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Li W, Ma H, Li S, Ma J. Computational and data driven molecular material design assisted by low scaling quantum mechanics calculations and machine learning. Chem Sci 2021; 12:14987-15006. [PMID: 34909141 PMCID: PMC8612375 DOI: 10.1039/d1sc02574k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Electronic structure methods based on quantum mechanics (QM) are widely employed in the computational predictions of the molecular properties and optoelectronic properties of molecular materials. The computational costs of these QM methods, ranging from density functional theory (DFT) or time-dependent DFT (TDDFT) to wave-function theory (WFT), usually increase sharply with the system size, causing the curse of dimensionality and hindering the QM calculations for large sized systems such as long polymer oligomers and complex molecular aggregates. In such cases, in recent years low scaling QM methods and machine learning (ML) techniques have been adopted to reduce the computational costs and thus assist computational and data driven molecular material design. In this review, we illustrated low scaling ground-state and excited-state QM approaches and their applications to long oligomers, self-assembled supramolecular complexes, stimuli-responsive materials, mechanically interlocked molecules, and excited state processes in molecular aggregates. Variable electrostatic parameters were also introduced in the modified force fields with the polarization model. On the basis of QM computational or experimental datasets, several ML algorithms, including explainable models, deep learning, and on-line learning methods, have been employed to predict the molecular energies, forces, electronic structure properties, and optical or electrical properties of materials. It can be conceived that low scaling algorithms with periodic boundary conditions are expected to be further applicable to functional materials, perhaps in combination with machine learning to fast predict the lattice energy, crystal structures, and spectroscopic properties of periodic functional materials.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Haibo Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 China
- Jiangsu Key Laboratory of Advanced Organic Materials, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University Nanjing 210023 China
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2
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Thakur K, Wang D, Lindeman SV, Rathore R. Synthesis of Doubly Annulated m-Terphenyl-Based Molecular Tweezers and Their Charge-Transfer Complexes with DDQ as a Guest. Chemistry 2018; 24:13106-13109. [PMID: 30033629 DOI: 10.1002/chem.201803137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/19/2018] [Indexed: 11/06/2022]
Abstract
The synthesis of a doubly-annulated m-terphenyl-based tweezer platform has been developed, which affords ready incorporation of various pincer units from monobenzenoid to polybenzenoid electron donors. The complexation study with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as guest has been carried out, and the crystal structure of T-Py∩DDQ reveals the sandwich-type binding mode in the solid state.
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Affiliation(s)
- Khushabu Thakur
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201-1881, USA
| | - Denan Wang
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201-1881, USA
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201-1881, USA
| | - Rajendra Rathore
- Department of Chemistry, Marquette University, Milwaukee, WI, 53201-1881, USA
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3
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Expanded aromatic carboxylate anion induced molecular sandwich construction via a tetracationic imidazolium macrocycle conversion from molecular box to molecular tweezer. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Sundholm D, Rauhalahti M, Özcan N, Mera-Adasme R, Kussmann J, Luenser A, Ochsenfeld C. Nuclear Magnetic Shieldings of Stacked Aromatic and Antiaromatic Molecules. J Chem Theory Comput 2017; 13:1952-1962. [PMID: 28287722 DOI: 10.1021/acs.jctc.6b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dage Sundholm
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Markus Rauhalahti
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Nergiz Özcan
- Department
of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtanens plats
1, FIN-00014 Helsinki, Finland
| | - Raúl Mera-Adasme
- Departamento
de Ciencias del Ambiente, Universidad de Santiago de Chile (USACH), Av. Libertador Bernardo O’Higgins 3363, 9170022 Estación Central, Chile
| | - Jörg Kussmann
- Department
of Chemistry, University of Munich (LMU), München D-81377, Germany
| | - Arne Luenser
- Department
of Chemistry, University of Munich (LMU), München D-81377, Germany
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5
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Wang SY, Fu JH, Liang YP, He YJ, Chen YS, Chan YT. Metallo-Supramolecular Self-Assembly of a Multicomponent Ditrigon Based on Complementary Terpyridine Ligand Pairing. J Am Chem Soc 2016; 138:3651-4. [DOI: 10.1021/jacs.6b01005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shih-Yu Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Jun-Hao Fu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yen-Peng Liang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yun-Jui He
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Sheng Chen
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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6
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Sumowski CV, Hanni M, Schweizer S, Ochsenfeld C. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. J Chem Theory Comput 2015; 10:122-33. [PMID: 26579896 DOI: 10.1021/ct400713t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
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Affiliation(s)
- Chris Vanessa Sumowski
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Matti Hanni
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Sabine Schweizer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
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7
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Robertson AJ, Pandey MK, Marsh A, Nishiyama Y, Brown SP. The use of a selective saturation pulse to suppress t1 noise in two-dimensional (1)H fast magic angle spinning solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:89-97. [PMID: 26432398 DOI: 10.1016/j.jmr.2015.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
A selective saturation pulse at fast magic angle spinning (MAS) frequencies (60+kHz) suppresses t1 noise in the indirect dimension of two-dimensional (1)H MAS NMR spectra. The method is applied to a synthetic nucleoside with an intense methyl (1)H signal due to triisopropylsilyl (TIPS) protecting groups. Enhanced performance in terms of suppressing the methyl signal while minimising the loss of signal intensity of nearby resonances of interest relies on reducing spin diffusion--this is quantified by comparing two-dimensional (1)H NOESY-like spin diffusion spectra recorded at 30-70 kHz MAS. For a saturation pulse centred at the methyl resonance, the effect of changing the nutation frequency at different MAS frequencies as well as the effect of changing the pulse duration is investigated. By applying a pulse of duration 30 ms and nutation frequency 725 Hz at 70 kHz MAS, a good compromise of significant suppression of the methyl resonance combined with the signal intensity of resonances greater than 5 ppm away from the methyl resonance being largely unaffected is achieved. The effectiveness of using a selective saturation pulse is demonstrated for both homonuclear (1)H-(1)H double quantum (DQ)/single quantum (SQ) MAS and (14)N-(1)H heteronuclear multiple quantum coherence (HMQC) two-dimensional solid-state NMR experiments.
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Affiliation(s)
- Aiden J Robertson
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan
| | - Andrew Marsh
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Centre, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.
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8
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Myers E, Herrero-Gómez E, Albrecht I, Lachs J, Mayer P, Hanni M, Ochsenfeld C, Trauner D. Total Synthesis of the Proposed Structure of Trichodermatide A. J Org Chem 2014; 79:9812-7. [DOI: 10.1021/jo501206k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eddie Myers
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Elena Herrero-Gómez
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Irina Albrecht
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Jennifer Lachs
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Peter Mayer
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Matti Hanni
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
- Department
of Physics, Department of Radiology, University of Oulu, FIN-90014 Oulu, Finland
| | - Christian Ochsenfeld
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Dirk Trauner
- Department
of Chemistry and Center for Integrated Protein Science, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
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9
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Yasuda M, Baba A. Fine Tuning of Lewis Acidity by Cage-Shaped Ligand Structure toward Catalytic Reactions. J SYN ORG CHEM JPN 2013. [DOI: 10.5059/yukigoseikyokaishi.71.1294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Dudenko DV, Yates JR, Harris KDM, Brown SP. An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide. CrystEngComm 2013. [DOI: 10.1039/c3ce41240g] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Greenland BW, Bird MB, Burattini S, Cramer R, O'Reilly RK, Patterson JP, Hayes W, Cardin CJ, Colquhoun HM. Mutual binding of polymer end-groups by complementary π–π-stacking: a molecular “Roman Handshake”. Chem Commun (Camb) 2013; 49:454-6. [DOI: 10.1039/c2cc35965k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Bonhomme C, Gervais C, Babonneau F, Coelho C, Pourpoint F, Azaïs T, Ashbrook SE, Griffin JM, Yates JR, Mauri F, Pickard CJ. First-principles calculation of NMR parameters using the gauge including projector augmented wave method: a chemist's point of view. Chem Rev 2012; 112:5733-79. [PMID: 23113537 DOI: 10.1021/cr300108a] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris, Université Pierre et Marie Curie, CNRS UMR, Collège de France, France.
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13
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Rossini AJ, Zagdoun A, Hegner F, Schwarzwälder M, Gajan D, Copéret C, Lesage A, Emsley L. Dynamic nuclear polarization NMR spectroscopy of microcrystalline solids. J Am Chem Soc 2012; 134:16899-908. [PMID: 22967206 DOI: 10.1021/ja308135r] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic nuclear polarization (DNP) solid-state NMR has been applied to powdered microcrystalline solids to obtain sensitivity enhancements on the order of 100. Glucose, sulfathiazole, and paracetamol were impregnated with bis-nitroxide biradical (bis-cyclohexyl-TEMPO-bisketal, bCTbK) solutions of organic solvents. The organic solvents were carefully chosen to be nonsolvents for the compounds, so that DNP-enhanced solid-state NMR spectra of the unaltered solids could be acquired. A theoretical model is presented that illustrates that for externally doped organic solids characterized by long spin-lattice relaxation times (T(1)((1)H) > 200 s), (1)H-(1)H spin diffusion can relay enhanced polarization over micrometer length scales yielding substantial DNP enhancements (ε). ε on the order of 60 are obtained for microcrystalline glucose and sulfathiazole at 9.4 T and with temperatures of ca. 105 K. The large gain in sensitivity enables the rapid acquisition of (13)C-(13)C correlation spectra at natural isotopic abundance. It is anticipated that this will be a general method for enhancing the sensitivity of solid-state NMR experiments of organic solids.
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Affiliation(s)
- Aaron J Rossini
- Centre de RMN a Tres Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
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14
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Nakajima H, Yasuda M, Takeda R, Baba A. Recognition of Aromatic Compounds by π Pocket within a Cage-Shaped Borate Catalyst. Angew Chem Int Ed Engl 2012; 51:3867-70. [DOI: 10.1002/anie.201200346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Indexed: 11/07/2022]
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15
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Nakajima H, Yasuda M, Takeda R, Baba A. Recognition of Aromatic Compounds by π Pocket within a Cage-Shaped Borate Catalyst. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200346] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Brown SP. Applications of high-resolution 1H solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 41:1-27. [PMID: 22177472 DOI: 10.1016/j.ssnmr.2011.11.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 05/25/2023]
Abstract
This article reviews the large increase in applications of high-resolution (1)H magic-angle spinning (MAS) solid-state NMR, in particular two-dimensional heteronuclear and homonuclear (double-quantum and spin-diffusion NOESY-like exchange) experiments, in the last five years. These applications benefit from faster MAS frequencies (up to 80 kHz), higher magnetic fields (up to 1 GHz) and pulse sequence developments (e.g., homonuclear decoupling sequences applicable under moderate and fast MAS). (1)H solid-state NMR techniques are shown to provide unique structural insight for a diverse range of systems including pharmaceuticals, self-assembled supramolecular structures and silica-based inorganic-organic materials, such as microporous and mesoporous materials and heterogeneous organometallic catalysts, for which single-crystal diffraction structures cannot be obtained. The power of NMR crystallography approaches that combine experiment with first-principles calculations of NMR parameters (notably using the GIPAW approach) are demonstrated, e.g., to yield quantitative insight into hydrogen-bonding and aromatic CH-π interactions, as well as to generate trial three-dimensional packing arrangements. It is shown how temperature-dependent changes in the (1)H chemical shift, linewidth and DQ-filtered signal intensity can be analysed to determine the thermodynamics and kinetics of molecular level processes, such as the making and breaking of hydrogen bonds, with particular application to proton-conducting materials. Other applications to polymers and biopolymers, inorganic compounds and bioinorganic systems, paramagnetic compounds and proteins are presented. The potential of new technological advances such as DNP methods and new microcoil designs is described.
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Affiliation(s)
- Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom.
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17
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Ogoshi T, Ueshima N, Yamagishi TA, Toyota Y, Matsumi N. Ionic liquid pillar[5]arene: its ionic conductivity and solvent-free complexation with a guest. Chem Commun (Camb) 2012; 48:3536-8. [DOI: 10.1039/c2cc30589e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Zhu Z, Cardin CJ, Gan Y, Murray CA, White AJP, Williams DJ, Colquhoun HM. Conformational Modulation of Sequence Recognition in Synthetic Macromolecules. J Am Chem Soc 2011; 133:19442-7. [DOI: 10.1021/ja2067115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhixue Zhu
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Christine J. Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Yu Gan
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Claire A. Murray
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Andrew J. P. White
- Chemical Crystallography Laboratory, Department of Chemistry, Imperial College, London, SW7 2AY, United Kingdom
| | - David J. Williams
- Chemical Crystallography Laboratory, Department of Chemistry, Imperial College, London, SW7 2AY, United Kingdom
| | - Howard M. Colquhoun
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
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19
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1165] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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21
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Webber AL, Emsley L, Claramunt RM, Brown SP. NMR crystallography of campho[2,3-c]pyrazole (Z' = 6): combining high-resolution 1H-13C solid-state MAS NMR spectroscopy and GIPAW chemical-shift calculations. J Phys Chem A 2011; 114:10435-42. [PMID: 20815383 DOI: 10.1021/jp104901j] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
(1)H-(13)C two-dimensional magic-angle spinning (MAS) solid-state NMR correlation spectra, recorded with the MAS-J-HMQC experiment, are presented for campho[2,3-c]pyrazole. For each (13)C moiety, there are six resonances associated with the six distinct molecules in the asymmetric unit cell (Z' = 6). The one-bond C-H correlations observed in the 2D (1)H-(13)C MAS-J-HMQC spectra allow the experimental determination of the (1)H and (13)C chemical shifts associated with the separate CH, CH(2), and CH(3) groups. (1)H and (13)C chemical shifts calculated by using the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach are presented. Calculations for the whole unit cell (12 × 29 = 348 atoms, with geometry optimization of all atoms) allow the assignment of the experimental (1)H and (13)C chemical shifts to the six distinct molecules. The calculated chemical shifts for the full crystal structure are compared with those for isolated molecules as extracted from the geometry-optimized crystal structure. In this way, the effect of intermolecular interactions on the observed chemical shifts is quantified. In particular, the calculations are sufficiently precise to differentiate the small (<1 ppm) differences between the (1)H chemical shifts of the six resonances associated with each distinct CH or CH(2) moiety.
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Affiliation(s)
- Amy L Webber
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
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22
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Webber AL, Elena B, Griffin JM, Yates JR, Pham TN, Mauri F, Pickard CJ, Gil AM, Stein R, Lesage A, Emsley L, Brown SP. Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations. Phys Chem Chem Phys 2010; 12:6970-83. [PMID: 20480118 DOI: 10.1039/c001290d] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A disaccharide is a challenging case for high-resolution (1)H solid-state NMR because of the 24 distinct protons (14 aliphatic and 10 OH) having (1)H chemical shifts that all fall within a narrow range of approximately 3 to 7 ppm. High-resolution (1)H (500 MHz) double-quantum (DQ) combined rotation and multiple pulse sequence (CRAMPS) solid-state NMR spectra of beta-maltose monohydrate are presented. (1)H-(1)H DQ-SQ CRAMPS spectra are presented together with (1)H (DQ)-(13)C correlation spectra obtained with a new pulse sequence that correlates a high-resolution (1)H DQ dimension with a (13)C single quantum (SQ) dimension using the refocused INEPT pulse-sequence element to transfer magnetization via one-bond (13)C-(1)H J couplings. Compared to the observation of only a single broad peak in a (1)H DQ spectrum recorded at 30 kHz magic-angle spinning (MAS), the use of DUMBO (1)H homonuclear decoupling in the (1)H DQ CRAMPS experiment allows the resolution of distinct DQ correlation peaks which, in combination with first-principles chemical shift calculations based on the GIPAW (Gauge Including Projector Augmented Waves) plane-wave pseudopotential approach, enables the assignment of the (1)H resonances to the 24 distinct protons. We believe this to be the first experimental solid-state NMR determination of the hydroxyl OH (1)H chemical shifts for a simple sugar. Variable-temperature (1)H-(1)H DQ CRAMPS spectra reveal small increases in the (1)H chemical shifts of the OH resonances upon decreasing the temperature from 348 K to 248 K.
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Affiliation(s)
- Amy L Webber
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
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Etzkorn M, Timmerman JC, Brooker MD, Yu X, Gerken M. Preparation, structures and preliminary host-guest studies of fluorinated syn-bis-quinoxaline molecular tweezers. Beilstein J Org Chem 2010; 6:39. [PMID: 20502656 PMCID: PMC2874330 DOI: 10.3762/bjoc.6.39] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 03/23/2010] [Indexed: 01/25/2023] Open
Abstract
A series of polycyclic frameworks with fluorinated syn-facial quinoxaline sidewalls has been prepared as potential molecular tweezers for electron-rich guest compounds. Our synthetic route to the cyclooctadiene-derived scaffolds 16a-d takes advantage of the facile isolation of a novel spirocyclic precursor 9b with the crucial syn-orientation of its two alkene moieties. The crystal structure of 16c displays two features typical of a molecular tweezer: inclusion of a solvent molecule in the molecular cleft and self-association of the self-complementary scaffolds. Furthermore, host-guest NMR studies of compound 16c in solution show chemical exchange between the unbound and bound electron-rich guest, N,N,N',N'-tetramethyl-p-phenylenediamine.
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Affiliation(s)
- Markus Etzkorn
- Department of Chemistry, The University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA.
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Zienau J, Kussmann J, Ochsenfeld C. Quantum-chemical simulation of solid-state NMR spectra: the example of a molecular tweezer host–guest complex. Mol Phys 2010. [DOI: 10.1080/00268970903476647] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Cahill LS, Rana UA, Forsyth M, Smith ME. Investigation of proton dynamics and the proton transport pathway in choline dihydrogen phosphate using solid-state NMR. Phys Chem Chem Phys 2010; 12:5431-8. [DOI: 10.1039/b916422g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Branchi B, Ceroni P, Balzani V, Bergamini G, Klärner FG, Vögtle F. Adducts between Dansylated Poly(propylene amine) Dendrimers and Anthracene Clips Mediated by ZnIIIons: Highly Efficient Photoinduced Energy Transfer. Chemistry 2009; 15:7876-7882. [DOI: 10.1002/chem.200802300] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bradley JP, Tripon C, Filip C, Brown SP. Determining relative proton-proton proximities from the build-up of two-dimensional correlation peaks in 1H double-quantum MAS NMR: insight from multi-spin density-matrix simulations. Phys Chem Chem Phys 2009; 11:6941-52. [PMID: 19652828 DOI: 10.1039/b906400a] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The build-up of intensity-as a function of the number, n(rcpl), of POST-C7 elements used for the excitation and reconversion of double-quantum (DQ) coherence (DQC)-is analysed for the fifteen distinct DQ correlation peaks that are observed experimentally for the eight separate (1)H resonances in a (1)H (500 MHz) DQ CRAMPS solid-state (12.5 kHz MAS) NMR spectrum of the dipeptide beta-AspAla (S. P. Brown, A. Lesage, B. Elena, and L. Emsley, J. Am. Chem. Soc., 2004, 126, 13230). The simulation in SPINEVOLUTION (M. Veshtort and R. G. Griffin, J. Magn. Reson., 2006, 178, 248) of t(1) ((1)H DQ evolution) FIDs for clusters of eight dipolar-coupled protons gives separate simulated (1)H DQ build-up curves for the CH(2)(a), CH(2)(b), CH(Asp), CH(Ala), NH and OH (1)H single-quantum (SQ) (1)H resonances. An analysis of both the simulated and experimental (1)H DQ build-up leads to the following general observations: (i) considering the build-up of (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the DQC corresponding to the shortest H-H distance; (ii) for the maximum intensity (1)H DQ peak at a particular SQ frequency, the recoupling time for the observed maximum intensity depends on the corresponding H-H distance, e.g., maximum intensity for the CH(2)(a)-CH(2)(b) (H-H distance = 1.55 A) and OH-CH(Asp) (H-H distance = 2.49 A) DQ peaks is observed at n(rcpl) = 2 and 3, respectively; (iii) for DQ peaks involving a CH(2) proton at a non-CH(2) SQ frequency, there is much reduced intensity and a maximum intensity at a short recoupling time; (iv) for the other lower intensity (1)H DQ peaks at a particular SQ frequency, maximum intensity is observed for the same (or close to the same) recoupling time, but the relative intensity of the DQ peaks is a reliable indicator of the relative H-H distance-the ratio of the maximum intensities for the peaks at the CH(Ala) SQ frequency due to the two DQCs with the NH and OH protons are found to be approximately in the ratio of the squares of the corresponding dipolar coupling constants. While the simulated (1)H DQ build-up curves reproduce most of the features of the experimental curves, maximum intensity is often observed at a longer recoupling time in simulations. In this respect, simulations for two to eight spins show a trend towards a faster decay for an increasing number of considered spins. Finally, simulations show that increasing either the Larmor frequency (to 1 GHz) or the MAS frequency (to 125 kHz) does not lead to changes in the marked differences between the (1)H DQ build-up curves at the CH(Asp) SQ frequency for DQCs to the CH(2)(a) and OH protons that correspond to similar H-H distances (2.39 A and 2.49 A, respectively).
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Brown SP. Recent Advances in Solid-State MAS NMR Methodology for Probing Structure and Dynamics in Polymeric and Supramolecular Systems. Macromol Rapid Commun 2009; 30:688-716. [DOI: 10.1002/marc.200800816] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 02/06/2009] [Indexed: 01/12/2023]
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Sharma G, Mavroidis C, Rege K, Yarmush ML, Budil D. Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications. Int J Rob Res 2009. [DOI: 10.1177/0278364908100278] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The design hypothesis, architectures, and computational modeling of a novel peptide-based nanoactuator are presented in this paper. We engineered the α-helical coiled-coil portion of the yeast transcriptional activator peptide called GCN4 to obtain an environmentally responsive nanoactuator. The dimeric coiled-coil peptide consists of two identical approximately 4.5 nm long and approximately 3 nm wide polypeptide chains. The actuation mechanism depends on the modification of electrostatic charges along the peptide by varying the pH of the solution resulting in the reversible movement of helices and, therefore, creating the motion of an actuator. Using molecular dynamics simulations we showed that pH changes led to a reversible opening of up to 1.5 nm which is approximately 150% of the initial separation of the nanoactuator. We also investigated the forces generated by the nanoactuator upon pH actuation, using a new method based on a modified steered molecular dynamics technique. Owing to its open and close motion resembling that of tweezers, the new nanoactuator can potentially be used as a nanogripper in various nanomanipulation tasks such as detection and removal of heavy metal ions during nanofabrication processes or as a molecular switch.
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Affiliation(s)
- Gaurav Sharma
- Department of Mechanical and Industrial Engineering, 360 Huntington Avenue, Northeastern University, Boston, MA 02115, USA
| | - Constantinos Mavroidis
- Department of Mechanical and Industrial Engineering, 360 Huntington Avenue, Northeastern University, Boston, MA 02115, USA,
| | - Kaushal Rege
- The Center for Engineering in Medicine (CEM), Massachusetts General Hospital and Harvard Medical School, 51 Blossom Street, Boston, MA 02114, USA, Department of Chemical Engineering, Arizona State University, Tempe, AZ, USA
| | - Martin L. Yarmush
- The Center for Engineering in Medicine (CEM), Massachusetts General Hospital and Harvard Medical School, 51 Blossom Street, Boston, MA 02114, USA
| | - David Budil
- Department of Chemistry and Chemical Biology, 60 Huntington Avenue, Northeastern University, Boston, MA 02115, USA
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30
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Gnandt D, Utz N, Blumen A, Koslowski T. Protein displacements under external forces: An atomistic Langevin dynamics approach. J Chem Phys 2009; 130:085104. [DOI: 10.1063/1.3077005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Moon C, Brunklaus G, Sebastiani D, Rudzevich Y, Böhmer V, Spiess HW. Solid-state NMR and computational studies of tetratolyl urea calix[4]arene inclusion compounds. Phys Chem Chem Phys 2009; 11:9241-9. [DOI: 10.1039/b822535d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Poudel PP, Chen J, Cammers A. Intramolecular π-Stacking in Isostructural Conformational Probes Depends Strongly on Charge Separation, a Proton NMR Study. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Bolz I, Moon C, Enkelmann V, Brunklaus G, Spange S. Probing Molecular Recognition in the Solid-State by Use of an Enolizable Chromophoric Barbituric Acid. J Org Chem 2008; 73:4783-93. [DOI: 10.1021/jo800598z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ina Bolz
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany, and Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
| | - Chulsoon Moon
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany, and Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
| | - Volker Enkelmann
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany, and Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
| | - Gunther Brunklaus
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany, and Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
| | - Stefan Spange
- Institut für Chemie, Technische Universität Chemnitz, D-09107 Chemnitz, Germany, and Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
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34
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Jensen F. Basis Set Convergence of Nuclear Magnetic Shielding Constants Calculated by Density Functional Methods. J Chem Theory Comput 2008; 4:719-27. [PMID: 26621087 DOI: 10.1021/ct800013z] [Citation(s) in RCA: 259] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frank Jensen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus, Denmark
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35
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Khan M, Brunklaus G, Enkelmann V, Spiess HW. Transient States in [2 + 2] Photodimerization of Cinnamic Acid: Correlation of Solid-State NMR and X-ray Analysis. J Am Chem Soc 2008; 130:1741-8. [DOI: 10.1021/ja0773711] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mujeeb Khan
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
| | - Gunther Brunklaus
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
| | - Volker Enkelmann
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
| | - Hans-Wolfgang Spiess
- Max-Planck-Institut für Polymerforschung, Postfach 31 48, D-55021 Mainz, Germany
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36
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Uldry AC, Griffin JM, Yates JR, Pérez-Torralba M, Santa María MD, Webber AL, Beaumont MLL, Samoson A, Claramunt RM, Pickard CJ, Brown SP. Quantifying Weak Hydrogen Bonding in Uracil and 4-Cyano-4‘-ethynylbiphenyl: A Combined Computational and Experimental Investigation of NMR Chemical Shifts in the Solid State. J Am Chem Soc 2008; 130:945-54. [DOI: 10.1021/ja075892i] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Anne-Christine Uldry
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - John M. Griffin
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Jonathan R. Yates
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Marta Pérez-Torralba
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - M. Dolores Santa María
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Amy L. Webber
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Maximus L. L. Beaumont
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Ago Samoson
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Rosa María Claramunt
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Chris J. Pickard
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
| | - Steven P. Brown
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K., Department of Physics, University of Warwick, Coventry CV4 7AL, U.K., TCM Group, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 OHE, U.K., Departamento de Química Orgánica y Bio-Orgánica, UNED, Senda del Rey 9, 28040 Madrid, Spain, and National Institute for Chemical Physics and Biophysics, Akadeemia Tee 23, Tallinn, Estonia
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Kussmann J, Ochsenfeld C. A density matrix-based method for the linear-scaling calculation of dynamic second- and third-order properties at the Hartree-Fock and Kohn-Sham density functional theory levels. J Chem Phys 2007; 127:204103. [DOI: 10.1063/1.2794033] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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38
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Kussmann J, Ochsenfeld C. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory. J Chem Phys 2007; 127:054103. [PMID: 17688330 DOI: 10.1063/1.2749509] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.
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Affiliation(s)
- Jörg Kussmann
- Theoretische Chemie, Universität Tübingen, Auf der Morgenstelle 8, D-72076 Tübingen, Germany
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39
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Hydrogen bonding-driven elastic bis(zinc)porphyrin receptors for neutral and cationic electron-deficient guests with a sandwich-styled complexing pattern. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.06.161] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Brunklaus G, Koch A, Sebastiani D, Spiess HW. Selectivity of guest–host interactions in self-assembled hydrogen-bonded nanostructures observed by NMR. Phys Chem Chem Phys 2007; 9:4545-51. [PMID: 17690780 DOI: 10.1039/b704269h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied the incorporation of various small guest molecules into calix[4]hydroquinone nanotubes and nanoclusters using solid-state proton NMR spectroscopy in combination with quantum chemical calculations. While the molecules exhibit different types of hydrogen bonding and van der Waals interactions, they show different affinities to the nanotube host structures. As the guest molecules are located inside the complexes, they experience a shift in the NMR resonance line caused by screening effects from the aromatic electrons of the host superstructure. The abilities to fill the otherwise empty space within the tubes can hence be measured indirectly by the displacement of the NMR lines relative to the free molecules. In this way, we can probe which guest molecules are recognized by the calix[4]hydroquinones as suitable for filling their nanoporous superstructures. Selective guest-host interactions have been successfully achieved for the three component mixture of water and acetone with either 2-methyl-2-propanol or 2-propanol. In both cases, the alcohols were superior to acetone in filling the CHQ tubes.
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Affiliation(s)
- Gunther Brunklaus
- Max-Planck-Institute for Polymer Research, NMR Division, Postfach 3148, 55021, Mainz, Germany
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41
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Zienau J, Kussmann J, Koziol F, Ochsenfeld C. Molecular recognition in molecular tweezers systems: quantum-chemical calculation of NMR chemical shifts. Phys Chem Chem Phys 2007; 9:4552-62. [PMID: 17690781 DOI: 10.1039/b706045a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.
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Affiliation(s)
- Jan Zienau
- Institut für Physikalische und Theoretische Chemie, Auf der Morgenstelle 8, Universität Tübingen, D-72076, Tübingen, Germany
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