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Đorđević Zlatković MR, Radulović NS, Dangalov M, Vassilev NG. Conformation Analysis and Stereodynamics of Symmetrically ortho-Disubstituted Carvacrol Derivatives. Molecules 2024; 29:1962. [PMID: 38731453 PMCID: PMC11085911 DOI: 10.3390/molecules29091962] [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: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
The design and synthesis of analogs of natural products can be a valuable source of medicinal preparations for the pharmaceutical industry. In the present study, the structural elucidation of eleven derivatives of 2,4-dihalogeno substituted synthetic analogues of the natural compound carvacrol was carried out by means of NMR experiments, and of another thirteen by DFT calculations. By selective NOE experiments and the irradiation of CH signals of the isopropyl group, individual conformers were assigned as syn and anti. By comparing GIAO/B3LYP/6-311++G(d,p)-calculated and experimentally measured vicinal 3JCH spin-spin constants, this assignment was confirmed. An unusual relationship is reported for proton-carbon vicinal couplings: 3JCH (180°) < 3JCH (0°). The conformational mobility of carvacrols was studied by 2D EXSY spectra. The application of homonuclear decoupling technique (HOBS) to these spectra simplifies the spectra, improves resolution without reducing the sensitivity, and allows a systematic examination of the rotational barrier of all compounds via their CH signals of the isopropyl group in a wider temperature interval. The rate constants of the isopropyl rotation between syn and anti conformers were determined and the corresponding energy barriers (14-17 kcal/mol) were calculated. DFT calculations of the energy barriers in carvacrol derivatives allowed the determination of the steric origin of the restricted isopropyl rotation. The barrier height depends on the size of the 2- and 4-position substituents, and is independent of the derivatization of the OH group.
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Affiliation(s)
| | - Niko S. Radulović
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia;
| | - Miroslav Dangalov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bontchev Str. Bl. 9, 1113 Sofia, Bulgaria;
| | - Nikolay G. Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bontchev Str. Bl. 9, 1113 Sofia, Bulgaria;
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2
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Belmonte-Sánchez E, García-López J, Navarro Y, Iglesias MJ, Fernández I, López-Ortiz F. Crystal, Solution, and Computational Study of the Structure of Ortho-Lithium N,N-Diisopropyl-P,P-Diphenylphosphinothioic Amide. Chemistry 2024; 30:e202303785. [PMID: 38134366 DOI: 10.1002/chem.202303785] [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: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/24/2023]
Abstract
The first crystal structure of an ortho-lithium phosphinothioic amide complexed with tetramethylethylenediamine 12 is reported. The complex consists of a spirane in which the spiro-lithium is N,N- and C,S-chelated by the diamine and organophosphorus ligands, respectively. The analogous ortho anion 14 obtained by Sn(IV)/Li transmetallation in THF has also been synthesized. Nuclear magnetic resonance study of both anions showed that they exist as monomers in solution and are involved in dynamic processes including the restricted rotation around the P-N bond. 14 is converted at room temperature by nucleophilic cyclization to the dearomatized anion 15, which evolves after a few hours to the benzophosphindole sulfide 16. Density functional theory calculations supported the aggregation state in solution and were used to explore the conformational space of anion 12, the mechanism of ortho-lithiation directed by P(X)-N (X=O, S) groups, and the mechanism of formation of 15.
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Affiliation(s)
- Eva Belmonte-Sánchez
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
| | - Jesús García-López
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
| | - Yolanda Navarro
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
| | - María José Iglesias
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
| | - Ignacio Fernández
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
| | - Fernando López-Ortiz
- Área de Química Orgánica, Centro de Investigación CIAIMBITAL, Universidad de Almería, 04120, Almería, Spain
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3
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Santos Neto AP, Rivelino R, Pagola GI, Provasi PF. High‐Level Electron Correlation of the Indirect Nuclear Spin‐Spin Coupling Constants in Some Small Diboranes and Lithium‐Doped Diboranes. ChemistrySelect 2021. [DOI: 10.1002/slct.202100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Roberto Rivelino
- Instituto de Física Universidade Federal da Bahia 40210-340 Salvador Bahia Brazil
| | - Gabriel I. Pagola
- Departamento de Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires IFIBA-CONICET Ciudad Universitaria, Pab. I 1428 Buenos Aires Argentina
| | - Patricio F. Provasi
- Department of Physics University of Northeastern IMIT-CONICET. Av. Libertad 5500, W 3404 AAS Corrientes Argentina
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Abstract
A simple, fast and cost-effective three-step synthesis of 1-methyl-8-phenyl-1,3-diazaspiro[4.5]decane-2,4-dione has been developed. The reactions described herein proceed readily, with high yields and no further purification. Therefore, the proposed method, with an overall yield of 60%, offers a facile pathway to the synthesis of N-1 monosubstituted spiro carbocyclic imidazolidine-2,4-diones (hydantoins), which constitute a privileged class of heterocyclic scaffolds with pharmacological interest.
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Paschoal DFS, Dos Santos HF. Predicting the structure and NMR coupling constant 1J( 129Xe- 19F) of XeF 6 using quantum mechanics methods. Phys Chem Chem Phys 2021; 23:7240-7246. [PMID: 33876084 DOI: 10.1039/d0cp06555b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The XeF6 molecule exists as a monomer in the gas phase and as the (XeF6)4 tetramer in solution. Herein we used distinct quantum mechanics methods to study the conformational equilibrium for the XeF6 monomer, which is represented mainly by Oh and C3v symmetric geometries, and for the (XeF6)4 structure found in condensate phases. The NMR 1J(129Xe-19F) coupling constant is predicted using our own NMR-DKH basis set, designed for NMR properties. The C3v conformer of XeF6 was stable only with HF, CCSD, and hybrid DFT functionals with at least 28% exact HF exchange. Increasing the % of HF exchange improves the description of the geometry and the Oh→C3v equilibrium. The BMK, BHandHLYP and LC-ωPBE functionals produce results in excellent agreement with experiments and high-level calculations for the XeF6 molecule. When it comes to the 1J(129Xe-19F) coupling constant, the (XeF6)4 structure must be considered. For that compound, BHandHLYP leads to the best structure, and BMK leads to the best coupling constant; therefore, the generalized protocol BMK/NMR-DKH//BHandHLYP/def2-SVP is recommended to study the XeF6 molecule in the gas phase and solution.
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Affiliation(s)
- Diego F S Paschoal
- NQTCM: Núcleo de Química Teórica e Computacional de Macaé, Polo Ajuda, Universidade Federal do Rio de Janeiro, Campus UFRJ-Macaé, 27.971-525, Macaé, RJ, Brazil.
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Ghiasi R, Zandiyeh Z. Theoretical study of the influence of solvent polarity on the 31P and 13C NMR parameters of the Ru(PH3)4(η2-benzyne) complex. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2020.108412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
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Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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Tong KKH, Hanif M, Lovett JH, Hummitzsch K, Harris HH, Söhnel T, Jamieson SMF, Hartinger CG. Thiourea-Derived Chelating Ligands and Their Organometallic Compounds: Investigations into Their Anticancer Activity. Molecules 2020; 25:molecules25163661. [PMID: 32796732 PMCID: PMC7464268 DOI: 10.3390/molecules25163661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 11/16/2022] Open
Abstract
Thiones have been investigated as ligands in metal complexes with catalytic and biological activity. We report the synthesis, characterization, and biological evaluation of a series of MII/III complexes of the general formulae [MII(cym)(L)Cl]X (cym = η6-p-cymene) or [MIII(Cp*)(L)Cl]X (Cp* = η5-pentamethylcyclopentadienyl), where X = Cl- or PF6-, and L represents heterocyclic derivatives of thiourea. The thiones feature a benzyl-triazolyl pendant and they act as bidentate ligands via N,S-coordination to the metal centers. Several derivatives have been investigated by single-crystal X-ray diffraction analysis. NMR investigations showed a counterion-dependent shift of several protons due to the interaction with the counterions. These NMR investigations were complemented with X-ray diffraction analysis data and the effects of different counterions on the secondary coordination sphere were also investigated by DFT calculations. In biological studies, the Ir benzimidazole derivative was found to accumulate in the cytoplasm and it was the most cytotoxic derivative investigated.
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Affiliation(s)
- Kelvin K. H. Tong
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (K.K.H.T.); (M.H.); (T.S.)
| | - Muhammad Hanif
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (K.K.H.T.); (M.H.); (T.S.)
| | - James H. Lovett
- Department of Chemistry, The University of Adelaide, Adelaide, SA 5005, Australia; (J.H.L.); (H.H.H.)
| | - Katja Hummitzsch
- Discipline of Obstetrics and Gynecology, The University of Adelaide, Robinson Research Institute, Adelaide, SA 5005, Australia;
| | - Hugh H. Harris
- Department of Chemistry, The University of Adelaide, Adelaide, SA 5005, Australia; (J.H.L.); (H.H.H.)
| | - Tilo Söhnel
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (K.K.H.T.); (M.H.); (T.S.)
| | - Stephen M. F. Jamieson
- Auckland Cancer Society Research Centre, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Christian G. Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; (K.K.H.T.); (M.H.); (T.S.)
- Correspondence: ; Tel.: +64-9-373-7599-83220
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9
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Hansen PE, Saeed BA, Rutu RS, Kupka T. One-bond 1 J( 15 N,H) coupling constants at sp 2 -hybridized nitrogen of Schiff bases, enaminones and similar compounds: A theoretical study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:750-762. [PMID: 32415997 DOI: 10.1002/mrc.5052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
1 J(15 N,H) coupling constants for enaminones and NH-forms of intramolecularly hydrogen-bonded Schiff bases as model compounds for sp2 -hybridized nitrogen atoms are evaluated using density functional theory (DFT) to find the optimal functionals and basis sets. Ammonia is used as a test molecule and its one-bond coupling constant is compared with experiment. A methylamine Schiff base of a truncated molecule of gossypol is used for checking the performance of selected B3LYP, O3LYP, PBE, BHandH, and APFD density functionals and standard, modified, and dedicated basis sets for coupling constants. Both in vacuum and in chloroform, modeled by the simple continuum model of solvent, the modified basis sets predict significantly better the 1 J(15 N,H) value in ammonia and in the methylamine Schiff base of a truncated molecule of gossypol than the standard basis sets. This procure is then used on a broad set of intramolecularly hydrogen-bonded molecules, and a good correlation between calculated and experimental one-bond NH coupling constants is obtained. The 1 J(15 N,H) couplings are slightly overestimated. The calculated data show for hydrogen-bonded NH interatomic distances that the calculated values depend on the NH bond lengths. The shorter the bond lengths, the larger the 1 J(15 N,H). A useful correlation between 1 J(15 N,H) and NH bond length is derived that enables realistic predictions of one-bond NH coupling constants. The calculations reproduce experimentally observed trends for the studied molecules.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Bahjat A Saeed
- Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Iraq
| | - Rita S Rutu
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Basrah, Iraq
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Opole, Poland
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10
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Chaudhuri P, Ducati LC, Ghosh A. Spin–spin coupling constants in linear substituted HCN clusters. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1537528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Puspitapallab Chaudhuri
- Department of Physics, Federal University of Amazonas, Manaus, Brazil
- Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Lucas C. Ducati
- Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Angsula Ghosh
- Department of Physics, Federal University of Amazonas, Manaus, Brazil
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11
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Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
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Affiliation(s)
- Leonid B Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia.
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12
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Aggelund PA, Sauer SPA, Jensen F. Development of polarization consistent basis sets for spin-spin coupling constant calculations for the atoms Li, Be, Na, and Mg. J Chem Phys 2018; 149:044117. [PMID: 30068157 DOI: 10.1063/1.5034109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The pcJ-n basis set, optimized for spin-spin coupling constant calculations using density functional theory methods, are expanded to also include the s-block elements Li, Be, Na, and Mg, by studying several small molecules containing these elements. This is done by decontracting the underlying pc-n basis sets, followed by augmentation with additional tight functions. As was the case for the p-block elements, the convergence of the results can be significantly improved by augmentation with tight s-functions. For the p-block elements, additional tight functions of higher angular momentum were also needed, but this is not the case for the s-block elements. A search for the optimum contraction scheme is carried out using the criterion that the contraction error should be lower than the inherent error of the uncontracted pcJ-n relative to the uncontracted pcJ-4 basis set. A large search over possible contraction schemes is done for the Li2 and Na2 molecules, and based on this search contracted pcJ-n basis sets for the four atoms are recommended. This work shows that it is more difficult to contract the pcJ-n basis sets, than the underlying pc-n basis sets. However, it also shows that the pcJ-n basis sets for Li and Be can be more strongly contracted than the pcJ-n basis sets for the p-block elements. For Na and Mg, the contractions are to the same degree as for the p-block elements.
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Affiliation(s)
- Patrick A Aggelund
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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de Souza Fernandes F, Cormanich RA, Zeoly LA, Formiga ALB, Coelho F. Employing Small Polyfunctionalized Molecules for a Diastereoselective Synthesis of Highly Substituted Indolines. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fábio de Souza Fernandes
- Institute of Chemistry; Department of Organic Chemistry; University of Campinas; Campinas Brazil
| | - Rodrigo A. Cormanich
- Institute of Chemistry; Department of Organic Chemistry; University of Campinas; Campinas Brazil
| | - Lucas A. Zeoly
- Institute of Chemistry; Department of Organic Chemistry; University of Campinas; Campinas Brazil
| | - André Luiz B. Formiga
- Institute of Chemistry; Department of Inorganic Chemistry; University of Campinas; Rua Josué de Castro, s/n - P.O. Box 6154 13083-970 Campinas SP Brazil
| | - Fernando Coelho
- Institute of Chemistry; Department of Organic Chemistry; University of Campinas; Campinas Brazil
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14
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Faber R, Sauer SPA. On the convergence of the ccJ-pVXZ and pcJ-n basis sets in CCSD calculations of nuclear spin–spin coupling constants: some difficult cases. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2217-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Adamson J, Nazarski RB, Jarvet J, Pehk T, Aav R. Shortfall of B3LYP in Reproducing NMR J
CH
Couplings in Some Isomeric Epoxy Structures with Strong Stereoelectronic Effects: A Benchmark Study on DFT Functionals. Chemphyschem 2018; 19:631-642. [DOI: 10.1002/cphc.201701125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/17/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jasper Adamson
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Ryszard B. Nazarski
- Theoretical and Structural Chemistry Group; Department of Physical Chemistry; Faculty of Chemistry; University of Lodz; Pomorska 163/165 90-236 Łódź Poland
| | - Jüri Jarvet
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
- Current address: Department of Biochemistry and Biophysics; Arrhenius Laboratories; Stockholm University; Svante Arrhenius väg 16 10691 Stockholm Sweden
| | - Tõnis Pehk
- National Institute of Chemical Physics and Biophysics; Akadeemia tee 23 12618 Tallinn Estonia
| | - Riina Aav
- Department of Chemistry and Biotechnology; Tallinn University of Technology; Akadeemia tee 15 12618 Tallinn Estonia
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Powell J, Valenti D, Bobnar H, Drain E, Elliott B, Frank S, McCullough T, Moore S, Kettring A, Iuliucci R, Harper JK. Evaluating the accuracy of theoretical one-bond 13 C─ 13 C scalar couplings and their ability to predict structure in a natural product. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:979-989. [PMID: 28557141 DOI: 10.1002/mrc.4616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
This study explores the feasibility of using a combination of experimental and theoretical 1-bond 13 C─13 C scalar couplings (1 JCC ) to establish structure in organic compounds, including unknowns. Historically, n JCC and n JCH studies have emphasized 2 and 3-bond couplings, yet 1 JCC couplings exhibit significantly larger variations. Moreover, recent improvements in experimental measurement and data processing methods have made 1 JCC data more available. Herein, an approach is evaluated in which a collection of theoretical structures is created from a partial nuclear magnetic resonance structural characterization. Computed 1 JCC values are compared to experimental data to identify candidates giving the best agreement. This process requires knowledge of the error in theoretical methods, thus the B3LYP, B3PW91, and PBE0 functionals are evaluated by comparing to 27 experimental values from INADEQUATE. Respective errors of ±1.2, ±3.8, and ±2.3 Hz are observed. An initial test of this methodology involves the natural product 5-methylmellein. In this case, only a single candidate matches experimental data with high statistical confidence. This analysis establishes the intramolecular hydrogen-bonding arrangement, ring heteroatom identity, and conformation at one position. This approach is then extended to hydroheptelidic acid, a natural product not fully characterized in prior studies. The experimental/theoretical approach proposed herein identifies a single best-fit structure from among 26 candidates and establishes, for the first time, 1 configuration and 3 conformations to complete the characterization. These results suggest that accurate and complete structural characterizations of many moderately sized organic structures (<800 Da) may be possible using only 1 JCC data.
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Affiliation(s)
- Jacob Powell
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Domenic Valenti
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Harley Bobnar
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Erika Drain
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Blaine Elliott
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sydney Frank
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Tyler McCullough
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Sean Moore
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Andrew Kettring
- Burnett School of Biomedical Sciences, University of Central Florida, 4111 Libra Dr., Orlando, FL, 32816, USA
| | - Robbie Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, PA, 15301, USA
| | - James K Harper
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
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17
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Vila JA, Scheraga HA. Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH. J Mol Struct 2017; 1134:576-581. [PMID: 28919647 PMCID: PMC5596661 DOI: 10.1016/j.molstruc.2017.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Assessment of the relative amounts of the forms of the imidazole ring of Histidine (His), namely the protonated (H+) and the tautomeric Nε2-H and Nδ1-H forms, respectively, is a challenging task in NMR spectroscopy. Indeed, their determination by direct observation of the 15N and 13C chemical shifts or the one-bond C-H, 1JCH, Spin-Spin Coupling Constants (SSCC) requires knowledge of the "canonical" limiting values of these forms in which each one is present to the extent of 100%. In particular, at high-pH, an accurate determination of these "canonical" limiting values, at which the tautomeric forms of His coexist, is an elusive problem in NMR spectroscopy. Among different NMR-based approaches to treat this problem, we focus here on the computation, at the DFT level of theory, of the high-pH limiting value for the 1JCH SSCC of the imidazole ring of His. Solvent effects were considered by using the polarizable continuum model approach. The results of this computation suggest, first, that the value of 1JCε1H = 205 ± 1.0 Hz should be adopted as the canonical high-pH limiting value for this SSCC; second, the variation of 1JCε1H SSCC during tautomeric changes is minor, i.e., within ±1Hz; and, finally, the value of 1JCδ2H SSCC upon tautomeric changes is large (15 Hz) indicating that, at high-pH or for non-protonated His at any pH, the tautomeric fractions of the imidazole ring of His can be predicted accurately as a function of the observed value of 1JCδ2H SSCC.
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Affiliation(s)
- Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700-San Luis, Argentina
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18
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Riley LE, Krämer T, McMullin CL, Ellis D, Rosair GM, Sivaev IB, Welch AJ. Large, weakly basic bis(carboranyl)phosphines: an experimental and computational study. Dalton Trans 2017; 46:5218-5228. [PMID: 28378864 DOI: 10.1039/c7dt00485k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bis(carboranyl)phosphines and their {AuCl} and {Se} derivatives have been the subject of experimental and computational studies.
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Affiliation(s)
- Laura E. Riley
- Institute of Chemical Sciences
- Heriot-Watt University
- Edinburgh
- UK EH14 4AS
| | - Tobias Krämer
- Institute of Chemical Sciences
- Heriot-Watt University
- Edinburgh
- UK EH14 4AS
| | | | - David Ellis
- Institute of Chemical Sciences
- Heriot-Watt University
- Edinburgh
- UK EH14 4AS
| | - Georgina M. Rosair
- Institute of Chemical Sciences
- Heriot-Watt University
- Edinburgh
- UK EH14 4AS
| | - Igor B. Sivaev
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Alan J. Welch
- Institute of Chemical Sciences
- Heriot-Watt University
- Edinburgh
- UK EH14 4AS
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19
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Tahara A, Tanaka H, Sunada Y, Shiota Y, Yoshizawa K, Nagashima H. Theoretical Study of the Catalytic Hydrogenation of Alkenes by a Disilaferracyclic Complex: Can the Fe-Si σ-Bond-Assisted Activation of H-H Bonds Allow Development of a Catalysis of Iron? J Org Chem 2016; 81:10900-10911. [PMID: 27704834 DOI: 10.1021/acs.joc.6b01961] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanisms associated with the hydrogenation of alkenes catalyzed by the iron complex Fe(cis-CO)2{o-(SiMe2)2C6H4}2(H)2 (1) were investigated by DFT calculations. The complex 1 has a structure in which the iron center is bonded to four silicon atoms and two hydrides. Secondary Si···H···Si interactions were also observed. The exchange of a 1,2-bis(dimethylsilyl)benzene ligand with ethylene and hydrogen gives a disilaferracycle bearing η2-(CH2═CH2) and η2-H2 ligands. The catalytic cycle initiated from the disilaferracycle involves cleavage of a H-H linkage assisted by an Fe-Si bond to form Fe-H and η1-(H-Si) moieties (step 1), hydrogen migration from the Fe-H group to the η2-(CH2═CH2) ligand which accomplishes the insertion of ethylene into the Fe-H bond (step 2), and reaction of the resulting β-agostic ethyl moiety with the η2-(H-Si) group to form ethane on the iron atom (step 3). The octahedral geometry of 1 as well as the presence of π-acidic CO ligands and Fe-Si σ-bonds contributes to all of the catalytic intermediates and the transition states being in the low-spin state. Steps 1 and 3 correspond to the σ-complex-assisted metathesis (σ-CAM) mechanisms proposed by Perutz and Sabo-Etienne, suggesting that these mechanisms can assist in the design of iron-based hydrogenation catalysts operating under mild conditions.
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Affiliation(s)
| | | | | | | | | | - Hideo Nagashima
- CREST, Japan Science and Technology Agency , Tokyo 102-0076, Japan
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20
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Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations. J Mol Model 2016; 22:273. [PMID: 27783230 DOI: 10.1007/s00894-016-3139-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
Abstract
Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of 3J(HαHβ), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.
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21
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Alipour M, Fallahzadeh P. First principles optimally tuned range-separated density functional theory for prediction of phosphorus–hydrogen spin–spin coupling constants. Phys Chem Chem Phys 2016; 18:18431-40. [DOI: 10.1039/c6cp02648f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The novel optimally tuned range-separated approximations for predicting NMR spin–spin coupling constants are proposed and benchmarked numerically.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
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22
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Taurian OE, Contreras RH, De Kowalewski DG, Pérez JE, Tormena CF. Lone-Pair Orientation Effect of an α-Oxygen Atom on (1)JCC NMR Spin-Spin Coupling Constants in o-Substituted Phenols. Experimental and DFT Study. J Chem Theory Comput 2015; 3:1284-94. [PMID: 26633202 DOI: 10.1021/ct7000396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The well-known N lone-pair orientation effect on (1)JCC spin-spin coupling constants (SSCCs) in oximes and their derivatives was used to study how negative hyperconjugative interactions of type LP1(O) → σ*CC depend on ortho interactions involving the OH group. This study demanded the following analyses: (i) a qualitative estimation of how (1)JCC SSCCs are affected by hyperconjugative interactions, (ii) a study of similar stereochemical effects to those in oximes, but in (1)JC1C2 and (1)JC1C6in a series of 2-substituted phenols, and (iii) a quantitative estimation, with the natural bond order approach, of some key electron delocalization interactions. A few unexpected results are quoted. LP1(O) → σ*CC interactions are affected by proximity interactions as follows: (a) they are enhanced by hydrogen bonds transferring charge into the (O-H)* antibonding orbital; (b) they are enhanced by proximity interactions of type LP1(O)···H-C; (c) they are inhibited by interactions of type LP(O1)···H-O. Consequences of these observations are discussed.
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Affiliation(s)
- Oscar E Taurian
- Department of Physics, FCEFQyN, National University of Río Cuarto, Ruta Nacional No. 36, Km 601, 5800 Río Cuarto, Argentina, Physical Chemistry Section, School of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco and Pedernera, 5700 San Luis, Argentina, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Ciudad Universitaria, Pab. 1, (C1428EHA) Buenos Aires, Argentina, and Chemistry Institute, State University of Campinas, CP 6154, CEP: 13084-971, Campinas, SP, Brazil
| | - Rubén H Contreras
- Department of Physics, FCEFQyN, National University of Río Cuarto, Ruta Nacional No. 36, Km 601, 5800 Río Cuarto, Argentina, Physical Chemistry Section, School of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco and Pedernera, 5700 San Luis, Argentina, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Ciudad Universitaria, Pab. 1, (C1428EHA) Buenos Aires, Argentina, and Chemistry Institute, State University of Campinas, CP 6154, CEP: 13084-971, Campinas, SP, Brazil
| | - Dora G De Kowalewski
- Department of Physics, FCEFQyN, National University of Río Cuarto, Ruta Nacional No. 36, Km 601, 5800 Río Cuarto, Argentina, Physical Chemistry Section, School of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco and Pedernera, 5700 San Luis, Argentina, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Ciudad Universitaria, Pab. 1, (C1428EHA) Buenos Aires, Argentina, and Chemistry Institute, State University of Campinas, CP 6154, CEP: 13084-971, Campinas, SP, Brazil
| | - Jorge E Pérez
- Department of Physics, FCEFQyN, National University of Río Cuarto, Ruta Nacional No. 36, Km 601, 5800 Río Cuarto, Argentina, Physical Chemistry Section, School of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco and Pedernera, 5700 San Luis, Argentina, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Ciudad Universitaria, Pab. 1, (C1428EHA) Buenos Aires, Argentina, and Chemistry Institute, State University of Campinas, CP 6154, CEP: 13084-971, Campinas, SP, Brazil
| | - Cláudio F Tormena
- Department of Physics, FCEFQyN, National University of Río Cuarto, Ruta Nacional No. 36, Km 601, 5800 Río Cuarto, Argentina, Physical Chemistry Section, School of Chemistry, Biochemistry and Pharmacy, National University of San Luis, Chacabuco and Pedernera, 5700 San Luis, Argentina, Department of Physics, FCEyN, University of Buenos Aires and CONICET, Ciudad Universitaria, Pab. 1, (C1428EHA) Buenos Aires, Argentina, and Chemistry Institute, State University of Campinas, CP 6154, CEP: 13084-971, Campinas, SP, Brazil
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23
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Deng W, Cheeseman JR, Frisch MJ. Calculation of Nuclear Spin-Spin Coupling Constants of Molecules with First and Second Row Atoms in Study of Basis Set Dependence. J Chem Theory Comput 2015; 2:1028-37. [PMID: 26633062 DOI: 10.1021/ct600110u] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper proposes a systematic way to modify standard basis sets for use in NMR spin-spin coupling calculations, which allows the high sensitivity of this property to the basis set to be handled in a manner which remains computationally feasible. The new basis set series is derived by uncontracting a standard basis set, such as correlation-consistent aug-cc-pVTZ, and extending it by systematically adding tight s and d functions. For elements in different rows of the periodic table, different progressions of functions are added. The new basis sets are shown to approach the basis set limit for calculations on a range of molecules containing hydrogen and first and second row atoms.
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Affiliation(s)
- Wei Deng
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520.,Gaussian Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492
| | - James R Cheeseman
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520.,Gaussian Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492
| | - Michael J Frisch
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520.,Gaussian Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492
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24
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Suardíaz R, Pérez C, Crespo-Otero R, García de la Vega JM, Fabián JS. Influence of Density Functionals and Basis Sets on One-Bond Carbon-Carbon NMR Spin-Spin Coupling Constants. J Chem Theory Comput 2015; 4:448-56. [PMID: 26620785 DOI: 10.1021/ct7003287] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The basis set and the functional dependence of one-bond carbon-carbon NMR spin-spin coupling constants (SSCC) have been analyzed using density functional theory. Four basis sets (6-311G**, TZVP, EPR-III, and aug-cc-pVTZ-J) and four functionals (PBE, PW91, B3LYP, and B3P86) are tested by comparison with 70 experimental values corresponding to 49 molecules that represent multiple types of hybridization of the carbon atoms. The two hybrid functionals B3P86 and B3LYP combined either EPR-III or aug-cc-pVTZ-J basis sets lead to the best accuracy of calculated SSCC. However, a simple linear regression allows for the obtaining of scaled coupling constants that fit much better with the experimental data and where the differences between the different basis sets and/or functional results are significantly reduced. For large molecules the TZVP basis set can be an appropriate election presenting a good compromise between quality of results and computational cost.
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Affiliation(s)
- R Suardíaz
- Departmento de Química Física, Facultad de Química, Universidad de la Habana, La Habana 10400, Cuba, and Departmento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - C Pérez
- Departmento de Química Física, Facultad de Química, Universidad de la Habana, La Habana 10400, Cuba, and Departmento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - R Crespo-Otero
- Departmento de Química Física, Facultad de Química, Universidad de la Habana, La Habana 10400, Cuba, and Departmento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José M García de la Vega
- Departmento de Química Física, Facultad de Química, Universidad de la Habana, La Habana 10400, Cuba, and Departmento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Jesús San Fabián
- Departmento de Química Física, Facultad de Química, Universidad de la Habana, La Habana 10400, Cuba, and Departmento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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25
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26
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Wrackmeyer B. The B-N Bond in Some Aminoboranes and an Iminoborane, Studied by11B and15N NMR Spectroscopy and DFT Methods. Z Anorg Allg Chem 2015. [DOI: 10.1002/zaac.201500653] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Wrackmeyer B, Schanz HJ. 2,5-Bridged 1-Carba-arachno-pentaborane(10) Derivatives – Intermediates on the Way to Pentaalkyl-1,5-dicarba-closo-pentaboranes(5). ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2015. [DOI: 10.1515/znb-2015-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Stimulated by a report from (R. Köster, G. Benedikt, M. A. Grassberger, Liebigs Ann. Chem. 1968, 719, 187.) on a carbaborane, for which the structure of 2,3,4,5,-tetraethlyl-1-methyl-2,5-μ-(ethyl-1′,1′-diyl)-1-carba-arachno-pentaborane(10) 1 was proposed, an independent synthesis was developed. Diethyl(ethynyl)borane was generated in situ in the presence of a large excess of “Et2B–H” (hydride bath) by ethynyl/H exchange, using ethynyl(trioctyl)tin to react in a mixture with diethyl(vinyl)borane at low temperature. Hydroboration and Et2B–H-catalysed condensation afforded 1, as shown by 11B, 13C NMR spectroscopy and DFT calculations. Thermal degradation of 1 gave 2,3,4-triethyl-1,5-dimethyl-1,5-dicarba-closo-pentaborane(5), whereas the pentaethyl-1,5-dicarba-closo-pentaborane(5) resulted from thermally induced decomposition of other suitably substituted arachno carbaboranes.
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Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Hans-Joerg Schanz
- Department of Chemistry, Georgia Southern University, P.O. Box 8064, Statesboro, GA 30460, USA
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28
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McKemmish LK, Gilbert ATB. Accurate Electron Densities at Nuclei Using Small Ramp-Gaussian Basis Sets. J Chem Theory Comput 2015; 11:3679-83. [PMID: 26574451 DOI: 10.1021/acs.jctc.5b00528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron densities at nuclei are difficult to calculate accurately with all-Gaussian basis sets because they lack an electron-nuclear cusp. The newly developed mixed ramp-Gaussian basis sets, such as R-31G, possess electron-nuclear cusps due to the presence of ramp functions in the basis. The R-31G basis set is a general-purpose mixed ramp-Gaussian basis set modeled on the 6-31G basis set. The prediction of electron densities at nuclei using R-31G basis sets for Li-F outperforms Dunning, Pople, and Jensen general purpose all-Gaussian basis sets of triple-ζ quality or lower and the cc-pVQZ basis set. It is of similar quality to the specialized pcJ-0 basis set which was developed with partial decontraction of core functions and extra high exponent s-Gaussians to predict electron density at the nucleus. These results show significant advantages in the properties of mixed ramp-Gaussian basis sets compared to all-Gaussian basis sets.
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Affiliation(s)
- Laura K McKemmish
- Department of Physics and Astronomy, University College London , London WC1E 6BT, United Kingdom.,Research School of Chemistry, Australian National University , Canberra 2601, Australia
| | - Andrew T B Gilbert
- Research School of Chemistry, Australian National University , Canberra 2601, Australia
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29
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Wrackmeyer B, Schanz H, Milius W, Veith M. Hexaethyl‐2,3,5‐tricarba‐
nido
‐hexaborane(7), Its Monoanion and the (Triphenylphosphane)gold and Dicarbonylrhodium Complexes. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany, http://www.ac2.uni‐bayreuth.de/catalyst‐design.php
| | - Hans‐Joerg Schanz
- Department of Chemistry, Georgia Southern University, P. O. Box 8064, Statesboro, GA 30460, USA
| | - Wolfgang Milius
- Anorganische Chemie I, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Michael Veith
- Anorganische Chemie, Fachbereich 8.11, Universität des Saarlandes, Gebäude C 4.1, Postfach 151150, 66041 Saarbrücken, Germany
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30
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Affiliation(s)
| | - J. San Fabián
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Madrid, Spain
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31
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Khan E, Wrackmeyer B, Kempe R, Glatz G. Synthesis of 4-silaspiro[3.4]octa-1,5-diene derivatives: hybrid spiro compounds. Appl Organomet Chem 2015. [DOI: 10.1002/aoc.3303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ezzat Khan
- Department of Chemistry; University of Malakand; 18550 Chakdara, Dir (Lower) Khyber Pakhtunkhwa Pakistan
| | - Bernd Wrackmeyer
- Anorganische Chemie II; Universität Bayreuth; D-95440 Bayreuth Germany
| | - Rhett Kempe
- Anorganische Chemie II; Universität Bayreuth; D-95440 Bayreuth Germany
| | - Germund Glatz
- Anorganische Chemie II; Universität Bayreuth; D-95440 Bayreuth Germany
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32
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Sproviero EM. Opsin Effect on the Electronic Structure of the Retinylidene Chromophore in Rhodopsin. J Chem Theory Comput 2015; 11:1206-19. [PMID: 26579769 DOI: 10.1021/ct500612n] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Direct examination of experimental NMR parameters combined with electronic structure analysis was used to provide a first-principle interpretation of NMR experiments and give a precise evaluation of how the electronic perturbation of the protein environment affects the electronic properties of the retinylidene chromophere in rhodopsin. To this end, we pursued a theoretical analysis using a combination of tools including quantum mechanics/molecular mechanics (QM/MM) at the Density Functional Theory (DFT) level, in conjunction with gauge independent atomic orbital (GIAO) calculations of (13)C NMR chemical shieldings and (1)J(CC) spin-spin coupling constants obtained with the Coupled Perturbed DFT (CPDFT) method. The opsin effect on the retinylidene chromophere is interpreted as an inductive effect of Glu-113 which readjusts the weighting factors of resonance substructures of the conjugated chain of the chromophere. These changes give a rationalization to the alternating effect of the (13)C chemical shifts magnitudes when comparing the retinylidene chromophere in the presence and absence of the protein environment. Conversely, perturbation of π orbitals has little to no effect over (1)J (13)C-(13)C spin-spin coupling constants, as they are mainly dominated by the Fermi contact term, and hence the counteraion effect is restricted to the vicinity of the perturbation. Thus, the apparent contradiction between experimental findings based on chemical shifts (deep penetration) and one-bond J-couplings (localized effects of the protonated Schiff base at the chain terminus) is in fact a consequence of different properties responding differently to the same external perturbation.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia , 600 South 43rd Street, Philadelphia, Pennsylvania 19104-4495, United States
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33
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Ring- and side-group conformational properties of di-O-acylated xylopyranosides: A computational study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Alipour M. In search of the appropriate theoretically justified mixing coefficient in parameter-free hybrid functionals for computing the NMR parameters. RSC Adv 2015. [DOI: 10.1039/c4ra13186j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The parameter-free hybrid density functionals, with theoretically justified mixing coefficients, are recommended to predict the NMR parameters.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
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35
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Fabián JS, García de la Vega JM, San Fabián E. Improvements in DFT Calculations of Spin–Spin Coupling Constants. J Chem Theory Comput 2014; 10:4938-49. [DOI: 10.1021/ct500676m] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- J. San Fabián
- Departamento
de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - J. M. García de la Vega
- Departamento
de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - E. San Fabián
- Departamento
de Química Física, Unidad Asociada del CSIC and Instituto
Universitario de Materiales, Universidad de Alicante, San Vicente
del Raspeig, 03690 Alicante, Spain
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36
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Bañuelos-Hernández AE, Mendoza-Espinoza JA. Synthesis of the 2,3,4-triacetyl-1,6-dideoxy-L-mannose and tetracetyl-3,6-dideoxy-L-mannitol and the study of the reaction mechanism by molecular modeling. RUSS J GEN CHEM+ 2014. [DOI: 10.1134/s1070363214070342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Khan E, Wrackmeyer B, Döring C, Kempe R. Synthesis and Characterization of Spirosilanes – 1,2‐Hydroboration and 1,1‐Carboboration. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ezzat Khan
- Department of Chemistry, University of Malakand, 18550 Chakdara, Khyber Pakhtunkhwa, Pakistan http://www.uom.edu.pk
| | - Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Cristian Döring
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Rhett Kempe
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany
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38
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Sensitivity of 3He NMR Parameters to the Proximity of Heterocyclic Rings. The Helium–Furan Dimer. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1490-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Bañuelos-Hernández AE, Mendoza-Espinoza JA, Pereda-Miranda R, Cerda-García-Rojas CM. Studies of (−)-Pironetin Binding to α-Tubulin: Conformation, Docking, and Molecular Dynamics. J Org Chem 2014; 79:3752-64. [DOI: 10.1021/jo500420j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Angel E. Bañuelos-Hernández
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
| | - José Alberto Mendoza-Espinoza
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
| | - Rogelio Pereda-Miranda
- Departamento
de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Circuito Exterior Ciudad Universitaria, México D. F. 04510, Mexico
| | - Carlos M. Cerda-García-Rojas
- Departamento
de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, A. P. 14-740, México D. F. 07000, Mexico
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40
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Khan E, Tok OL, Wrackmeyer B. Synthesis of 1-silacyclopent-2-ene derivatives using 1,2-hydroboration, 1,1-organoboration and protodeborylation. Appl Organomet Chem 2014. [DOI: 10.1002/aoc.3121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ezzat Khan
- Department of Chemistry; University of Malakand; Chakdara 18550 Dir (Lower), Khyber Pakhtunkhwa Pakistan
| | - Oleg L. Tok
- Anorganische Chemie II; Universität Bayreuth; D-95440 Bayreuth Germany
| | - Bernd Wrackmeyer
- Anorganische Chemie II; Universität Bayreuth; D-95440 Bayreuth Germany
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41
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Wrackmeyer B, Klimkina EV, Milius W. 1,3,2-Dithiaphospholanes with an annelated 1,2-dicarba-closo-dodecaborane(12) unit: formation and reactivity. Dalton Trans 2014; 43:5021-43. [DOI: 10.1039/c3dt52753k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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42
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N-Trimethylsilyl-aminophosphines: Solution-state Structures, Studied by Multinuclear Magnetic Resonance and DFT Methods. Z Anorg Allg Chem 2014. [DOI: 10.1002/zaac.201300365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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San Fabián J, García de la Vega JM, Suardíaz R, Fernández-Oliva M, Pérez C, Crespo-Otero R, Contreras RH. Computational NMR coupling constants: shifting and scaling factors for evaluating 1JCH. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:775-787. [PMID: 24123317 DOI: 10.1002/mrc.4014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 06/02/2023]
Abstract
Optimized shifting and/or scaling factors for calculating one-bond carbon-hydrogen spin-spin coupling constants have been determined for 35 combinations of representative functionals (PBE, B3LYP, B3P86, B97-2 and M06-L) and basis sets (TZVP, HIII-su3, EPR-III, aug-cc-pVTZ-J, ccJ-pVDZ, ccJ-pVTZ, ccJ-pVQZ, pcJ-2 and pcJ-3) using 68 organic molecular systems with 88 (1)JCH couplings including different types of hybridized carbon atoms. Density functional theory assessment for the determination of (1)JCH coupling constants is examined, comparing the computed and experimental values. The use of shifting constants for obtaining the calculated coupling improves substantially the results, and most models become qualitatively similar. Thus, for the whole set of couplings and for all approaches excluding those using the M06 functional, the root-mean-square deviations lie between 4.7 and 16.4 Hz and are reduced to 4-6.5 Hz when shifting constants are considered. Alternatively, when a specific rovibrational contribution of 5 Hz is subtracted from the experimental values, good results are obtained with PBE, B3P86 and B97-2 functionals in combination with HIII-su3, aug-cc-pVTZ-J and pcJ-2 basis sets.
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Affiliation(s)
- J San Fabián
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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44
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Wrackmeyer B, Klimkina EV, Milius W. 1,3,2‐Dioxaphospholanes with an Annelated 1,2‐Dicarba‐
closo
‐dodecaborane(12) Unit: Formation and Dimerization. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201301219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bernd Wrackmeyer
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Elena V. Klimkina
- Anorganische Chemie II, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Wolfgang Milius
- Anorganische Chemie I, Universität Bayreuth, 95440 Bayreuth, Germany
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45
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Dunlop-Brière AF, Baird MC, Budzelaar PHM. [Cp2TiCH2CHMe(SiMe3)]+, an Alkyl–Titanium Complex Which (a) Exists in Equilibrium between a β-Agostic and a Lower Energy γ-Agostic Isomer and (b) Undergoes Hydrogen Atom Exchange between α-, β-, and γ-Sites via a Combination of Conventional β-Hydrogen Elimination–Reinsertion and a Nonconventional CH Bond Activation Process Which Involves Proton Tunnelling. J Am Chem Soc 2013; 135:17514-27. [DOI: 10.1021/ja4092775] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Michael C. Baird
- Department of Chemistry, Queen’s University, Kingston, ON K7L
3N6, Canada
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46
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Isolation and characterization of bioactive compounds from the bark of Litsea costalis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 128:85-91. [DOI: 10.1016/j.jphotobiol.2013.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/08/2013] [Accepted: 08/01/2013] [Indexed: 11/22/2022]
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47
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Kupka T, Stachów M, Stobiński L, Kaminský J. 3He NMR: from free gas to its encapsulation in fullerene. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:463-468. [PMID: 23737362 DOI: 10.1002/mrc.3972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/16/2013] [Accepted: 05/01/2013] [Indexed: 06/02/2023]
Abstract
The (3)He nuclear magnetic shieldings were calculated for single helium atom, its dimer, simple models of fullerene cages (He@Cn), and single wall carbon nanotubes. The performances of several levels of theory (HF, MP2, DFT-VSXC, CCSD, CCSD(T), and CCSDT) were tested. Two sets of polarization-consistent basis sets were used (pcS-n and aug-pcS-n), and an estimate of (3)He nuclear magnetic shieldings in the complete basis set limit using a two-parameter fit was established. Theoretical (3)He results reproduced accurately previously reported theoretical values for helium gas, dimer, and helium probe inside several fullerene cages. Excellent agreement with experimental values was achieved. (3)He nuclear magnetic shieldings of single helium atom approaching various points of benzene ring were tested, and an impact of (3)He confinement within fullerene cages of different size on the (3)He chemical shift was determined.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
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48
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Si⋅⋅⋅H Interligand Interactions in Cobalt(V) and Iridium(V) Bis(silyl)bis(hydride) Complexes. Chempluschem 2013; 78:1073-1081. [DOI: 10.1002/cplu.201300174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/18/2013] [Indexed: 11/07/2022]
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49
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Afonin AV, Pavlov DV, Albanov AI, Tarasova OA, Nedolya NA. Experimental and theoretical study of the intramolecular C-H···N and C-H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2-(alkylsulfanyl)-5-amino-1-vinylpyrroles: a particular state of amine nitrogen. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:414-423. [PMID: 23695830 DOI: 10.1002/mrc.3967] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/21/2013] [Accepted: 04/22/2013] [Indexed: 06/02/2023]
Abstract
In the (1)H NMR spectra of the 1-vinylpyrroles with amino- and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the HA and HB terminal methylene protons of the vinyl group is discovered. Also, the one-bond (1)J(C(β),H(B)) coupling constant is surprisingly greater than the (1)J(C(β),H(A)) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π-system of the pyrrole ring so that it is directed toward the HB hydrogen. These factors are favorable to the emergence of the intramolecular C-HB •••N hydrogen bonding in the s-cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the HB hydrogen provides an opportunity of the intramolecular C-HB •••S hydrogen bonding in the s-cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C-H•••N and C-H•••S hydrogen bonding. Therefore, an unusual high-frequency shift of the HB signal and the increase in the (1)J(C(β),H(B)) coupling constant can be explained by the effects of hydrogen bonding.
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Affiliation(s)
- Andrei V Afonin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St 1, 664033, Irkutsk, Russia
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50
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Pudasaini B, Janesko BG. Evaluation of Approximate Exchange-Correlation Functionals in Predicting One-Bond (31)P-(1)H NMR Indirect Spin-Spin Coupling Constants. J Chem Theory Comput 2013; 9:1443-51. [PMID: 26587606 DOI: 10.1021/ct3010613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work benchmarks density functional theory, with several different exchange-correlation functionals, for prediction of isotropic one-bond phosphorus-hydrogen NMR spin-spin coupling constants (SSCCs). Our test set consists of experimental SSCCs from 30 diverse molecules representing multiple phosphorus bonding environments. The results suggest the importance of a balance between the choice of correlation functional and the admixture of nonlocal exchange. Overall, standard DFT methods appear to suffice for usefully accurate predictions of (31)P-(1)H SSCCs.
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Affiliation(s)
- Bimal Pudasaini
- Texas Christian University , 2800 South University Drive, Fort Worth, Texas 76129, United States
| | - Benjamin G Janesko
- Texas Christian University , 2800 South University Drive, Fort Worth, Texas 76129, United States
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