1
|
Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang LP, Mobley DL. Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields. J Phys Chem B 2024; 128:7888-7902. [PMID: 39087913 DOI: 10.1021/acs.jpcb.4c03167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.
Collapse
Affiliation(s)
- Pavan Kumar Behara
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Hyesu Jang
- Chemistry Department, University of California at Davis, Davis, California 95616, United States
- OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States
| | - Joshua T Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Trevor Gokey
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - David L Dotson
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States
- Datryllic LLC, Phoenix, Arizona 85003, United States
| | | | | | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
| | - Lee-Ping Wang
- Chemistry Department, University of California at Davis, Davis, California 95616, United States
| | - David L Mobley
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
| |
Collapse
|
2
|
Zhang Y, Li C, Zhao H, Yu Z, Tang X, Zhang J, Chen Z, Zeng J, Zhang P, Han L, Chen H. Synchronized crystallization in tin-lead perovskite solar cells. Nat Commun 2024; 15:6887. [PMID: 39134557 PMCID: PMC11319464 DOI: 10.1038/s41467-024-51361-2] [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: 07/02/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Tin-lead halide perovskites with a bandgap near 1.2 electron-volt hold great promise for thin-film photovoltaics. However, the film quality of solution-processed Sn-Pb perovskites is compromised by the asynchronous crystallization behavior between Sn and Pb components, where the crystallization of Sn-based perovskites tends to occur faster than that of Pb. Here we show that the rapid crystallization of Sn is rooted in its stereochemically active lone pair, which impedes coordination between the metal ion and Lewis base ligands in the perovskite precursor. From this perspective, we introduce a noncovalent binding agent targeting the open metal site of coordinatively unsaturated Sn(II) solvates, thereby synchronizing crystallization kinetics and homogenizing Sn-Pb alloying. The resultant single-junction Sn-Pb perovskite solar cells achieve a certified power conversion efficiency of 24.13 per cent. The encapsulated device retains 90 per cent of the initial efficiency after 795 h of maximum power point operation under simulated one-sun illumination.
Collapse
Affiliation(s)
- Yao Zhang
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Li
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Zhao
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Zhongxun Yu
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Jiao Tong University JA Technology New Energy Materials Joint Research Center, Shanghai, China
| | - Xiaoan Tang
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Jixiang Zhang
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Jiao Tong University JA Technology New Energy Materials Joint Research Center, Shanghai, China
| | - Zhenhua Chen
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jianrong Zeng
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Peng Zhang
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
- Joint Research Center for Clean Energy Materials, Shanghai Jiao Tong University, Shanghai, China
| | - Liyuan Han
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Han Chen
- State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China.
- Innovation Center for Future Materials, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China.
- Joint Research Center for Clean Energy Materials, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
3
|
Zhang WW, Feng Z, You SL, Zheng C. Electrophile-Arene Affinity: An Energy Scale for Evaluating the Thermodynamics of Electrophilic Dearomatization Reactions. J Org Chem 2024. [PMID: 39077910 DOI: 10.1021/acs.joc.4c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Rational design and development of organic reactions are lofty goals in synthetic chemistry. Quantitative description of the properties of molecules and reactions by physical organic parameters plays an important role in this regard. In this Article, we report an energy scale, namely, electrophile-arene affinity (EAA), for evaluating the thermodynamics of electrophilic dearomatization reactions, a class of important transformations that can rapidly build up molecular complexity and structural diversity by converting planar aromatic compounds into three-dimensional cyclic molecules. The acquisition of EAA data can be readily achieved by theoretically calculating the enthalpy changes (ΔH) of the hypothetical reactions of various (cationic) electrophiles with aromatic systems (taking the 1-methylnaphthalen-2-olate ion as an example in this study). Linear correlations are found between the calculated ΔH values and established physical organic parameters such as the percentage of buried volume %VBur (steric effect), Hammett's σ or Brown's σ+ (electronic effect), and Mayr's E (reaction kinetics). Careful analysis of the ΔH values leads to the rational design of a dearomative alkynylation reaction using alkynyl hypervalent iodonium reagents as the electrophiles.
Collapse
Affiliation(s)
- Wen-Wen Zhang
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Zuolijun Feng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Shu-Li You
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
- Shanghai-Hong Kong Joint Laboratory of Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| |
Collapse
|
4
|
De Snoo W, Kong WY, Tantillo DJ. Allyl-Allyl Coupling Promoted by Catalyst Systems with two Palladium Atoms - A Plethora of Potentially Pericyclic Processes. Angew Chem Int Ed Engl 2024; 63:e202406095. [PMID: 38709849 DOI: 10.1002/anie.202406095] [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: 03/29/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Recently, Huang and co-workers reported a catalytic reaction that utilizes H2 as the sole reductant for a C-C coupling of allyl groups with yields up to 96 %. Here we use computational quantum chemistry to identify several key features of this reaction that provide clarity on how it proceeds. We propose the involvement of a Pd-Pd bound dimer precatalyst, demonstrate the importance of ligand π-π interactions and counterions, and identify a new, energetically viable, mechanism involving two dimerized, outer-sphere reductive elimination transition structures that determine both the rate and selectivity. Although we rule out the previously proposed transmetalation step on energetic grounds, we show it to have an unusual aromatic transition structure in which two Pd atoms support rearranging electrons. The prevalence of potential metal-supported pericyclic reactions in this system suggests that one should consider such processes regularly, but the results of our calculations also indicate that one should do so with caution.
Collapse
Affiliation(s)
- William De Snoo
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| |
Collapse
|
5
|
Grotjahn R, Purnomo J, Jin D, Lutfi N, Furche F. Chemically Accurate Singlet-Triplet Gaps of Arylcarbenes from Local Hybrid Density Functionals. J Phys Chem A 2024; 128:6046-6060. [PMID: 39012067 DOI: 10.1021/acs.jpca.4c02852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Singlet-triplet (ST) gaps are key descriptors of carbenes, because their properties and reactivity are strongly spin-dependent. However, the theoretical prediction of ST gaps is challenging and generally thought to require elaborate correlated wave function methods or double-hybrid density functionals. By evaluating two recent test sets of arylcarbenes (AC12 and AC18), we show that local hybrid functionals based on the "common t" local mixing function (LMF) model achieve mean absolute errors below 1 kcal/mol at a computational cost only slightly higher than that of global hybrid functionals. An analysis of correlation contributions to the ST gaps suggests that the accuracy of the common t-LMF model is mainly due to an improved description of nondynamical correlation which, unlike exchange, is not additive in each spin-channel. Although spin-nonadditivity can be achieved using the local spin polarization alone, using the "common", i.e., spin-unresolved, iso-orbital indicator t for constructing the LMF is found to be critical for consistent accuracy in ST gaps of arylcarbenes. The results support the view of LHs as vehicles to improve the description of nondynamical correlation rather than sophisticated exchange mixing approaches.
Collapse
Affiliation(s)
- Robin Grotjahn
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Justin Purnomo
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dayun Jin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Nicolas Lutfi
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| |
Collapse
|
6
|
Chamkin AA, Chamkina ES. Assessment of the applicability of DFT methods to [Cp*Rh]-catalyzed hydrogen evolution processes. J Comput Chem 2024. [PMID: 39052232 DOI: 10.1002/jcc.27468] [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: 02/11/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
The present computational study provides a benchmark of density functional theory (DFT) methods in describing hydrogen evolution processes catalyzed by [Cp*Rh]-containing organometallic complexes. A test set was composed of 26 elementary reactions featuring chemical transformations and bonding situations essential for the field, including the emerging concept of non-innocent Cp* behavior. Reference values were obtained from a highly accurate 3/4 complete basis set and 6/7 complete PNO space extrapolated DLPNO-CCSD(T) energies. The performance of lower-level extrapolation procedures was also assessed. We considered 84 density functionals (DF) (including 13 generalized gradient approximations (GGA), nine meta-GGAs, 33 hybrids, and 29 double-hybrids) and three composite methods (HF-3c, PBEh-3c, and r2SCAN-3c), combined with different types of dispersion corrections (D3(0), D3BJ, D4, and VV10). The most accurate approach is the PBE0-DH-D3BJ (MAD of 1.36 kcal mol-1) followed by TPSS0-D3BJ (MAD of 1.60 kcal mol-1). Low-cost r2SCAN-3c composite provides a less accurate but much faster alternative (MAD of 2.39 kcal mol-1). The widely used Minnesota-family M06-L, M06, and M06-2X DFs should be avoided (MADs of 3.70, 3.94, and 4.01 kcal mol-1, respectively).
Collapse
Affiliation(s)
- Aleksandr A Chamkin
- A.N.Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Moscow, Russia
| | - Elena S Chamkina
- A.N.Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
7
|
Alessandrini S, Melosso M, Bizzocchi L, Barone V, Puzzarini C. The Semiexperimental Approach at Work: Equilibrium Structure of Radical Species. J Phys Chem A 2024; 128:5833-5855. [PMID: 38991181 DOI: 10.1021/acs.jpca.4c01758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The so-called semiexperimental (SE) approach is a powerful technique for obtaining highly accurate equilibrium structures for isolated systems. This Featured Article describes its extension to open-shell species, thus providing the first systematic investigation on radical equilibrium geometries to be used for benchmarking purposes. The small yet significant database obtained demonstrates that there is no reduction in accuracy when moving from closed-shell species to radicals. We also provide an extension of the applicability of the SE approach to medium-/large-sized radicals by exploiting the so-called "Lego-brick" approach, which is based on the assumption that a molecular system can be seen as formed by smaller fragments for which the SE equilibrium structure is available. In this Featured Article we show that this model can be successfully applied also to open-shell species.
Collapse
Affiliation(s)
- Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| |
Collapse
|
8
|
Li N, Yang X, Li X, Peng Z, Yin Z, Jiang C, Huang Z, Li Y. Enhancing the detonation performance of azobistriazole energetic derivatives via inducing N-oxide groups. Phys Chem Chem Phys 2024; 26:19863-19875. [PMID: 38989787 DOI: 10.1039/d4cp00183d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The N-oxide strategy plays a crucial role in regulating the performance and safety of energetic materials. This study mainly addresses the question of how the N-oxide group affects the properties of azobistriazole and its derivatives. Our findings indicate that the N-oxide group can increase the density of the system, and its effect on the enthalpy of formation depends on the specific situation. The N-oxide groups can effectively improve the density and energetic properties. Some of the energetic derivatives containing N-oxide groups have a density as high as 2.097 g cm-3 (D3-NO(2)) and a detonation velocity as high as 10 275 m s-1 (C6-NO(2)). The effect of N-oxide groups on the enthalpy of formation depends on the specific circumstances. The effect of N-oxide groups on the stability of azobistriazole energetic derivatives is relatively complex. Among them, the N-oxide group on the triazole ring has an opposite effect on the bond dissociation enthalpy of functional groups. When the N-oxide group is on the 1,2,3-triazole ring, it can improve C-R (R is equal to C(NO2)3, NF2, NHNO2, NO2, and ONO2 respectively) bond dissociation enthalpy, and when it is on the 1,2,4-triazole ring, it will reduce the C-R bond dissociation enthalpy. When the N-oxide group is located on the azo bond, the bond dissociation enthalpy of the azo bond will be significantly reduced. This article systematically explores the effect of N-oxide groups on the properties of azobistriazole energetic derivatives, which will help people better utilize N-oxide groups to design and synthesize new energetic materials.
Collapse
Affiliation(s)
- Nan Li
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Xinbo Yang
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
- School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Xiuyuan Li
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Zihuan Peng
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Zehong Yin
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Chongwen Jiang
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Zhihong Huang
- School of Mechatronical Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| | - Yuchuan Li
- School of Material Science & Engineering, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, P. R. China.
| |
Collapse
|
9
|
Hancock AC, Giudici E, Goerigk L. How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models. J Comput Chem 2024; 45:1667-1681. [PMID: 38553847 DOI: 10.1002/jcc.27351] [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: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 06/04/2024]
Abstract
Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group (M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165). So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work (A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964). The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS- ω PBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.
Collapse
Affiliation(s)
- Amy C Hancock
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| | - Erica Giudici
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
10
|
Puzzarini C, Alessandrini S. Carbamic acid and its dimer: A computational study. J Comput Chem 2024. [PMID: 38970400 DOI: 10.1002/jcc.27442] [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: 02/15/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 07/08/2024]
Abstract
A recent work by Marks et al. on the formation of carbamic acid in NH3 $$ {}_3 $$ -CO2 $$ {}_2 $$ interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.
Collapse
Affiliation(s)
- Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| | - Silvia Alessandrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| |
Collapse
|
11
|
Lv W, Cao H, Guan Y, Wu M, Liu H, Guo X, Yao T, Chen P, Sheng L, Wu J. Mediating peroxymonosulfate activation path in Fenton-like reaction via doping different metal atoms into g-C 3N 5. J Colloid Interface Sci 2024; 674:416-427. [PMID: 38943909 DOI: 10.1016/j.jcis.2024.06.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/01/2024]
Abstract
Peroxymonosulfate (PMS) could be activated by either radical path or non-radical path, how to rationally mediate these two routines was an important unresolved issue. This work has introduced a simple way to address this problem via metal atom doping. It was found that Fe-doped nitrogen-rich graphitic carbon nitride (Fe-C3N5) exhibited high activity towards PMS activation for tetracycline degradation, and the degradation rate was 3.14 times higher than that of Co-doped nitrogen-rich graphitic carbon nitride (Co-C3N5). Radical trapping experiment revealed the contributions of reactive species over two catalysts were different. Electron paramagnetic resonance analysis further uncovered the non-radical activation path played a dominated role on Fe-C3N5 surface, while the radical activation path was the main routine on Co-C3N5 surface. Density functional theory calculations, X-ray photoelectron spectroscopy analysis, and electrochemical experiments provided convincing evidence to support these views. This study supplied a novel method to mediate PMS activation path via changing the doped metal atom in g-C3N5 skeleton, and it allowed us to better optimize the PMS activation efficiency.
Collapse
Affiliation(s)
- Wenwen Lv
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Huijun Cao
- State Key Lab Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yina Guan
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Maoquan Wu
- State Key Lab Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Hongyan Liu
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Xu Guo
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Tongjie Yao
- State Key Lab Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Peng Chen
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China
| | - Li Sheng
- State Key Lab Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China.
| | - Jie Wu
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin, China.
| |
Collapse
|
12
|
Li J, Yang W. Chemical Potentials and the One-Electron Hamiltonian of the Second-Order Perturbation Theory from the Functional Derivative Approach. J Phys Chem A 2024; 128:4876-4885. [PMID: 38842399 DOI: 10.1021/acs.jpca.4c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
We develop a functional derivative approach to calculate the chemical potentials of second-order perturbation theory (MP2). In the functional derivative approach, the correlation part of the MP2 chemical potential, which is the derivative of the MP2 correlation energy with respect to the occupation number of frontier orbitals, is obtained from the chain rule via the noninteracting Green's function. First, the MP2 correlation energy is expressed in terms of the noninteracting Green's function, and its functional derivative to the noninteracting Green's function is the second-order self-energy. Then, the derivative of the noninteracting Green's function to the occupation number is obtained by including the orbital relaxation effect. We show that the MP2 chemical potentials obtained from the functional derivative approach agree with that obtained from the finite difference approach. The one-electron Hamiltonian, defined as the derivative of the MP2 energy with respect to the one particle density matrix, is also derived using the functional derivative approach, which can be used in the self-consistent calculations of MP2 and double-hybrid density functionals. The developed functional derivative approach is promising for calculating the chemical potentials and the one-electron Hamiltonian of approximate functionals and many-body perturbation approaches dependent explicitly on the noninteracting Green's function.
Collapse
Affiliation(s)
- Jiachen Li
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
- RIKEN Center for Computational Science, Kobe, Japan
| |
Collapse
|
14
|
Becke AD. A remarkably simple dispersion damping scheme and the DH24 double hybrid density functional. J Chem Phys 2024; 160:204118. [PMID: 38818895 DOI: 10.1063/5.0207682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
In recent papers, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] and then Becke [J. Chem. Phys. 159, 241101 (2023)] have developed a novel double hybrid density functional, "DH23," whose terms are based on good local physics. Its 12 coefficients are trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.73 kcal/mol for the revDH23 variant). Here, we simplify DH23 by introducing a dispersion damping scheme involving atomic numbers only and one global parameter. The resulting new functional, "DH24," performs as well as its predecessors.
Collapse
Affiliation(s)
- Axel D Becke
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
15
|
Ferreira P, Neves RPP, Miranda FP, Cunha AV, Havenith RWA, Ramos MJ, Fernandes PA. DszA Catalyzes C-S Bond Cleavage through N 5-Hydroperoxyl Formation. J Chem Inf Model 2024; 64:4218-4230. [PMID: 38684937 PMCID: PMC11134501 DOI: 10.1021/acs.jcim.4c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.
Collapse
Affiliation(s)
- Pedro Ferreira
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Rui P. P. Neves
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Filipa P. Miranda
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana V. Cunha
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp 2000, Belgium
| | - Remco W. A. Havenith
- Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), Ghent B-9000, Belgium
| | - Maria J. Ramos
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A. Fernandes
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| |
Collapse
|
16
|
Ojea V, Ruiz M. DLPNO-CCSD(T) and DFT study of the acetate-assisted C-H activation of benzaldimine at [RuCl 2( p-cymene)] 2: the relevance of ligand exchange processes at ruthenium(II) complexes in polar protic media. Dalton Trans 2024; 53:8662-8679. [PMID: 38695752 DOI: 10.1039/d4dt00380b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
To gain mechanistic insights into the acetate-assisted cyclometallations of arylimines promoted by [RuCl2(p-cymene)]2 in polar protic media, DFT geometry optimizations (with M06 and ωB97X-D3 functionals and the cc-pVDZ-PP[Ru] basis set) followed by DLPNO-CCSD(T)/CBS energy evaluations were performed using benzaldimine as a model substrate and methanol as the solvent (with CPCM or SMD models). The calculation results show that coordination of the imine to an acetate ruthenium precursor is followed by anion (chloride or acetate) dissociation as the rate-determining step of the process. H-Bonding of two explicit MeOH to the anion reduces the calculated activation energy to ca. 23 kcal mol-1, in good agreement with the experimental half-life at room temperature. Subsequent AMLA/CMD C-H activation of the intermediate cationic complexes is a faster, reversible process. Alternative reaction pathways involving neutral diacetate ruthenium complexes offer AMLA/CMD transition state structures of lower energy but are precluded due to higher energy barriers for the initial ligand exchange processes at ruthenium. Solvent assistance accelerates the final chloride/acetate exchange processes on the cycloruthenate intermediates, particularly when compression in the condensed phase is taken into consideration. The performance of six DFT functionals (with the aug-pVTZ-PP[Ru] basis set) was assessed using the DLPNO-CCSD(T)/CBS reference energies. Neutral diacetate ruthenium complexes were incorrectly predicted as being kinetically relevant when using hybrid DFT methods (PBE0-D3(BJ), M06-2X or ωB97M-V). Good agreement between the calculated barrier heights and our benchmark energy results was obtained by using double-hybrid DFT methods. PWPB95 with D3(BJ) or D4 dispersion energy corrections was found to be the most accurate (ΔG≠ MUE of ca. 1 kcal mol-1). This study may aid our understanding of and help with further experimental investigations of synthetically useful carboxylate-assisted C-H bond functionalizations involving (N,C)-cyclometallated (p-cymene)Ru(II) intermediate complexes in sustainable polar protic solvents.
Collapse
Affiliation(s)
- Vicente Ojea
- Departamento de Química, Facultade de Ciencias, Universidade da Coruña, E-15078 A Coruña, Spain.
| | - María Ruiz
- Departamento de Química, Facultade de Ciencias, Universidade da Coruña, E-15078 A Coruña, Spain.
| |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- Sven Tobisch
- University of St Andrews, School of Chemistry, Purdie Building, North Haugh, St Andrews, KY16 9ST, UK.
| |
Collapse
|
18
|
Gasevic T, Bursch M, Ma Q, Grimme S, Werner HJ, Hansen A. The p-block challenge: assessing quantum chemistry methods for inorganic heterocycle dimerizations. Phys Chem Chem Phys 2024; 26:13884-13908. [PMID: 38661329 DOI: 10.1039/d3cp06217a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The elements of the p-block of the periodic table are of high interest in various chemical and technical applications like frustrated Lewis-pairs (FLP) or opto-electronics. However, high-quality benchmark data to assess approximate density functional theory (DFT) for their theoretical description are sparse. In this work, we present a benchmark set of 604 dimerization energies of 302 "inorganic benzenes" composed of all non-carbon p-block elements of main groups III to VI up to polonium. This so-called IHD302 test set comprises two classes of structures formed by covalent bonding and by weaker donor-acceptor (WDA) interactions, respectively. Generating reliable reference data with ab initio methods is challenging due to large electron correlation contributions, core-valence correlation effects, and especially the slow basis set convergence. To compute reference values for these dimerization reactions, after thorough testing, we applied a computational protocol using state-of-the-art explicitly correlated local coupled cluster theory termed PNO-LCCSD(T)-F12/cc-VTZ-PP-F12(corr.). It includes a basis set correction at the PNO-LMP2-F12/aug-cc-pwCVTZ level. Based on these reference data, we assess 26 DFT methods in combination with three different dispersion corrections and the def2-QZVPP basis set, five composite DFT approaches, and five semi-empirical quantum mechanical methods. For the covalent dimerizations, the r2SCAN-D4 meta-GGA, the r2SCAN0-D4 and ωB97M-V hybrids, and the revDSD-PBEP86-D4 double-hybrid functional are found to be the best-performing methods among the evaluated functionals of the respective class. However, since def2 basis sets for the 4th period are not associated to relativistic pseudo-potentials, we obtained significant errors in the covalent dimerization energies (up to 6 kcal mol-1) for molecules containing p-block elements of the 4th period. Significant improvements were achieved for systems containing 4th row elements by using ECP10MDF pseudopotentials along with re-contracted aug-cc-pVQZ-PP-KS basis sets introduced in this work with the contraction coefficients taken from atomic DFT (PBE0) calculations. Overall, the IHD302 set represents a challenge to contemporary quantum chemical methods. This is due to a large number of spatially close p-element bonds which are underrepresented in other benchmark sets, and the partial covalent bonding character for the WDA interactions. The IHD302 set may be helpful to develop more robust and transferable approximate quantum chemical methods in the future.
Collapse
Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- FACCTs GmbH, 50677, Koeln, Germany
| | - Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| |
Collapse
|
19
|
Kraemer Y, Buldt JA, Kong WY, Stephens AM, Ragan AN, Park S, Haidar ZC, Patel AH, Shey R, Dagan R, McLoughlin CP, Fettinger JC, Tantillo DJ, Pitts CR. Overcoming a Radical Polarity Mismatch in Strain-Release Pentafluorosulfanylation of [1.1.0]Bicyclobutanes: An Entryway to Sulfone- and Carbonyl-Containing SF 5-Cyclobutanes. Angew Chem Int Ed Engl 2024; 63:e202319930. [PMID: 38237059 PMCID: PMC11045327 DOI: 10.1002/anie.202319930] [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: 12/23/2023] [Indexed: 04/26/2024]
Abstract
The first assortment of achiral pentafluorosulfanylated cyclobutanes (SF5-CBs) are now synthetically accessible through strain-release functionalization of [1.1.0]bicyclobutanes (BCBs) using SF5Cl. Methods for both chloropentafluorosulfanylation and hydropentafluorosulfanylation of sulfone-based BCBs are detailed herein, as well as proof-of-concept that the logic extends to tetrafluoro(aryl)sulfanylation, tetrafluoro(trifluoromethyl)sulfanylation, and three-component pentafluorosulfanylation reactions. The methods presented enable isolation of both syn and anti isomers of SF5-CBs, but we also demonstrate that this innate selectivity can be overridden in chloropentafluorosulfanylation; that is, an anti-stereoselective variant of SF5Cl addition across sulfone-based BCBs can be achieved by using inexpensive copper salt additives. Considering the SF5 group and CBs have been employed individually as nonclassical bioisosteres, structural aspects of these unique SF5-CB "hybrid isosteres" were then contextualized using SC-XRD. From a mechanistic standpoint, chloropentafluorosulfanylation ostensibly proceeds through a curious polarity mismatch addition of electrophilic SF5 radicals to the electrophilic sites of the BCBs. Upon examining carbonyl-containing BCBs, we also observed rare instances whereby radical addition to the 1-position of a BCB occurs. The nature of the key C(sp3)-SF5 bond formation step - among other mechanistic features of the methods we disclose - was investigated experimentally and with DFT calculations. Lastly, we demonstrate compatibility of SF5-CBs with various downstream functionalizations.
Collapse
Affiliation(s)
- Yannick Kraemer
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Jón Atiba Buldt
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Alexander M Stephens
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Abbey N Ragan
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Soojun Park
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Zane C Haidar
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Ansh Hiten Patel
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Rachel Shey
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Roee Dagan
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Connor P McLoughlin
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - James C Fettinger
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Dean J Tantillo
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Cody Ross Pitts
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
20
|
Bruckhoff T, Ballmann J, Gade LH. Radicalizing CO by Mononuclear Palladium(I). Angew Chem Int Ed Engl 2024; 63:e202320064. [PMID: 38498121 DOI: 10.1002/anie.202320064] [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: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
A mononuclear, T-shaped palladium(I) d9 metalloradical (3), stabilized by a bulky carbazole-based PNP-ligand, was obtained by reduction of palladium chloride or thermal Pd-C bond homolysis of the corresponding neopentyl complex. Pressurizing with CO gave the Pd(I) carbonyl complex, which was structurally characterized by X-ray diffraction. Delocalization of the unpaired electron to the carbonyl carbon was detected by EPR spectroscopy and theoretically modeled by DFT and ab initio methods. The partially reduced and radicalized CO slowly reacts with di(tert-butyl) disulfide under homolytic S-S cleavage and C-S bond formation to give the corresponding metallathioester.
Collapse
Affiliation(s)
- Tim Bruckhoff
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 276, 69120, Heidelberg, Germany
| | - Joachim Ballmann
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 276, 69120, Heidelberg, Germany
| | - Lutz H Gade
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 276, 69120, Heidelberg, Germany
| |
Collapse
|
21
|
Jin H, Merz KM. Modeling Zinc Complexes Using Neural Networks. J Chem Inf Model 2024; 64:3140-3148. [PMID: 38587510 PMCID: PMC11040731 DOI: 10.1021/acs.jcim.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
Understanding the energetic landscapes of large molecules is necessary for the study of chemical and biological systems. Recently, deep learning has greatly accelerated the development of models based on quantum chemistry, making it possible to build potential energy surfaces and explore chemical space. However, most of this work has focused on organic molecules due to the simplicity of their electronic structures as well as the availability of data sets. In this work, we build a deep learning architecture to model the energetics of zinc organometallic complexes. To achieve this, we have compiled a configurationally and conformationally diverse data set of zinc complexes using metadynamics to overcome the limitations of traditional sampling methods. In terms of the neural network potentials, our results indicate that for zinc complexes, partial charges play an important role in modeling the long-range interactions with a neural network. Our developed model outperforms semiempirical methods in predicting the relative energy of zinc conformers, yielding a mean absolute error (MAE) of 1.32 kcal/mol with reference to the double-hybrid PWPB95 method.
Collapse
Affiliation(s)
- Hongni Jin
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
22
|
Zahara AJ, Haines BE, Wilkerson-Hill SM. Programmed Heterocycle Synthesis Using Halomucononitriles as Pyridinimine Precursors. Org Lett 2024; 26:2976-2981. [PMID: 38557087 DOI: 10.1021/acs.orglett.4c00547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Herein we report a method to convert primary amines, ubiquitous motifs found in pharmaceutical libraries, to either imidazo[1,2-a]pyridines or 7-alkyl azaindoles in two steps from known compounds. Using halomucononitrile reagents, we can directly access 5-bromo-6-imino-1-alkyl-1,6-dihydropyridine-2-carbonitriles (pyridinimines) in a single step from primary amines (25-93% yield) through the cyclization of transient aminomucononitrile intermediates. We then demonstrate that these compounds can be readily converted to 7-alkylazaindoles using Sonogashira cross-coupling conditions (13 examples, up to 91% yield). Under oxidative conditions, the pyridinimines serve as directing groups for C-H functionalization reactions to afford imidazo[1,2-a]pyridines. We also studied the mechanism of the cyclization event using DFT calculations and propose that this takes place via sequential base-mediated E/Z isomerization and cyclization steps.
Collapse
Affiliation(s)
- Adam J Zahara
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Brandon E Haines
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Sidney M Wilkerson-Hill
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
23
|
M Zahir FZ, Hay MA, Janetzki JT, Gable RW, Goerigk L, Boskovic C. Predicting valence tautomerism in diverse cobalt-dioxolene complexes: elucidation of the role of ligands and solvent. Chem Sci 2024; 15:5694-5710. [PMID: 38638213 PMCID: PMC11023039 DOI: 10.1039/d3sc04493a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
The ability of molecular switches to reversibly interconvert between different forms promises potential applications at the scale of single molecules up to bulk materials. One type of molecular switch comprises cobalt-dioxolene compounds that exhibit thermally-induced valence tautomerism (VT) interconversions between low spin Co(iii)-catecholate (LS-CoIII-cat) and high spin Co(ii)-semiquinonate (HS-CoII-sq) forms. Two families of these compounds have been investigated for decades but have generally been considered separately: neutral [Co(diox)(sq)(N2L)] and cationic [Co(diox)(N4L)]+ complexes (diox = generic dioxolene, N2L/N4L = bidentate/tetradentate N-donor ancillary ligand). Computational identification of promising new candidate compounds prior to experimental exploration is beneficial for environmental and cost considerations but requires a thorough understanding of the underlying thermochemical parameters that influence the switching. Herein, we report a robust approach for the analysis of both cobalt-dioxolene families, which involved a quantitative density functional theory-based study benchmarked with reliable quasi-experimental references. The best-performing M06L-D4/def2-TZVPP level of theory has subsequently been verified by the synthesis and experimental investigation of three new complexes, two of which exhibit thermally-induced VT, while the third remains in the LS-CoIII-cat form across all temperatures, in agreement with prediction. Valence tautomerism in solution is markedly solvent-dependent, but the origin of this has not been definitively established. We have extended our computational approach to elucidate the correlation of VT transition temperature with solvent stabilisation energy and change in dipole moment. This new understanding may inform the development of VT compounds for applications in soft materials including films, gels, and polymers.
Collapse
Affiliation(s)
- F Zahra M Zahir
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Moya A Hay
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Jett T Janetzki
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Robert W Gable
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Lars Goerigk
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| | - Colette Boskovic
- School of Chemistry, University of Melbourne Victoria 3010 Australia
| |
Collapse
|
24
|
Wu L, Yang F, Niu K, Zhao J, Zhang X, Lu X, Li X, Huang Y, Chen J. Single-Mg-Atom Catalyst with a Dual Active Center as an Emerging Promising Sensing Platform. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38607228 DOI: 10.1021/acsami.4c03081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bisphenol compounds [bisphenol A (BPA), etc.] are one class of the most important and widespread pollutants in food and environment, which pose severe endocrine disrupting effect, reproductive toxicity, immunotoxicity, and metabolic toxicity on humans and animals. Simultaneous rapid determination of BPA and its analogues (bisphenol S, bisphenol AF, etc.) with extraordinary potential resolution and sensitivity is of great significance but still extremely challenging. Herein, a series of single-atom catalysts (SACs) were synthesized by anchoring different metal atoms (Mg, Co, Ni, and Cu) on N-doped carbon materials and used as sensing materials for simultaneous detection of bisphenols with similar chemical structures. The Mg-based SAC enables the potential discrimination and simultaneous rapid detection of multiple bisphenols, showing outstanding analytical performances, outperforming all other SACs and traditional electrode materials. Our experiments and density functional theory calculations show that pyrrolic N serves as the adsorption site for the adsorption of bisphenols and the Mg atom serves as the active site for the electrocatalytic oxidation of bisphenols, which play a synergistic role as dual active centers in improving the sensing performance. The results of this work may pave the way for the rational design of SACs as advanced sensing and catalytic materials.
Collapse
Affiliation(s)
- Lingxia Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
- School of Environmental & Municipal Engineering, Qingdao University of Technology, Qingdao 266033, China
| | - Feifei Yang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Kai Niu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Xiong Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Xianbo Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Xuning Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Yanqiang Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Jiping Chen
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, China
| |
Collapse
|
25
|
Nemirovich T, Young B, Brezina K, Mason PE, Seidel R, Stemer D, Winter B, Jungwirth P, Bradforth SE, Schewe HC. Stability and Reactivity of Aromatic Radical Anions in Solution with Relevance to Birch Reduction. J Am Chem Soc 2024; 146:8043-8057. [PMID: 38363862 PMCID: PMC10979400 DOI: 10.1021/jacs.3c11655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
We investigate the electronic structure of aromatic radical anions in the solution phase employing a combination of liquid-jet (LJ) photoelectron (PE) spectroscopy measurements and electronic structure calculations. By using recently developed protocols, we accurately determine the vertical ionization energies of valence electrons of both the solvent and the solute molecules. In particular, we first characterize the pure solvent of tetrahydrofuran (THF) by LJ-PE measurements in conjunction with ab initio molecular dynamics simulations and G0W0 calculations. Next, we determine the electronic structure of neutral naphthalene (Np) and benzophenone (Bp) as well as their radical anion counterparts Np- and Bp- in THF. Wherever feasible, we performed orbital assignments of the measured PE features of the aromatic radical anions, with comparisons to UV-vis absorption spectra of the corresponding neutral molecules being instrumental in rationalizing the assignments. Analysis of the electronic structure differences between the neutral species and their anionic counterparts provides understanding of the primarily electrostatic stabilization of the radical anions in solution. Finally, we obtain a very good agreement of the reduction potentials extracted from the present LJ-PES measurements of Np- and Bp- in THF with previous electrochemical data from cyclic voltammetry measurements. In this context, we discuss how the choice of solvent holds significant implications for optimizing conditions for the Birch reduction process, wherein aromatic radical anions play crucial roles as reactive intermediates.
Collapse
Affiliation(s)
- Tatiana Nemirovich
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Brandon Young
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Krystof Brezina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Philip E. Mason
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Robert Seidel
- Helmholtz-Zentrum
Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Dominik Stemer
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Bernd Winter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Stephen E. Bradforth
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - H. Christian Schewe
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech
Republic
| |
Collapse
|
26
|
Wang Y, Du J, Huang H. Reversible Thiyl Radical Addition-Fragmentation Chain Transfer Polymerization. Angew Chem Int Ed Engl 2024; 63:e202318898. [PMID: 38284482 DOI: 10.1002/anie.202318898] [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: 12/08/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Developing reversible-deactivation radical polymerization (RDRP) methods that could directly control the thiyl radical propagation is highly desirable yet remains challenging in modern polymer chemistry. Here, we reported the first reversible thiyl radical addition-fragmentation chain transfer (SRAFT) polymerization strategy, which utilizes allyl sulfides as chain transfer agents for reversibly deactivating the propagating thiyl radicals, thus allowing us to directly control a challenging thiyl radical chain polymerization to afford polymers with well-defined architectures. A linear dependence of molecular weight on conversion, high chain-end fidelity, and efficient chain extension proved good controllability of the polymerization. In addition, density functional theory calculations provided insight into the reversible deactivation ability of allyl sulfides. The SRAFT strategy developed in this work represents a promising platform for discovering new controlled polymerizations based on thiyl radical chemistry.
Collapse
Affiliation(s)
- Yongjin Wang
- School of Materials Science and Engineering, Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Jiaman Du
- School of Materials Science and Engineering, Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hanchu Huang
- School of Materials Science and Engineering, Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-Sen University, Guangzhou, 510006, China
| |
Collapse
|
27
|
Plett C, Grimme S, Hansen A. Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules. J Comput Chem 2024; 45:419-429. [PMID: 37982322 DOI: 10.1002/jcc.27248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and ω B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol- 1 . If more efficient methods are required, the composite DFT-method r2 SCAN-3c (MAD of 1.2 kcal mol- 1 ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.
Collapse
Affiliation(s)
- Christoph Plett
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius-Institut für Physikalische und Theoretische Chemie, Universität Bonn, Bonn, Germany
| |
Collapse
|
28
|
Du H, Sato M, Komuro A, Ono R. Theoretical Prediction of the Reaction Probabilities of H, O, and OH Radicals on the Polypropylene Surface. J Phys Chem A 2024; 128:1041-1048. [PMID: 38311924 DOI: 10.1021/acs.jpca.3c07531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
To determine the H-abstraction reaction probabilities of H/O/OH radicals with a polypropylene (PP) surface, a first-principles calculation was performed based on the DLPNO-CCSD(T)/CBS//M06-2X-D3/def-TZVP theory level. The PP chain model used in this study was 2,4,6-trimethylheptane. The rate constants of the H/O/OH radicals with the isolated PP chain model were calculated based on the conventional transition-state theory. By comparing the experimental values and considering the error factors and their compensation, it was concluded that the orders of magnitude of the predicted rate constants were accurate. The resulting rate constants were converted to reaction probabilities between the H/O/OH radicals and the PP surface. The method used in this study is applicable for obtaining theoretical values of surface reaction probabilities based on first-principles calculations. The calculation at the DLPNO-CCSD(T)/CBS theory level has high accuracy but consumes a large amount of computational resources. The study also demonstrated that the double-hybrid functionals, wB97x-2-D3(BJ) and rev-DSD-PBEP86-D3(BJ), with a 3-ζ or 4-ζ basis set, could reproduce the electronic energy values obtained from DLPNO-CCSD(T)/CBS while using only approximately 1/100 of the computational resources required by the latter under our computer configuration.
Collapse
Affiliation(s)
- Hao Du
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masahiro Sato
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo 113-0032, Japan
| | - Atsushi Komuro
- Department of Advanced Energy, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ryo Ono
- Department of Advanced Energy, The University of Tokyo, Tokyo 113-0032, Japan
| |
Collapse
|
29
|
Xu X, Rades T, Grohganz H. Molecular interactions of hydrated co-amorphous systems of prilocaine and lidocaine. Int J Pharm 2024; 651:123807. [PMID: 38220121 DOI: 10.1016/j.ijpharm.2024.123807] [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: 11/17/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
It is generally accepted that water as a plasticizer can decrease the glass transition temperatures (Tgs) of amorphous drugs and drug excipient systems. However, previous studies suggest that water, as an anti-plasticizer, can increase the Tgs of co-amorphous systems of prilocaine (PRL) and lidocaine (LID). In order to investigate the intermolecular interactions between water and co-amorphous PRL-LID systems, Fourier transform infrared spectroscopy (FTIR) and principal component analysis (PCA) were conducted. Water was found to bind with the carbonyl groups of PRL and LID molecularly evenly in the hydrated co-amorphous PRL-LID systems. Quantum chemical simulations visually confirmed the interactions between water and co-amorphous PRL-LID systems. Furthermore, the physical stability of hydrated co-amorphous PRL-LID systems was improved due to the anti-plasticizing effect of water, compared with the anhydrous samples. The preference of water to interact with the carbonyl groups of PRL and LID as binding sites could be associated with the anti-plasticizing effect of water on the co-amorphous PRL-LID systems.
Collapse
Affiliation(s)
- Xiaoyue Xu
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Thomas Rades
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Holger Grohganz
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| |
Collapse
|
30
|
Zhou X, Huang Z, He X. Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters. J Chem Phys 2024; 160:054103. [PMID: 38310472 DOI: 10.1063/5.0182164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024] Open
Abstract
Proton exchange reactions are of key importance in many processes in water. However, it is nontrivial to achieve reliable barrier heights for multiple proton exchanges and complexation energies in hydrogen-bonded systems theoretically. Performance of the fixed-node diffusion quantum Monte Carlo (FN-DMC) with the single-Slater-Jastrow trial wavefunction on total energies, barrier heights of multiple proton exchanges, and complexation energies of small water, ammonia, and hydrogen fluoride clusters is investigated in this study. Effects of basis sets and those of locality approximation (LA), T-move approximation (T-move), and determinant localization approximation (DLA) schemes in dealing with the nonlocal part of pseudopotentials on FN-DMC results are evaluated. According to our results, diffuse basis functions are important in achieving reliable barrier heights and complexation energies with FN-DMC, although the cardinal number of the basis set is more important than diffuse basis functions on total energies of these systems. Our results also show that the time step bias with DLA and LA is smaller than T-move; however, the time step bias of DMC energies with respect to time steps using the T-move is roughly linear up to 0.06 a.u., while this is not the case with LA and DLA. Barrier heights and complexation energies with FN-DMC using these three schemes are always within chemical accuracy. Taking into account the fact that T-move and DLA are typically more stable than LA, FN-DMC calculations with the T-move or DLA scheme and basis sets containing diffuse basis functions are suggested for barrier heights of multiple proton exchanges and complexation energies of hydrogen-bonded clusters.
Collapse
Affiliation(s)
- Xiaojun Zhou
- 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 200062, People's Republic of China
- School of Physics & Information Science, Shaanxi University of Science and Technology, Xi'an 710021, People's Republic of China
| | - Zhiru Huang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu, People's Republic of 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 200062, People's Republic of China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, People's Republic of China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, People's Republic of China
| |
Collapse
|
31
|
Gasevic T, Bamberg M, Wicke J, Bolte M, Virovets A, Lerner HW, Grimme S, Hansen A, Wagner M, Bursch M. Confined Lewis Pairs: Investigation of the X - →Si 20 Interaction in Halogen-Encapsulating Silafulleranes. Angew Chem Int Ed Engl 2024; 63:e202314238. [PMID: 38059423 DOI: 10.1002/anie.202314238] [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: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
A joint theoretical and experimental study on 32 endohedral silafullerane derivatives [X@Si20 Y20 ]- (X=F-I; Y=F-I, H, Me, Et) andT h ${T_h }$ -[Cl@Si20 H12 Y8 ]- (Y=F-I) is presented. First, we evaluated the structure-determining template effect of Cl- in a systematic series of concave silapolyquinane model systems. Second, we investigated the X- →Si20 interaction energy (E int ${E_{{\rm{int}}} }$ ) as a function of X- and Y and found the largestE int ${E_{{\rm{int}}} }$ values for electron-withdrawing exohedral substituents Y. Given that X- ions can be considered as Lewis bases and empty Si20 Y20 clusters as Lewis acids, we classify our inseparable host-guest complexes [X@Si20 Y20 ]- as "confined Lewis pairs". Third, 35 Cl NMR spectroscopy proved to be highly diagnostic for an experimental assessment of the Cl- →Si20 interaction as the paramagnetic shielding and, in turn, δ ${\delta }$ (35 Cl) of the endohedral Cl- ion correlate inversely withE int ${E_{{\rm{int}}} }$ . Finally, we disclose the synthesis of [PPN][Cl@Si20 Y20 ] (Y=Me, Et, Br) and provide a thorough characterization of these new silafulleranes.
Collapse
Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Marcel Bamberg
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Julius Wicke
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Michael Bolte
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Alexander Virovets
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Hans-Wolfram Lerner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Matthias Wagner
- Institut für Anorganische und Analytische Chemie, Goethe-Universität Frankfurt am Main, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| |
Collapse
|
32
|
Wappett DA, Goerigk L. Exploring CPS-Extrapolated DLPNO-CCSD(T 1) Reference Values for Benchmarking DFT Methods on Enzymatically Catalyzed Reactions. J Phys Chem A 2024; 128:62-72. [PMID: 38124376 DOI: 10.1021/acs.jpca.3c05086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Domain-based local pair natural orbital coupled-cluster singles doubles with perturbative triples [DLPNO-CCSD(T)] is regularly used to calculate reliable benchmark reference values at a computational cost significantly lower than that of canonical CCSD(T). Recent work has shown that even greater accuracy can be obtained at only a small additional cost through extrapolation to the complete PNO space (CPS) limit. Herein, we test two levels of CPS extrapolation, CPS(5,6), which approximates the accuracy of standard TightPNO, and CPS(6,7), which surpasses it, as benchmark values to test density functional approximations (DFAs) on a small set of organic and transition-metal-dependent enzyme active site models. Between the different reference levels of theory, there are changes in the magnitudes of the absolute deviations for all functionals, but these are small and there is minimal impact on the relative rankings of the tested DFAs. The differences are more significant for the metalloenzymes than the organic enzymes, so we repeat the tests on our entire ENZYMES22 set of organic enzyme active site models [Wappett, D. A.; Goerigk, L. J. Phys. Chem. A 2019, 123, 7057-7074] to confirm that using the CPS extrapolations for the reference values has negligible impact on the benchmarking outcomes. This means that we can particularly recommend CPS(5,6) as an alternative to standard TightPNO settings for calculating reference values, increasing the applicability of DLPNO-CCSD(T) in benchmarking reaction energies and barrier heights of larger models of organic enzymes. DLPNO-CCSD(T1)/CPS(6,7) energies for ENZYMES22 are finally presented as updated reference values for the set, reflecting the recent improvements in the method.
Collapse
Affiliation(s)
- Dominique A Wappett
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
33
|
Zhu Y, Alqahtani S, Hu X. An Assessment of Dispersion-Corrected DFT Methods for Modeling Nonbonded Interactions in Protein Kinase Inhibitor Complexes. Molecules 2024; 29:304. [PMID: 38257217 PMCID: PMC11154270 DOI: 10.3390/molecules29020304] [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: 10/31/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quantifying the strengths of these key protein-ligand interactions. However, the accuracy of DFT methods can vary substantially depending on the choice of exchange-correlation functionals and associated basis sets. In this study, a comprehensive benchmarking of nine widely used DFT methods was carried out to identify an optimal approach for quantitative modeling of nonbonded interactions, balancing both accuracy and computational efficiency. From a database of 2139 kinase-inhibitor crystal structures, a diverse library of 49 nonbonded interaction motifs was extracted, encompassing CH-π, π-π stacking, cation-π, hydrogen bonding, and salt bridge interactions. The strengths of nonbonded interaction energies for all 49 motifs were calculated at the advanced CCSD(T)/CBS level of theory, which serve as references for a systematic benchmarking of BLYP, TPSS, B97, ωB97X, B3LYP, M062X, PW6B95, B2PLYP, and PWPB95 functionals with D3BJ dispersion correction alongside def2-SVP, def2-TZVP, and def2-QZVP basis sets. The RI, RIJK, and RIJCOSX approximations were used for selected functionals. It was found that the B3LYP/def2-TZVP and RIJK RI-B2PLYP/def2-QZVP methods delivered the best combination of accuracy and computational efficiency, making them well-suited for efficient modeling of nonbonded interactions responsible for molecular recognition of protein kinase inhibitors in their targets.
Collapse
Affiliation(s)
- Yan Zhu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
| | - Saad Alqahtani
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
- Department of Chemistry, King Saud University, Riyadh 12372, Saudi Arabia
| | - Xiche Hu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA; (Y.Z.); (S.A.)
| |
Collapse
|
34
|
Bednarzick U, Gerlach J, Schulte M, Iovkova L, Tymann D, Hiersemann M. Intramolecular Alkyne-de Mayo Reaction Using the Enol Methylene Acetal Linker: Experimental Implementation and Computational Simulation. J Org Chem 2024. [PMID: 38170916 DOI: 10.1021/acs.joc.3c02022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The enol-linked intramolecular alkyne-de Mayo reaction is a photochemically triggered cascade reaction suitable for the synthesis of substituted dihydrotropones by two-carbon ring expansion of enol ethers of cyclopentane-1,3-dion. We report on the implementation of the methylene acetal linker and the isolation of the initial (2 + 2) photocycloadduct in substances. We have investigated in depth the modus operandi of the ring-opening of the π-donor-π-acceptor cyclobutene derivatives by computational chemistry.
Collapse
Affiliation(s)
- Ulf Bednarzick
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Jonas Gerlach
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Marcel Schulte
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Ljuba Iovkova
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - David Tymann
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Martin Hiersemann
- Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, 44227 Dortmund, Germany
| |
Collapse
|
35
|
Bursch M, Grimme S, Hansen A. Influence of Steric and Dispersion Interactions on the Thermochemistry of Crowded (Fluoro)alkyl Compounds. Acc Chem Res 2024; 57:153-163. [PMID: 38102118 DOI: 10.1021/acs.accounts.3c00634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
ConspectusAlkanes play a pivotal role in industrial, environmental, and biological processes. They are characterized by their carbon-carbon single-bond structure, remarkable stability, and conformational diversity. Fluorination of such compounds imparts unique physicochemical properties that often enhance pharmacokinetic profiles, metabolic stability, and receptor interactions while keeping beneficial properties. However, such per- and polyfluoroalkyl substances (PFAS) show a persistent presence in the environment and potential adverse health effects, which propelled them to the forefront of global environmental and health discussions. Alkyl compounds are also prototypical for stereoelectronic (SE) effects that are widely applied in chemistry. Substituents are typically described as electron-density-donating/withdrawing and/or responsible for sterically interacting with reagents or strategic groups in the molecule. That alkane branching can result in higher stability compared to less-branched isomers has been investigated in detail also by testing quantum chemical methods, in particular density functional theory (DFT). Alkane branching results in spatially compact structures with close intramolecular contacts so that at a specific size the detailed balance of attractive London dispersion and covalent versus repulsive Pauli exchange interactions shifts to new, chemically unfragile situations. This may lead to dissociation at room temperature and opens the central question: what is the smallest crowed alkane that cannot be made synthetically? In this Account, we try to shed light on the interplay among the various (free) energy components for crowded (fluoro)alkane dissociation. In this context, homolytic cleavage of the central C-C bond in a series of model alkanes of increasing size with tert-butyl (tBu), adamantyl (Ad), and [1.1.1]propellanyl (Prop) substituents is investigated. Reference energies are calculated at the PNO-LCCSD(T)-F12b level and used to benchmark the performance of contemporary DFT functionals. In line with previous conclusions, the application of dispersion corrections to density functionals is mandatory. For crowed structures, the accurate description of the midrange correlation effects, specifically repulsive van der Waals interactions, is crucial, and we observed that the density-dependent VV10 correction is superior to D4 in this context, although the asymptotic region is better described by the latter. The best available dispersion-inclusive functionals show systematic and reasonably small residual errors and can be safely applied to large systems (>100 atoms), for which coupled cluster methods with large basis sets are not computationally feasible anymore. For qualitatively correct predictions of synthetic accessibility under equilibrium conditions (free energy), the inclusion of thermostatistical (entropy) contributions is also essential. According to our results, tetra-tert-butylmethane (C17tBu) is the largest and most crowded system with a positive dissociation free energy and should be synthesizable. The difference between hydrogenated and perfluorinated systems originates from the increase in the steric repulsion of spatially close substituents, which is not compensated to the same extent by attractive orbital and dispersion interactions. A sometimes-assumed similar steric demand for fluorine and hydrogen atoms is not corroborated by our investigations on crowded systems. Perfluorination is found to substantially decrease thermal stability, rendering perfluorinated hexamethylethane (C8tBuF) the last potentially stable representative.
Collapse
Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Beringstraße 4, D-53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Beringstraße 4, D-53115 Bonn, Germany
| |
Collapse
|
36
|
Becke AD. Doubling down on density-functional theory. J Chem Phys 2023; 159:241101. [PMID: 38146827 DOI: 10.1063/5.0178236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023] Open
Abstract
In a recent paper, Becke et al. [J. Chem. Phys. 158, 151103 (2023)] presented a novel double hybrid density functional, "DH23," whose terms are based on good physics. Its 12 coefficients were trained on the GMTKN55 (general main-group thermochemistry, kinetics, and noncovalent interactions) chemical database of Goerigk et al. [Phys. Chem. Chem. Phys. 19, 32184 (2017)]. The lowest GMTKN55 "WTMAD2" error to date for any hybrid or double hybrid density functional was obtained (1.76 kcal/mol). Here, we make some revisions to DH23 and test its efficacy on reference data beyond GMTKN55, namely, organometallic reaction energies and barrier heights. The results confirm that DH23 is robust outside its training set. In the process, a slightly smaller GMTKN55 WTMAD2 of 1.73 kcal/mol is achieved.
Collapse
Affiliation(s)
- Axel D Becke
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, P.O. Box 15000, Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
37
|
Klippenstein SJ, Elliott SN. OH Roaming during the Ozonolysis of α-Pinene: A New Route to Highly Oxygenated Molecules? J Phys Chem A 2023; 127:10647-10662. [PMID: 38055299 DOI: 10.1021/acs.jpca.3c05179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The formation of low-volatility organic compounds in the ozonolysis of α-pinene, the dominant atmospheric monoterpene, provides an important route to aerosol formation. In this work, we consider a previously unexplored set of pathways for the formation of highly oxygenated molecules in α-pinene ozonolysis. Pioneering, direct experimental observations of Lester and co-workers have demonstrated a significant production of hydroxycarbonyl products in the dissociation of Criegee intermediates. Theoretical analyses indicate that this production arises from OH roaming-induced pathways during the OO fission of the vinylhydroperoxides (VHPs), which in turn come from internal H transfers in the Criegee intermediates. Ab initio kinetics computations are used here to explore the OH roaming-induced channels that arise from the ozonolysis of α-pinene. For computational reasons, the calculations consider a surrogate for α-pinene, where two spectator methyl groups are replaced with H atoms. Multireference electronic structure calculations are used to illustrate a variety of energetically accessible OH roaming pathways for the four VHPs arising from the ozonolysis of this α-pinene surrogate. Ab initio transition-state theory-based master equation calculations indicate that for the dissociation of stabilized VHPs, these OH roaming pathways are kinetically significant with a branching that generally increases from ∼20% at room temperature up to ∼70% at lower temperatures representative of the troposphere. For one of the VHPs, this branching already exceeds 60% at room temperature. For the overall ozonolysis process, these branching ratios would be greatly reduced by a limited branching to the stabilized VHP, although there would also be some modest roaming fraction for the nonthermal VHP dissociation process. The strong exothermicities of the roaming-induced isomerizations/additions and abstractions suggest new routes to fission of the cyclobutane rings. Such ring fissions would facilitate further autoxidation reactions, thereby providing a new route for producing highly oxygenated nonvolatile precursors to aerosol formation.
Collapse
Affiliation(s)
- Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarah N Elliott
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| |
Collapse
|
38
|
Martínez-Haya B, Avilés-Moreno JR, Gámez F, Martens J, Oomens J, Berden G. Correlated proton dynamics in hydrogen bonding networks: the benchmark case of 3-hydroxyglutaric acid. Phys Chem Chem Phys 2023; 26:198-208. [PMID: 38053486 DOI: 10.1039/d3cp04514e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born-Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]-·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations.
Collapse
Affiliation(s)
- Bruno Martínez-Haya
- Center for Nanoscience and Sustainable Technologies (CNATS), Universidad Pablo de Olavide, E-41013 Seville, Spain.
| | - Juan Ramón Avilés-Moreno
- Department of Applied Physical Chemistry, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Francisco Gámez
- Departamento de Química Física, Universidad Complutense, E-28040 Madrid, Spain
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| |
Collapse
|
39
|
Lv J, Hua R. LiO tBu-Promoted Intramolecular 1,3-Dipolar Cycloaddition of the 2'-Alkynyl-biaryl-2-aldehyde N-Tosylhydrazones Approach to 3-Substituted 1 H-Dibenzo[ e, g]indazoles. Molecules 2023; 28:8061. [PMID: 38138554 PMCID: PMC10745680 DOI: 10.3390/molecules28248061] [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: 10/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
A two-step, one-pot synthesis of 3-substituted 1H-dibenzo[e,g]indazoles in good to high yields via a LiOtBu-promoted intramolecular 1,3-dipolar cyclization of 2'-alkynyl-biaryl-2-aldehyde N-tosylhydrazones was developed. The N-Ts-hydrazones used were prepared in situ via the reactions of 2'-alkynyl-biaryl-2-aldehydes and TsNHNH2(p-methylbenzenesulfonohydrazide). Two types of signals related to the hydrogen bonds, forming in several products, were observed in the 1H NMR spectra recorded in DMSO-d6, assigned to N-H bonds in their dimeric species of product and tautomer.
Collapse
Affiliation(s)
- Jiaying Lv
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China;
| | - Ruimao Hua
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China;
- State Key Laboratory of Chemistry and Utilization of Carbon-Based Energy Resources, College of Chemistry, Xinjiang University, Urumqi 830017, China
| |
Collapse
|
40
|
Hancock AC, Goerigk L. Noncovalently bound excited-state dimers: a perspective on current time-dependent density functional theory approaches applied to aromatic excimer models. RSC Adv 2023; 13:35964-35984. [PMID: 38090083 PMCID: PMC10712016 DOI: 10.1039/d3ra07381e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 05/12/2024] Open
Abstract
Excimers are supramolecular systems whose binding strength is influenced by many factors that are ongoing challenges for computational methods, such as charge transfer, exciton coupling, and London dispersion interactions. Treating the various intricacies of excimer binding at an adequate level is expected to be particularly challenging for time-dependent Density Functional Theory (TD-DFT) methods. In addition to well-known limitations for some TD-DFT methods in the description of charge transfer or exciton coupling, the inherent London dispersion problem from ground-state DFT translates to TD-DFT. While techniques to appropriately treat dispersion in DFT are well-developed for electronic ground states, these dispersion corrections remain largely untested for excited states. Herein, we aim to shed light on current TD-DFT methods, including some of the newest developments. The binding of four model excimers is studied across nine density functionals with and without the application of additive dispersion corrections against a wave function reference of SCS-CC2/CBS(3,4) quality, which approximates select CCSDR(3)/CBS data adequately. To our knowledge, this is the first study that presents single-reference wave function dissociation curves at the complete basis set level for the assessed model systems. It is also the first time range-separated double-hybrid density functionals are applied to excimers. In fact, those functionals turn out to be the most promising for the description of excimer binding followed by global double hybrids. Range-separated and global hybrids-particularly with large fractions of Fock exchange-are outperformed by double hybrids and yield worse dissociation energies and inter-molecular equilibrium distances. The deviation between each assessed functional and reference increases with system size, most likely due to missing dispersion interactions. Additive dispersion corrections of the DFT-D3(BJ) and DFT-D4 types reduce the average errors for TD-DFT methods but do so inconsistently and therefore do not offer a black-box solution in their ground-state parametrised form. The lack of appropriate description of dispersion effects for TD-DFT methods is likely hindering the practical application of the herein identified more efficient methods. Dispersion corrections parametrised for excited states appear to be an important next step to improve the applicability of TD-DFT methods and we hope that our work assists with the future development of such corrections.
Collapse
Affiliation(s)
- Amy C Hancock
- School of Chemistry, The University of Melbourne Parkville Australia +61-(0)3-8344 6784
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne Parkville Australia +61-(0)3-8344 6784
| |
Collapse
|
41
|
Wappett D, Goerigk L. Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set. J Chem Theory Comput 2023; 19:8365-8383. [PMID: 37943578 PMCID: PMC10688432 DOI: 10.1021/acs.jctc.3c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
Collapse
Affiliation(s)
- Dominique
A. Wappett
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| |
Collapse
|
42
|
Jacquemin D, Kossoski F, Gam F, Boggio-Pasqua M, Loos PF. Reference Vertical Excitation Energies for Transition Metal Compounds. J Chem Theory Comput 2023. [PMID: 37965941 DOI: 10.1021/acs.jctc.3c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
To enrich and enhance the diversity of the quest database of highly accurate excitation energies [Véril, M.; et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2021, 11, e1517], we report vertical transition energies in transition metal compounds. Eleven diatomic molecules with a singlet or doublet ground state containing a fourth-row transition metal (CuCl, CuF, CuH, ScF, ScH, ScO, ScS, TiN, ZnH, ZnO, and ZnS) are considered, and the corresponding excitation energies are computed using high-level coupled-cluster (CC) methods, namely, CC3, CCSDT, CC4, and CCSDTQ, as well as multiconfigurational methods such as CASPT2 and NEVPT2. In many cases, to provide more comprehensive benchmark data, we also provide full configuration interaction estimates computed with the configuration interaction using a perturbative selection made iteratively (CIPSI) method. Based on these calculations, theoretical best estimates of the transition energies are established in both the aug-cc-pVDZ and aug-cc-pVTZ basis sets. This allows us to accurately assess the performance of the CC and multiconfigurational methods for this specific set of challenging transitions. Furthermore, comparisons with experimental data and previous theoretical results are also reported.
Collapse
Affiliation(s)
- Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Franck Gam
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| |
Collapse
|
43
|
Ibraimo Patia R, Singh K, Davies DL, Lelj F. Photoisomerisation of Exo-Imine Complexes and the Role of MECP in the Reverse Thermal Equilibrium: An Experimental and DFT Computational Investigation. Chemistry 2023; 29:e202301570. [PMID: 37578687 DOI: 10.1002/chem.202301570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023]
Abstract
Complexes [MCl2 Cp*]2 (M=Ir, Rh), [RuCl2 (p-cymene)]2 and [Ir(C^N)2 Cl]2 (HC^N=a, phenylpyridine ; b, phenylpyrazole,) react with imine ligands derived from ο-aminophenol to yield complexes with an exocyclic C=N bond which has a cis or trans configuration. The trans isomer is favoured except for sterically crowded complexes Cp*M (M=Ir, Rh) when the imine has a mesityl substituent, for which the cis isomer is favoured. The complexes undergo photoisomerisation in visible light but revert back to the original isomer over time or when heated. The rate of the thermal reverse isomerisation depends on the imine substituent and the metal fragment. DFT calculations correctly reproduce the favoured isomer and suggest that the reverse isomerisation occurs by a rehybridisation at the N atom as found in organic imines. In addition, a triplet state, thermally accessible by a Minimum Energy Crossing Point (MECP) provides a low energy pathway for reverse isomerisation in the case of the half-sandwich complexes.
Collapse
Affiliation(s)
- Raissa Ibraimo Patia
- School of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Kuldip Singh
- School of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - David L Davies
- School of Chemistry, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Francesco Lelj
- LASCAMM-CR-INSTM, Unità INSTM della Basilicata, Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
| |
Collapse
|
44
|
Graf D, Thom AJW. Corrected density functional theory and the random phase approximation: Improved accuracy at little extra cost. J Chem Phys 2023; 159:174106. [PMID: 37921249 DOI: 10.1063/5.0168569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
We recently introduced an efficient methodology to perform density-corrected Hartree-Fock density functional theory [DC(HF)-DFT] calculations and an extension to it we called "corrected" HF DFT [C(HF)-DFT] [Graf and Thom, J. Chem. Theory Comput. 19 5427-5438 (2023)]. In this work, we take a further step and combine C(HF)-DFT, augmented with a straightforward orbital energy correction, with the random phase approximation (RPA). We refer to the resulting methodology as corrected HF RPA [C(HF)-RPA]. We evaluate the proposed methodology across various RPA methods: direct RPA (dRPA), RPA with an approximate exchange kernel, and RPA with second-order screened exchange. C(HF)-dRPA demonstrates very promising performance; for RPA with exchange methods, on the other hand, we often find over-corrections.
Collapse
Affiliation(s)
- Daniel Graf
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| | - Alex J W Thom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, England
| |
Collapse
|
45
|
Ma HZ, Canty AJ, O'Hair RAJ. Liberation of carbon monoxide from formic acid mediated by molybdenum oxyanions. Dalton Trans 2023; 52:15734-15746. [PMID: 37843527 DOI: 10.1039/d3dt01983g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Multistage mass spectrometry experiments, isotope labelling and DFT calculations were used to explore whether selective decarbonylation of formic acid could be mediated by molybdate anions [(MoO3)x(OH)]- (x = 1 and 2) via a formal catalytic cycle involving two steps. In step 1, both molybdate anions undergo gas-phase ion-molecule reactions (IMR) with formic acid to produce the coordinated formates [(MoO3)x(O2CH)]- and H2O. In step 2, both coordinated formates [(MoO3)x(O2CH)]- undergo decarbonylation under collision-induced dissociation (CID) conditions to reform the molybdate anions [(MoO3)x(OH)]- (x = 1 and 2), thus closing a formal catalytic cycle. In the case of [MoO3(O2CH)]- an additional decarboxylation channel also occurs to yield [MoO3(H)]-, which is unreactive towards formic acid. The reaction between [Mo18O3(18OH)]- and formic acid gives rise to [Mo18O3(O2CH)]- highlighting that ligand substitution occurs without 18O/16O exchange between the coordinated 18OH ligand and HC16O2H. The reaction between [(MoO3)x(OD)]- (x = 1 and 2) and DCO2H initially produces [(MoO3)x(OH)]- (x = 1 and 2), indicating that D/H exchange occurs. DFT calculations were carried out to investigate the reaction mechanisms and energetics associated with both steps of the formal catalytic cycle and to better understand the competition between decarbonylation and decarboxylation, which is crucial in developing a selective catalyst. The CO and CO2 loss channels from the monomolybdate anion [MoO3(O2CH)]- have similar barrier heights which is in agreement with experimental results where both fragmentation channels are observed. In contrast, the dimolybdate anion is more selective, since the decarbonylation pathway of [(MoO3)2(O2CH)]- is both kinetically and thermodynamically favoured, which agrees with experimental observations where the CO loss channel is solely observed.
Collapse
Affiliation(s)
- Howard Z Ma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.
| | - Allan J Canty
- School of Natural Sciences - Chemistry, University of Tasmania, Private Bag 75, Hobart, Tasmania, 7001, Australia
| | - Richard A J O'Hair
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.
| |
Collapse
|
46
|
Brémond E, Rodríguez-Mayorga M, Pérez-Jiménez AJ, Adamo C, Sancho-García JC. Assessment of the nonempirical r2SCAN-QIDH double-hybrid density functional against large and diverse datasets. J Chem Phys 2023; 159:141101. [PMID: 37811824 DOI: 10.1063/5.0157259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
We update the Quadratic Integrand Double-Hybrid (QIDH) model [J. Chem. Phys. 141, 031101 (2014)] by incorporating the nonempirical restored-regularized Strongly Constrained and Appropriately Normed (r2SCAN) meta-generalized gradient approximation exchange-correlation functional, thus devising a robust density functional approximation free of any empirical parameter and incorporating all the constraints so far known for the exchange-correlation kernel. We assessed the new r2SCAN-QIDH expression on the GMTKN55 database and further extend its application to various types of non-covalent interactions (e.g., S66 × 8, O24 × 5). The assessment done shows that the model becomes very competitive in accuracy with respect to parent exchange-correlation functionals of any type, but without relying on any fitted parameter or numerical training.
Collapse
Affiliation(s)
- E Brémond
- Université de Paris Cité, ITODYS, CNRS, F-75006 Paris, France
| | - M Rodríguez-Mayorga
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - A J Pérez-Jiménez
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| | - C Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), FRE 2027, F-75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - J C Sancho-García
- Department of Physical Chemistry, University of Alicante, E-03080 Alicante, Spain
| |
Collapse
|
47
|
Li WL, Chen K, Rossomme E, Head-Gordon M, Head-Gordon T. Greater transferability and accuracy of norm-conserving pseudopotentials using nonlinear core corrections. Chem Sci 2023; 14:10934-10943. [PMID: 37829021 PMCID: PMC10566506 DOI: 10.1039/d3sc03709f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
We present an investigation into the transferability of pseudopotentials (PPs) with a nonlinear core correction (NLCC) using the Goedecker, Teter, and Hutter (GTH) protocol across a range of pure GGA, meta-GGA and hybrid functionals, and their impact on thermochemical and non-thermochemical properties. The GTH-NLCC PP for the PBE density functional demonstrates remarkable transferability to the PBE0 and ωB97X-V exchange-correlation functionals, and relative to no NLCC, improves agreement significantly for thermochemical benchmarks compared to all-electron calculations. On the other hand, the B97M-rV meta-GGA functional performs poorly with the PBE-derived GTH-NLCC PP, which is mitigated by reoptimizing the NLCC parameters for this specific functional. The findings reveal that atomization energies exhibit the greatest improvements from use of the NLCC, which thus provides an important correction needed for covalent interactions relevant to applications involving chemical reactivity. Finally we test the NLCC-GTH PPs when combined with medium-size TZV2P molecularly optimized (MOLOPT) basis sets which are typically utilized in condensed phase simulations, and show that they lead to consistently good results when compared to all-electron calculations for atomization energies, ionization potentials, barrier heights, and non-covalent interactions, but lead to somewhat larger errors for electron affinities.
Collapse
Affiliation(s)
- Wan-Lu Li
- Kenneth S. Pitzer Center for Theoretical Chemistry USA
- Department of Chemistry USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory USA
- Department of Nanoengineering and Materials Science and Engineering Program, University of California San Diego La Jolla California 92093 USA
| | - Kaixuan Chen
- Kenneth S. Pitzer Center for Theoretical Chemistry USA
- Department of Chemistry USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory USA
| | - Elliot Rossomme
- Kenneth S. Pitzer Center for Theoretical Chemistry USA
- Department of Chemistry USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry USA
- Department of Chemistry USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory USA
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry USA
- Department of Chemistry USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory USA
- Department of Chemical and Biomolecular Engineering USA
- Department of Bioengineering, University of California, Berkeley Berkeley California 94720 USA
| |
Collapse
|
48
|
O’Reilly RJ, Karton A. The influence of substituents in governing the strength of the P-X bonds of substituted halophosphines R 1R 2P-X (X = F and Cl). Front Chem 2023; 11:1283418. [PMID: 37854977 PMCID: PMC10579588 DOI: 10.3389/fchem.2023.1283418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/15/2023] [Indexed: 10/20/2023] Open
Abstract
In this study, the gas-phase homolytic P-F and P-Cl bond dissociation energies (BDEs) of a set of thirty fluorophosphine (R1R2P-F) and thirty chlorophosphine-type (R1R2P-Cl) molecules have been obtained using the high-level W2 thermochemical protocol. For the R1R2P-F species, the P-F BDEs (at 298 K) differ by up to 117.0 kJ mol-1, with (H3Si)2P-F having the lowest BDE (439.5 kJ mol-1) and F2P-F having the largest BDE (556.5 kJ mol-1). In the case of the chlorophosphine-type molecules, the difference in BDEs is considerably smaller (i.e., 72.6 kJ mol-1), with (NC)2P-Cl having the lowest P-Cl BDE (299.8 kJ mol-1) and (HO)2P-Cl having the largest (372.4 kJ mol-1). We have further analyzed the effect of substituents in governing the P-F and P-Cl BDEs by considering the effect of substituents in the parent halogenated precursors (using molecule stabilization enthalpies) and the effect of substituents in the product radicals (using radical stabilization enthalpies). Finally, we have also assessed the performance of a wide range of DFT methods for their ability to compute the gas-phase P-F and P-Cl BDEs contained in this dataset. We find that, overall, the double hybrid functional DSD-PBEB95 offers the best performance for both bond types, with mean absolute deviations of just 2.1 (P-F BDEs) and 2.2 (P-Cl BDEs) kJ mol-1.
Collapse
Affiliation(s)
- Robert J. O’Reilly
- School of Science and Technology, University of New England, Armidale, NSW, Australia
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW, Australia
| |
Collapse
|
49
|
Scheele T, Neudecker T. Investigating the accuracy of density functional methods for molecules in electric fields. J Chem Phys 2023; 159:124111. [PMID: 38127387 DOI: 10.1063/5.0164372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/05/2023] [Indexed: 12/23/2023] Open
Abstract
The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical reactions has gained traction in recent years. Electronic structure calculations using OEEFs are commonly done using methods based on density functional theory (DFT), but until now, the performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more general scope. Looking at the accuracy of molecular geometries, electronic energies, and electric dipole moments compared to accurate coupled-cluster with perturbative triples data, we have investigated a wide variety of density functionals using different basis sets to determine how well the individual functionals perform on various types of chemical bonds. We found that most functionals accurately calculate geometries in OEEFs and that small basis sets are sufficient in many cases. Calculations of electronic energies show a significant error introduced by the OEEF, which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages that they bring.
Collapse
Affiliation(s)
- Tarek Scheele
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359 Bremen, Germany
| | - Tim Neudecker
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße NW2, D-28359 Bremen, Germany
- Bremen Center for Computational Materials Science, University of Bremen, Am Fallturm 1, D-28359 Bremen, Germany
- MAPEX Center for Materials and Processes, University of Bremen, Bibliothekstraße 1, D-28359 Bremen, Germany
| |
Collapse
|
50
|
Chi S, Yu Y, Zhang M. Theoretical Insights into Midchain Radicals and Branching Characteristics in Solution Copolymerization of Ethylene and Vinyl Acetate. J Phys Chem B 2023; 127:8268-8281. [PMID: 37715720 DOI: 10.1021/acs.jpcb.3c04570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
Abstract
The kinetics of intermolecular chain transfer to polymer (CTP) and chain transfer to monomer (CTM), as well as backbiting in solution copolymerization of ethylene and vinyl acetate (VAc), are calculated by density functional theory. An intrinsic rate coefficient for each reaction type, whose Arrhenius parameters are expressed as functions of unreacted monomer composition, is extracted from calculated elementary reactions, and hence it applies to a wide range of fragment compositions of EVA. Backbiting controls the generation of midchain radicals (MCRs) on the backbone, and its rate maximizes at a medium fraction of VAc in the unreacted monomers. CTP plays an insignificant role in MCR generation even at high conversion rates due to its low pre-exponential factor. The concentration of MCRs is quantified and is close to that of ECRs at high conversions and high fractions of VAc in monomers. Additionally, branching characteristics are explored; concentrations of short-chain branching (SCB) and long-chain branching (LCB) are about 0.7-2.5 and 0.1-0.4%, respectively, and drop with VAc fraction rapidly. The role of the migration of MCRs is highlighted, which transforms about 10% of SCB points into LCB points. Disagreeing with insights from laboratory experiments, it is the migration, rather than CTP, which increases the LCB concentration at high conversions.
Collapse
Affiliation(s)
- Suocheng Chi
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, PR China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang 315201, PR China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, PR China
| | - Yingzhe Yu
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, PR China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang 315201, PR China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, PR China
| | - Minhua Zhang
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University, Tianjin 300072, PR China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang 315201, PR China
- State Key Laboratory of Engines, Tianjin University, Tianjin 300072, PR China
| |
Collapse
|