Utilizing proton transfer to produce molecular salts in bromanilic acid substituted-pyridine molecular complexes – predictable synthons?

2013 ◽  
Vol 69 (11) ◽  
pp. 1279-1288 ◽  
Author(s):  
Lynne H. Thomas ◽  
Martin S. Adam ◽  
Andrew O'Neill ◽  
Chick C. Wilson
Keyword(s):  
Proton Transfer ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Molecular Complexes ◽  
Design Tool ◽  
Acid Molecule ◽  
Protonation State ◽  
Molecular Salts ◽  
Potential Strategy ◽  
A Charge

Controlled introduction of proton transfer into the design of a series of molecular complexes is described, delivering the systematic production of ionic molecular complexes (molecular salts). The controlled production of molecular salts has relevance as a potential strategy in the design of pharmaceutical materials. In nine molecular complexes consisting of bromanilic acid with the N-heterocyclic compounds 2-, 3- and 4-picoline [bis(2/3/4-methylpyridinium) 2,5-dibromo-3,6-dioxocyclohexa-1,4-diene-1,4-diolate, 2C6H8N+·C6Br2O42−], 2,3-, 2,4-, 2,5- and 3,5-lutidine [2,3/2,4/2,5/3,5-dimethylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C7H10N+·C6HBr2O4−], and 3-bromo-4-methylpyridine [3-bromo-4-methylpyridinium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate, C6H7BrN+·C6HBr2O4−] and 2-bromo-3-methylpyridine [2-bromo-3-methylpyridine–2,5-dibromo-3,6-dihydroxycyclohexa-2,5-diene-1,4-dione (1/1), C6H6BrN·C6H2Br2O4], proton transfer occurs readily between the bromanilic acid molecule and the N heteroatom of the pyridine ring, in all cases producing a charge-assisted bifurcated N—H...O hydrogen bond. This reinforces the value of this motif as a design tool in the crystal engineering of such complexes. The protonation state (and stoichiometry) significantly affect the supramolecular synthons obtained, but 1:2 stoichiometries reliably give rise to PBP synthons and 1:1 stoichiometries to PBBP synthons (where P indicates a methylpyridine co-molecule and B a bromanilic acid molecule). The influence of halogen interactions on the wider crystal packing is also discussed, with C—H...Br and Br...O interactions the most prevalent; only one Br...Br interaction is found.

scholarly journals Tuning colour in multi-component complexes: Molecular disorder as a design tool

2014 ◽  
Vol 70 (a1) ◽  
pp. C1007-C1007
Author(s):  
Charlotte Jones ◽  
Chick Wilson ◽  
Lynne Thomas
Keyword(s):  
Single Crystal ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Colour Change ◽  
Molecular Complexes ◽  
Design Tool ◽  
Layered Crystal ◽  
Molecular Rearrangement ◽  
Organic Systems ◽  
Inorganic Systems

The key aim of multi-component crystallisation is modification of the physicochemical properties for a specific task.[1] Tuning colour using molecular components is a relatively unexplored area, which is surprising given the possible advantages in pigment development. In crystalline materials, the optical characteristics are not solely dependent on the molecules but also on the crystal packing;[2] it follows that the optical properties could be modified using crystal engineering techniques. We have systematically investigated co-crystallising haloanilines with dinitrobenzoic acids to build an understanding of the intermolecular interactions. Molecular disorder of one or more of the components tends to lead to layered crystal structures that include stacking interactions and therefore strong colour, indicating that molecular disorder is desirable. Defects in inorganic systems are routinely exploited as a route to enhancing or introducing physical properties but similar effects in organic systems are yet to be properly exploited. We will discuss the methods by which disorder can be designed into molecular complexes, and the local ordering effects which give rise to strong diffuse scattering. Additionally we have identified a pair of thermochromic molecular complexes, 2-iodoaniline/2-bromoaniline 3,4-dinitrobenzoic acid, where disorder appears to be crucial in lending the materials their properties. Both complexes undergo a temperature-induced colour change from red to yellow corresponding to a significant molecular rearrangement. The thermochromic transition is a single-crystal to single-crystal effect; the role of molecular disorder as a facilitator for the molecular rearrangement, maintaining the crystal integrity, will be discussed. Despite the complexes being isostructural, only the bromoaniline complex shows reversible thermochromic behaviour; subtleties in the manifestation of this disorder can explain the differences in the reversibility of the transition.

scholarly journals A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3111
Author(s):  
Massimiliano Aschi ◽  
Giorgia Toto Brocchi ◽  
Gustavo Portalone
Keyword(s):  
Proton Transfer ◽  
Crystal Packing ◽  
Computational Study ◽  
Theoretical Calculations ◽  
Bromine Atom ◽  
Lone Pair ◽  
Organic Salts ◽  
Dna And Rna ◽  
Molecular Salts ◽  
Derivatives Of

Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C–Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).

scholarly journals Zn(II) Heteroleptic Halide Complexes with 2-Halopyridines: Features of Halogen Bonding in Solid State

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3393
Author(s):  
Mikhail A. Vershinin ◽  
Marianna I. Rakhmanova ◽  
Alexander S. Novikov ◽  
Maxim N. Sokolov ◽  
Sergey A. Adonin
Keyword(s):  
Solid State ◽  
Quantum Yield ◽  
Crystal Packing ◽  
Halogen Bonding ◽  
Molecular Complexes ◽  
Substituted Pyridines ◽  
Halide Complexes

Reactions between Zn(II) dihalides and 2-halogen-substituted pyridines 2-XPy result in a series of heteroleptic molecular complexes [(2-XPy)2ZnY2] (Y = Cl, X = Cl (1), Br (2), I (3); Y = Br, X = Cl (4), Br (5), I (6), Y = I, X = Cl (7), Br (8), and I (9)). Moreover, 1–7 are isostructural (triclinic), while 8 and 9 are monoclinic. In all cases, halogen bonding plays an important role in formation of crystal packing. Moreover, 1–9 demonstrate luminescence in asolid state; for the best emitting complexes, quantum yield (QY) exceeds 21%.

Structural diversity of salts of terpyridine derivatives with europium(III) located in both, cation and anion, in comparison to molecular complexes

2020 ◽  
Vol 235 (8-9) ◽  
pp. 353-363
Author(s):  
Alexander E. Sedykh ◽  
Robin Bissert ◽  
Dirk G. Kurth ◽  
Klaus Müller-Buschbaum
Keyword(s):  
Thermal Properties ◽  
Crystal Packing ◽  
Side Reaction ◽  
Molecular Complexes ◽  
Structural Diversity ◽  
Organic Ligands ◽  
Ionic Complexes ◽  
Structural Variability ◽  
Dimeric Complexes ◽  
The Common

AbstractThree salts of the common composition [EuCl2(X-tpy)2][EuCl4(X-tpy)]·nMeCN were obtained from EuCl3·6H2O and the respective organic ligands (X-tpy = 4′-phenyl-2,2′:6′,2″-terpyridine ptpy, 4′-(pyridin-4-yl)-2,2′:6′,2″-terpyridine 4-pytpy, and 4′-(pyridin-3-yl)-2,2′:6′,2″-terpyridine 3-pytpy). These ionic complexes are examples of salts, in which both cation and anion contain Eu3+ with the same organic ligands and chlorine atoms coordinated. As side reaction, acetonitrile transforms into acetamide resulting in the crystallization of the complex [EuCl3(ptpy)(acetamide)] (4). Salts [EuCl2(ptpy)2][EuCl4(ptpy)]·2.34MeCN (1), [EuCl2(4-pytpy)2][EuCl4(4-pytpy)]·0.11MeCN (2), and [EuCl2(3-pytpy)2][EuCl4(3-pytpy)]·MeCN (3) crystallize in different structures (varying in space group and crystal packing) due to variation of the rear atom of the ligand to a coordinative site. Additionally, we show and compare structural variability through the dimeric complexes [Eu2Cl6(ptpy)2(N,N′-spacer)]·N,N′-spacer (5, 6, 7) obtained from [EuCl3(ptpy)(py)] by exchanging the end-on ligand pyridine with several bipyridines (4,4′-bipyridine bipy, 1,2-bis(4-pyridyl)ethane bpa, and 1,2-bis(2-pyridyl)ethylene bpe). In addition, photophysical (photoluminescence) and thermal properties are presented.

scholarly journals Cavity hydration dynamics in cytochrome c oxidase and functional implications

2017 ◽  
Vol 114 (42) ◽  
pp. E8830-E8836 ◽  
Author(s):  
Chang Yun Son ◽  
Arun Yethiraj ◽  
Qiang Cui
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Protein ◽  
Wetting Transition ◽  
Protonation State ◽  
Hydration Level ◽  
Level Change ◽  
Dynamics Simulations

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

Organic crystal engineering with piperazine-2,5-diones. 2. Crystal packing of weakly dipolar piperazinediones derived from 2-amino-4-bromo-7-methoxyindan-2-carboxylic acid

Tetrahedron ◽  
1999 ◽  
Vol 55 (50) ◽  
pp. 14301-14322 ◽  
Author(s):  
Lawrence J. Williams ◽  
B. Jagadish ◽  
Michael G. Lansdown ◽  
Michael D. Carducci ◽  
Eugene A. Mash
Keyword(s):  
Carboxylic Acid ◽  
Crystal Engineering ◽  
Crystal Packing ◽  
Organic Crystal

scholarly journals Towards computer-guided tuning of the crystal packing of porous organic cages

2014 ◽  
Vol 70 (a1) ◽  
pp. C667-C667
Author(s):  
Angeles Pulido ◽  
Ming Liu ◽  
Paul Reiss ◽  
Anna Slater ◽  
Sam Chong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Engineering ◽  
Molecular Sieves ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Aromatic Aldehydes ◽  
Lattice Energy ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Computational Techniques

Among microporous materials, there has been an increasing recent interest in porous organic cage (POC) crystals, which can display permanent intrinsic (molecular) and extrinsic (crystal network) porosity. These materials can be used as molecular sieves for gas separation and potential applications as enzyme mimics have been suggested since they exhibit structural response toward guest molecules[1]. Small structural modifications of the initial building blocks of the porous organic molecules can lead to quite different molecular assembly[1]. Moreover, the crystal packing of POCs is based on weak molecular interactions and is less predictable that other porous materials such as MOFs or zeolites.[2] In this contribution, we show that computational techniques -molecular conformational searches and crystal structure prediction- can be successfully used to understand POC crystal packing preferences. Computational results will be presented for a series of closely related tetrahedral imine- and amine-linked porous molecules, formed by [4+6] condensation of aromatic aldehydes and cyclohexyl linked diamines. While the basic cage is known to have one strongly preferred crystal structure, the presence of small alkyl groups on the POC modifies its crystal packing preferences, leading to extensive polymorphism. Calculations were able to successfully identify these trends as well as to predict the structures obtained experimentally, demonstrating the potential for computational pre-screening in the design of POCs within targeted crystal structures. Moreover, the need of accurate molecular (ab initio calculations) and crystal (based on atom-atom potential lattice energy minimization) modelling for computer-guided crystal engineering will be discussed.

scholarly journals Crystal structures of 2-aminopyridine citric acid salts: C5H7N2 +·C6H7O7 − and 3C5H7N2 +·C6H5O7 3−

2018 ◽  
Vol 74 (8) ◽  
pp. 1111-1116 ◽  
Author(s):  
Shet M. Prakash ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
Ismail Warad
Keyword(s):  
Hydrogen Bond ◽  
Citric Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Almost All

2-Aminopyridine and citric acid mixed in 1:1 and 3:1 ratios in ethanol yielded crystals of two 2-aminopyridinium citrate salts, viz. C5H7N2 +·C6H7O7 − (I) (systematic name: 2-aminopyridin-1-ium 3-carboxy-2-carboxymethyl-2-hydroxypropanoate), and 3C5H7N2 +·C6H5O7 3− (II) [systematic name: tris(2-aminopyridin-1-ium) 2-hydroxypropane-1,2,3-tricarboxylate]. The supramolecular synthons present are analysed and their effect upon the crystal packing is presented in the context of crystal engineering. Salt I is formed by the protonation of the pyridine N atom and deprotonation of the central carboxylic group of citric acid, while in II all three carboxylic groups of the acid are deprotonated and the charges are compensated for by three 2-aminopyridinium cations. In both structures, a complex supramolecular three-dimensional architecture is formed. In I, the supramolecular aggregation results from Namino—H...Oacid, Oacid...H—Oacid, Oalcohol—H...Oacid, Namino—H...Oalcohol, Npy—H...Oalcohol and Car—H...Oacid interactions. The molecular conformation of the citrate ion (CA3−) in II is stabilized by an intramolecular Oalcohol—H...Oacid hydrogen bond that encloses an S(6) ring motif. The complex three-dimensional structure of II features Namino—H...Oacid, Npy—H...Oacid and several Car—H...Oacid hydrogen bonds. In the crystal of I, the common charge-assisted 2-aminopyridinium–carboxylate heterosynthon exhibited in many 2-aminopyridinium carboxylates is not observed, instead chains of N—H...O hydrogen bonds and hetero O—H...O dimers are formed. In the crystal of II, the 2-aminopyridinium–carboxylate heterosynthon is sustained, while hetero O—H...O dimers are not observed. The crystal structures of both salts display a variety of hydrogen bonds as almost all of the hydrogen-bond donors and acceptors present are involved in hydrogen bonding.

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