1
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Zhang J, Bhattacharya S, Khsara BE, Nisar T, Müller AB, Besora M, Poblet JM, Wagner V, Kuhnert N, Kortz U. Pt IV-Containing Hexaplatinate(II) [Pt IVPt II6O 6(AsO 2(CH 3) 2) 6] 2- and Hexapalladate(II) [Pt IVPd II6O 6(AsO 2(CH 3) 2) 6] 2. Inorg Chem 2023; 62:13184-13194. [PMID: 37440284 DOI: 10.1021/acs.inorgchem.3c00832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The first PtIV-containing discrete polyoxoplatinate(II) [PtIVPtII6O6(AsO2(CH3)2)6]2- (Pt7) and polyoxopalladate(II) [PtIVPdII6O6(AsO2(CH3)2)6]2- (PtPd6) have been prepared and characterized in the solid state, in solution, and in the gas phase. The molecular structures of the noble metal-oxo clusters Pt7 and PtPd6 comprise a central, octahedral PtIVO6 hetero group surrounded by six square-planar MO4 (M = PtII, PdII) units, which are capped by six dimethylarsinate ligands. The polyanions were prepared under simple one-pot aqueous solution conditions by reacting H2Pt(OH)6 with either K2PtCl4 or Pd(NO3)2 in sodium dimethylarsinate buffer (pH 7) at 80 °C. Catalytic studies were performed on Pt7 supported on SBA15-apts for o-xylene hydrogenation at 300 °C and 90 bar H2 pressure and indicated excellent activity and recyclability with low activation temperature.
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Affiliation(s)
- Jiayao Zhang
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Saurav Bhattacharya
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
- Department of Chemistry, BITS Pilani K. K. Birla Goa Campus, K. K. Birla Goa Campus, 403726 Goa, India
| | - Bahaa E Khsara
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Talha Nisar
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Anja B Müller
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Maria Besora
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Josep M Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Veit Wagner
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Nikolai Kuhnert
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kortz
- School of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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2
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Mondal S, Jana G, Srivastava HK, Sastry GN, Chattaraj PK. Structure and stability of the sH binary hydrate cavity and host-guest versus guest-guest interactions therein: A DFT approach. J Comput Chem 2023; 44:1446-1453. [PMID: 36916825 DOI: 10.1002/jcc.27102] [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: 01/05/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
The intrinsic ability of clathrate hydrates to encage gaseous molecules is explored. Encapsulation ability depends on the cavity size and the type of guest gaseous species in addition to the physical parameters, temperature and pressure. Here we have reported the structure, stability and nature of interaction in dissimilar guest occupied sH hydrate cavity. Diatomic gas molecules and small polyatomic hydrocarbons are considered as guests. The irregular icosahedron (512 68 ) cavity of sH hydrate is the host. Different thermodynamic parameters for the guest molecules encapsulation were calculated using three different hybrid DFT functionals, B3LYP, M05-2X, M06, and moreover using dispersion correction (PBE0-D3). With the consideration of large H-bonded systems the 6-31G* and cc-pVTZ basis sets were used for two set of computations. To disclose the nature of interaction between the host-guest systems as well as the interaction between the guest molecules inside the host the non-covalent interaction (NCI) indices and energy decomposition analysis (EDA) were done. Impact of host-guest and guest-guest interactions are discussed.
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Affiliation(s)
- Sukanta Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.,Department of Education, A. M. School of Educational Sciences, Assam University, Silchar, Assam, India
| | - Gourhari Jana
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
| | - Hemant K Srivastava
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India.,Department of Medicinal Chemistry, NIPER, Guwahati, Assam, India
| | - Garikapati N Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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3
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Stojičkov M, Zlatar M, Pio Mazzeo P, Bacchi A, Radovanović D, Stevanović N, Jevtović M, Novaković I, Anđelković K, Sladić D, Čobeljić B, Gruden M. The interplay between spin states, geometries and biological activity of Fe(III) and Mn(II) complexes with thiosemicarbazone. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Lonsdale DR, Goerigk L. One-electron self-interaction error and its relationship to geometry and higher orbital occupation. J Chem Phys 2023; 158:044102. [PMID: 36725505 DOI: 10.1063/5.0129820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Density Functional Theory (DFT) sees prominent use in computational chemistry and physics; however, problems due to the self-interaction error (SIE) pose additional challenges to obtaining qualitatively correct results. As an unphysical energy an electron exerts on itself, the SIE impacts most practical DFT calculations. We conduct an in-depth analysis of the one-electron SIE in which we replicate delocalization effects for simple geometries. We present a simple visualization of such effects, which may help in future qualitative analysis of the one-electron SIE. By increasing the number of nuclei in a linear arrangement, the SIE increases dramatically. We also show how molecular shape impacts the SIE. Two- and three-dimensional shapes show an even greater SIE stemming mainly from the exchange functional with some error compensation from the one-electron error, which we previously defined [D. R. Lonsdale and L. Goerigk, Phys. Chem. Chem. Phys. 22, 15805 (2020)]. Most tested geometries are affected by the functional error, while some suffer from the density error. For the latter, we establish a potential connection with electrons being unequally delocalized by the DFT methods. We also show how the SIE increases if electrons occupy higher-lying atomic orbitals; seemingly one-electron SIE free methods in a ground are no longer SIE free in excited states, which is an important insight for some popular, non-empirical density functional approximations (DFAs). We conclude that the erratic behavior of the SIE in even the simplest geometries shows that robust DFAs are needed. Our test systems can be used as a future benchmark or contribute toward DFT development.
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Affiliation(s)
- Dale R Lonsdale
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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5
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Reimann M, Kaupp M. Spin-State Splittings in 3d Transition-Metal Complexes Revisited: Benchmarking Approximate Methods for Adiabatic Spin-State Energy Differences in Fe(II) Complexes. J Chem Theory Comput 2022; 18:7442-7456. [PMID: 36417564 DOI: 10.1021/acs.jctc.2c00924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The CASPT2+δMRCI composite approach reported in a companion paper has been extended and used to provide high-quality reference data for a series of adiabatic spin gaps (defined as ΔE = Equintet - Esinglet) of [FeIIL6]2+ complexes (L = CNH, CO, NCH, NH3, H2O), either at nonrelativistic level or including scalar relativistic effects. These highly accurate data have been used to evaluate the performance of various more approximate methods. Coupled-cluster theory with singles, doubles, and perturbative triples, CCSD(T), is found to agree well with the new reference data for Werner-type complexes but exhibits larger underestimates by up to 70 kJ/mol for the π-acceptor ligands, due to appreciable static correlation in the low-spin states of these systems. Widely used domain-based local CCSD(T) calculations, DLPNO-CCSD(T), are shown to depend very sensitively on the cutoff values used to construct the localized domains, and standard values are not sufficient. A large number of density functional approximations have been evaluated against the new reference data. The B2PLYP double hybrid gives the smallest deviations, but several functionals from different rungs of the usual ladder hierarchy give mean absolute deviations below 20 kJ/mol. This includes the B97-D semilocal functional, the PBE0* global hybrid with 15% exact-exchange admixture, as well as the local hybrids LH07s-SVWN and LH07t-SVWN. Several further functionals achieve mean absolute errors below 30 kJ/mol (M06L-D4, SSB-D, B97-1-D4, LC-ωPBE-D4, LH12ct-SsirPW92-D4, LH12ct-SsifPW92-D4, LH14t-calPBE-D4, LHJ-HFcal-D4, and several further double hybrids) and thereby also still overall outperform CCSD(T) or uncorrected CASPT2. While exact-exchange admixture is a crucial factor in favoring high-spin states, the present evaluations confirm that other aspects can be important as well. A number of the better-performing functionals underestimate the spin gaps for the π-acceptor ligands but overestimate them for L = NH3, H2O. In contrast to a previous suggestion, non-self-consistent density functional theory (DFT) computations on top of Hartree-Fock orbitals are not a promising path to produce accurate spin gaps in such complexes.
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Affiliation(s)
- Marc Reimann
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
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6
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de Andrade TFCB, Dos Santos HF, Fonseca Guerra C, Paschoal DFS. Computational Prediction of Tc-99 NMR Chemical Shifts in Technetium Complexes with Radiopharmaceutical Applications. J Phys Chem A 2022; 126:5434-5448. [PMID: 35930743 DOI: 10.1021/acs.jpca.2c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Tc-99m nucleus is the most used nuclide in radiopharmaceuticals designed for imaging diagnosis. The metal can exist in nine distinct oxidation states and forms distinct coordination complexes with a variety of chelating agents and geometries. These complexes are usually characterized through Tc-99 NMR that is very sensitive to the Tc coordination sphere. Therefore, predicting Tc-99 NMR might be useful to assist experimentalists in structural characterization. In the present study, we propose three computational protocols for predicting Tc-99 NMR chemical shifts based on density functional theory calculations using relativistic and nonrelativistic Hamiltonians: the relativistic Model 1, the nonrelativistic Model 2, and the empirical nonrelativistic Model 3. In Models 2 and 3, the NMR-DKH basis set was used for all atoms, including the Tc, for which it was developed here. All models were applied for a set of 41 Tc-complexes with metal oxidation states 0, I, and V, for which the Tc-99 chemical shift was available experimentally. The mean absolute deviation and the mean relative deviation were 67 ppm and 4.8% (Model 1), 92 ppm and 6.2% (Model 2), and 65 ppm and 4.9% (Model 3), respectively. Last, the effect of the explicit solvent was evaluated for the [TcO2(en)2]+─Tc(V) complex. The calculated results for the Tc-99 NMR chemical shift at SO-ZORA-SSB-D/TZ2P-ZORA/COSMO//TPSS/def2-SVP/IEF-PCM(UFF) show that the inclusion of 14 water molecules (first solvation shell) together with the implicit solvation model leads to an absolute deviation of only 7 ppm (0.3%) from the experimental value, indicating that the solvent effects play a key role in predicting Tc-99 NMR.
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Affiliation(s)
- Taís F C B de Andrade
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal do Rio de Janeiro, Macaé, 27.971-525 Rio de Janeiro, Brasil
| | - Hélio F Dos Santos
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química - ICE, Universidade Federal de Juiz de Fora, Campus Universitário, 36.036-900 Juiz de Fora, Minas Gerais, Brasil
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Diego F S Paschoal
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal do Rio de Janeiro, Macaé, 27.971-525 Rio de Janeiro, Brasil
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7
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Rajan A, Elcheikh Mahmoud M, Wang F, Bhattacharya S, Mougharbel AS, Ma X, Müller AB, Nisar T, Taffa DH, Poblet JM, Kuhnert N, Wagner V, Wark M, Kortz U. Discovery of Polythioplatinate(II) [Pt 3S 2(SO 3) 6] 10- and Study of Its Solution and Catalytic Properties. Inorg Chem 2022; 61:11529-11538. [PMID: 35866749 DOI: 10.1021/acs.inorgchem.2c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have discovered the first polythioplatinate(II), [PtII3S2(SO3)6]10- (1), which was synthesized in aqueous basic medium (pH 11) by hydrothermal heating at 150 °C. Polyanion 1 comprises a discrete, triangular assembly of three Pt2+ ions linked by two μ3-sulfido ligands, and their square-planar coordination geometry is completed by two terminal S-bound sulfito ligands. Polyanion 1 was isolated as a hydrated sodium salt, Na10[PtII3(μ3-S)2(SO3)6]·22H2O (Na-1), which was characterized in the solid state by single-crystal X-ray diffraction, Fourier-transform infrared spectroscopy, thermogravimetric analysis, X-ray photoelectron spectra, and elemental analysis, in solution by 195Pt NMR and atomic absorption spectroscopy, and in the gas phase by electrospray ionization mass spectrometry. Density functional theory calculations were performed, and the 195Pt NMR chemical shifts of 1 were computed theoretically and shown to match well with the experimental data. Furthermore, the discrete title polyanion 1 was immobilized on mesoporous SBA-15 support and used as a precatalyst for the hydrogenation of o-xylene.
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Affiliation(s)
- Ananthu Rajan
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Mahmoud Elcheikh Mahmoud
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Fei Wang
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Saurav Bhattacharya
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Ali S Mougharbel
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Xiang Ma
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Anja B Müller
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Talha Nisar
- Department of Physics and Earth Sciences, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Dereje H Taffa
- Institute of Chemistry, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Josep M Poblet
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Nikolai Kuhnert
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Veit Wagner
- Department of Physics and Earth Sciences, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Michael Wark
- Institute of Chemistry, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Ulrich Kortz
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
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8
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Drosou M, Mitsopoulou CA, Pantazis DA. Reconciling Local Coupled Cluster with Multireference Approaches for Transition Metal Spin-State Energetics. J Chem Theory Comput 2022; 18:3538-3548. [PMID: 35582788 PMCID: PMC9202354 DOI: 10.1021/acs.jctc.2c00265] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Spin-state energetics
of transition metal complexes remain one
of the most challenging targets for electronic structure methods.
Among single-reference wave function approaches, local correlation
approximations to coupled cluster theory, most notably the domain-based
local pair natural orbital (DLPNO) approach, hold the promise of bringing
the accuracy of coupled cluster theory with single, double, and perturbative
triple excitations, CCSD(T), to molecular systems of realistic size
with acceptable computational cost. However, recent studies on spin-state
energetics of iron-containing systems raised doubts about the ability
of the DLPNO approach to adequately and systematically approximate
energetics obtained by the reference-quality complete active space
second-order perturbation theory with coupled-cluster semicore correlation,
CASPT2/CC. Here, we revisit this problem using a diverse set of iron
complexes and examine several aspects of the application of the DLPNO
approach. We show that DLPNO-CCSD(T) can accurately reproduce both
CASPT2/CC and canonical CCSD(T) results if two basic principles are
followed. These include the consistent use of the improved iterative
(T1) versus the semicanonical perturbative triple corrections
and, most importantly, a simple two-point extrapolation to the PNO
space limit. The latter practically eliminates errors arising from
the default truncation of electron-pair correlation spaces and should
be viewed as standard practice in applications of the method to transition
metal spin-state energetics. Our results show that reference-quality
results can be readily achieved with DLPNO-CCSD(T) if these principles
are followed. This is important also in view of the applicability
of the method to larger single-reference systems and multinuclear
clusters, whose treatment of dynamic correlation would be challenging
for multireference-based approaches.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Christiana A Mitsopoulou
- Inorganic Chemistry Laboratory, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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9
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de Azevedo Santos L, Ramalho TC, Hamlin TA, Bickelhaupt FM. Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study. J Comput Chem 2021; 42:688-698. [PMID: 33543482 PMCID: PMC7986859 DOI: 10.1002/jcc.26489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/27/2022]
Abstract
We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP) with and without diffuse functions. The highest-level ZORA-CCSD(T)/ma-ZORA-def2-QZVPP counterpoise-corrected complexation energies (ΔECPC ) are converged within 1.1-3.4 kcal mol-1 and 1.5-3.1 kcal mol-1 with respect to the method and basis set, respectively. Next, we used the ZORA-CCSD(T)/ma-ZORA-def2-QZVPP (ΔECPC ) as reference data for analyzing the performance of 13 different ZORA-relativistic DFT approaches in combination with the Slater-type QZ4P basis set. We find that the three-best performing functionals are M06-2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol-1 , respectively. The MAE for BLYP-D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol-1 , respectively.
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Affiliation(s)
- Lucas de Azevedo Santos
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Institute of Natural SciencesFederal University of LavrasLavrasBrazil
- Center for Basic and Applied ResearchUniversity Hradec KraloveHradec KraloveCzech Republic
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamAmsterdamNetherlands
- Institute for Molecules and MaterialsRadboud University NijmegenNijmegenNetherlands
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10
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Melidis L, Styles IB, Hannon MJ. Targeting structural features of viral genomes with a nano-sized supramolecular drug. Chem Sci 2021; 12:7174-7184. [PMID: 34123344 PMCID: PMC8153246 DOI: 10.1039/d1sc00933h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022] Open
Abstract
RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Iain B Styles
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Computer Science, University of Birmingham Edgbaston Birmingham B15 2TT UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham The Midlands UK
- Alan Turing Institute London UK
| | - Michael J Hannon
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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11
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Abstract
Applications of density-functional theory (DFT) in computational chemistry rely on an approximate exchange-correlation (xc) functional. However, existing approximations can fail dramatically for open-shell molecules, in particular for transition-metal complexes or radicals. Most importantly, predicting energy differences between different spin-states with approximate exchange-correlation functionals remains extremely challenging. Formally, it is known that the exact xc functional should be spin-state dependent, but none of the available approximations feature such an explicit spin-state dependence [C. R. Jacob and M. Reiher, Int. J. Quantum Chem., 2012, 112, 3661-3684]. Thus, to find novel approximations for the xc functional for open-shell systems, the development of spin-state dependent xc functionals appears to be a promising avenue. Here, we set out to shed light on the spin-state dependence of the xc functional by investigating the underlying xc holes, which we extract from configuration interaction calculations for model systems. We analyze the similarities and differences between the xc holes of the lowest-energy singlet and triplet states of the dihydrogen molecule, the helium atom, and the lithium dimer. To shed further light on the spin-state dependence of these xc holes we also discuss exact conditions that can be derived from the spin structure of the reduced two-electron density matrix. Altogether, our results suggest several possible routes towards the construction of explicitly spin-state dependent approximations for the xc functional.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany.
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12
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Prokopiou G, Autschbach J, Kronik L. Assessment of the Performance of Optimally Tuned Range‐Separated Hybrid Functionals for Nuclear Magnetic Shielding Calculations. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Georgia Prokopiou
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
| | - Jochen Autschbach
- Department of ChemistryState University of New York at BuffaloBuffalo NY 14260‐3000 USA
| | - Leeor Kronik
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
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13
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Gupta M, Chatterjee N, De D, Saha R, Chattaraj PK, Oliver CL, Bharadwaj PK. Metal-Organic Frameworks of Cu(II) Constructed from Functionalized Ligands for High Capacity H 2 and CO 2 Gas Adsorption and Catalytic Studies. Inorg Chem 2020; 59:1810-1822. [PMID: 31965795 DOI: 10.1021/acs.inorgchem.9b03012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two Cu(II)-based metal-organic frameworks (MOFs) having paddle-wheel secondary building units (SBUs), namely, 1Me and 1ipr, were synthesized solvothermally using two new bent di-isophthalate ligands incorporating different substituents. The MOFs showed high porosity (BET surface area, 2191 m2/g for 1Me and 1402 m2/g for 1ipr). For 1Me, very high CO2 adsorption (98.5 wt % at 195 K, 42.9 wt % at 273 K, 23.3 wt % at 298 K) at 1 bar was found, while for 1ipr, it was significantly less (14.3 wt % at 298 K and 1 bar, 54.4 wt % at 298 K at 50 bar). 1Me exhibited H2 uptake of 3.2 wt % at 77 K and 1 bar of pressure, which compares well with other benchmark MOFs. For 1ipr, the H2 uptake was found to be 2.54 wt % under similar experimental conditions. The significant adsorption of H2 and CO2 for 1Me could be due to the presence of micropores as well as unsaturated metal sites in these MOFs besides the presence of substituents that interact with the gas molecules. The experimental adsorption behavior of the MOFs could be justified by theoretical calculations. Additionally, catalytic conversions of CO2 and CS2 into useful chemicals like cyclic carbonates, cyclic trithiocarbonates, and cyclic dithiocarbonates could be achieved.
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Affiliation(s)
- Mayank Gupta
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur 208016 , India
| | - Nabanita Chatterjee
- Centre for Supramolecular Chemistry Research (CSCR), Department of Chemistry , University of Cape Town , Cape Town , South Africa
| | - Dinesh De
- Department of Basic Science, Vishwavidyalaya Engineering College, Lakhanpur , Sarguja University , Lakhanpur , Chhattisgarh - 497116 , India
| | - Ranajit Saha
- Department of Chemistry and Center for Theoretical Studies , Indian Institute of Technology Kharagpur , Kharagpur 721302 , India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Center for Theoretical Studies , Indian Institute of Technology Kharagpur , Kharagpur 721302 , India.,Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India
| | - Clive L Oliver
- Centre for Supramolecular Chemistry Research (CSCR), Department of Chemistry , University of Cape Town , Cape Town , South Africa
| | - Parimal K Bharadwaj
- Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur 208016 , India.,Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India
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14
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15
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Siig OS, Kepp KP. Iron(II) and Iron(III) Spin Crossover: Toward an Optimal Density Functional. J Phys Chem A 2018; 122:4208-4217. [PMID: 29630380 DOI: 10.1021/acs.jpca.8b02027] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Spin crossover (SCO) plays a major role in biochemistry, catalysis, materials, and emerging technologies such as molecular electronics and sensors, and thus accurate prediction and design of SCO systems is of high priority. However, the main tool for this purpose, density functional theory (DFT), is very sensitive to applied methodology. The most abundant SCO systems are Fe(II) and Fe(III) systems. Even with average good agreement, a functional may be significantly more accurate for Fe(II) or Fe(III) systems, preventing balanced study of SCO candidates of both types. The present work investigates DFT's performance for well-known Fe(II) and Fe(III) SCO complexes, using various design types and customized versions of GGA, hybrid, meta-GGA, meta-hybrid, double-hybrid, and long-range-corrected hybrid functionals. We explore the limits of DFT performance and identify proficient Fe(II)-Fe(III)-balanced functionals. We identify and quantify remarkable differences in the DFT description of Fe(II) and Fe(III) systems. Most functionals become more accurate once Hartree-Fock exchange is adjusted to 10-17%, regardless of the type of functionals involved. However, this typically introduces a clear Fe(II)-Fe(III) bias. The most accurate functionals measured by mean absolute errors <10 kJ/mol are CAMB3LYP-17, B3LYP*, and B97-15 with 15-17% Hartree-Fock exchange, closely followed by CAMB3LYP and CAMB3LYP-15, OPBE, rPBE-10, and B3P86-15. While GGA functionals display a small Fe(II)-Fe(III) bias, they are generally inaccurate, except the O exchange functional. Hybrid functionals (including B2PLYP double hybrids and meta hybrids) tend to favor HS too much in Fe(II) vs Fe(III), which is important in many studies where the oxidation state of iron can vary, e.g. rational SCO design and studies of catalytic processes involving iron. The only functional with a combined bias <5 kJ/mol and a decent MAE (15 kJ/mol) is our customized PBE0-12 functional. Alternatively one has to sacrifice Fe(II)-Fe(III) balance to use the best functionals for each group separately. We also investigated the precision (measured as the standard deviation of errors) and show that the target accuracy for iron SCO is 10 kJ/mol for accuracy and 5 kJ/mol for precision, and DFT is probably not going to break this limit in the near future. Importantly, all four types of functional behavior (accurate/precise, accurate/imprecise, inaccurate/precise, inaccurate/imprecise) are observed. More generally, our work illustrates the importance not only of overall accuracy but also of balanced accuracy for systems likely to occur in context.
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Affiliation(s)
- Oliver S Siig
- DTU Chemistry , Technical University of Denmark , Building 206 , 2800 Kgs. Lyngby , Denmark
| | - Kasper P Kepp
- DTU Chemistry , Technical University of Denmark , Building 206 , 2800 Kgs. Lyngby , Denmark
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16
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Stepanović S, Angelone D, Gruden M, Swart M. The role of spin states in the catalytic mechanism of the intra- and extradiol cleavage of catechols by O 2. Org Biomol Chem 2018; 15:7860-7868. [PMID: 28880037 DOI: 10.1039/c7ob01814b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-dependent enzymes and biomimetic iron complexes can catalyze the ring cleavage of very inert, aromatic compounds. The mechanisms of these transformations and the factors that lead either to extradiol cleavage or intradiol cleavage have not been fully understood. By using density functional theory we have elucidated the mechanism of the catalytic cycle for two biomimetic complexes, and explained the difference in the experimentally obtained products.
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Affiliation(s)
- S Stepanović
- Center for Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade Njegoseva 12, 11001 Belgrade, Serbia
| | - D Angelone
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi (Ciències), 17003 Girona, Spain
| | - M Gruden
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11001 Belgrade, Serbia.
| | - M Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi (Ciències), 17003 Girona, Spain and ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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17
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Merlini ML, Britovsek GJP, Swart M, Belanzoni P. Understanding the Catalase-Like Activity of a Bioinspired Manganese(II) Complex with a Pentadentate NSNSN Ligand Framework. A Computational Insight into the Mechanism. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03559] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Letizia Merlini
- Laboratoire de Chimie et Biochimie Computationnelles, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Av. F.-A. Forel 2, CH-1015 Lausanne, Switzerland
| | - George J. P. Britovsek
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Facultat de Ciències, 17003 Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Paola Belanzoni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Istituto di Scienze e Tecnologie Molecolari del CNR CNR-ISTM, c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123 Perugia, Italy
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18
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Iron MA. Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals. J Chem Theory Comput 2017; 13:5798-5819. [PMID: 29016125 DOI: 10.1021/acs.jctc.7b00772] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The various factors influencing the accuracy of 13C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
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19
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Aebersold LE, Yuwono SH, Schoendorff G, Wilson AK. Efficacy of Density Functionals and Relativistic Effective Core Potentials for Lanthanide-Containing Species: The Ln54 Molecule Set. J Chem Theory Comput 2017; 13:2831-2839. [DOI: 10.1021/acs.jctc.6b01223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas E. Aebersold
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Stephen H. Yuwono
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - George Schoendorff
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Angela K. Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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20
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Artiukhin DG, Stein CJ, Reiher M, Neugebauer J. Quantum Chemical Spin Densities for Radical Cations of Photosynthetic Pigment Models. Photochem Photobiol 2017; 93:815-833. [DOI: 10.1111/php.12757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/30/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Denis G. Artiukhin
- Theoretische Organische Chemie; Organisch-Chemisches Institut and Center for Multiscale Theory and Simulation; Westfälische Wilhelms-Universität Münster; Münster Germany
| | | | - Markus Reiher
- Laboratorium für Physikalische Chemie; ETH Zürich; Zürich Switzerland
| | - Johannes Neugebauer
- Theoretische Organische Chemie; Organisch-Chemisches Institut and Center for Multiscale Theory and Simulation; Westfälische Wilhelms-Universität Münster; Münster Germany
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21
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Goerigk L, Hansen A, Bauer C, Ehrlich S, Najibi A, Grimme S. A look at the density functional theory zoo with the advanced GMTKN55 database for general main group thermochemistry, kinetics and noncovalent interactions. Phys Chem Chem Phys 2017; 19:32184-32215. [DOI: 10.1039/c7cp04913g] [Citation(s) in RCA: 854] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present the updated and extended GMTKN55 benchmark database for more accurate and extensive energetic evaluation of density functionals and other electronic structure methods with detailed guidelines for method users.
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Affiliation(s)
- Lars Goerigk
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Andreas Hansen
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Christoph Bauer
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Stephan Ehrlich
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
| | - Asim Najibi
- School of Chemistry
- The University of Melbourne
- Parkville
- Australia
| | - Stefan Grimme
- Universität Bonn
- Mulliken Center for Theoretical Chemistry
- Bonn
- Germany
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22
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Abstract
The great diversity and richness of transition metal chemistry, such as the features of an open d-shell, opened a way to numerous areas of scientific research and technological applications. Depending on the nature of the metal and its environment, there are often several energetically accessible spin states, and the progress in accurate theoretical treatment of this complicated phenomenon is presented in this Account. The spin state energetics of a transition metal complex can be predicted theoretically on the basis of density functional theory (DFT) or wave function based methodology, where DFT has advantages since it can be applied routinely to medium-to-large-sized molecules and spin-state consistent density functionals are now available. Additional factors such as the effect of the basis set, thermochemical contributions, solvation, relativity, and dispersion, have been investigated by many researchers, but challenges in unambiguous assignment of spin states still remain. The first DFT studies showed intrinsic spin-state preferences of hybrid functionals for high spin and early generalized gradient approximation functionals for low spin. Progress in the development of density functional approximations (DFAs) then led to a class of specially designed DFAs, such as OPBE, SSB-D, and S12g, and brought a very intriguing and fascinating observation that the spin states of transition metals and the SN2 barriers of organic molecules are somehow intimately linked. Among the many noteworthy results that emerged from the search for the appropriate description of the complicated spin state preferences in transition metals, we mainly focused on the examination of the connection between the spin state and the structures or coordination modes of the transition metal complexes. Changes in spin states normally lead only to changes in the metal-ligand bond lengths, but to the best of our knowledge, the dapsox ligand showed the first example of a transition-metal complex where a change in spin state leads also to changes in the coordination, switching between pentagonal-bipyramidal and capped-octahedron. Moreover, we have summarized the results of the thorough study that corrected the experimental assignment of the nature of the recently synthesized Sc3+ adduct of [FeIV(O)(TMC)]2+ (TMC = 1,4,8,11-tetramethylcyclam) and firmly established that the Sc3+-capped iron-oxygen complex corresponds to high-spin FeIII. Last, but not least, we have provided deeper insight and rationalization of the observation that unlike in metalloenzymes, where the FeIV-oxo is usually observed with high spin, biomimetic FeIV-oxo complexes typically have a intermediate spin state. Energy decomposition analyses on the trigonal-bypiramidal (TBP) and octahedral model systems with ammonia ligands have revealed that the interaction energy of the prepared metal ion in the intermediate spin state is much smaller for the TBP structure. This sheds light on the origin of the intermediate spin state of the biomimetic TBP FeIV-oxo complexes.
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Affiliation(s)
- Marcel Swart
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut de Química Computacional i Catàlisi (IQCC) & Dept. Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain
| | - Maja Gruden
- Center
for Computational Chemistry and Bioinformatics, Faculty of Chemistry, University of Belgrade, Belgrade 11000, Serbia
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23
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Hill EA, Weitz AC, Onderko E, Romero-Rivera A, Guo Y, Swart M, Bominaar EL, Green MT, Hendrich MP, Lacy DC, Borovik AS. Reactivity of an Fe IV-Oxo Complex with Protons and Oxidants. J Am Chem Soc 2016; 138:13143-13146. [PMID: 27647293 PMCID: PMC5110122 DOI: 10.1021/jacs.6b07633] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-valent Fe-OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme FeIV-OH complexes, we demonstrate the reversible protonation of a synthetic FeIV-oxo species containing a tris-urea tripodal ligand. The same protonated FeIV-oxo species can be prepared via oxidation, suggesting that a putative FeV-oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the FeIV-oxo complex most likely occurs on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular H-bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar protonated high-valent Fe-oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high-valent Fe-OH species to mechanisms.
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Affiliation(s)
- Ethan A. Hill
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
| | - Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Elizabeth Onderko
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi & Dept. Química, Universitat de Girona, 17003, Spain
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi & Dept. Química, Universitat de Girona, 17003, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Michael T. Green
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | | | - David C. Lacy
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
| | - A. S. Borovik
- Department of Chemistry, University of California-Irvine, 1102 Natural Sciences II, Irvine, CA 92697
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24
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Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. PLoS One 2016; 11:e0162031. [PMID: 27656882 PMCID: PMC5033481 DOI: 10.1371/journal.pone.0162031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 08/16/2016] [Indexed: 11/19/2022] Open
Abstract
Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys2[2Fe-2S]His2 and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.
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25
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Application of discrete solvent reaction field to second-order susceptibility of organic molecular crystal. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1938-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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27
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Grimmel S, Schoendorff G, Wilson AK. Gauging the Performance of Density Functionals for Lanthanide-Containing Molecules. J Chem Theory Comput 2016; 12:1259-66. [DOI: 10.1021/acs.jctc.5b01193] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephanie Grimmel
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry and Biochemistry, Karlsruher Institut für Technologie, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - George Schoendorff
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Angela K. Wilson
- Department
of Chemistry and Center for Advanced Scientific Computing and Modeling
(CASCaM), University of North Texas, Denton, Texas 76203-5017, United States
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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28
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Dunbar RC, Martens J, Berden G, Oomens J. Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate. Phys Chem Chem Phys 2016; 18:26923-26932. [DOI: 10.1039/c6cp03974j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Giel Berden
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
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29
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Swart M, Solà M, Bickelhaupt FM. Density Functional Calculations of E2 and SN2 Reactions: Effects of the Choice of Method, Algorithm, and Numerical Accuracy. J Chem Theory Comput 2015; 6:3145-52. [PMID: 26616777 DOI: 10.1021/ct100454c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein we provide a detailed account on how the potential energy surfaces of the E2 and SN2 reactions of X(-) + CH3CH2X (X = F, Cl) depend on various methodological and technical choices in density functional calculations. We cover a choice of density functionals (OLYP, various M06-types, and the new SSB-D), basis sets (up to quintuple- and quadruple-ζ for Gaussian- and Slater-type orbitals, respectively, plus polarization and diffuse functions), and other aspects of the computations (among others: nonrelativistic versus zeroth-order regular approximation relativistic; numerical integration accuracy; all-electron versus frozen core; self-consistent field (SCF) versus post-SCF). The program codes ADF and NWChem are used for calculations with Slater- and Gaussian-type basis sets, respectively. The fluoride systems (X = F) appear to not only depend extremely sensitively on the basis set size (especially the presence of diffuse functions) but also on other technical settings, especially in the case of hybrid meta-generalized gradient approximation functionals. This work complements a recent contribution (Y. Zhao, D. G. Truhlar, J. Chem. Theory Comput. 2010, 6, 1104) and provides recommendations for density functionals, basis sets, and technical settings.
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Affiliation(s)
- Marcel Swart
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, E-17071 Girona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, E-08010 Barcelona, Spain, and Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Miquel Solà
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, E-17071 Girona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, E-08010 Barcelona, Spain, and Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, E-17071 Girona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, E-08010 Barcelona, Spain, and Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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Vlahović F, Perić M, Gruden-Pavlović M, Zlatar M. Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes. J Chem Phys 2015; 142:214111. [DOI: 10.1063/1.4922111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filip Vlahović
- Innovation center of the Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Republic of Serbia
| | - Marko Perić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Republic of Serbia
| | - Maja Gruden-Pavlović
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Republic of Serbia
| | - Matija Zlatar
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Republic of Serbia
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32
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Pan S, Mandal S, Chattaraj PK. Cucurbit[6]uril: A Possible Host for Noble Gas Atoms. J Phys Chem B 2015; 119:10962-74. [DOI: 10.1021/acs.jpcb.5b01396] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sudip Pan
- Department of Chemistry and
Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, 721302, India
| | - Subhajit Mandal
- Department of Chemistry and
Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, 721302, India
| | - Pratim K. Chattaraj
- Department of Chemistry and
Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, 721302, India
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33
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Daub CD, Åstrand PO, Bresme F. Lithium Ion–Water Clusters in Strong Electric Fields: A Quantum Chemical Study. J Phys Chem A 2015; 119:4983-92. [DOI: 10.1021/acs.jpca.5b01822] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher D. Daub
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
| | - Per-Olof Åstrand
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
| | - Fernando Bresme
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
- Department
of Chemistry, Imperial College London SW7 2AZ, London, United Kingdom
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34
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San LK, Bukovsky EV, Larson BW, Whitaker JB, Deng SHM, Kopidakis N, Rumbles G, Popov AA, Chen YS, Wang XB, Boltalina OV, Strauss SH. A faux hawk fullerene with PCBM-like properties. Chem Sci 2015; 6:1801-1815. [PMID: 29142669 PMCID: PMC5653957 DOI: 10.1039/c4sc02970d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/13/2014] [Indexed: 01/27/2023] Open
Abstract
Reaction of C60, C6F5CF2I, and SnH(n-Bu)3 produced, among other unidentified fullerene derivatives, the two new compounds 1,9-C60(CF2C6F5)H (1) and 1,9-C60(cyclo-CF2(2-C6F4)) (2). The highest isolated yield of 1 was 35% based on C60. Depending on the reaction conditions, the relative amounts of 1 and 2 generated in situ were as high as 85% and 71%, respectively, based on HPLC peak integration and summing over all fullerene species present other than unreacted C60. Compound 1 is thermally stable in 1,2-dichlorobenzene (oDCB) at 160 °C but was rapidly converted to 2 upon addition of Sn2(n-Bu)6 at this temperature. In contrast, complete conversion of 1 to 2 occurred within minutes, or hours, at 25 °C in 90/10 (v/v) PhCN/C6D6 by addition of stoichiometric, or sub-stoichiometric, amounts of proton sponge (PS) or cobaltocene (CoCp2). DFT calculations indicate that when 1 is deprotonated, the anion C60(CF2C6F5)- can undergo facile intramolecular SNAr annulation to form 2 with concomitant loss of F-. To our knowledge this is the first observation of a fullerene-cage carbanion acting as an SNAr nucleophile towards an aromatic C-F bond. The gas-phase electron affinity (EA) of 2 was determined to be 2.805(10) eV by low-temperature PES, higher by 0.12(1) eV than the EA of C60 and higher by 0.18(1) eV than the EA of phenyl-C61-butyric acid methyl ester (PCBM). In contrast, the relative E1/2(0/-) values of 2 and C60, -0.01(1) and 0.00(1) V, respectively, are virtually the same (on this scale, and under the same conditions, the E1/2(0/-) of PCBM is -0.09 V). Time-resolved microwave conductivity charge-carrier yield × mobility values for organic photovoltaic active-layer-type blends of 2 and poly-3-hexylthiophene (P3HT) were comparable to those for equimolar blends of PCBM and P3HT. The structure of solvent-free crystals of 2 was determined by single-crystal X-ray diffraction. The number of nearest-neighbor fullerene-fullerene interactions with centroid···centroid (⊙···⊙) distances of ≤10.34 Å is significantly greater, and the average ⊙···⊙ distance is shorter, for 2 (10 nearest neighbors; ave. ⊙···⊙ distance = 10.09 Å) than for solvent-free crystals of PCBM (7 nearest neighbors; ave. ⊙···⊙ distance = 10.17 Å). Finally, the thermal stability of 2 was found to be far greater than that of PCBM.
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Affiliation(s)
- Long K San
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
| | - Eric V Bukovsky
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
| | - Bryon W Larson
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
- National Renewable Energy Laboratory , Golden , CO 80401 , USA . ;
| | - James B Whitaker
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
| | - S H M Deng
- Physical Sciences Division , Pacific Northwest National Laboratory , MS K8-88, P.O. Box 999 , Richland , WA 99352 , USA .
| | - Nikos Kopidakis
- National Renewable Energy Laboratory , Golden , CO 80401 , USA . ;
| | - Garry Rumbles
- National Renewable Energy Laboratory , Golden , CO 80401 , USA . ;
| | - Alexey A Popov
- Leibniz Institute for Solid State and Materials Research , 01069 Dresden , Germany .
| | - Yu-Sheng Chen
- ChemMatCARS Beamline , University of Chicago Advanced Photon Source , Argonne , IL 60439 , USA .
| | - Xue-Bin Wang
- Physical Sciences Division , Pacific Northwest National Laboratory , MS K8-88, P.O. Box 999 , Richland , WA 99352 , USA .
| | - Olga V Boltalina
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
| | - Steven H Strauss
- Department of Chemistry , Colorado State University , Fort Collins , CO 80523 , USA . ;
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Ottonello G, Richet P, Vetuschi Zuccolini M. The wet solidus of silica: Predictions from the scaled particle theory and polarized continuum model. J Chem Phys 2015; 142:054503. [DOI: 10.1063/1.4906745] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- G. Ottonello
- DIPTERIS, Università di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - P. Richet
- Institut de Physique du Globe, Rue Jussieu 2, 75005 Paris, France
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Pascual-Borràs M, López X, Poblet JM. Accurate calculation of31P NMR chemical shifts in polyoxometalates. Phys Chem Chem Phys 2015; 17:8723-31. [DOI: 10.1039/c4cp05016a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We search for an optimal DFT/basis set combination for computationally reproducing31P NMR chemical shifts in polyoxometalates.
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Affiliation(s)
- Magda Pascual-Borràs
- Departament de Química Física i Inorgànica
- Universitat Rovira i Virgili
- 43007 Tarragona
- Spain
| | - Xavier López
- Departament de Química Física i Inorgànica
- Universitat Rovira i Virgili
- 43007 Tarragona
- Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica
- Universitat Rovira i Virgili
- 43007 Tarragona
- Spain
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37
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Hatz R, Hänninen V, Halonen L. Pair-potential approach to accurate dispersion energies between group 12 (Zn, Cd, Hg) clusters. J Phys Chem A 2014; 118:12274-9. [PMID: 25427295 DOI: 10.1021/jp510622u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dispersion interactions between group 12 (Zn, Cd, Hg) metal clusters are studied at the CCSD(T) level with triple-ζ basis sets. We use atomic orientation dependent C6 dispersion coefficients derived from simple model systems to calculate the intermolecular dispersion energy between larger metal clusters. By using an atomic pair-potential model, we are able to obtain highly accurate results comparable to the CCSD(T) level of theory. For all the systems studied, our method results in a robust description of the dispersion energy at long distances, and it is able to outperform the examined dispersion corrected DFT calculations.
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Affiliation(s)
- Richard Hatz
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki , P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland
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38
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Kolakkandy S, Pratihar S, Aquino AJA, Wang H, Hase WL. Properties of Complexes Formed by Na+, Mg2+, and Fe2+ Binding with Benzene Molecules. J Phys Chem A 2014; 118:9500-11. [DOI: 10.1021/jp5029257] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sujitha Kolakkandy
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Adelia J. A. Aquino
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Hai Wang
- Department
of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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39
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Mahmoodinia M, Ebadi M, Åstrand PO, Chen D, Cheng HY, Zhu YA. Structural and electronic properties of the Pt(n)-PAH complex (n = 1, 2) from density functional calculations. Phys Chem Chem Phys 2014; 16:18586-95. [PMID: 25076458 DOI: 10.1039/c4cp02488e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A detailed density functional study of the Pt atom and the Pt dimer adsorption on a polyaromatic hydrocarbon (PAH) is presented. The preferred adsorption site for a Pt atom is confirmed to be the bridge site. Upon adsorption of a single Pt atom, however, it is found here that the electronic ground state changes from the triplet state (5d(9)6s(1) configuration) to the closed-shell singlet state (5d(10)6s(0) configuration), which consequently will affect the catalytic activity of Pt when single Pt atoms bind to a carbon surface. The preferred adsorption site for the Pt dimer in the upright configuration is the hollow site. In contrast to the adsorption of a single Pt atom, the formation of a Pt-C bond in the adsorption of a Pt dimer is not accompanied by a change in the spin state, so the most stable electronic state is still the triplet state. While the atomic charge on the Pt atoms and dimers (in parallel configuration) in the Ptn-PAH complex is positive, a negative charge is found on the upper Pt atom for the upright configuration, indicating that single layers of Pt atoms will have a different catalytic activity as compared to Pt clusters on a carbon surface. Comparing the Pt-C bond length and the charge transfer on different sites, the magnitude of the charge transfer decreases with bond elongation, indicating that the catalytic activity of the Pt atom and dimer can be changed by modifying its chemical surroundings. The adsorption energy for the Pt dimer on a PAH surface is larger than that for two individual Pt atoms on the surface indicating that aggregation of Pt atoms on the PAH surface is favorable.
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Affiliation(s)
- Mehdi Mahmoodinia
- Department of Chemistry, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
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40
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Pascual-Borràs M, López X, Rodríguez-Fortea A, Errington RJ, Poblet JM. 17O NMR chemical shifts in oxometalates: from the simplest monometallic species to mixed-metal polyoxometalates. Chem Sci 2014. [DOI: 10.1039/c4sc00083h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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Gruden-Pavlović M, Stepanović S, Perić M, Güell M, Swart M. A density functional study of the spin state energetics of polypyrazolylborato complexes of first-row transition metals. Phys Chem Chem Phys 2014; 16:14514-22. [DOI: 10.1039/c3cp55488k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Stepanović S, Andjelković L, Zlatar M, Andjelković K, Gruden-Pavlović M, Swart M. Role of Spin State and Ligand Charge in Coordination Patterns in Complexes of 2,6-Diacetylpyridinebis(semioxamazide) with 3d-Block Metal Ions: A Density Functional Theory Study. Inorg Chem 2013; 52:13415-23. [DOI: 10.1021/ic401752n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | | | | | - Marcel Swart
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Facultat de Ciències, 17071 Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís
Companys 23, 08010 Barcelona, Spain
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43
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Gavette JV, Mills NS, Zakharov LN, Johnson CA, Johnson DW, Haley MM. An Anion-Modulated Three-Way Supramolecular Switch that Selectively Binds Dihydrogen Phosphate, H2PO4−. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302929] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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44
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Gavette JV, Mills NS, Zakharov LN, Johnson CA, Johnson DW, Haley MM. An anion-modulated three-way supramolecular switch that selectively binds dihydrogen phosphate, H2PO4-. Angew Chem Int Ed Engl 2013; 52:10270-4. [PMID: 23934912 DOI: 10.1002/anie.201302929] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/29/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Jesse V Gavette
- Department of Chemistry and Biochemistry & Materials Science Institute, University of Oregon, Eugene, OR 97403-1253 (USA)
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45
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Čobeljić B, Pevec A, Turel I, Swart M, Mitić D, Milenković M, Marković I, Jovanović M, Sladić D, Jeremić M, Anđelković K. Synthesis, characterization, DFT calculations and biological activity of derivatives of 3-acetylpyridine and the zinc(II) complex with the condensation product of 3-acetylpyridine and semicarbazide. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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47
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Swart M, Bickelhaupt FM. Benchmark study on the smallest bimolecular nucleophilic substitution reaction: H⁻+CH₄-->CH₄+H⁻. Molecules 2013; 18:7726-38. [PMID: 23823873 PMCID: PMC6270058 DOI: 10.3390/molecules18077726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/03/2013] [Accepted: 06/28/2013] [Indexed: 11/16/2022] Open
Abstract
We report here a benchmark study on the bimolecular nucleophilic substitution (S(N)2) reaction between hydride and methane, for which we have obtained reference energies at the coupled cluster toward full configuration-interaction limit (CC-cf/CBS). Several wavefunction (HF, MP2, coupled cluster) and density functional methods are compared for their reliability regarding these reference data.
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Affiliation(s)
- Marcel Swart
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry & Amsterdam Center for Multiscale Modeling, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands; E-Mail:
- Institute of Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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48
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Adsorption of a single Pt atom on polyaromatic hydrocarbons from first-principle calculations. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.04.077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Groß L, Steenbock T, Herrmann C. The angular dependence of spin-state energy splittings in the core. Mol Phys 2013. [DOI: 10.1080/00268976.2013.799297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Lynn Groß
- a Institute of Inorganic and Applied Chemistry , University of Hamburg , Martin-Luther-King-Platz 6, Hamburg , 20146 , Germany
| | - Torben Steenbock
- a Institute of Inorganic and Applied Chemistry , University of Hamburg , Martin-Luther-King-Platz 6, Hamburg , 20146 , Germany
| | - Carmen Herrmann
- a Institute of Inorganic and Applied Chemistry , University of Hamburg , Martin-Luther-King-Platz 6, Hamburg , 20146 , Germany
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50
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Armangué L, Solà M, Swart M. Nuclear magnetic resonance shieldings of water clusters: is it possible to reach the complete basis set limit by extrapolation? Mol Phys 2013. [DOI: 10.1080/00268976.2013.793832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Lluís Armangué
- a Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi , Girona , Spain
| | - Miquel Solà
- a Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi , Girona , Spain
| | - Marcel Swart
- a Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi , Girona , Spain
- b Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys , Barcelona , Spain
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