation functionals through the correlation factor approach. J Chem Phys 2015; 143:144102. [DOI: 10.1063/1.4932074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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583
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Tran F, Blaha P, Schwarz K. How close are the Slater and Becke-Roussel potentials in solids? J Chem Theory Comput 2015; 11:4717-26. [PMID: 26500460 PMCID: PMC4606396 DOI: 10.1021/acs.jctc.5b00675] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Indexed: 11/30/2022]
Abstract
The Becke–Roussel (BR) potential [Phys. Rev. A 1989, 39, 3761] was proposed as an approximation to the Slater potential, which is the Coulomb potential generated by the exact exchange hole. In the present work, a detailed comparison between the Slater and BR potentials in solids is presented. It is shown that the two potentials usually lead to very similar results for the electronic structure; however, in a few cases, e.g., Si, Ge, or strongly correlated systems like NiO, the fundamental band gap or magnetic properties can differ markedly. Such differences should not be neglected when the computationally expensive Slater potential is replaced by the cheap semilocal BR potential in approximations to the exact-exchange Kohn–Sham potential, such as the one proposed by Becke and Johnson [J. Chem. Phys. 2006, 124, 221101].
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Affiliation(s)
- Fabien Tran
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Peter Blaha
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
| | - Karlheinz Schwarz
- Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria
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584
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Li TL, Lu WC. Application of Koopmans' theorem for density functional theory to full valence-band photoemission spectroscopy modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 149:434-440. [PMID: 25974677 DOI: 10.1016/j.saa.2015.04.084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/25/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
In this work, Koopmans' theorem for Kohn-Sham density functional theory (KS-DFT) is applied to the photoemission spectra (PES) modeling over the entire valence-band. To examine the validity of this application, a PES modeling scheme is developed to facilitate a full valence-band comparison of theoretical PES spectra with experiments. The PES model incorporates the variations of electron ionization cross-sections over atomic orbitals and a linear dispersion of spectral broadening widths. KS-DFT simulations of pristine rubrene (5,6,11,12-tetraphenyltetracene) and potassium-rubrene complex are performed, and the simulation results are used as the input to the PES models. Two conclusions are reached. First, decompositions of the theoretical total spectra show that the dissociated electron of the potassium mainly remains on the backbone and has little effect on the electronic structures of phenyl side groups. This and other electronic-structure results deduced from the spectral decompositions have been qualitatively obtained with the anionic approximation to potassium-rubrene complexes. The qualitative validity of the anionic approximation is thus verified. Second, comparison of the theoretical PES with the experiments shows that the full-scale simulations combined with the PES modeling methods greatly enhance the agreement on spectral shapes over the anionic approximation. This agreement of the theoretical PES spectra with the experiments over the full valence-band can be regarded, to some extent, as a collective validation of the application of Koopmans' theorem for KS-DFT to valence-band PES, at least, for this hydrocarbon and its alkali-adsorbed complex.
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Affiliation(s)
- Tsung-Lung Li
- Department of Electrophysics, National Chia-Yi University, Chiayi 60004, Taiwan
| | - Wen-Cai Lu
- Laboratory of Fiber Materials and Modern Textile and Growing Base for State Key Laboratory, College of Physics, Qingdao University, Qingdao, Shandong 266071, PR China; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130021, PR China
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585
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Dawson W, Gygi F. Performance and Accuracy of Recursive Subspace Bisection for Hybrid DFT Calculations in Inhomogeneous Systems. J Chem Theory Comput 2015; 11:4655-63. [DOI: 10.1021/acs.jctc.5b00826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William Dawson
- Department of Computer Science, University of California Davis, Davis, California 95616, United States
| | - François Gygi
- Department of Computer Science, University of California Davis, Davis, California 95616, United States
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586
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Janesko BG, Fisher HC, Bridle MJ, Montchamp JL. P(═O)H to P–OH Tautomerism: A Theoretical and Experimental Study. J Org Chem 2015; 80:10025-32. [DOI: 10.1021/acs.joc.5b01618] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Benjamin G. Janesko
- Department of Chemistry, Texas Christian University, Box 298860, Fort Worth, Texas 76129, United States
| | - Henry C. Fisher
- Department of Chemistry, Texas Christian University, Box 298860, Fort Worth, Texas 76129, United States
| | - Mark J. Bridle
- Department of Chemistry, Texas Christian University, Box 298860, Fort Worth, Texas 76129, United States
| | - Jean-Luc Montchamp
- Department of Chemistry, Texas Christian University, Box 298860, Fort Worth, Texas 76129, United States
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587
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Zhou Y, Bahmann H, Ernzerhof M. Construction of exchange-correlation functionals through interpolation between the non-interacting and the strong-correlation limit. J Chem Phys 2015; 143:124103. [PMID: 26428992 DOI: 10.1063/1.4931160] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Drawing on the adiabatic connection of density functional theory, exchange-correlation functionals of Kohn-Sham density functional theory are constructed which interpolate between the extreme limits of the electron-electron interaction strength. The first limit is the non-interacting one, where there is only exchange. The second limit is the strong correlated one, characterized as the minimum of the electron-electron repulsion energy. The exchange-correlation energy in the strong-correlation limit is approximated through a model for the exchange-correlation hole that is referred to as nonlocal-radius model [L. O. Wagner and P. Gori-Giorgi, Phys. Rev. A 90, 052512 (2014)]. Using the non-interacting and strong-correlated extremes, various interpolation schemes are presented that yield new approximations to the adiabatic connection and thus to the exchange-correlation energy. Some of them rely on empiricism while others do not. Several of the proposed approximations yield the exact exchange-correlation energy for one-electron systems where local and semi-local approximations often fail badly. Other proposed approximations generalize existing global hybrids by using a fraction of the exchange-correlation energy in the strong-correlation limit to replace an equal fraction of the semi-local approximation to the exchange-correlation energy in the strong-correlation limit. The performance of the proposed approximations is evaluated for molecular atomization energies, total atomic energies, and ionization potentials.
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Affiliation(s)
- Yongxi Zhou
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale A, Montréal, Québec H3C 3J7, Canada
| | - Hilke Bahmann
- Department of Chemistry, Technische Universität Berlin, Strasse des 17 Juni, Berlin, Germany
| | - Matthias Ernzerhof
- Département de Chimie, Université de Montréal, C.P. 6128, Succursale A, Montréal, Québec H3C 3J7, Canada
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588
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Teale AM, Helgaker T, Savin A. Alternative Representations of the Correlation Energy in Density-Functional Theory: A Kinetic-Energy Based Adiabatic Connection. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201500132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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589
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Patrick CE, Thygesen KS. Adiabatic-connection fluctuation-dissipation DFT for the structural properties of solids—The renormalized ALDA and electron gas kernels. J Chem Phys 2015; 143:102802. [DOI: 10.1063/1.4919236] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Christopher E. Patrick
- Center for Atomic-Scale Materials Design (CAMD), Department of Physics, Technical University of Denmark, DK—2800 Kongens Lyngby, Denmark
| | - Kristian S. Thygesen
- Center for Atomic-Scale Materials Design (CAMD), Department of Physics, Technical University of Denmark, DK—2800 Kongens Lyngby, Denmark
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590
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Kraisler E, Schmidt T, Kümmel S, Kronik L. Effect of ensemble generalization on the highest-occupied Kohn-Sham eigenvalue. J Chem Phys 2015; 143:104105. [DOI: 10.1063/1.4930119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eli Kraisler
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Tobias Schmidt
- Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, 95440 Bayreuth, Germany
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
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591
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Wagner JP, Schreiner PR. London’sche Dispersionswechselwirkungen in der Molekülchemie - eine Neubetrachtung sterischer Effekte. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503476] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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592
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Hartley MK, Vine S, Walsh E, Avrantinis S, Daub GW, Cave RJ. Comparison of Relative Activation Energies Obtained by Density Functional Theory and the Random Phase Approximation for Several Claisen Rearrangements. J Phys Chem B 2015; 120:1486-96. [DOI: 10.1021/acs.jpcb.5b06646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madeline K. Hartley
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
| | - Seanna Vine
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
| | - Elizabeth Walsh
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
| | - Sara Avrantinis
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
| | - G. William Daub
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
| | - Robert J. Cave
- Department of Chemistry, Harvey Mudd College, 241 Platt Blvd., Claremont, California 91711, United States
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593
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Mao Y, Chen J, Wang H, Hu P. Catalyst screening: Refinement of the origin of the volcano curve and its implication in heterogeneous catalysis. CHINESE JOURNAL OF CATALYSIS 2015. [DOI: 10.1016/s1872-2067(15)60875-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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594
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Gaus M, Jin H, Demapan D, Christensen AS, Goyal P, Elstner M, Cui Q. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput 2015; 11:4205-19. [PMID: 26575916 PMCID: PMC4827604 DOI: 10.1021/acs.jctc.5b00600] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the parametrization of a density functional tight binding method (DFTB3) for copper in a spin-polarized formulation. The parametrization is consistent with the framework of 3OB for main group elements (ONCHPS) and can be readily used for biological applications that involve copper proteins/peptides. The key to our parametrization is to introduce orbital angular momentum dependence of the Hubbard parameter and its charge derivative, thus allowing the 3d and 4s orbitals to adopt different sizes and responses to the change of charge state. The parametrization has been tested by applying to a fairly broad set of molecules of biological relevance, and the properties of interest include optimized geometries, ligand binding energies, and ligand proton affinities. Compared to the reference QM level (B3LYP/aug-cc-pVTZ, which is shown here to be similar to the B97-1 and CCSD(T) results, in terms of many properties of interest for a set of small copper containing molecules), our parametrization generally gives reliable structural properties for both Cu(I) and Cu(II) compounds, although several exceptions are also noted. For energetics, the results are more accurate for neutral ligands than for charged ligands, likely reflecting the minimal basis limitation of DFTB3; the results generally outperform NDDO based methods such as PM6 and even PBE with the 6-31+G(d,p) basis. For all ligand types, single-point B3LYP calculations at DFTB3 geometries give results very close (∼1-2 kcal/mol) to the reference B3LYP values, highlighting the consistency between DFTB3 and B3LYP structures. Possible further developments of the DFTB3 model for a better treatment of transition-metal ions are also discussed. In the current form, our first generation of DFTB3 copper model is expected to be particularly valuable as a method that drives sampling in systems that feature a dynamical copper binding site.
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Affiliation(s)
- Michael Gaus
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Haiyun Jin
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Darren Demapan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Anders S Christensen
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Puja Goyal
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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595
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Wagner JP, Schreiner PR. London dispersion in molecular chemistry--reconsidering steric effects. Angew Chem Int Ed Engl 2015; 54:12274-96. [PMID: 26262562 DOI: 10.1002/anie.201503476] [Citation(s) in RCA: 638] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/15/2022]
Abstract
London dispersion, which constitutes the attractive part of the famous van der Waals potential, has long been underappreciated in molecular chemistry as an important element of structural stability, and thus affects chemical reactivity and catalysis. This negligence is due to the common notion that dispersion is weak, which is only true for one pair of interacting atoms. For increasingly larger structures, the overall dispersion contribution grows rapidly and can amount to tens of kcal mol(-1) . This Review collects and emphasizes the importance of inter- and intramolecular dispersion for molecules consisting mostly of first row atoms. The synergy of experiment and theory has now reached a stage where dispersion effects can be examined in fine detail. This forces us to reconsider our perception of steric hindrance and stereoelectronic effects. The quantitation of dispersion energy donors will improve our ability to design sophisticated molecular structures and much better catalysts.
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Affiliation(s)
- J Philipp Wagner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany)
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen (Germany).
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596
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Gaiduk AP, Gygi F, Galli G. Density and Compressibility of Liquid Water and Ice from First-Principles Simulations with Hybrid Functionals. J Phys Chem Lett 2015; 6:2902-2908. [PMID: 26267178 DOI: 10.1021/acs.jpclett.5b00901] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We determined the equilibrium density and compressibility of water and ice from first-principles molecular dynamics simulations using gradient-corrected (PBE) and hybrid (PBE0) functionals. Both functionals predicted the density of ice to be larger than that of water, by 15 (PBE) and 35% (PBE0). The PBE0 functional yielded a lower density of both ice and water with respect to PBE, leading to better agreement with experiment for ice but not for liquid water. Approximate inclusion of dispersion interactions on computed molecular-dynamics trajectories led to a substantial improvement of the PBE0 results for the density of liquid water, which, however, resulted to be slightly lower than that of ice.
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Affiliation(s)
- Alex P Gaiduk
- †Institute for Molecular Engineering, The University of Chicago, 5747 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - François Gygi
- ‡Department of Computer Science, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Giulia Galli
- †Institute for Molecular Engineering, The University of Chicago, 5747 South Ellis Avenue, Chicago, Illinois 60637, United States
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597
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Liakos DG, Neese F. Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory. J Chem Theory Comput 2015; 11:4054-63. [DOI: 10.1021/acs.jctc.5b00359] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, D-45470 Mülheim an der Ruhr, Germany
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598
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Kerner L, Kicková A, Filo J, Kedžuch S, Putala M. Elucidation of Photoisomerization-Related Structural Changes in an Acrylamide-Bridged Binaphthalene–Diazene Macrocyclic Chiroptical Switch by Experimental Electronic Circular Dichroism Spectra Simulation: Role of Dispersion Corrections. J Phys Chem A 2015; 119:8588-98. [DOI: 10.1021/acs.jpca.5b03474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lukáš Kerner
- Department of Organic Chemistry, Faculty
of Natural Sciences, Comenius University in Bratislava, Mlynská
dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Anna Kicková
- Department of Organic Chemistry, Faculty
of Natural Sciences, Comenius University in Bratislava, Mlynská
dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Juraj Filo
- Department of Organic Chemistry, Faculty
of Natural Sciences, Comenius University in Bratislava, Mlynská
dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Stanislav Kedžuch
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská
cesta 9, 845 36 Bratislava, Slovak Republic
| | - Martin Putala
- Department of Organic Chemistry, Faculty
of Natural Sciences, Comenius University in Bratislava, Mlynská
dolina, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
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599
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Sperger T, Sanhueza IA, Kalvet I, Schoenebeck F. Computational Studies of Synthetically Relevant Homogeneous Organometallic Catalysis Involving Ni, Pd, Ir, and Rh: An Overview of Commonly Employed DFT Methods and Mechanistic Insights. Chem Rev 2015. [PMID: 26207572 DOI: 10.1021/acs.chemrev.5b00163] [Citation(s) in RCA: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Theresa Sperger
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, 52074 Aachen, Germany
| | - Italo A Sanhueza
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, 52074 Aachen, Germany.,Laboratory of Organic Chemistry, ETH Zürich , Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Indrek Kalvet
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, 52074 Aachen, Germany
| | - Franziska Schoenebeck
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, 52074 Aachen, Germany
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600
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Shepard R, Brozell SR, Gidofalvi G. The Representation and Parametrization of Orthogonal Matrices. J Phys Chem A 2015; 119:7924-39. [PMID: 25946418 DOI: 10.1021/acs.jpca.5b02015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four representations and parametrizations of orthogonal matrices Q ∈ R(m×n) in terms of the minimal number of essential parameters {φ} are discussed: the exponential representation, the Householder reflector representation, the Givens rotation representation, and the rational Cayley transform representation. Both square n = m and rectangular n < m situations are considered. Two separate kinds of parametrizations are considered: one in which the individual columns of Q are distinct, the Stiefel manifold, and the other in which only span(Q) is significant, the Grassmann manifold. The practical issues of numerical stability, continuity, and uniqueness are discussed. The computation of Q in terms of the essential parameters {φ}, and also the extraction of {φ} for a given Q are considered for all of the parametrizations. The transformation of gradient arrays between the Q and {φ} variables is discussed for all representations. It is our hope that developers of new methods will benefit from this comparative presentation of an important but rarely analyzed subject.
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Scott R Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Gergely Gidofalvi
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
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