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Panwaria P, Das A. N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations. J Phys Chem A 2024; 128:4685-4693. [PMID: 38814588 DOI: 10.1021/acs.jpca.4c02181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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2
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Ma W, Kirchhoff JL, Strohmann C, Grabe B, Loh CCJ. Cooperative Bifurcated Chalcogen Bonding and Hydrogen Bonding as Stereocontrolling Elements for Selective Strain-Release Septanosylation. J Am Chem Soc 2023; 145:26611-26622. [PMID: 38032866 PMCID: PMC10722516 DOI: 10.1021/jacs.3c06984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
The exploitation of noncovalent interactions (NCIs) is emerging as a vital handle in tackling broad stereoselectivity challenges in synthesis. In particular, there has been significant recent interest in the harnessing of unconventional NCIs to surmount difficult selectivity challenges in glycosylations. Herein, we disclose the exploitation of an unconventional bifurcated chalcogen bonding and hydrogen bonding (HB) network, which paves the way for a robust catalytic strategy into biologically useful seven-membered ring sugars. Through 13C nuclear magnetic resonance (NMR) in situ monitoring, NMR titration experiments, and density functional theory (DFT) modeling, we propose a remarkable contemporaneous activation of multiple functional groups consisting of a bifurcated chalcogen bonding mechanism working hand-in-hand with HB activation. Significantly, the ester moiety installed on the glycosyl donor is critical in the establishment of the postulated ternary complex for stereocontrol. Through the 13C kinetic isotopic effect and kinetic studies, our data corroborated that a dissociative SNi-type mechanism forms the stereocontrolling basis for the excellent α-selectivity.
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Affiliation(s)
- Wenpeng Ma
- Abteilung
Chemische Biologie, Max-Planck-Institut
für Molekulare Physiologie, Otto-Hahn-Straße 11, Dortmund 44227, Germany
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
| | - Jan-Lukas Kirchhoff
- Fakultät
für Chemie und Chemische Biologie, Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straße 6, Dortmund 44227, Germany
| | - Carsten Strohmann
- Fakultät
für Chemie und Chemische Biologie, Anorganische Chemie, Technische Universität Dortmund, Otto-Hahn-Straße 6, Dortmund 44227, Germany
| | - Bastian Grabe
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
| | - Charles C. J. Loh
- Abteilung
Chemische Biologie, Max-Planck-Institut
für Molekulare Physiologie, Otto-Hahn-Straße 11, Dortmund 44227, Germany
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 4a, Dortmund 44227, Germany
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3
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Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [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
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
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4
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Horstmann JS, Klabunde S, Hepp A, Layh M, Hansen MR, Eckert H, Würthwein E, Uhl W. Reactions of Al‐N Based Active Lewis Pairs with Ketones and 1,2‐Diketones: Insertion into Al‐N Bonds, C‐C and C‐N Bond Formation and a Tricyclic Saturated Tetraaza Compound. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Julia Silissa Horstmann
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Sina Klabunde
- Institut für Physikalische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Marcus Layh
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Michael Ryan Hansen
- Institut für Physikalische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Hellmut Eckert
- Institut für Physikalische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
| | - Ernst‐Ulrich Würthwein
- Organisch‐chemisches Institut and Center for Multiscale Theory and Computation (CMTC) Universität Münster Corrensstrasse 40 48149 Münster Germany
| | - Werner Uhl
- Institut für Anorganische und Analytische Chemie Universität Münster Corrensstraße 30 48149 Münster Germany
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5
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Pozharskii AF, Dyablo OV, Pogosova OG, Ozeryanskii VA, Filarowski A, Vasilikhina KM, Dzhangiryan NA. Modeling Biologically Important NH···π Interactions Using peri-Disubstituted Naphthalenes. J Org Chem 2020; 85:12468-12481. [DOI: 10.1021/acs.joc.0c01697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alexander F. Pozharskii
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
| | - Olga V. Dyablo
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
| | - Olga G. Pogosova
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
| | - Valery A. Ozeryanskii
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
| | - Aleksander Filarowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Kseniya M. Vasilikhina
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
| | - Narek A. Dzhangiryan
- Department of Organic Chemistry, Southern Federal University, Zorge 7, 344090 Rostov-on-Don, Russian Federation
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6
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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7
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Bristow JC, Naftalin I, Cliff SVA, Yang S, Carravetta M, Heinmaa I, Stern R, Wallis JD. Modelling of an aza-Michael reaction from crystalline naphthalene derivatives containing peri–peri interactions: very long N–C bonds? CrystEngComm 2020. [DOI: 10.1039/d0ce01137a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A correlation between N–C bond formation and CC bond breaking is constructed from the structures of a family of peri-naphthalenes with a second set of peri substituents.
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Affiliation(s)
- Jonathan C. Bristow
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Isaac Naftalin
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Stacey V. A. Cliff
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | - Songjie Yang
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
| | | | - Ivo Heinmaa
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - Raivo Stern
- Laboratory of Chemical Physics
- National Institute of Chemical Physics and Biophysics
- Tallinn
- Estonia
| | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS
- UK
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8
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Noohinejad L, van Smaalen S, Petříček V, Schönleber A. Incommensurately modulated structure of morpholinium tetrafluoroborate and configurational versus chemical entropies at the incommensurate and lock-in phase transitions. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:836-843. [PMID: 28980987 DOI: 10.1107/s2052520617009398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
Morpholinium tetrafluoroborate, [C4H10NO]+[BF4]-, belongs to a class of ferroelectric compounds ABX4. However, [C4H10NO]+[BF4]- does not develop ferroelectric properties because the incommensurate phase below Tc,I = 153 K is centrosymmetric with superspace group Pnam(σ100)00s and σ1 = 0.42193 (12) at T = 130 K; the threefold superstructure below Tc,II = 117-118 K possesses the acentric but non-ferroelectric space group P212121. At ambient conditions, [C4H10NO]+[BF4]- comprises orientationally disordered [BF4]- anions accommodated in cavities between four morpholinium cations. A structure model for the incommensurately modulated phase, which involves modulated orientational ordering of [BF4]- together with modulated distortions and displacements of the morpholinium ions is reported. A mechanism is proposed for the phase transitions, whereby at low temperatures morpholinium cations are shaped around the tetrafluoroborate anion in order to optimize the interactions with one orientation of this anion and, thus, forcing [BF4]- into this orientation. This mechanism is essentially different from a pure order-disorder phase transition. It is supported by consideration of the transition entropy. The difference in configurational entropy between the disordered and incommensurate phases has been computed from the structure models. It is shown to be much smaller than the experimental transition entropy reported by Owczarek et al. [Chem. Phys. (2011), 381, 11-20]. These features show that the order-disorder contribution is only a minor contribution to the transition entropy and that other factors, such as conformational changes, play a larger role in the phase transitions.
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Affiliation(s)
- Leila Noohinejad
- Laboratory of Crystallography, University of Bayreuth, 95440 Bayreuth, Germany
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, 95440 Bayreuth, Germany
| | - Václav Petříček
- Institute of Physics, Academy of Sciences of the Czech Republic, 18221 Praha 8, Czech Republic
| | - Andreas Schönleber
- Laboratory of Crystallography, University of Bayreuth, 95440 Bayreuth, Germany
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9
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Leclaire J, Poisson G, Ziarelli F, Pepe G, Fotiadu F, Paruzzo FM, Rossini AJ, Dumez JN, Elena-Herrmann B, Emsley L. Structure elucidation of a complex CO 2-based organic framework material by NMR crystallography. Chem Sci 2016; 7:4379-4390. [PMID: 30155085 PMCID: PMC6014084 DOI: 10.1039/c5sc03810c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/22/2016] [Indexed: 12/23/2022] Open
Abstract
A three-dimensional structural model of a complex CO2-based organic framework made from high molecular weight, self-assembled, flexible and multi-functional oligomeric constituents has been determined de novo by solid-state NMR including DNP-enhanced experiments. The complete assignment of the 15N, 13C and 1H resonances was obtained from a series of two-dimensional through space and through bond correlation experiments. MM-QM calculations were used to generate different model structures for the material which were then evaluated by comparing multiple experimental and calculated NMR parameters. Both NMR and powder X-ray diffraction were evaluated as tools to determine the packing by crystal modelling, and at the level of structural modelling used here PXRD was found not to be a useful complement. The structure determined reveals a highly optimised H-bonding network that explains the unusual selectivity of the self-assembly process which generates the material. The NMR crystallography approach used here should be applicable for the structure determination of other complex solid materials.
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Affiliation(s)
- Julien Leclaire
- Univ Lyon , Université Claude Bernard , CNRS, INSA, CPE , ICBMS UMR 5246 , 69622 Villeurbanne , France .
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Guillaume Poisson
- Univ Lyon , Université Claude Bernard , CNRS, INSA, CPE , ICBMS UMR 5246 , 69622 Villeurbanne , France .
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Fabio Ziarelli
- Aix-Marseille Université , Fédération des Sciences Chimiques , Spectropôle , 13397 Marseille , France
| | - Gerard Pepe
- Aix-Marseille Université , CNRS , UMR 7325 CINaM , 13288 Marseille , France
| | - Frédéric Fotiadu
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aaron J Rossini
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Jean-Nicolas Dumez
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
| | - Bénédicte Elena-Herrmann
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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10
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Saritemur G, Nomen Miralles L, Husson D, Pitak MB, Coles SJ, Wallis JD. Two modes of peri-interaction between an aldehyde group and a carboxylate anion in naphthalaldehydate salts. CrystEngComm 2016. [DOI: 10.1039/c5ce02282g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The naphthalaldehydate anion shows two modes of interaction between its functional groups: either a carboxylate oxygen atom makes an n–π* interaction with the aldehyde carbon atom, or the aldehyde hydrogen atom is directed to the face of the carboxylate group.
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Affiliation(s)
- Gizem Saritemur
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS, UK
| | - Laura Nomen Miralles
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS, UK
| | - Deborah Husson
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS, UK
| | - Mateusz B. Pitak
- UK National Crystallography Service, Chemistry
- University of Southampton
- Southampton, UK
| | - Simon J. Coles
- UK National Crystallography Service, Chemistry
- University of Southampton
- Southampton, UK
| | - John D. Wallis
- School of Science and Technology
- Nottingham Trent University
- Nottingham NG11 8NS, UK
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11
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Kerr HE, Mason HE, Sparkes HA, Hodgkinson P. Testing the limits of NMR crystallography: the case of caffeine–citric acid hydrate. CrystEngComm 2016. [DOI: 10.1039/c6ce01453d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The effects of geometry optimisation on the ability to predict linewidths due to disorder and crystal packing energies is investigated on a previously unreported caffeine citric acid cocrystal system.
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Affiliation(s)
- Hannah E. Kerr
- Department of Chemistry
- Durham University
- Durham DH1 3LE, UK
| | - Helen E. Mason
- Department of Chemistry
- Durham University
- Durham DH1 3LE, UK
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12
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Breton GW, Crasto CJ. Substituted 2-(Dimethylamino)biphenyl-2′-carboxaldehydes as Substrates for Studying n→π* Interactions and as a Promising Framework for Tracing the Bürgi–Dunitz Trajectory. J Org Chem 2015; 80:7375-84. [DOI: 10.1021/acs.joc.5b00766] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gary W. Breton
- Department
of Chemistry, Berry College, Mount Berry, Georgia 30149, United States
| | - Chiquito J. Crasto
- Center
for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas 79409, United States
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