scholarly journals A robust and tunable halogen bond organocatalyzed 2-deoxyglycosylation involving quantum tunneling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunfa Xu ◽  
V. U. Bhaskara Rao ◽  
Julia Weigen ◽  
Charles C. J. Loh
Keyword(s):  
Quantum Tunneling ◽  
Halogen Bond ◽  
Reaction Network ◽  
Halogen Bonding ◽  
Isotopic Effect ◽  
Rate Determining Step ◽  
Important Addition ◽  
Substrate Tolerance ◽  
Kinetic Investigations

Abstract The development of noncovalent halogen bonding (XB) catalysis is rapidly gaining traction, as isolated reports documented better performance than the well-established hydrogen bonding thiourea catalysis. However, convincing cases allowing XB activation to be competitive in challenging bond formations are lacking. Herein, we report a robust XB catalyzed 2-deoxyglycosylation, featuring a biomimetic reaction network indicative of dynamic XB activation. Benchmarking studies uncovered an improved substrate tolerance compared to thiourea-catalyzed protocols. Kinetic investigations reveal an autoinductive sigmoidal kinetic profile, supporting an in situ amplification of a XB dependent active catalytic species. Kinetic isotopic effect measurements further support quantum tunneling in the rate determining step. Furthermore, we demonstrate XB catalysis tunability via a halogen swapping strategy, facilitating 2-deoxyribosylations of D-ribals. This protocol showcases the clear emergence of XB catalysis as a versatile activation mode in noncovalent organocatalysis, and as an important addition to the catalytic toolbox of chemical glycosylations.

scholarly journals In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1589 ◽  
Author(s):  
Yunwen Tao ◽  
Yue Qiu ◽  
Wenli Zou ◽  
Sadisha Nanayakkara ◽  
Seth Yannacone ◽  
...  
Keyword(s):  
Bond Strength ◽  
Vibrational Mode ◽  
Halogen Bond ◽  
Molecular Crystals ◽  
Halogen Bonding ◽  
Halogen Bonds ◽  
Mode Theory ◽  
Local Vibrational Mode ◽  
Intrinsic Strength

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ -hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n → σ ∗ (X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

scholarly journals Hydrogen and Halogen Bond Mediated Coordination Polymers of Chloro-Substituted Pyrazin-2-Amine Copper(I) Bromide Complexes

Chemistry ◽  
2020 ◽  
Vol 2 (3) ◽  
pp. 700-713
Author(s):  
Aaron Mailman ◽  
Rakesh Puttreddy ◽  
Manu Lahtinen ◽  
Noora Svahn ◽  
Kari Rissanen
Keyword(s):  
Coordination Polymers ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
X Ray Diffraction ◽  
New Class ◽  
Monodentate Ligands ◽  
High Yields ◽  
Polymeric Structures ◽  
Mode Of Coordination

A new class of six mono- (1; 3-Cl-, 2; 5-Cl-, 3; 6-Cl-) and di-(4; 3,6-Cl, 5; 5,6-Cl-, 6; 3,5-Cl-) chloro-substituted pyrazin-2-amine ligands (1–6) form complexes with copper (I) bromide, to give 1D and 2D coordination polymers through a combination of halogen and hydrogen bonding that were characterized by X-ray diffraction analysis. These Cu(I) complexes were prepared indirectly from the ligands and CuBr2 via an in situ redox process in moderate to high yields. Four of the pyrazine ligands, 1, 4–6 were found to favor a monodentate mode of coordination to one CuI ion. The absence of a C6-chloro substituent in ligands 1, 2 and 6 supported N1–Cu coordination over the alternative N4–Cu coordination mode evidenced for ligands 4 and 5. These monodentate systems afforded predominantly hydrogen bond (HB) networks containing a catenated (μ3-bromo)-CuI ‘staircase’ motif, with a network of ‘cooperative’ halogen bonds (XB), leading to infinite polymeric structures. Alternatively, ligands 2 and 3 preferred a μ2-N,N’ bridging mode leading to three different polymeric structures. These adopt the (μ3-bromo)-CuI ‘staircase’ motif observed in the monodentate ligands, a unique single (μ2-bromo)-CuI chain, or a discrete Cu2Br2 rhomboid (μ2-bromo)-CuI dimer. Two main HB patterns afforded by self-complimentary dimerization of the amino pyrazines described by the graph set notation R22(8) and non-cyclic intermolecular N–H∙∙∙N’ or N–H∙∙∙Br–Cu leading to infinite polymeric structures are discussed. The cooperative halogen bonding between C–Cl∙∙∙Cl–C and the C–Cl∙∙∙Br–Cu XB contacts are less than the sum of the van der Waals radii of participating atoms, with the latter ranging from 3.4178(14) to 3.582(15) Å. In all cases, the mode of coordination and pyrazine ring substituents affect the pattern of HBs and XBs in these supramolecular structures.

scholarly journals Selenium– and tellurium–halogen reagents

2018 ◽  
Vol 3 (12) ◽  
Author(s):  
Tristram Chivers ◽  
Risto S. Laitinen
Keyword(s):  
Oxidation State ◽  
Halogen Bond ◽  
The Other ◽  
Oxidation States ◽  
Alkyl Aryl ◽  
Organic Selenium ◽  
Formal Oxidation State ◽  
Wide Range ◽  
Inorganic And Organic

Abstract Selenium and tellurium form binary halides in which the chalcogen can be in formal oxidation states (IV), (II) or (I). They are versatile reagents for the preparation of a wide range of inorganic and organic selenium and tellurium compounds taking advantage of the reactivity of the chalcogen–halogen bond. With the exception of the tetrafluorides, the tetrahalides are either commercially available or readily prepared. On the other hand, the low-valent species, EX2 (E = Se, Te; X = Cl, Br) and E2X2 (E = Se, Te; X = Cl, Br) are unstable with respect to disproportionation and must be used as in situ reagents. Organoselenium and tellurium halides are well-known in oxidation states (IV) and (II), as exemplified by REX3, R2EX2 and REX (R = alkyl, aryl; E = Se, Te; X = F, Cl, Br, I); mixed-valent (IV/II) compounds of the type RTeX2TeR are also known. This chapter surveys the availability and/or preparative methods for these widely used reagents followed by examples of their applications in synthetic inorganic and organic selenium and tellurium chemistry. For both the binary halides and their organic derivatives, the discussion is subdivided according to the formal oxidation state of the chalcogen.

scholarly journals Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 224 ◽  
Author(s):  
Yannick Roselló ◽  
Mónica Benito ◽  
Elies Molins ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera
Keyword(s):  
Density Functional ◽  
Halogen Bond ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Adenine Ring ◽  
Bonding Interaction ◽  
Donor Ability ◽  
Adenine Derivative

In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.

A kinetic study of mechanochemical halogen bond formation by in situ31P solid-state NMR spectroscopy

2017 ◽  
Vol 53 (71) ◽  
pp. 9930-9933 ◽  
Author(s):  
Yijue Xu ◽  
Lysiane Champion ◽  
Bulat Gabidullin ◽  
David L. Bryce
Keyword(s):  
Activation Energy ◽  
Solid State ◽  
Nmr Spectroscopy ◽  
Kinetic Study ◽  
Solid State Nmr ◽  
Halogen Bond ◽  
Bond Formation ◽  
Nmr Studies ◽  
Solid State Nmr Spectroscopy

In situ 31P solid-state NMR studies of mechanochemical halogen bond formation provide insights into the cocrystallisation process and an estimate of the activation energy.

scholarly journals In situ X-ray Diffraction Investigation of the Crystallisation of Perfluorinated Ce(IV)-based Metal-Organic Frameworks with UiO-66 and MIL-140 architectures

2020 ◽  
Author(s):  
Stephen Shearan ◽  
Jannick Jacobsen ◽  
Ferdinando Costantino ◽  
Roberto D’Amato ◽  
Dmitri Novikov ◽  
...  
Keyword(s):  
Crystal Growth ◽  
Metal Organic Frameworks ◽  
Building Blocks ◽  
Nucleation And Growth ◽  
X Ray Diffraction ◽  
X Ray ◽  
Rate Determining Step ◽  
Wide Range ◽  
Metal Organic

We report on the results of a thorough <i>in situ</i> synchrotron powder X-ray diffraction study of the crystallisation in aqueous medium of two recently discovered perfluorinated Ce(IV)-based metal-organic frameworks (MOFs), analogues of the already well investigated Zr(IV)-based UiO-66 and MIL-140A, namely, F4_UiO-66(Ce) and F4_MIL-140A(Ce). The two MOFs were originally obtained in pure form in similar conditions, using ammonium cerium nitrate and tetrafluoroterephthalic acid as building blocks, and small variations of the reaction parameters were found to yield mixed phases. Here, we investigate the crystallisation of these compounds <i>in situ</i> in a wide range of conditions, varying parameters such as temperature, amount of the protonation modulator nitric acid (HNO<sub>3</sub>) and amount of the coordination modulator acetic acid (AcOH). When only HNO<sub>3</sub> is present in the reaction environment, F4_MIL-140A(Ce) is obtained as a pure phase. Heating preferentially accelerates nucleation, which becomes rate determining below 57 °C, whereas the modulator influences nucleation and crystal growth to a similar extent. Upon addition of AcOH to the system, alongside HNO<sub>3</sub>, mixed-phased products, consisting of F4_MIL-140A(Ce) and F4_UiO-66(Ce), are obtained. In these conditions, F4_UiO-66(Ce) is always formed faster and no interconversion between the two phases occurs. In the case of F4_UiO-66(Ce), crystal growth is always the rate determining step. An increase in the amount of HNO<sub>3</sub> slows down both nucleation and growth rates for F4_MIL-140A(Ce), whereas nucleation is mainly affected for F4_UiO-66(Ce). In addition, a higher amount HNO<sub>3</sub> favours the formation of F4_MIL-140A(Ce). Similarly, increasing the amount of AcOH leads to slowing down of the nucleation and growth rate, but favours the formation of F4_UiO-66(Ce). The pure F4_UiO-66(Ce) phase could also be obtained when using larger amounts of AcOH in the presence of minimal HNO<sub>3</sub>. Based on these <i>in situ</i> results, a new optimised route to achieving a pure, high quality F4_MIL-140A(Ce) phase in mild conditions (60 °C, 1 h) is also identified.

Cyclic networks of halogen-bonding interactions in molecular self-assemblies: a theoretical N—X...NversusC—X...N investigation

2017 ◽  
Vol 73 (2) ◽  
pp. 179-187
Author(s):  
Ruben D. Parra ◽  
Álvaro Castillo
Keyword(s):  
Electron Density ◽  
Self Assembly ◽  
Metal Ion ◽  
Halogen Atom ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Nbo Analysis ◽  
Binding Energies ◽  
Cyclic Network ◽  
Ability To Drive

The geometries and energetics of molecular self-assembly structures that contain a sequential network of cyclic halogen-bonding interactions are investigated theoretically. The strength of the halogen-bonding interactions is assessed by examining binding energies, electron charge transfer (NBO analysis) and electron density at halogen-bond critical points (AIM theory). Specifically, structural motifs having intramolecular N—X...N (X= Cl, Br, or I) interactions and the ability to drive molecular self-assemblyviathe same type of interactions are used to construct larger self-assemblies of up to three unit motifs. N—X...N halogen-bond cooperativity as a function of the self-assembly size, and the nature of the halogen atom is also examined. The cyclic network of the halogen-bonding interactions provides a suitable cavity rich in electron density (from the halogen atom lone pairs not involved in the halogen bonds) that can potentially bind an electron-deficient species such as a metal ion. This possibility is explored by examining the ability of the N—X...N network to bind Na+. Likewise, molecular self-assembly structures driven by the weaker C—X...N halogen-bonding interactions are investigated and the results compared with those of their N—X...N counterparts.

Cooperative halogen bonding and polarized π-stacking in the formation of coloured charge-transfer co-crystals

2018 ◽  
Vol 42 (13) ◽  
pp. 10615-10622 ◽  
Author(s):  
Chideraa I. Nwachukwu ◽  
Zachary R. Kehoe ◽  
Nathan P. Bowling ◽  
Erin D. Speetzen ◽  
Eric Bosch
Keyword(s):  
Charge Transfer ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Π Stacking

Matched electron rich halogen bond acceptors and donor have been synthesized and the halogen bonded charge transfer cocrystals characterized.

Tetradentate halogen bonding macrocyclic anion receptor inspired by the “Texas-sized” molecular box

2022 ◽  
Author(s):  
Tian Zhao ◽  
Vincent Lynch ◽  
Jonathan L. Sessler
Keyword(s):  
Click Chemistry ◽  
Halogen Bond ◽  
Halogen Bonding ◽  
Anion Receptor

Inspired by the tetracationic “Texas-sized” molecular box, a neutral analogue containing four iodotriazole halogen bond-promoting subunits (“Ibox”) was synthesized. This new macrocycle was prepared by means of azide-alkyne click chemistry....

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