1
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Nakajima Y, Ohmura T, Seino J. Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. J Comput Chem 2024; 45:1870-1879. [PMID: 38686778 DOI: 10.1002/jcc.27375] [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: 11/12/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.
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Affiliation(s)
- Yuya Nakajima
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Takuto Ohmura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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2
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Chan B. Limiting factors in the accuracy of DFT calculation for redox potentials. J Comput Chem 2024; 45:1177-1186. [PMID: 38311976 DOI: 10.1002/jcc.27320] [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: 11/13/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024]
Abstract
In the present study, we have investigated factors affecting the accuracy of computational chemistry calculation of redox potentials, namely the gas-phase ionization energy (IE) and electron affinity (EA), and the continuum solvation effect. In general, double-hybrid density functional theory methods yield IEs and EAs that are on average within ~0.1 eV of our high-level W3X-L benchmark, with the best performing method being DSD-BLYP/ma-def2-QZVPP. For lower-cost methods, the average errors are ~0.2-0.3 eV, with ωB97X-3c being the most accurate (~0.15 eV). For the solvation component, essentially all methods have an average error of ~0.3 eV, which shows the limitation of the continuum solvation model. Curiously, the directly calculated redox potentials show errors of ~0.3 eV for all methods. These errors are notably smaller than what can be expected from error propagation with the two components (IE and EA, and solvation effect). Such a discrepancy can be attributed to the cancellation of errors, with the lowest-cost GFN2-xTB method benefiting the most, and the most accurate ωB97X-3c method benefiting the least. For organometallic species, the redox potentials show large deviations exceeding ~0.5 eV even for DSD-BLYP. The large errors are attributed to those for the gas-phase IEs and EAs, which represents a major barrier to the accurate calculation of redox potentials for such systems.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
- RIKEN Center for Computational Science, Kobe, Japan
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3
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Tobisch S. Copper-catalysed electrophilic carboamination of terminal alkynes with benzyne looked at through the computational lens. Dalton Trans 2024; 53:8154-8167. [PMID: 38536069 DOI: 10.1039/d3dt04301k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
A detailed computational mechanistic study of the copper-catalysed three-component-type electrophilic carboamination of terminal alkynes with benzyne and an archetypal O-benzoylhydroxylamine electrophile is presented. Probing various plausible pathways for relevant elementary steps and scrutinising performance degradation pathways, with the aid of a reliable computational protocol applied to a realistic catalyst model combined with kinetic analysis, identified the pathways preferably traversed in productive catalysis. It entails rapid alkynylcupration of in situ generated benzyne to deliver the arylcopper nucleophile that undergoes amination with the O-benzoylhydroxylamine electrophile to afford copper benzoate. Umpolung-enabled electrophilic amination favours a multistep SN2-type oxidative addition/N-C bond-forming reductive elimination sequence involving a short-lived formal {P^P}CuIII carboxylate amido aryl intermediate. SN2-type displacement of the benzoate leaving group at the arylcopper nucleophile, which represents the catalyst resting state, is predicted to be the turnover limiting step. Alkynolysis transforms copper benzoate back to catalytically competent alkynylcopper. The computational probe of a wider range of substrates reveals that only severely ring-strained C6-arynes, C6-cycloalkynes and electron-deficient cyclopropenes featuring a highly reactive C≡C linkage could replace benzyne. Moreover, strict control of stationary benzyne concentration is indispensable for electrophilic carboamination to ever become achievable.
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Affiliation(s)
- Sven Tobisch
- University of St Andrews, School of Chemistry, Purdie Building, North Haugh, St Andrews, KY16 9ST, UK.
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4
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Mészáros D, Matejčík Š, Papp P. Formation of negative ions from cobalt tricarbonyl nitrosyl Co(CO) 3NO clusters. Phys Chem Chem Phys 2024; 26:7522-7533. [PMID: 38357994 DOI: 10.1039/d3cp05601e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Electron attachment and corresponding dissociative electron attachment (DEA) to cobalt tricarbonyl nitrosyl (Co(CO)3NO) clusters have been studied by co-expansion with Ar gas into a high vacuum. A monochromatic electron beam was utilized to generate negative ions and the resulting reaction products were identified using mass spectrometry. The ion fragments corresponding to Co(CO)3NO monomers closely resemble results from earlier gas phase experiments and studies conducted on Co(CO)3NO in He nanodroplets. However, contrary to the gas phase or He nanodroplet ion yields, a resonance structure comprising several peaks at energies above ∼4 eV was observed both in the case of molecular clusters [Co(CO)3NO]n- (with n = 1, 2, 3) and clusters comprising DEA fragments. Additionally, the ion yields of numerous other clusters such as ions without nitrosyl ([Co(CO)4]-, [Co2(CO)5]-), clusters consisting of two fragments such as ([Co2(CO)NO]-, [Co2(CO)(NO)2]-, [Co2(CO)2NO]-, [Co2(CO)2(NO)2]-, [Co3(CO)(NO)3]-, [Co3(CO)8(NO)3]-, [Co3(CO)(NO)2]-, [Co3(CO)3(NO)2]-, and [Co3(CO)5(NO)2]-) were recorded. Moreover, NO bond dissociation was confirmed with the [Co(CO)2N]-ion and with N- or O-retaining cluster ions, such as [Co2(CO)(NO)N]-, [Co2(CO)2(NO)N]-, [Co3(CO)2(NO)N]-, [Co3(CO)3(NO)N]- and [Co3(CO)(NO)2N]-, or [Co2(CO)2O]-, [Co2(CO)3O]-, [Co3(CO)3O]-, [Co3(CO)4O]-and [Co3(CO)2(NO)O]- respectively.
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Affiliation(s)
- Dušan Mészáros
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
| | - Štefan Matejčík
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
| | - Peter Papp
- Department of Experimental Physics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina F2, 842 48 Bratislava, Slovakia.
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5
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Chan B. DAPD Set of Pd-Containing Diatomic Molecules: Accurate Molecular Properties and the Great Lengths to Obtain Them. J Chem Theory Comput 2023; 19:9260-9268. [PMID: 38096563 DOI: 10.1021/acs.jctc.3c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
In the present study, we obtained reliable bond energy, bond length, and zero-point vibrational frequency for a set of diatomic Pd species (the DAPD set). It includes PdH, Pd2, and PdX (X = B, C, N, O, F, Al, Si, P, S, and Cl). Our highest-level protocol (W4X-L) represents scalar and spin-orbit relativistic, valence- and inner-valence correlated, extrapolated CCSDTQ(5) energy. The DAPD set of molecules is challenging for computational chemistry methods in different manners; for Pd2, the spin-orbit contribution to the bond energy is fairly large, whereas for PdC and PdSi, the post-CCSD(T) correlation components are considerable. The diverse range of requirements represents a significant challenge for lower-level methods. While density functional theory (DFT) methods generally yield good agreements for bond lengths and vibrational frequencies, large deviations are found for bond energies. In general, hybrid DFT methods are more accurate than nonhybrid functionals, but the agreement in individual cases varies. This illustrates the critical role that new high-quality reference data would play in the continual development of lower-cost methods.
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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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6
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Semidalas E, Martin JML. Correlation Consistent Basis Sets for Explicitly Correlated Theory: The Transition Metals. J Chem Theory Comput 2023; 19:5806-5820. [PMID: 37540641 PMCID: PMC10500978 DOI: 10.1021/acs.jctc.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 08/06/2023]
Abstract
We present correlation consistent basis sets for explicitly correlated (F12) calculations, denoted VnZ(-PP)-F12-wis (n = D,T), for the d-block elements. The cc-pVDZ-F12-wis basis set is contracted to [8s7p5d2f] for the 3d-block, while its ECP counterpart for the 4d and 5d-blocks, cc-pVDZ-PP-F12-wis, is contracted to [6s6p5d2f]. The corresponding contracted sizes for cc-pVTZ(-PP)-F12-wis are [9s8p6d3f2g] for the 3d-block elements and [7s7p6d3f2g] for the 4d and 5d-block elements. Our VnZ(-PP)-F12-wis basis sets are evaluated on challenging test sets for metal-organic barrier heights (MOBH35) and group-11 metal clusters (CUAGAU-2). In F12 calculations, they are found to be about as close to the complete basis set limit as the combination of standard cc-pVnZ-F12 on main-group elements with the standard aug-cc-pV(n+1)Z(-PP) basis sets on the transition metal(s). While our basis sets are somewhat more compact than aug-cc-pV(n+1)Z(-PP), the CPU time benefit is negligible for catalytic complexes that contain only one or two transition metals among dozens of main-group elements; however, it is somewhat more significant for metal clusters.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
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7
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Chan B. Compilation of Ionic Clusters with the Rock Salt Structure: Accurate Benchmark Thermochemical Data, Assessment of Quantum Chemistry Methods, and the Convergence Behavior of Lattice Energies. J Phys Chem A 2023. [PMID: 37368538 DOI: 10.1021/acs.jpca.3c01880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In the present study, computational quantum chemistry is used to obtain lattice energies (LEs) for a range of ionic clusters with the NaCl structure. Specifically, the compounds include NaF, NaCl, MgO, MgS, KF, CaO, and CaS clusters, (MX)n, with n = 1, 2, 4, 6, 8, 12, 16, 24, 32, 40, 50, 60, 75, 90, and 108. The highest-level W2 and W1X-2 methods are applied to the small clusters with n = 1 to 8 (the MX35 data set). The assessment with MX35 shows that, for the calculation of geometries and vibrational frequencies, the PBE0-D3(BJ) and PBE-D3(BJ) DFT methods are reasonable, but the calculation of atomization energies is more challenging. This is a result of different systematic deviations for clusters of different species. Thus, species-specific adjustments are applied for larger clusters, which are calculated with the DuT-D3 double-hybrid DFT method, the MN15 DFT method, and the PM7 semi-empirical method. They yield smoothly converging LEs to the bulk values. It is also found that, for the alkali-metal species, the LEs for a single molecule are ∼70% of the bulk values, while for the alkali-earth species, they are ∼80%. This has enabled a straightforward means to the first-principles estimation of LEs for similarly structured ionic compounds.
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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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8
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Liu Y, Zhang C, Liu Z, Truhlar DG, Wang Y, He X. Supervised learning of a chemistry functional with damped dispersion. NATURE COMPUTATIONAL SCIENCE 2023; 3:48-58. [PMID: 38177952 PMCID: PMC10766516 DOI: 10.1038/s43588-022-00371-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2024]
Abstract
Kohn-Sham density functional theory is widely used in chemistry, but no functional can accurately predict the whole range of chemical properties, although recent progress by some doubly hybrid functionals comes close. Here, we optimized a singly hybrid functional called CF22D with higher across-the-board accuracy for chemistry than most of the existing non-doubly hybrid functionals by using a flexible functional form that combines a global hybrid meta-nonseparable gradient approximation that depends on density and occupied orbitals with a damped dispersion term that depends on geometry. We optimized this energy functional by using a large database and performance-triggered iterative supervised training. We combined several databases to create a very large, combined database whose use demonstrated the good performance of CF22D on barrier heights, isomerization energies, thermochemistry, noncovalent interactions, radical and nonradical chemistry, small and large systems, simple and complex systems and transition-metal chemistry.
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Affiliation(s)
- Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Cheng Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, China.
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9
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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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10
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Chan B. High-Level Quantum Chemistry Reference Heats of Formation for a Large Set of C, H, N, and O Species in the NIST Chemistry Webbook and the Identification and Validation of Reliable Protocols for Their Rapid Computation. J Phys Chem A 2022; 126:4981-4990. [PMID: 35878062 DOI: 10.1021/acs.jpca.2c03846] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A recent study has examined the accuracy of NIST heats of formation for a set of C, H, and O-containing species with a proposed low-cost quantum chemistry approach. In the present study, we have used high-level methods such as W1X-2 to obtain these data more rigorously, which we have then used to assess the NIST and the previously computed values. We find that many of these NIST data that are as suggested to be unreliable by the previous study are indeed inconsistent with our high-level reference values. However, we also find substantial deviations for the previously computed values from our benchmark. Thus, we have assessed the performance of alternative low-cost methods. In our assessment, we have additionally examined C, H, N, and O-containing species for which heats of formation are available from the NIST database. We find the ωB97M-V/ma-def2-TZVP, DSD-PBEP86/ma-def2-TZVP, and CCSD(T)-F12b/aug'-cc-pVDZ methods to be adequate for obtaining heats of formation with the atomization approach, once their atomic energies are optimized with our benchmark. Notably, the low-cost ωB97M-V method yields values that agree to be within 10 kJ mol-1 for more than 90% of the (∼1500) species. A higher 20 kJ mol-1 threshold captures 98% of the data. The outlier species typically contain many electron-withdrawing (nitro) groups. In these cases, the use of isodesmic-type reactions rather than the atomization approach is more reliable. Our assessment has also identified significant outliers from the NIST database, for which experimental re-determination of the heats of formation would be desirable.
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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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11
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Chan B. A step-by-step investigation of sodium chloride clusters: accurate references, assessment of low-cost methods, and convergence from molecule to salt. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2088422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
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12
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Semidalas E, Martin JM. The MOBH35 Metal–Organic Barrier Heights Reconsidered: Performance of Local-Orbital Coupled Cluster Approaches in Different Static Correlation Regimes. J Chem Theory Comput 2022; 18:883-898. [PMID: 35045709 PMCID: PMC8830049 DOI: 10.1021/acs.jctc.1c01126] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
We have revisited
the MOBH35 (Metal–Organic Barrier Heights,
35 reactions) benchmark [Iron, Janes, , 2019, 123 ( (17), ), 3761−378130973722; ibid. 2019, 123, 6379–6380] for realistic organometallic catalytic reactions, using both canonical
CCSD(T) and localized orbital approximations to it. For low levels
of static correlation, all of DLPNO-CCSD(T), PNO-LCCSD(T), and LNO-CCSD(T)
perform well; for moderately strong levels of static correlation,
DLPNO-CCSD(T) and (T1) may break down catastrophically,
and PNO-LCCSD(T) is vulnerable as well. In contrast, LNO-CCSD(T) converges
smoothly to the canonical CCSD(T) answer with increasingly tight convergence
settings. The only two reactions for which our revised MOBH35 reference
values differ substantially from the original ones are reaction 9
and to a lesser extent 8, both involving iron. For the purpose of
evaluating density functional theory (DFT) methods for MOBH35, it
would be best to remove reaction 9 entirely as its severe level of
static correlation makes it just too demanding for a test. The magnitude
of the difference between DLPNO-CCSD(T) and DLPNO-CCSD(T1) is a reasonably good predictor for errors in DLPNO-CCSD(T1) compared to canonical CCSD(T); otherwise, monitoring all of T1, D1, max|tiA|, and 1/(εLUMO – εHOMO) should provide adequate warning
for potential problems. Our conclusions are not specific to the def2-SVP
basis set but are largely conserved for the larger def2-TZVPP, as
they are for the smaller def2-SV(P): the latter may be an economical
choice for calibrating against canonical CCSD(T). Finally, diagnostics
for static correlation are statistically clustered into groups corresponding
to (1) importance of single excitations in the wavefunction; (2a)
the small band gap, weakly separated from (2b) correlation entropy;
and (3) thermochemical importance of correlation energy, as well as
the slope of the DFT reaction energy with respect to the percentage
of HF exchange. Finally, a variable reduction analysis reveals that
much information on the multireference character is provided by T1, IND/Itot, and the exchange-based diagnostic A100[TPSS].
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Affiliation(s)
- Emmanouil Semidalas
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Reḥovot 7610001, Israel
| | - Jan M.L. Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Reḥovot 7610001, Israel
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13
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Maurer LR, Bursch M, Grimme S, Hansen A. Assessing Density Functional Theory for Chemically Relevant Open-Shell Transition Metal Reactions. J Chem Theory Comput 2021; 17:6134-6151. [PMID: 34546754 DOI: 10.1021/acs.jctc.1c00659] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to the principle lack of systematic improvement possibilities of density functional theory, careful assessment of the performance of density functional approximations (DFAs) on well-designed benchmark sets, for example, for reaction energies and barrier heights, is crucial. While main-group chemistry is well covered by several available sets, benchmark data for transition metal chemistry is sparse. This is especially the case for larger, chemically relevant molecules. Addressing this issue, we recently introduced the MOR41 benchmark which covers chemically relevant reactions of closed-shell complexes. In this work, we extend these efforts to single-reference open-shell systems and introduce the "reactions of open-shell single-reference transition metal complexes" (ROST61) benchmark set. ROST61 includes accurate coupled-cluster reference values for 61 reaction energies with a mean reaction energy of -42.8 kcal mol-1. Complexes with 13-93 atoms covering 20 d-block elements are included, but due to the restriction to single-reference open-shell systems, important elements such as iron or platinum could not be taken into account, or only to a small extent. We assess the performance of 31 DFAs in combination with three London dispersion (LD) correction schemes. Further, DFT-based composite methods, MP2, and a few semiempirical quantum chemical methods are evaluated. Consistent with the results for the MOR41 closed-shell benchmark, we find that the ordering of DFAs according to Jacob's ladder is preserved and that adding an LD correction is crucial, clearly improving almost all tested methods. The recently introduced r2SCAN-3c composite method stands out with a remarkable mean absolute deviation (MAD) of only 2.9 kcal mol-1, which is surpassed only by hybrid DFAs with low amounts of Fock exchange (e.g., 2.3 kcal mol-1 for TPSS0-D4/def2-QZVPP) and double-hybrid (DH) DFAs but at a significantly higher computational cost. The lowest MAD of only 1.6 kcal mol-1 is obtained with the DH DFA PWPB95-D4 in the def2-QZVPP basis set approaching the estimated accuracy of the reference method. Overall, the ROST61 set adds important reference data to a sparsely sampled but practically relevant area of chemistry. At this point, it provides valuable orientation for the application and development of new DFAs and electronic structure methods in general.
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Affiliation(s)
- Leonard R Maurer
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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14
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Chan B. Accurate Thermochemistry for Main-Group Elements up to Xenon with the W n-P34 Series of Composite Methods. J Chem Theory Comput 2021; 17:5704-5714. [PMID: 34410730 DOI: 10.1021/acs.jctc.1c00598] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In the present study, we introduce the accurate Wn-P34 quantum chemistry composite methods with applicability to heavy p-block elements up to xenon. For a set of thermochemical properties for prototypical third- and fourth-row species and for a diverse set of small light-main-group species, they show accuracies of ∼3 kJ mol-1 or better. Overall, the Wn-P34 methods are comparable in accuracy to Wn, with a widened applicability to heavier elements. We have used Wn-P34 to compile the P34 set of accurate thermochemical values for heavy p-block species, and we have applied this set to assess a wide range of lower-cost methods. The results of our assessment show that the G4(MP2)-XK composite method provides adequate treatments for these species, but several widely used double-hybrid density functional theory (DH-DFT) methods show uncharacteristically large deviations. In contrast, we find it presently surprising that some pure and hybrid DFT methods such as TPSS and SCANh perform quite well. We hope that our findings and new tools would facilitate the application of computational chemistry for heavy elements, of which the properties are yet to be broadly explored.
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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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15
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Chan B. Re-examining the electronic structure of fluorescent tetra-silver clusters in zeolites. Phys Chem Chem Phys 2021; 23:1984-1993. [PMID: 33437977 DOI: 10.1039/d0cp05105e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, we have examined the electronic structures related to the fluorescence properties of small Ag42+ complexes encapsulated in zeolites. We find that interaction between Ag42+ and coordinated water molecules, which was previously proposed to be the origin of fluorescence, may not be a sufficient condition by itself. Refinement of the previously used all-silicon-cage model to include framework Al atoms leads to an asymmetric environment, and this alters the electronic structure in favor of fluorescence. We have further examined the substitution of the H2O ligands by NH3, H2S, PH3, CO and CS. Among these systems, Ag42+ binds most strongly to NH3 but the energetics for the H2S and PH3 complexes is also reasonable. The energy of the fluorescent light is related to the energy of the lowest-energy triplet state, and these energies for the H2O, NH3, H2S and PH3 systems span the range of ∼2-3 eV, i.e., roughly the visible range. Thus, the use of different ligands appears to be an attractive means for tailoring the luminescence properties.
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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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16
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Chan B, Luo Y, Kimura M. Hydride Affinities for Main-Group Hydride Reductants: Assessment of Density Functionals and Trends in Reactivities. J Phys Chem A 2021; 125:835-842. [PMID: 33449696 DOI: 10.1021/acs.jpca.0c10543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present study, we have examined hydride affinities relevant to a range of group 13 and group 14 reductants. We use the high-level W1X-G0, G4(MP2)-XK, and DSD-PBEP86 methods to obtain the RHA42 set of accurate reductant hydride affinities. Assessment of DFT methods with the RHA42 set shows that all functionals that we have examined are fairly accurate. Overall, we find ωB97X-V to be the most accurate. The MN12-SX screened-exchange functional and the nonhybrid B97-D3BJ method also perform well, and they may provide a lower-cost means for obtaining hydride affinities. The trend in the hydride affinities suggests an increased reducing power when one moves down the periodic table, e.g., with TlH3 being a stronger reductant than BH3. We also find that group 13 hydrides are stronger reductants than the group 13 analogues. In general, substitution of a hydrogen, e.g., BH2+ → BHMe+, and the formation of dimer, e.g., BH2+ → B2H5+, also lead to stronger reductants. A notable observation is the small hydride affinities for silyl cations, which are indicative of the potential of silanes as strong reducing agents. In particular, poly(methylhydrosiloxane) (PMHS) cations are associated with especially small hydride affinities owing to the presence of intramolecular oxygen atoms that can stabilize the cation center. We have further found the germanium analogues of the silanes to be more reactive, and they may further widen the scope of main-group hydride reducing agents.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Ying Luo
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki 852-8521, Japan
| | - Masanari Kimura
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki 852-8521, Japan
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17
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Chan B. Fullerene Thermochemical Stability: Accurate Heats of Formation for Small Fullerenes, the Importance of Structural Deformation on Reactivity, and the Special Stability of C 60. J Phys Chem A 2020; 124:6688-6698. [PMID: 32786665 DOI: 10.1021/acs.jpca.0c04732] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have used quantum chemistry computations, in conjunction with isodesmic-type reactions, to obtain accurate heats of formation (HoFs) for the small fullerenes C20 (2358.2 ± 8.0 kJ mol-1), C24 (2566.2 ± 7.6), and the lowest-energy isomers of C32 (2461.1 ± 15.4), C42 (2629.0 ± 20.5), and C54 (2686.2 ± 25.3). As part of this endeavor, we have also obtained accurate HoFs for several medium-sized molecules, namely 216.6 ± 1.4 for fulvene, 375.5 ± 1.5 for pentalene, 670.8 ± 2.9 for acepentalene, and 262.7 ± 2.5 for acenaphthylene. We combine the energies of the small fullerenes and previously obtained energies for larger fullerenes (from C60 to C6000) into a full picture of fullerene thermochemical stability. In general, the per-carbon energies can be reasonably approximated by the "R+D" model that we have previously developed [Chan et al. J. Chem. Theory Comput. 2019, 15, 1255-1264], which takes into account Resonance and structural Deformation factors. In a case study on C54, we find that most of the high-deformation-energy atoms correspond to the sites of the C-Cl bond in the experimentally captured C54Cl8. In another case study, we find that C60 has the lowest value for the maximum local-deformation energy when compared with similar-sized fullerenes, which is consistent with its "special stability". These results are indicative of structural deformation playing an important role in the reactivity of fullerenes.
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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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18
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Semidalas E, Martin JML. Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT? J Chem Theory Comput 2020; 16:4238-4255. [PMID: 32456427 PMCID: PMC7366511 DOI: 10.1021/acs.jctc.0c00189] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
large and chemically diverse GMTKN55 benchmark was used as
a training set for parametrizing composite wave function thermochemistry
protocols akin to G4(MP2)XK theory (Chan, B.; Karton, A.; Raghavachari,
K. J. Chem. Theory Comput. 2019, 15, 4478–4484). On account of their availability
for elements H through Rn, Karlsruhe def2 basis sets were employed.
Even after reparametrization, the GMTKN55 WTMAD2 (weighted mean absolute
deviation, type 2) for G4(MP2)-XK is actually inferior to that of
the best rung-4 DFT functional, ωB97M-V. By increasing the basis
set for the MP2 part to def2-QZVPPD, we were able to substantially
improve performance at modest cost (if an RI-MP2 approximation is
made), with WTMAD2 for this G4(MP2)-XK-D method now comparable to
the better rung-5 functionals (albeit at greater cost). A three-tier
approach with a scaled MP3/def2-TZVPP intermediate step, however,
leads to a G4(MP3)-D method that is markedly superior to even the
best double hybrids ωB97M(2) and revDSD-PBEP86-D4. Evaluating
the CCSD(T) component with a triple-ζ, rather than split-valence,
basis set yields only a modest further improvement that is incommensurate
with the drastic increase in computational cost. G4(MP3)-D and G4(MP2)-XK-D
have about 40% better WTMAD2, at similar or lower computational cost,
than their counterparts G4 and G4(MP2), respectively: detailed comparison
reveals that the difference lies in larger molecules due to basis
set incompleteness error. An E2/{T,Q} extrapolation and a CCSD(T)/def2-TZVP
step provided the G4-T method of high accuracy and with just three
fitted parameters. Using KS orbitals in MP2 leads to the G4(MP3|KS)-D
method, which entirely eliminates the CCSD(T) step and has no steps
costlier than scaled MP3; this shows a path forward to further improvements
in double-hybrid density functional methods. None of our final selections
require an empirical HLC correction; this cuts the number of empirical
parameters in half and avoids discontinuities on potential energy
surfaces. G4-T-DLPNO, a variant in which post-MP2 corrections are
evaluated at the DLPNO-CCSD(T) level, achieves nearly the accuracy
of G4-T but is applicable to much larger systems.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḩovot, Israel
| | - Jan M L Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḩovot, Israel
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19
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Shuman NS, Ard SG, Sweeny BC, Viggiano AA, Owen CJ, Armentrout PB. Methane Adducts of Gold Dimer Cations: Thermochemistry and Structure from Collision-Induced Dissociation and Association Kinetics. J Phys Chem A 2020; 124:3335-3346. [PMID: 32176490 DOI: 10.1021/acs.jpca.0c01217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bond dissociation energies at 0 K (BDE) of Au2+-CH4 and Au2CH4+-CH4 have been determined using two separate experimental methods. Analyses of collision-induced dissociation cross sections for Au2CH4+ + Xe and Au2(CH4)2+ + Xe measured using a guided ion beam tandem mass spectrometer (GIBMS) yield BDEs of 0.71 ± 0.05 and 0.57 ± 0.07 eV, respectively. Statistical modeling of association kinetics of Au2(CH4)0-2+ + CH4 + He measured from 200 to 400 K and at 0.3-0.9 Torr using a selected-ion flow tube (SIFT) apparatus yields slightly higher values of 0.81 ± 0.21 and 0.75 ± 0.25 eV. The SIFT data also place a lower limit on the BDE of Au2C2H8+-CH4 of 0.35 eV, likely an activated isomer, not Au2(CH4)2+-CH4. Particular emphasis is placed on determining the uncertainty in the derivation from association kinetics measurements, including uncertainties in collisional energy transfer, calculated harmonic frequencies, and possible contribution of isomerization of the association complexes. This evaluation indicates that an uncertainty of ±0.2 eV should be expected and that an uncertainty of better than ±0.1 eV is unlikely to be reasonable.
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Affiliation(s)
- Nicholas S Shuman
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, Albuquerque, New Mexico 87117, United States
| | - Shaun G Ard
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, Albuquerque, New Mexico 87117, United States
| | - Brendan C Sweeny
- NRC Postdoc at Air Force Research Laboratory, Space Vehicles Directorate, Kirtland Air Force Base, Albuquerque, New Mexico 87117, United States
| | - Albert A Viggiano
- Air Force Research Laboratory, Space Vehicles Directorate, Kirtland AFB, Albuquerque, New Mexico 87117, United States
| | - Cameron J Owen
- Department of Chemistry, University of Utah, 315 S. 1400 E., Rm 2020, Salt Lake City, Utah 84112, United States
| | - P B Armentrout
- Department of Chemistry, University of Utah, 315 S. 1400 E., Rm 2020, Salt Lake City, Utah 84112, United States
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20
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Chan B. Aqueous-Phase Conformations of Lactose, Maltose, and Sucrose and the Assessment of Low-Cost DFT Methods with the DSCONF Set of Conformers for the Three Disaccharides. J Phys Chem A 2020; 124:582-590. [PMID: 31927999 DOI: 10.1021/acs.jpca.9b10932] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present study, we have examined a range of quantum chemistry methods for the calculation of conformers for lactose, maltose, and sucrose. We find that the DSD-PBE-P86/aug'-cc-pVTZ//B3-LYP-D3BJ/6-311+G(2d,p) protocol yields good relative energies in comparison with reference CCSD(T)/CBS//B3-LYP-D3BJ/maug-cc-pVTZ values. We have surveyed a total of ∼550 conformers for the three disaccharides with the chosen DSD-PBE-P86 method in conjunction with continuum aqueous solvation. In each case, the lowest free energy conformer is characterized by hydrogen bond(s) between the two rings. Another finding is that the major contributors to the overall variations in aqueous free energies are the electronic energies and the solvation energies. To facilitate investigations of larger systems, we have compiled the DSCONF set of conformers for the three disaccharides, and we have assessed lower cost methods with this set. We find MS1-D3/6-31+G(2d,p) to be cost-effective and accurate for both geometry optimization and the calculation of relative energies for disaccharides. In addition, we note that MS1-D3 has previously been found to yield good relative energies for the WATER27 set of water clusters. We thus deem this method to be appropriate for the study of saccharide conformations in both gas phase and aqueous solution.
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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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