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Karton A. Big data benchmarking: how do DFT methods across the rungs of Jacob's ladder perform for a dataset of 122k CCSD(T) total atomization energies? Phys Chem Chem Phys 2024; 26:14594-14606. [PMID: 38738470 DOI: 10.1039/d4cp00387j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Total atomization energies (TAEs) are a central quantity in density functional theory (DFT) benchmark studies. However, so far TAE databases obtained from experiment or high-level ab initio wavefunction theory included up to hundreds of TAEs. Here, we use the GDB-9 database of 133k CCSD(T) TAEs generated by Curtiss and co-workers [B. Narayanan, P. C. Redfern, R. S. Assary and L. A. Curtiss, Chem. Sci., 2019, 10, 7449] to evaluate the performance of 14 representative DFT methods across the rungs of Jacob's ladder (namely, PBE, BLYP, B97-D, M06-L, τ-HCTH, PBE0, B3LYP, B3PW91, ωB97X-D, τ-HCTHh, PW6B95, M06, M06-2X, and MN15). We first use the A25[PBE] diagnostic for nondynamical correlation to eliminate systems that potentially include significant multireference effects, for which the CCSD(T) TAEs might not be sufficiently reliable. The resulting database (denoted by GDB9-nonMR) includes 122k species. Of the considered functionals, B3LYP attains the best performance relative to the G4(MP2) reference TAEs, with a mean absolute deviation (MAD) of 4.09 kcal mol-1. This first-generation hybrid functional, in which the three mixing coefficients were fitted against a small set of TAEs, is one of the few functionals that are not systematically biased towards overestimating the G4(MP2) TAEs, as demonstrated by a mean-signed deviation (MSD) of 0.45 kcal mol-1. The relatively good performance of B3LYP is followed by the heavily parameterized M06-L meta-GGA functional, which attains a MAD of 6.24 kcal mol-1. The PW6B95, M06, M06-2X, and MN15 functionals tend to systematically overestimate the G4(MP2) TAEs and attain MADs ranging between 18.69 (M06) and 28.54 (MN15) kcal mol-1. However, PW6B95 and M06-2X exhibit particularly narrow error distributions. Thus, scaling their TAEs by an empirical scaling factor reduces their MADs to merely 3.38 (PW6B95) and 2.85 (M06-2X) kcal mol-1. Empirical dispersion corrections (e.g., D3 and D4) are attractive, and therefore, their inclusion worsens the performance of methods that systematically overestimate the TAEs.
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Affiliation(s)
- Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
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2
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Xu H, Wang B, Liao L, Wang Y, Zhu Q, Ren H. High-Throughput Predictions of Accurate Enthalpies of Formation for Larger Molecules Utilizing the Bond Difference Correction Method. J Phys Chem Lett 2024; 15:998-1005. [PMID: 38252697 DOI: 10.1021/acs.jpclett.3c03390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The prediction of standard enthalpies of formation (EOFs) for larger molecules involves a trade-off between accuracy and cost, often resulting in non-negligible errors. The connectivity-based hierarchy (CBH) and simple bond additivity correction (BAC) are two promising means for evaluating EOFs, although they cannot achieve strict chemical accuracy. Calculated errors in the CBH are confirmed from accumulated systematic errors associated with bond differences in chemical environments. On the basis of a new set of bond descriptors, our developed bond difference correction (BDC) method effectively solves incremental errors with molecular size and inability applications for aromatic molecules. To balance the accuracy between non-aromatic and aromatic molecules, a more accurate BAC-based method with unpaired electrons and p hybrid orbitals (BAC-EP) is developed. With the incorporation of the two methods above, strict chemical accuracy by the largest deviation is achieved at low costs. These universal, ultrafast, and high-throughput methods greatly contribute to self-consistent thermodynamic parameters in combustion mechanisms.
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Affiliation(s)
- Huajie Xu
- Research Institute of Frontier Science, Southwest Jiao Tong University, Chengdu, Sichuan 610065, People's Republic of China
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Bo Wang
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Lingxian Liao
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Yang Wang
- Research Institute of Frontier Science, Southwest Jiao Tong University, Chengdu, Sichuan 610065, People's Republic of China
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Haisheng Ren
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
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3
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Mitzel NW, Lamm JH. Phase-Dependence of Molecular Structures Arising from Weak London Dispersion Interactions. Acc Chem Res 2023; 56:3379-3391. [PMID: 37852201 DOI: 10.1021/acs.accounts.3c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
ConspectusThe structures of molecules can be different in different phases. Intermolecular forces, even those of weak noncovalent interactions (WNCIs), can lead to a preference for quite different conformations in the solid, the gas, and the liquid phases. WNCIs can cause variations in bond lengths, angles, and torsional angles. Since structure is a fundamental concept in chemistry, the knowledge of structural changes with phase is important to understand the source and effects of distorting contributions from WNCIs but also as a predictive tool for the design and stabilization of new bonding situations.X-ray crystallography is ubiquitous and now mostly straightforward to perform, but facilities for the determination of accurate gas-phase structure determination are rare, and gas-phase work is laborious and time-consuming. There are currently about 1.25 million crystal structures and more than 12 500 experimental gas-phase structures, but the intersection of the two data sets that can tell us about the structural differences of the same molecule in different phases is surprisingly small.In this Account, we describe several cases of WNCI-dominated systems for which accurate experimental structure determinations exist for both the gas phase and the solid state and, in one case, also for solution. The examples include aryl-aryl, aryl-alkyl, and alkyl-alkyl interactions; systems with chalcogen and halogen bonding; and fluorine-based interactions in arylboranes. We work out the role of WNCIs in stabilizing large, strained, or sterically overloaded molecules. We will show how flexible molecules will fold under the action of WNCIs when isolated in the gas and how they fold or unfold when they are embedded in an environment of neighbors in crystals. We will show how they can vary in strength when the substitution patterns in aryl groups are changed by different halogens and how intramolecular WNCIs, such as those forming rings, change when such systems experience additional intermolecular WNCIs.Overall, we hope that this Account will give the reader an idea of the type and magnitude of structural changes that can be expected from a free molecule in the gas phase or a single molecule calculated by quantum chemistry compared with one embedded in a crystal. This should define the limits of comparability and provide some predictive concepts of the distortions and variations to be expected.
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Affiliation(s)
- Norbert W Mitzel
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Jan-Hendrik Lamm
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
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4
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Baroudi A, Jaradat K, Karton A. 6-Endo-dig versus 5-exo-dig: Exploring Radical Cyclization Preference with First-, Second-, and Third-row Linkers using High-level Quantum Chemical Methods. Chemphyschem 2023; 24:e202300426. [PMID: 37392178 DOI: 10.1002/cphc.202300426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
As an expansion upon Baldwin rules, the cyclization reactions of hex-5-yn-1-yl radical systems with different first-, second-, and third-row linkers are explored at the CCSD(T) level via means of the SMD(benzene)-G4(MP2) thermochemical protocol. Unlike C, O, and N linkers, systems with B, Si, P, S, Ge, As, and Se linkers are shown to favor 6-endo-dig cyclization. This offers fundamental insights into the rational synthetic design of cyclic compounds. A thorough analysis of stereoelectronic effects, cyclization barriers, and intrinsic barriers illustrates that structural changes alter the cyclization preference by mainly impacting 5-exo-dig reaction barriers. Based on the high-level computational modeling, we proceed to develop a new tool for cyclization preference prediction from the correlation between cyclization barriers and radical structural parameters (e. g., linker bond length and bond angle). A strong correlation is found between the radical attack trajectory angle and the reaction barrier heights, i. e., cyclization preference. Finally, the influence of stereoelectronic effects on the two radical cyclization pathways is further investigated in stereoisomers of hypervalent silicon system, which provides novel insight into cyclization control.
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Affiliation(s)
- Abdulkader Baroudi
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Khaled Jaradat
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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5
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Ruth M, Gerbig D, Schreiner PR. Machine Learning for Bridging the Gap between Density Functional Theory and Coupled Cluster Energies. J Chem Theory Comput 2023. [PMID: 37418619 DOI: 10.1021/acs.jctc.3c00274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Accurate electronic energies and properties are crucial for successful reaction design and mechanistic investigations. Computing energies and properties of molecular structures has proven extremely useful, and, with increasing computational power, the limits of high-level approaches (such as coupled cluster theory) are expanding to ever larger systems. However, because scaling is highly unfavorable, these methods are still not universally applicable to larger systems. To address the need for fast and accurate electronic energies of larger systems, we created a database of around 8000 small organic monomers (2000 dimers) optimized at the B3LYP-D3(BJ)/cc-pVTZ level of theory. This database also includes single-point energies computed at various levels of theory, including PBE1PBE, ωΒ97Χ, M06-2X, revTPSS, B3LYP, and BP86, for density functional theory as well as DLPNO-CCSD(T) and CCSD(T) for coupled cluster theory, all in conjunction with a cc-pVTZ basis. We used this database to train machine learning models based on graph neural networks using two different graph representations. Our models are able to make energy predictions from B3LYP-D3(BJ)/cc-pVTZ inputs to CCSD(T)/cc-pVTZ outputs with a mean absolute error of 0.78 and to DLPNO-CCSD(T)/cc-pVTZ with an mean absolute error of 0.50 and 0.18 kcal mol-1 for monomers and dimers, respectively. The model for dimers was further validated on the S22 database, and the monomer model was tested on challenging systems, including those with highly conjugated or functionally complex molecules.
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Affiliation(s)
- Marcel Ruth
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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6
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Karton A, Greatrex BW, O'Reilly RJ. Intramolecular Proton-Coupled Hydride Transfers with Relatively Low Activation Barriers. J Phys Chem A 2023. [PMID: 37368352 DOI: 10.1021/acs.jpca.3c03166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We report that bifunctional molecules containing hydroxyl and carbonyl functional groups can undergo an effective transfer hydrogenation via an intramolecular proton-coupled hydride transfer (PCHT) mechanism. In this reaction mechanism, a hydride transfer between two carbon atoms is coupled with a proton transfer between two oxygen atoms via a cyclic bond rearrangement transition structure. The coupled transfer of the two hydrogens as Hδ+ and Hδ- is supported by atomic polar tensor charges. The activation energy for the PCHT reaction is strongly dependent on the length of the alkyl chain between the hydroxyl and carbonyl functional groups but relatively weakly dependent on the functional groups attached to the hydroxyl and carbonyl carbons. We investigate the PCHT reaction mechanism using the Gaussian-4 thermochemical protocol and obtain high activation energy barriers (ΔH‡298) of 210.5-228.3 kJ mol-1 for chain lengths of one carbon atom and 160.2-163.9 kJ mol-1 for chain lengths of two carbon atoms. However, for longer chain lengths containing 3-4 carbon atoms, we obtain ΔH‡298 values as low as 101.9 kJ mol-1. Importantly, the hydride transfer between two carbon atoms proceeds without the need for a catalyst or hydride transfer activating agent. These results indicate that the intramolecular PCHT reaction provides an effective avenue for uncatalyzed, metal-free hydride transfers at ambient temperatures.
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Affiliation(s)
- Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Ben W Greatrex
- School of Rural Medicine, University of New England, Armidale, NSW 2351, Australia
| | - Robert J O'Reilly
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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7
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Rzhevskiy SA, Minaeva LI, Topchiy MA, Melnikov IN, Kiselev VG, Pivkina AN, Fomenkov IV, Asachenko AF. Synthesis, Characterization, and Properties of High-Energy Fillers Derived from Nitroisobutylglycerol. Int J Mol Sci 2023; 24:8541. [PMID: 37239887 PMCID: PMC10218491 DOI: 10.3390/ijms24108541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Herein we report a comprehensive laboratory synthesis of a series of energetic azidonitrate derivatives (ANDP, SMX, AMDNNM, NIBTN, NPN, 2-nitro-1,3-dinitro-oxypropane) starting from the readily available nitroisobutylglycerol. This simple protocol allows obtaining the high-energy additives from the available precursor in yields higher than those reported using safe and simple operations not presented in previous works. A detailed characterization of the physical, chemical, and energetic properties including impact sensitivity and thermal behavior of these species was performed for the systematic evaluation and comparison of the corresponding class of energetic compounds.
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Affiliation(s)
- Sergey A. Rzhevskiy
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, 119991 Moscow, Russia; (S.A.R.); (L.I.M.); (M.A.T.)
| | - Lidiya I. Minaeva
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, 119991 Moscow, Russia; (S.A.R.); (L.I.M.); (M.A.T.)
| | - Maxim A. Topchiy
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, 119991 Moscow, Russia; (S.A.R.); (L.I.M.); (M.A.T.)
| | - Igor N. Melnikov
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia; (I.N.M.); (A.N.P.)
| | - Vitaly G. Kiselev
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia;
| | - Alla N. Pivkina
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia; (I.N.M.); (A.N.P.)
| | - Igor V. Fomenkov
- Zelinsky Institute of Organic Chemistry RAS, 47 Leninsky Ave., 119991 Moscow, Russia;
| | - Andrey F. Asachenko
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, 119991 Moscow, Russia; (S.A.R.); (L.I.M.); (M.A.T.)
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8
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Melnikov IN, Kiselev VG, Dalinger IL, Starosotnikov AM, Muravyev NV, Pivkina AN. Thermochemistry, Tautomerism, and Thermal Stability of 5,7-Dinitrobenzotriazoles. Int J Mol Sci 2023; 24:ijms24065330. [PMID: 36982405 PMCID: PMC10049112 DOI: 10.3390/ijms24065330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/09/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Nitro derivatives of benzotriazoles are safe energetic materials with remarkable thermal stability. In the present study, we report on the kinetics and mechanism of thermal decomposition for 5,7-dinitrobenzotriazole (DBT) and 4-amino-5,7-dinitrobenzotriazole (ADBT). The pressure differential scanning calorimetry was employed to study the decomposition kinetics of DBT experimentally because the measurements under atmospheric pressure are disturbed by competing evaporation. The thermolysis of DBT in the melt is described by a kinetic scheme with two global reactions. The first stage is a strong autocatalytic process that includes the first-order reaction (Ea1I = 173.9 ± 0.9 kJ mol−1, log(A1I/s−1) = 12.82 ± 0.09) and the catalytic reaction of the second order with Ea2I = 136.5 ± 0.8 kJ mol−1, log(A2I/s−1) = 11.04 ± 0.07. The experimental study was complemented by predictive quantum chemical calculations (DLPNO-CCSD(T)). The calculations reveal that the 1H tautomer is the most energetically preferable form for both DBT and ADBT. Theory suggests the same decomposition mechanisms for DBT and ADBT, with the most favorable channels being nitro-nitrite isomerization and C–NO2 bond cleavage. The former channel has lower activation barriers (267 and 276 kJ mol−1 for DBT and ADBT, respectively) and dominates at lower temperatures. At the same time, due to the higher preexponential factor, the radical bond cleavage, with reaction enthalpies of 298 and 320 kJ mol−1, dominates in the experimental temperature range for both DBT and ADBT. In line with the theoretical predictions of C–NO2 bond energies, ADBT is more thermally stable than DBT. We also determined a reliable and mutually consistent set of thermochemical values for DBT and ADBT by combining the theoretically calculated (W1-F12 multilevel procedure) gas-phase enthalpies of formation and experimentally measured sublimation enthalpies.
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Affiliation(s)
- Igor N. Melnikov
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
| | - Vitaly G. Kiselev
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
- Physics Department, Novosibirsk State University, 1 Pirogova Str., 630090 Novosibirsk, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
| | - Igor L. Dalinger
- Zelinsky Institute of Organic Chemistry RAS, 47 Leninsky Ave., 119991 Moscow, Russia
| | | | - Nikita V. Muravyev
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-499-137-8203
| | - Alla N. Pivkina
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
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9
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Rosenberg M, Brinker UH. Carbene Routes to Cyclopropatetrahedrane. J Org Chem 2022; 87:16902-16906. [PMID: 36446051 PMCID: PMC9764353 DOI: 10.1021/acs.joc.2c02217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 11/30/2022]
Abstract
The formation of cyclopropatetrahedrane (tetracyclo[2.1.0.01,3.02,4]pentane) via four different carbene reactions is computed using the (U)CCSD(T)(full)/cc-pVTZ//(U)ωB97X-D/cc-pVTZ + 1.3686(EZPVE) theoretical model. Intrinsic reaction coordinate plots confirm that each carbene is directly linked to cyclopropatetrahedrane via a unique cyclopropanation step. Each elementary step is assessed according to the structure and energy of its transition state.
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Affiliation(s)
- Murray
G. Rosenberg
- Department
of Chemistry, The State University of New
York at Binghamton, P.O. Box 6000, Binghamton, New York 13902-6000, United States
| | - Udo H. Brinker
- Institute
of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
- Department
of Chemistry, The State University of New
York at Binghamton, P.O. Box 6000, Binghamton, New York 13902-6000, United States
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10
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Energetic [1,2,5]oxadiazolo [2,3- a]pyrimidin-8-ium Perchlorates: Synthesis and Characterization. Molecules 2022; 27:molecules27238443. [PMID: 36500539 PMCID: PMC9740163 DOI: 10.3390/molecules27238443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022] Open
Abstract
A convenient method to access the above perchlorates has been developed, based on the cyclocondensation of 3-aminofurazans with 1,3-diketones in the presence of HClO4. All compounds were fully characterized by multinuclear NMR spectroscopy and X-ray crystal structure determinations. Initial safety testing (impact and friction sensitivity) and thermal stability measurements (DSC/DTA) were also carried out. Energetic performance was calculated by using the PILEM code based on calculated enthalpies of formation and experimental densities at r.t. These salts exhibit excellent burn rates and combustion behavior and are promising ingredients for energetic materials.
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11
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Karton A, Chan B. Performance of local G4(MP2) composite ab initio procedures for fullerene isomerization energies. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Chan B, Karton A. Assessment of DLPNO-CCSD(T)-F12 and its use for the formulation of the low-cost and reliable L-W1X composite method. J Comput Chem 2022; 43:1394-1402. [PMID: 35709311 DOI: 10.1002/jcc.26892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 04/28/2022] [Indexed: 02/03/2023]
Abstract
In the present study, we have investigated the performance of RIJCOSX DLPNO-CCSD(T)-F12 methods for a wide range of systems. Calculations with a high-accuracy option ["DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12"] extrapolated to the complete-basis-set limit using the maug-cc-pV[D+d,T+d]Z basis sets provides fairly good agreements with the canonical CCSD(T)/CBS reference for a diverse set of thermochemical and kinetic properties [with mean absolute deviations (MADs) of ~1-2 kJ mol-1 except for atomization energies]. On the other hand, the low-cost "RIJCOSX DLPNO-CCSD(T)-F12D" option leads to substantial deviations for certain properties, notably atomization energies (MADs of up to tens of kJ mol-1 ). With the high-accuracy CBS approach, we have formulated the L-W1X method, which further includes a low-cost core-valence plus scalar-relativistic term. It shows generally good accuracy. For improved accuracies in specific cases, we advise replacing maug-cc-pV(n+d)Z with jun-cc-pV(n+d)Z for the calculation of electron affinities, and using well-constructed isodesmic-type reactions to obtain atomization energies. For medium-sized systems, DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12 calculations are several times faster than the corresponding canonical computation; the use of the local approximations (RIJCOSX and DLPNO) leads to a better scaling than that for the canonical calculation (from ~6-7 down to ~2-4 for our test systems). Thus, the DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12 method, and the L-W1X protocol that based on it, represent a useful means for obtaining accurate thermochemical quantities for larger systems.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
| | - Amir Karton
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
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13
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Abstract
The computational modeling of fullerenes plays a fundamental role in designing low-dimension carbon nanostructures. Nevertheless, the relative energies of fullerenes larger than C20 and C24 have not been comprehensively examined by means of highly accurate ab initio methods, for example, the CCSD(T) method. Here we report such an investigation for a diverse set of 29 C40 isomers. We calculate the energies of the C40 fullerenes using the G4(MP2) composite ab initio method, which approximates the CCSD(T) energy in conjunction with a triple-ζ-quality basis set (CCSD(T)/TZ). The CCSD(T)/TZ isomerization energies span 43.1-763.3 kJ mol-1. We find a linear correlation (R2 = 0.96) between the CCSD(T)/TZ isomerization energies and the fullerene pentagon signatures (P1 index), which reflect the strain associated with fused pentagon-pentagon rings. Using the reference CCSD(T)/TZ isomerization energies, we examine the relationship between the percentage of exact Hartree-Fock (HF) exchange in hybrid density functional theory (DFT) methods and the pentagon-pentagon strain energies. We find that the performance of hybrid DFT methods deteriorates with the pentagon-pentagon strain energy. This deterioration in performance becomes more pronounced with the inclusion of high amounts of HF exchange. For example, for B3LYP (20% HF exchange), the root-mean-square deviation (RMSD) relative to G4(MP2) increases from 8.9 kJ mol-1 for the low-strain isomers (P1 = 11) to 18.0 kJ mol-1 for the high-strain isomers (P1 > 13). However, for BH&HLYP (50% HF exchange) the RMSD increases from 23.0 (P1 = 11) to 113.2 (P1 > 13) kJ mol-1. A similar trend is observed for the M06/M06-2X pair of functionals. Namely, for M06 (27% HF exchange) the RMSD increases from 0.8 (P1 = 11) to 21.0 (P1 > 13) kJ mol-1, whereas for M06-2X (54% HF exchange) the RMSD increases from 16.7 (P1 = 11) to 77.7 (P1 > 13) kJ mol-1. Overall, we find that the strain associated with pentagon adjacency is an inherently challenging problem for hybrid DFT methods involving high amounts of HF exchange and that there is an inverse relationship between the optimal percentage of HF exchange and the pentagon-pentagon strain energy. For example, for BLYP the optimal percentages of HF exchange are 13% (P1 = 11), 10% (P1 = 12), 7.5% (P1 = 13), and 6% (P1 > 13).
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Affiliation(s)
- Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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14
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Weber JL, Vuong H, Devlaminck PA, Shee J, Lee J, Reichman DR, Friesner RA. A Localized-Orbital Energy Evaluation for Auxiliary-Field Quantum Monte Carlo. J Chem Theory Comput 2022; 18:3447-3459. [PMID: 35507769 DOI: 10.1021/acs.jctc.2c00111] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) has recently emerged as a promising method for the production of benchmark-level simulations of medium- to large-sized molecules because of its accuracy and favorable polynomial scaling with system size. Unfortunately, the memory footprints of standard energy evaluation algorithms are nontrivial, which can significantly impact timings on graphical processing units (GPUs) where memory is limited. Previous attempts to reduce scaling by taking advantage of the low-rank structure of the Coulombic integrals have been successful but exhibit high prefactors, making their utility limited to very large systems. Here we present a complementary cubic-scaling route to reduce memory and computational scaling based on the low rank of the Coulombic interactions between localized orbitals, focusing on the application to ph-AFQMC. We show that the error due to this approximation, which we term localized-orbital AFQMC (LO-AFQMC), is systematic and controllable via a single variable and that the method is computationally favorable even for small systems. We present results demonstrating robust retention of accuracy versus both experiment and full ph-AFQMC for a variety of test cases chosen for their potential difficulty for localized-orbital-based methods, including the singlet-triplet gaps of the polyacenes benzene through pentacene, the heats of formation for a set of Platonic hydrocarbon cages, and the total energy of ferrocene, Fe(Cp)2. Finally, we reproduce our previous result for the gas-phase ionization energy of Ni(Cp)2, agreeing with full ph-AFQMC to within statistical error while using less than 1/15th of the computer time.
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Affiliation(s)
- John L Weber
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Hung Vuong
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Pierre A Devlaminck
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - James Shee
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Joonho Lee
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - David R Reichman
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
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15
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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16
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Shapeshifting radicals. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Recent Synthetic Efforts towards High Energy Density Materials: How to Design High-Performance Energetic Structures? FIREPHYSCHEM 2021. [DOI: 10.1016/j.fpc.2021.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Chan B, Karton A. Polycyclic aromatic hydrocarbons: from small molecules through nano-sized species towards bulk graphene. Phys Chem Chem Phys 2021; 23:17713-17723. [PMID: 34378574 DOI: 10.1039/d1cp01659h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have examined the use of systematic bond-separation reactions and purposely constructed chemistry-preserving isodesmic reactions for the thermochemical calculation of aromatic hydrocarbon species. The bond-separation approach yields somewhat disappointing accuracy even when the reaction energies are obtained with generally robust composite and double-hybrid (DH) density functional theory (DFT) methods. In contrast, for the purposely constructed reactions, we find a dramatic improvement in the accuracy for energies calculated with all methods examined. Notably, for medium-sized aromatic hydrocarbons, we find that an effective approach for formulating a well-balanced reaction is to split the target species into two halves with an aromatic overlapping region. Overall, the G4(MP2)-XK, MPW2PLYP, MN15, PBE, and DC-DFTB3 methods are reasonable within their respective classes of methods for the calculation of bond-separation as well as chemistry-preserving isodesmic reactions. We have further computed per-carbon atomization energy (AE) for a series of D6h benzene-type molecules, and thus obtained a formula for extrapolation to the graphene limit [AEn = 711.5 × (1 - 1/n0.640) kJ mol-1, where n = number of carbons]. It suggests that nano-graphene with a length larger than 10 nm would resemble properties of bulk graphene, and conversely, downsizing a nano-graphene beyond this point may lead to considerably altered properties from the bulk.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-Shi, Nagasaki 852-8521, Japan.
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19
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Muravyev NV, Monogarov KA, Melnikov IN, Pivkina AN, Kiselev VG. Learning to fly: thermochemistry of energetic materials by modified thermogravimetric analysis and highly accurate quantum chemical calculations. Phys Chem Chem Phys 2021; 23:15522-15542. [PMID: 34286759 DOI: 10.1039/d1cp02201f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The standard state enthalpy of formation and the enthalpy of sublimation are essential thermochemical parameters determining the performance and application prospects of energetic materials (EM). Direct experimental measurements of these properties are complicated by low volatility and high heat release in bomb calorimetry experiments. As a result, the uncertainties in the reported enthalpies of formation for a number of even well-known CHNO-containing compounds might amount up to tens kJ mol-1, while for some novel high-nitrogen molecules they reach even hundreds of kJ mol-1. The present study reports a facile approach to determining the solid-state formation enthalpies comprised of complementary high-level quantum chemical calculations of the gas-phase thermochemistry and advanced thermal analysis techniques yielding sublimation enthalpies. The thermogravimetric procedure for the measurement of sublimation enthalpy was modified by using low external pressures (down to 0.2 Pa). This allows for observing sublimation/vaporization instead of thermal decomposition of the compounds studied. Extensive benchmarking on nonenergetic and energetic compounds reveals the average and maximal absolute errors of the sublimation enthalpies of 3.3 and 11.0 kJ mol-1, respectively. The comparison of the results with those obtained from the widely used Trouton-Williams empirical equation shows that the latter underestimates the sublimation enthalpy up to 140 kJ mol-1. Therefore, we performed a reparametrization of the latter equation with simple chemical descriptors that reduces the mean error down to 30 kJ mol-1. Highly accurate multi-level procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach were used to calculate theoretically the gas-phase formation enthalpies. In several cases, the DLPNO-CCSD(T) enthalpies of isodesmic reactions were also employed to obtain the gas-phase thermochemistry for medium-sized important EMs. Combining the obtained thermochemical properties, we determined the solid-state enthalpies of formation for nearly 60 species containing various important explosophoric groups, from common nitroaromatics, nitroethers, and nitramines to novel nitrogen-rich heterocyclic species (e.g., the derivatives of pyrazole, tetrazole, furoxan, etc.). The large-scale benchmarking against the available experimental solid-state enthalpies of formation yielded the maximal inaccuracy of the proposed method of 25 kJ mol-1.
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Affiliation(s)
- Nikita V Muravyev
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Konstantin A Monogarov
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Igor N Melnikov
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Alla N Pivkina
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Vitaly G Kiselev
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia. and Novosibirsk State University, 1 Pirogova Str., 630090 Novosibirsk, Russia and Institute of Chemical Kinetics and Combustion, SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
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20
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21
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Larin AA, Bystrov DM, Fershtat LL, Konnov AA, Makhova NN, Monogarov KA, Meerov DB, Melnikov IN, Pivkina AN, Kiselev VG, Muravyev NV. Nitro-, Cyano-, and Methylfuroxans, and Their Bis-Derivatives: From Green Primary to Melt-Cast Explosives. Molecules 2020; 25:molecules25245836. [PMID: 33322001 PMCID: PMC7764251 DOI: 10.3390/molecules25245836] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/03/2022] Open
Abstract
In the present work, we studied in detail the thermochemistry, thermal stability, mechanical sensitivity, and detonation performance for 20 nitro-, cyano-, and methyl derivatives of 1,2,5-oxadiazole-2-oxide (furoxan), along with their bis-derivatives. For all species studied, we also determined the reliable values of the gas-phase formation enthalpies using highly accurate multilevel procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach and isodesmic reactions with the domain-based local pair natural orbital (DLPNO) modifications of the coupled-cluster techniques. Apart from this, we proposed reliable benchmark values of the formation enthalpies of furoxan and a number of its (azo)bis-derivatives. Additionally, we reported the previously unknown crystal structure of 3-cyano-4-nitrofuroxan. Among the monocyclic compounds, 3-nitro-4-cyclopropyl and dicyano derivatives of furoxan outperformed trinitrotoluene, a benchmark melt-cast explosive, exhibited decent thermal stability (decomposition temperature >200 °C) and insensitivity to mechanical stimuli while having notable volatility and low melting points. In turn, 4,4′-azobis-dicarbamoyl furoxan is proposed as a substitute of pentaerythritol tetranitrate, a benchmark brisant high explosive. Finally, the application prospects of 3,3′-azobis-dinitro furoxan, one of the most powerful energetic materials synthesized up to date, are limited due to the tremendously high mechanical sensitivity of this compound. Overall, the investigated derivatives of furoxan comprise multipurpose green energetic materials, including primary, secondary, melt-cast, low-sensitive explosives, and an energetic liquid.
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Affiliation(s)
- Alexander A. Larin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Ave., 119991 Moscow, Russia; (A.A.L.); (D.M.B.); (L.L.F.); (A.A.K.); (N.N.M.)
| | - Dmitry M. Bystrov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Ave., 119991 Moscow, Russia; (A.A.L.); (D.M.B.); (L.L.F.); (A.A.K.); (N.N.M.)
| | - Leonid L. Fershtat
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Ave., 119991 Moscow, Russia; (A.A.L.); (D.M.B.); (L.L.F.); (A.A.K.); (N.N.M.)
| | - Alexey A. Konnov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Ave., 119991 Moscow, Russia; (A.A.L.); (D.M.B.); (L.L.F.); (A.A.K.); (N.N.M.)
| | - Nina N. Makhova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky Ave., 119991 Moscow, Russia; (A.A.L.); (D.M.B.); (L.L.F.); (A.A.K.); (N.N.M.)
| | - Konstantin A. Monogarov
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
| | - Dmitry B. Meerov
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
| | - Igor N. Melnikov
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
| | - Alla N. Pivkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
| | - Vitaly G. Kiselev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
- Novosibirsk State University, 1 Pirogova Str., 630090 Novosibirsk, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
| | - Nikita V. Muravyev
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygina Str., 119991 Moscow, Russia; (K.A.M.); (D.B.M.); (I.N.M.); (A.N.P.); (V.G.K.)
- Correspondence: ; Tel.: +7-499-137-8203
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22
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Dorofeeva OV. Accurate prediction of norbornadiene cycle enthalpies by DLPNO-CCSD(T 1 )/CBS method. J Comput Chem 2020; 41:2352-2364. [PMID: 32798279 DOI: 10.1002/jcc.26394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/04/2020] [Accepted: 07/15/2020] [Indexed: 11/06/2022]
Abstract
The DLPNO-CCSD(T1 )/CBS method combined with simple reactions containing small reference species leads to an improvement in the accuracy of theoretically evaluated enthalpies of formation of medium-sized polyalicyclic hydrocarbons when compared with the widely used composite approach. The efficiency of the DLPNO-CCSD(T1 )/CBS method is most vividly demonstrated by comparing with the results of G4 calculations for adamantane. The most important factor in choosing appropriate working reaction is the same number of species on both sides of the equation. Among these reactions, the reactions with small enthalpy change usually provide a better cancellation of errors. The DLPNO-CCSD(T1 )/CBS method was used to calculate the enthalpies of formation of compounds belonging to the norbornadiene cycle (norbornadiene, quadricyclane, norbornene, nortricyclane, and norbornane). The most reliable experimental enthalpies of formation are recommended for these compounds by comparing calculated values with conflicting experimental data.
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Affiliation(s)
- Olga V Dorofeeva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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23
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Gorn MV, Gritsan NP, Goldsmith CF, Kiselev VG. Thermal Stability of Bis-Tetrazole and Bis-Triazole Derivatives with Long Catenated Nitrogen Chains: Quantitative Insights from High-Level Quantum Chemical Calculations. J Phys Chem A 2020; 124:7665-7677. [DOI: 10.1021/acs.jpca.0c04985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Margarita V. Gorn
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Street, Novosibirsk 630090, Russia
| | - Nina P. Gritsan
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Street, Novosibirsk 630090, Russia
| | - C. Franklin Goldsmith
- Brown University, School of Engineering, 184 Hope Street, Providence, Rhode Island 02912, United States
| | - Vitaly G. Kiselev
- Novosibirsk State University, 1 Pirogova Street, Novosibirsk 630090, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Street, Novosibirsk 630090, Russia
- Brown University, School of Engineering, 184 Hope Street, Providence, Rhode Island 02912, United States
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24
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Karton A. Effective basis set extrapolations for CCSDT, CCSDT(Q), and CCSDTQ correlation energies. J Chem Phys 2020; 153:024102. [PMID: 32668917 DOI: 10.1063/5.0011674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is well established that extrapolating the coupled-cluster single double triple [CCSD and (T)] correlation energies using empirically motivated extrapolation exponents can accelerate the basis set convergence. Here, we consider the extrapolation of coupled-cluster expansion terms beyond the CCSD(T) level to the complete basis set (CBS) limit. We obtain reference CCSDT-CCSD(T) [T3-(T)], CCSDT(Q)-CCSDT [(Q)], and CCSDTQ-CCSDT(Q) [T4-(Q)] contributions from cc-pV{5,6}Z extrapolations for a diverse set of 16 first- and second-row systems. We use these basis-set limit results to fit extrapolation exponents in conjunction with the cc-pV{D,T}Z, cc-pV{T,Q}Z, and cc-pV{Q,5}Z basis set pairs. The optimal extrapolation exponents result in noticeable improvements in performance (relative to α = 3.0) in conjunction with the cc-pV{T,Q}Z basis set pair; however, smaller improvements are obtained for the other basis sets. These results confirm that the basis sets and basis set extrapolations used for obtaining post-CCSD(T) components in composite thermochemical theories such as Weizmann-4 and HEAT are sufficiently close to the CBS limit for attaining sub-kJ/mole accuracy. The fitted extrapolation exponents demonstrate that the T3-(T) correlation component converges more slowly to the CBS limit than the (Q) and T4 terms. A systematic investigation of the effect of diffuse functions shows that it diminishes (i) in the order T3-(T) > (Q) > T4-(Q) and (ii) with the size of the basis set. Importantly, we find that diffuse functions tend to systematically reduce the T3-(T) contribution but systematically increases the (Q) contribution. Thus, the use of the cc-pVnZ basis sets benefits from a certain degree of error cancellation between these two components.
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Affiliation(s)
- Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
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25
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Lakmuang C, Kroeger AA, Karton A. Criegee intermediate decomposition pathways for the formation of o-toluic acid and 2-methylphenylformate. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Wiberg KB, Rablen PR. Increase in Strain Energy during Conversion of [4.4.4.5]Fenestrane to [4.4.4.4]Fenestrane: a Method for Estimating the Heats of Formation of Hydrocarbons and Their Derivatives from Ab Initio Energies. J Org Chem 2020; 85:4981-4987. [DOI: 10.1021/acs.joc.0c00187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenneth B. Wiberg
- Departments of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Paul R. Rablen
- Departments of Chemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
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27
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Bakowies D. Estimating Systematic Error and Uncertainty in Ab Initio Thermochemistry: II. ATOMIC(hc) Enthalpies of Formation for a Large Set of Hydrocarbons. J Chem Theory Comput 2019; 16:399-426. [DOI: 10.1021/acs.jctc.9b00974] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dirk Bakowies
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstr. 80, CH 4056 Basel, Switzerland
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28
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Kiselev VG, Goldsmith CF. Accurate Thermochemistry of Novel Energetic Fused Tricyclic 1,2,3,4-Tetrazine Nitro Derivatives from Local Coupled Cluster Methods. J Phys Chem A 2019; 123:9818-9827. [DOI: 10.1021/acs.jpca.9b08356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitaly G. Kiselev
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
- Semenov Institute of Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
- Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
| | - C. Franklin Goldsmith
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
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29
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Finkenstadt D, Mehl MJ, Pederson MR, Richardson SL. Theoretical studies of the vibrational properties of octahedrane (C 12H 12): A polyhedral caged hydrocarbon molecule. J Chem Phys 2019; 150:214304. [PMID: 31176345 DOI: 10.1063/1.5096404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational properties of octahedrane (C12H12) are calculated using density-functional theory employing two different computational methods: an all-electron Gaussian orbital approach and a Naval Research Laboratory-tight-binding scheme (NRL-TB) coupled with molecular dynamics (NRL-TBMD). Both approaches yield vibrational densities of states for octahedrane that are in good general agreement with each other. NRL Molecular Orbital Library can also provide accurate infrared and Raman spectra which can be analyzed and compared with experimental results, while NRL-TBMD can be conveniently scaled up for larger finite-temperature simulations. This latter approach is used in our paper to produce a theoretical prediction for a stable room temperature structure of octahedrane.
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Affiliation(s)
- Daniel Finkenstadt
- U.S. Naval Academy, Department of Physics, Annapolis, Maryland 21402, USA
| | - Michael J Mehl
- U.S. Naval Academy, Department of Physics, Annapolis, Maryland 21402, USA
| | - Mark R Pederson
- U.S. Department of Energy, Office of Basic Energy Sciences, Washington, DC 20585, USA
| | - Steven L Richardson
- U.S. Naval Research Laboratory, Center for Computational Materials Science, Washington, DC 20375, USA
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Santra G, Sylvetsky N, Martin JML. Minimally Empirical Double-Hybrid Functionals Trained against the GMTKN55 Database: revDSD-PBEP86-D4, revDOD-PBE-D4, and DOD-SCAN-D4. J Phys Chem A 2019; 123:5129-5143. [PMID: 31136709 PMCID: PMC9479158 DOI: 10.1021/acs.jpca.9b03157] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
We
present a family of minimally empirical double-hybrid DFT functionals
parametrized against the very large and diverse GMTKN55 benchmark.
The very recently proposed ωB97M(2) empirical double hybrid
(with 16 adjustable parameters) has the lowest WTMAD2 (weighted mean
absolute deviation over GMTKN55) ever reported at 2.19 kcal/mol. However,
refits of the DSD-BLYP and DSD-PBEP86 spin-component-scaled, dispersion-corrected
double hybrids can achieve WTMAD2 values as low as 2.33 with the very
recent D4 dispersion correction (2.42 kcal/mol with the D3(BJ) dispersion
term) using just a handful of adjustable parameters. If we use full
DFT correlation in the initial orbital evaluation, the xrevDSD-PBEP86-D4
functional reaches WTMAD2 = 2.23 kcal/mol, statistically indistinguishable
from ωB97M(2) but using just four nonarbitrary adjustable parameters
(and three semiarbitrary ones). The changes from the original DSD
parametrizations are primarily due to noncovalent interaction energies
for large systems, which were undersampled in the original parametrization
set. With the new parametrization, same-spin correlation can be eliminated
at minimal cost in performance, which permits revDOD-PBEP86-D4 and
revDOD-PBE-D4 functionals that scale as N4 or even N3 with the size of the system.
Dependence of WTMAD2 for DSD functionals on the percentage of HF exchange
is roughly quadratic; it is sufficiently weak that any reasonable
value in the 64% to 72% range can be chosen semiarbitrarily. DSD-SCAN
and DOD-SCAN double hybrids involving the SCAN nonempirical meta-GGA
as the semilocal component have also been considered and offer a good
alternative if one wishes to eliminate either the empirical dispersion
correction or the same-spin correlation component. noDispSD-SCAN66
achieves WTMAD2 = 3.0 kcal/mol, compared to 2.7 kcal/mol for DOD-SCAN66-D4.
However, the best performance without dispersion corrections (WTMAD2
= 2.8 kcal/mol) is reached by revωB97X-2, a slight reparametrization
of the Chai–Head-Gordon range-separated double hybrid. Finally,
in the context of double-hybrid functionals, the very recent D4 dispersion
correction is clearly superior over D3(BJ).
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Affiliation(s)
- Golokesh Santra
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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31
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Thermochemistry of phosphorus sulfide cages: an extreme challenge for high-level ab initio methods. Struct Chem 2019. [DOI: 10.1007/s11224-019-01352-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Kiselev VG, Goldsmith CF. Accurate Prediction of Bond Dissociation Energies and Barrier Heights for High-Energy Caged Nitro and Nitroamino Compounds Using a Coupled Cluster Theory. J Phys Chem A 2019; 123:4883-4890. [DOI: 10.1021/acs.jpca.9b01506] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vitaly G. Kiselev
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
- Novosibirsk State University, 2 Pirogova Str., 630090 Novosibirsk, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
| | - C. Franklin Goldsmith
- School of Engineering, Brown University, 184 Hope Str., Providence, Rhode Island 02912, United States
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33
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Dral PO, Wu X, Thiel W. Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections. J Chem Theory Comput 2019; 15:1743-1760. [PMID: 30735388 PMCID: PMC6416713 DOI: 10.1021/acs.jctc.8b01265] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/31/2022]
Abstract
We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E ABC for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
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Affiliation(s)
- Pavlo O. Dral
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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34
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Karton A. Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods. Aust J Chem 2019. [DOI: 10.1071/ch19276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).
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35
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Morgante P, Peverati R. ACCDB: A collection of chemistry databases for broad computational purposes. J Comput Chem 2018; 40:839-848. [DOI: 10.1002/jcc.25761] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 11/11/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
| | - Roberto Peverati
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
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36
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Zhang IY, Wu J, Xu X. Accurate heats of formation of polycyclic saturated hydrocarbons predicted by using the XYG3 type of doubly hybrid functionals. J Comput Chem 2018; 40:1113-1122. [PMID: 30379331 DOI: 10.1002/jcc.25726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 11/06/2022]
Abstract
Polycyclic saturated hydrocarbons (PSHs) are attractive candidates as hydrocarbon propellants. To assess their potential values, one of the key factors is to determine their energy contents, such as to calculate their heats of formation (HOF). In this work, we have calculated HOFs for a set of 36 PSHs including exo-Tricyclo[5.2.1.0(2,6) ] decane, the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. The results from B3LYP, B3LYP-D3BJ, M06-2X, B2PLYP, B2PLYP-D3BJ, and the XYG3 type of doubly hybrid (xDH) functionals are presented. It is demonstrated here that the xDH functionals yield accurate HOFs in good agreement with those from experiments or the G4 theory. In particular, XYGJ-OS, a low scaling xDH functional, is shown to hold the promise for accurate prediction of HOFs for PSHs of larger sizes. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jianming Wu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
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37
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CCSDT(Q)/CBS thermochemistry for the D5h → D10h isomerization in the C10 carbon cluster: Getting the right answer for the right reason. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.05.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Mardirossian N, Head-Gordon M. Survival of the most transferable at the top of Jacob's ladder: Defining and testing the ωB97M(2) double hybrid density functional. J Chem Phys 2018; 148:241736. [PMID: 29960332 PMCID: PMC5991970 DOI: 10.1063/1.5025226] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/09/2018] [Indexed: 01/19/2023] Open
Abstract
A meta-generalized gradient approximation, range-separated double hybrid (DH) density functional with VV10 non-local correlation is presented. The final 14-parameter functional form is determined by screening trillions of candidate fits through a combination of best subset selection, forward stepwise selection, and random sample consensus (RANSAC) outlier detection. The MGCDB84 database of 4986 data points is employed in this work, containing a training set of 870 data points, a validation set of 2964 data points, and a test set of 1152 data points. Following an xDH approach, orbitals from the ωB97M-V density functional are used to compute the second-order perturbation theory correction. The resulting functional, ωB97M(2), is benchmarked against a variety of leading double hybrid density functionals, including B2PLYP-D3(BJ), B2GPPLYP-D3(BJ), ωB97X-2(TQZ), XYG3, PTPSS-D3(0), XYGJ-OS, DSD-PBEP86-D3(BJ), and DSD-PBEPBE-D3(BJ). Encouragingly, the overall performance of ωB97M(2) on nearly 5000 data points clearly surpasses that of all of the tested density functionals. As a Rung 5 density functional, ωB97M(2) completes our family of combinatorially optimized functionals, complementing B97M-V on Rung 3, and ωB97X-V and ωB97M-V on Rung 4. The results suggest that ωB97M(2) has the potential to serve as a powerful predictive tool for accurate and efficient electronic structure calculations of main-group chemistry.
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Affiliation(s)
- Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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39
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Fokin AA, Zhuk TS, Blomeyer S, Pérez C, Chernish LV, Pashenko AE, Antony J, Vishnevskiy YV, Berger RJF, Grimme S, Logemann C, Schnell M, Mitzel NW, Schreiner PR. Intramolecular London Dispersion Interaction Effects on Gas-Phase and Solid-State Structures of Diamondoid Dimers. J Am Chem Soc 2017; 139:16696-16707. [PMID: 29037036 DOI: 10.1021/jacs.7b07884] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The covalent diamantyl (C28H38) and oxadiamantyl (C26H34O2) dimers are stabilized by London dispersion attractions between the dimer moieties. Their solid-state and gas-phase structures were studied using a multitechnique approach, including single-crystal X-ray diffraction (XRD), gas-phase electron diffraction (GED), a combined GED/microwave (MW) spectroscopy study, and quantum chemical calculations. The inclusion of medium-range electron correlation as well as the London dispersion energy in density functional theory is essential to reproduce the experimental geometries. The conformational dynamics computed for C26H34O2 agree well with solution NMR data and help in the assignment of the gas-phase MW data to individual diastereomers. Both in the solid state and the gas phase the central C-C bond is of similar length for the diamantyl [XRD, 1.642(2) Å; GED, 1.630(5) Å] and the oxadiamantyl dimers [XRD, 1.643(1) Å; GED, 1.632(9) Å; GED+MW, 1.632(5) Å], despite the presence of two oxygen atoms. Out of a larger series of quantum chemical computations, the best match with the experimental reference data is achieved with the PBEh-3c, PBE0-D3, PBE0, B3PW91-D3, and M06-2X approaches. This is the first gas-phase confirmation that the markedly elongated C-C bond is an intrinsic feature of the molecule and that crystal packing effects have only a minor influence.
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Affiliation(s)
- Andrey A Fokin
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine.,Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Tatyana S Zhuk
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Sebastian Blomeyer
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Cristóbal Pérez
- Max-Planck-Institut für Struktur und Dynamik der Materie , Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Lesya V Chernish
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Alexander E Pashenko
- Department of Organic Chemistry, Igor Sikorsky Kiev Polytechnic Institute , Prospekt Pobedy 37, 03056 Kiev, Ukraine
| | - Jens Antony
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Yury V Vishnevskiy
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Raphael J F Berger
- Materialchemie, Paris-Lodron Universität Salzburg , Hellbrunner Str. 34, A-5020 Salzburg, Austria
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Christian Logemann
- Institute of Inorganic and Analytical Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Melanie Schnell
- Max-Planck-Institut für Struktur und Dynamik der Materie , Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Norbert W Mitzel
- Lehrstuhl für Anorganische Chemie und Strukturchemie, Universität Bielefeld , Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University , Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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40
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Intramolekulare π-π-Wechselwirkungen in flexibel verbrückten, teilweise fluorierten Bisarenen in der Gasphase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Blomeyer S, Linnemannstöns M, Nissen JH, Paulus J, Neumann B, Stammler HG, Mitzel NW. Intramolecular π-π Interactions in Flexibly Linked Partially Fluorinated Bisarenes in the Gas Phase. Angew Chem Int Ed Engl 2017; 56:13259-13263. [DOI: 10.1002/anie.201707716] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/17/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Sebastian Blomeyer
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Marvin Linnemannstöns
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Jan Hendrick Nissen
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Jannik Paulus
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Beate Neumann
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Hans-Georg Stammler
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert W. Mitzel
- Lehrstuhl für Anorganische Chemie und Strukturchemie; Centrum für Molekulare Materialien CM 2; Fakultät für Chemie, Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
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42
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Peach ML, Cachau RE, Nicklaus MC. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit 2017; 30:10.1002/jmr.2618. [PMID: 28233410 PMCID: PMC5553890 DOI: 10.1002/jmr.2618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/25/2022]
Abstract
In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.
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Affiliation(s)
- Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raul E Cachau
- Data Science and Information Technology Program, Advanced Biomedical Computing Center, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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43
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Karton A, Sylvetsky N, Martin JML. W4‐17: A diverse and high‐confidence dataset of atomization energies for benchmarking high‐level electronic structure methods. J Comput Chem 2017; 38:2063-2075. [DOI: 10.1002/jcc.24854] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/10/2017] [Accepted: 05/18/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Amir Karton
- School of Molecular SciencesThe University of Western AustraliaPerth Western Australia6009 Australia
| | - Nitai Sylvetsky
- Department of Organic ChemistryWeizmann Institute of ScienceRehovot76100 Israel
| | - Jan M. L. Martin
- Department of Organic ChemistryWeizmann Institute of ScienceRehovot76100 Israel
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44
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Mardirossian N, Head-Gordon M. Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1333644] [Citation(s) in RCA: 709] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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45
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Abstract
We have devised the composite procedures WG and WGh to unify the W1X and the (computationally more economical) G4(MP2)-6X protocols. The WG procedure employs a combination of MP2, MP2-F12, CCSD-F12b, and CCSD(T) to approximate the all-electron scalar-relativistic CCSD(T)/CBS energy. In addition, it incorporates features such as the scaling of the energy components and an empirical "higher-level-correction" term. The WGh protocol represents a somewhat more economical variant of WG with partial removal of diffuse functions. Our benchmark shows that, in general, both WG and WGh have similar performance to that for W1X-2, with WGh (predictably) performing somewhat less well for electron affinities. In terms of computational efficiency, WG is approximately an order of magnitude less costly than W1X-2, while WGh gives not only a further slight savings in computer time but also a notably reduced disk requirement.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University , Bunkyo 1-14, Nagasaki 852-8521, Japan
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46
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Witte J, Mardirossian N, Neaton JB, Head-Gordon M. Assessing DFT-D3 Damping Functions Across Widely Used Density Functionals: Can We Do Better? J Chem Theory Comput 2017; 13:2043-2052. [DOI: 10.1021/acs.jctc.7b00176] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Jeffrey B. Neaton
- Kavli Energy
Nanosciences
Institute at Berkeley, Berkeley, California 94720, United States
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47
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Dorofeeva OV, Osina EL. Performance of DFT, MP2, and composite ab initio methods for the prediction of enthalpies of formations of CHON compounds using isodesmic reactions. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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48
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Sarrami F, Yu LJ, Karton A. Thermochemistry of icosahedral closo-dicarboranes: a composite ab initio quantum-chemical perspective. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We obtained accurate thermochemical properties for the ortho-, meta-, and para-dicarborane isomers (C2B10H12) by means of explicitly correlated high-level thermochemical procedures. The thermochemical properties include heats of formation, isomerization energies, C–H and B–H bond dissociation energies (BDEs), and ionization potentials. Of these only the ionization potentials are known experimentally. Our best theoretical ionization potentials, obtained by means of the ab initio W1–F12 thermochemical protocol, was 241.50 kcal mol–1 (para-dicarborane), 238.45 kcal mol–1 (meta-dicarborane), and 236.54 kcal mol–1 (ortho-dicarborane). These values agree with the experimental values adopted by the National Institute of Standards and Technology (NIST) thermochemical tables to within overlapping uncertainties. However, they suggest that the experimental values may represent significant underestimations. For all isomers, the C–H BDEs are systematically higher than the B–H BDEs because of the relative stability of the boron-centred radicals. The C–H BDEs for the three isomers cluster within a narrow energetic interval, namely between 110.8 kcal mol–1 (para-dicarborane) and 111.7 kcal mol–1 (meta-dicarborane). The B–H BDEs cluster within a larger interval ranging between 105.8 and 108.1 kcal mol–1 (both obtained for ortho-dicarborane). We used our benchmark W1–F12 data to assess the performance of a number of lower cost composite ab initio methods. We found that the Gaussian-3 procedures (G3(MP2)B3 and G3B3) result in excellent performance with overall root-mean-square deviations (RMSDs) of 0.3–0.4 kcal mol–1 for the isomerization, ionization, and bond dissociation energies. However, the Gaussian-4 procedures (G4, G4(MP2), and G4(MP2)-6X) showed relatively poor performance with overall RMSDs of 1.3–3.7 kcal mol–1.
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Affiliation(s)
- Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Li-Juan Yu
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
| | - Amir Karton
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009, Australia
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Mardirossian N, Head-Gordon M. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements? J Chem Theory Comput 2016; 12:4303-25. [PMID: 27537680 DOI: 10.1021/acs.jctc.6b00637] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses.
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Affiliation(s)
- Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California , Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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Mardirossian N, Head-Gordon M. ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation. J Chem Phys 2016; 144:214110. [DOI: 10.1063/1.4952647] [Citation(s) in RCA: 370] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Narbe Mardirossian
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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