Ortho-Substituent Effects on Halogen Bond Geometry for N-Haloimide⋯2-Substituted Pyridine Complexes

The nature of (imide)N-X⋯N(pyridine) halogen-bonded complexes formed by six N-haloimides and sixteen 2-substituted pyridines are studied using X-ray crystallography (68 crystal structures), Density Functional Theory (DFT) (86 complexation energies), and NMR spectroscopy (90 association constants). Strong halogen bond (XB) donors such as N-iodosuccinimide form only 1:1 haloimide:pyridine crystalline complexes, but even stronger N-iodosaccharin forms 1:1 haloimide:pyridine and three other distinct complexes. In 1:1 haloimide:pyridine crystalline complexes, the haloimide's N─X bond exhibits an unusual bond bending feature that is larger for stronger N-haloimides. DFT complexation energies (ΔEXB ) for iodoimide-pyridine complexes range from -44 to -99 kJ mol-1 , while for N-bromoimide-pyridine, they are between -31 and -77 kJ mol-1 . The ΔEXB of I⋯N XBs in 1:1 iodosaccharin:pyridine complexes are the largest of their kind, but they are substantially smaller than those in [bis(saccharinato)iodine(I)]pyridinium salts (-576 kJ mol-1 ), formed by N-iodosaccharin and pyridines. The NMR association constants and ΔEXB energies of 1:1 haloimide:pyridine complexes do not correlate as these complexes in solution are heavily influenced by secondary interactions, which DFT studies do not account for. Association constants follow the σ-hole strengths of N-haloimides, which agree with DFT and crystallography data. The haloimide:2-(N,N-dimethylamino)pyridine complex undergoes a halogenation reaction resulting in 5-iodo-2-dimethylaminopyridine.

Halogen Bonds of Halogen(I) Ions─Where Are We and Where to Go?

Halenium ions, X+, are particularly strong halogen-bond donors that interact with two Lewis bases simultaneously to form linear [D···X···D]+-type halonium complexes. Their three-center, four-electron halogen bond is both fundamentally interesting and technologically valuable as it tames the reactivity of halogen(I) ions, opening up new horizons in a variety of fields including synthetic organic and supramolecular chemistry. Understanding this bonding situation enables the development of improved halogen(I) transfer reactions and of advanced functional materials. Following a decade of investigations of basic principles, the range of applications is now rapidly widening. In this Perspective, we assess the status of the field and identify its key advances and the main bottlenecks. Clearing common misunderstandings that may hinder future progress, we aim to inspire and direct future research efforts.

N-X⋅⋅⋅O-N Halogen Bonds in Complexes of N-Haloimides and Pyridine-N-oxides: A Large Data Set Study

N-X⋅⋅⋅- O-N+ halogen-bonded systems formed by 27 pyridine N-oxides (PyNOs) as halogen-bond (XB) acceptors and two N-halosuccinimides, two N-halophthalimides, and two N-halosaccharins as XB donors are studied in silico, in solution, and in the solid state. This large set of data (132 DFT optimized structures, 75 crystal structures, and 168 1 H NMR titrations) provides a unique view to structural and bonding properties. In the computational part, a simple electrostatic model (SiElMo) for predicting XB energies using only the properties of halogen donors and oxygen acceptors is developed. The SiElMo energies are in perfect accord with energies calculated from XB complexes optimized with two high-level DFT approaches. Data from in silico bond energies and single-crystal X-ray structures correlate; however, data from solution do not. The polydentate bonding characteristic of the PyNOs' oxygen atom in solution, as revealed by solid-state structures, is attributed to the lack of correlation between DFT/solid-state and solution data. XB strength is only slightly affected by the PyNO oxygen properties [(atomic charge (Q), ionization energy (Is,min ) and local negative minima (Vs,min )], as the σ-hole (Vs,max ) of the donor halogen is the key determinant leading to the sequence N-halosaccharin>N-halosuccinimide>N-halophthalimide on the XB strength.

Competition between Binding to Various Sites of Substituted Imidazoliums

The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH₃ base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.

Carbonyl hypoiodites from pivalic and trimesic acid and their silver(I) intermediates

The first tris(O-I-N) carbonyl hypoiodites have been synthesised based on trimesic acid and pyridine or 4-methylpyridine, with their structures definitively confirmed by single crystal X-ray diffraction (SCXRD). The more soluble carbonyl hypoiodites based on pivalic acid have also been studied via NMR, SCXRD, and computational analyses, enabling the study of the direct silver(I) precursor and intermediates of the resulting carbonyl hypoiodites generated using a range of substituted pyridines.

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

N-Iodosaccharin-pyridine co-crystal system under pressure: experimental evidence of reversible twinning

This work presents a single-crystal X-ray diffraction study of an organic co-crystal composed of N-iodosaccharin and pyridine (NISac·py) under hydrostatic pressure ranging from 0.00 (5) GPa to 4.5 (2) GPa. NISac·py crystallizes in the monoclinic system (space group B2₁/e). The unconventional setting of the space group is adopted (the conventional setting is P2₁/c, No. 14) to emphasise the strongly pseudo-orthorhombic symmetry of the lattice, with a β angle very close to 90°. The crystal structure contains one molecule each of N-iodosaccharin (NISac) and pyridine (py) in the asymmetric unit (Z' = 1), linked via an N_sac...I...N'_py halogen-bonding motif. A gradual modification of this motif is observed under pressure as a result of changes in the crystalline environment. Mechanical twinning is observed under compression and the sample splits into two domains, spanning an unequal volume that is mapped by a twofold rotation about the [100] direction of the B2₁/e unit cell. The twinning is particularly significant at high pressure, being reversible when the pressure is released. The structure of the twinned sample reveals the continuity of a substantial substructure across the composition plane. The presence of this common substructure in the two orientations of the twinned individuals can be interpreted as a structural reason for the formation of the twin and is the first observed example in a molecular crystal. These results indicate that the anisotropy of intermolecular interactions in the crystal structure results in an anisotropic strain generated upon the action of hydrostatic compression. Periodic density functional theory calculations were carried out by considering an isotropic external pressure, the results showing good agreement with the experimental findings. The bulk modulus of the crystal was obtained from the equations of state, being 7 (1) GPa for experimental data and 6.8 (5) GPa for theoretical data.

Evaluation of Halogenopyridinium Cations as Halogen Bond Donors

We have performed a database survey and a structural and computational study of the potential and the limitations of halogenopyridinium cations as halogen bond donors. The database survey demonstrated that adding a positive charge on a halogenopyridine ring increases the probability that the halogen atom will participate in a halogen bond, although for chloropyridines it remains below 60%. Crystal structures of both protonated and N-methylated monohalogenated pyridinium cations revealed that the iodo- and bromopyridinium cations always form halogen-bonding contacts with the iodide anions shorter than the sum of the vdW radii, while chloropyridinium cations mostly participate in longer contacts or fail to form halogen bonds. Although a DFT study of the electrostatic potential has shown that both protonation and N-methylation of halogenopyridines leads to a considerable increase in the ESP of the halogen σ-hole, it is generally not the most positive site on the cation, allowing for alternate binding sites.

Dihypoiodites stabilised by 4-ethylpyridine through O-I-N halogen bonds

Four bis(O-I-N) compounds have been synthesised from various dihypoiodites and 4-ethylpyridine. The compounds were characterised in both the solution and solid states by NMR spectroscopy (¹H, ¹⁵N), X-ray diffraction, and computational calculations.

Halogen Bonding in N-Alkyl-3-halogenopyridinium Salts

We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.

Carbonyl Hypoiodites as Extremely Strong Halogen Bond Donors

Neutral halogen-bonded O-I-N complexes were prepared from in situ formed carbonyl hypoiodites and aromatic organic bases. The carbonyl hypoiodites have a strongly polarized iodine atom with larger σ-holes than any known uncharged halogen bond donor. Modulating the Lewis basicity of the selected pyridine derivatives and carboxylates leads to halogen-bonded complexes where the classical O-I⋅⋅⋅N halogen bond transforms more into a halogen-bonded COO- ⋅⋅⋅I-N+ ion-pair (salt) with an asymmetric O-I-N moiety. X-ray analyses, NMR studies, and calculations reveal the halogen bonding geometries of the carbonyl hypoiodite-based O-I-N complexes, confirming that in the solid-state the iodine atom is much closer to the N-atom of the pyridine derivatives than its original position at the carboxylate O-atom.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X–X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X–X···N with the chloride of N-chlorosuccinimide lead to Cl–X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔEint). The calculated ΔEint values for (imide)Br···N (−11.2 to −12.5 kcal/mol) are smaller than the values for (imide)I···N (−8.4 to −29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N–I covalent bond and I···N non-covalent bond of a (saccharin)N–I···N motif signify the covalent character for I···N halogen bonding.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔE_int). The calculated ΔE_int values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.

Halogen Bond of Halonium Ions: Benchmarking DFT Methods for the Description of NMR Chemical Shifts

Because of their anisotropic electron distribution and electron deficiency, halonium ions are unusually strong halogen-bond donors that form strong and directional three-center, four-electron halogen bonds. These halogen bonds have received considerable attention owing to their applicability in supramolecular and synthetic chemistry and have been intensely studied using spectroscopic and crystallographic techniques over the past decade. Their computational treatment faces different challenges to those of conventional weak and neutral halogen bonds. Literature studies have used a variety of wave functions and DFT functionals for prediction of their geometries and NMR chemical shifts, however, without any systematic evaluation of the accuracy of these methods being available. In order to provide guidance for future studies, we present the assessment of the accuracy of 12 common DFT functionals along with the Hartree-Fock (HF) and the second-order Møller-Plesset perturbation theory (MP2) methods, selected from an initial set of 36 prescreened functionals, for the prediction of 1H, 13C, and 15N NMR chemical shifts of [N-X-N]+ halogen-bond complexes, where X = F, Cl, Br, and I. Using a benchmark set of 14 complexes, providing 170 high-quality experimental chemical shifts, we show that the choice of the DFT functional is more important than that of the basis set. The M06 functional in combination with the aug-cc-pVTZ basis set is demonstrated to provide the overall most accurate NMR chemical shifts, whereas LC-ωPBE, ωB97X-D, LC-TPSS, CAM-B3LYP, and B3LYP to show acceptable performance. Our results are expected to provide a guideline to facilitate future developments and applications of the [N-X-N]+ halogen bond.

O-I-O halogen bond of halonium ions

The reactivity of halonium ions is conveniently modulated by three-center, four-electron halogen bonds. Such stabilized halonium complexes are valuable reagents for oxidations and halofunctionalization reactions. We report the first example of the stabilization of a halenium ion in a three-center, four-electron halogen bond with two oxygen ligands. The influence of electron density and solvent on the stability of the complexes is assessed. O-I-O halogen bond complexes are applicable as synthetic reagents and as supramolecular synthons.

Disentanglement of orthogonal hydrogen and halogen bonds via natural orbital for chemical valence: A charge displacement analysis

As known, the electron density of covalently bound halogen atoms is anisotropically distributed, making them potentially able to establish many weak interactions, acting at the same time as halogen bond donors and hydrogen bond acceptors. Indeed, there are many examples in which the halogen and hydrogen bond coexist in the same structure and, if a correct bond analysis is required, their separation is mandatory. Here, the advantages and limitations of coupling the charge displacement analysis with natural orbital for chemical valence method (NOCV-CD) to separately analyze orthogonal weak interactions are shown, for both symmetric and asymmetric adducts. The methodology gives optimal results with intermolecular adducts but, in the presence of an organometallic complex, also intramolecular interactions can be correctly analyzed. Beyond the methodological aspects, it is shown that correctly separate and quantify the interactions can give interesting chemical insights about the systems.

The Influence of Halogenated Hypercarbon on Crystal Packing in the Series of 1-Ph-2-X-1,2-dicarba-closo-dodecaboranes (X = F, Cl, Br, I)

Although 1-Ph-2-X-closo-1,2-C₂B₁₀H₁₀ (X = F, Cl, Br, I) derivatives had been computed to have positive values of the heat of formation, it was possible to prepare them. The corresponding solid-state structures were computationally analyzed. Electrostatic potential computations indicated the presence of highly positive σ-holes in the case of heavy halogens. Surprisingly, the halogen•••π interaction formed by the Br atom was found to be more favorable than that of I.

Halogen bonds of halonium ions

Halonium ions are particularly strong halogen bond donors, and are accordingly valuable tools for a variety of fields, such as supramolecular and synthetic organic chemistry.

Qualitative as well as quantitative analysis of interactions present in chlorine and bromine substituted aromatic organic crystals: A DFT linked Crystal Explorer study

The effect of noncovalent interactions in shaping a crystal structure is explored qualitatively as well as quantitatively in a DFT linked Crystal Explorer (CE) study of nine different Chlorine and Bromine substituted benzene derivatives. The qualitative approach to analyze interactions is based on Hirshfeld surface that locates electronic charge distribution on the surface, quantitative estimation is obtained by linking DFT computations withCE.In the halogen substituted benzene derivatives considered here, in addition to conventional hydrogen and halogen bonding other interactions such as those between Chlorine-Hydrogen, Bromine-Hydrogen, Bromine-Oxygen have been deciphered. The molecular crystal structure of a variety of halogen substituted aromatic molecules has been rationalized and attributed to specific interactions.

A Crystallographic Charge Density Study of the Partial Covalent Nature of Strong N⋅⋅⋅Br Halogen Bonds

The covalent nature of strong N-Br⋅⋅⋅N halogen bonds in a cocrystal (2) of N-bromosuccinimide (NBS) with 3,5-dimethylpyridine (lut) was determined from X-ray charge density studies and compared to a weak N-Br⋅⋅⋅O halogen bond in pure crystalline NBS (1) and a covalent bond in bis(3-methylpyridine)bromonium cation (in its perchlorate salt (3). In 2, the donor N-Br bond is elongated by 0.0954 Å, while the Br⋅⋅⋅acceptor distance of 2.3194(4) is 1.08 Å shorter than the sum of the van der Waals radii. A maximum electron density of 0.38 e Å^-3 along the Br⋅⋅⋅N halogen bond indicates a considerable covalent contribution to the total interaction. This value is intermediate to 0.067 e Å^-3 for the Br⋅⋅⋅O contact in 1, and approximately 0.7 e Å^-3 in both N-Br bonds of the bromonium cation in 3. A calculation of the natural bond order charges of the contact atoms, and the σ*(N1-Br) population of NBS as a function of distance between NBS and lut, have shown that charge transfer becomes significant at a Br⋅⋅⋅N distance below about 3 Å.

Benchmarking of Halogen Bond Strength in Solution with Nickel Fluorides: Bromine versus Iodine and Perfluoroaryl versus Perfluoroalkyl Donors

The energetics of halogen bond formation in solution have been investigated for a series of nickel fluoride halogen bond acceptors; trans-[NiF(2-C5 NF4 )(PEt3 )2 ] (A1), trans-[NiF{2-C5 NF3 (4-H)}(PEt3 )2 ] (A2), trans-[NiF{2-C5 NF3 (4-NMe2 )}(PEt3 )2 ] (A3) and trans-[NiF{2-C5 NF2 H(4-CF3 )}(PCy3 )2 ] (A4) with neutral organic halogen bond donors, iodopentafluorobenzene (D1), 1-iodononafluorobutane (D2) and bromopentafluorobenzene (D3), in order to establish the significance of changes from perfluoroaryl to perfluoroalkyl donors and from iodine to bromine donors. 19 F NMR titration experiments have been employed to obtain the association constants, enthalpy, and entropy for the halogen bond formed between these donor-acceptor partners in protiotoluene. For A2-A4, association constants of the halogen bonds formed with iodoperfluoroalkane (D2) are consistently larger than those obtained for analogous complexes with the iodoperfluoroarene (D1). For complexes formed with A2-A4, the strength of the halogen bond is significantly lowered upon modification of the halogen donor atom from I (in D1) to Br (in D3) (for D1: 5≤K285 ≤12 m-1 , for D3: 1.0≤K193 ≤1.6 m-1 ). The presence of the electron donating NMe2 substituent on the pyridyl ring of acceptor A3 led to an increase in -ΔH, and the association constants of the halogen bond complexes formed with D1-D3, compared to those formed by A1, A2 and A4 with the same donors.

Halogen Bond Asymmetry in Solution

Halogen bonding is the noncovalent interaction of halogen atoms in which they act as electron acceptors. Whereas three-center hydrogen bond complexes, [D···H···D]⁺ where D is an electron donor, exist in solution as rapidly equilibrating asymmetric species, the analogous halogen bonds, [D···X···D]⁺, have been observed so far only to adopt static and symmetric geometries. Herein, we investigate whether halogen bond asymmetry, i.e., a [D-X···D]⁺ bond geometry, in which one of the D-X bonds is shorter and stronger, could be induced by modulation of electronic or steric factors. We have also attempted to convert a static three-center halogen bond complex into a mixture of rapidly exchanging asymmetric isomers, [D···X-D]⁺ ⇄ [D-X···D]⁺, corresponding to the preferred form of the analogous hydrogen bonded complexes. Using ¹⁵N NMR, IPE NMR, and DFT, we prove that a static, asymmetric geometry, [D-X···D]⁺, is obtained upon desymmetrization of the electron density of a complex. We demonstrate computationally that conversion into a dynamic mixture of asymmetric geometries, [D···X-D]⁺ ⇄ [D-X···D]⁺, is achievable upon increasing the donor-donor distance. However, due to the high energetic gain upon formation of the three-center-four-electron halogen bond, the assessed complex strongly prefers to form a dimer with two static and symmetric three-center halogen bonds over a dynamic and asymmetric halogen bonded form. Our observations indicate a vastly different preference in the secondary bonding of H⁺ and X⁺. Understanding the consequences of electronic and steric influences on the strength and geometry of the three-center halogen bond provides useful knowledge on chemical bonding and for the development of improved halonium transfer agents.

Short is strong: experimental electron density in a very short N···I halogen bond

2,3,5,6-Tetrafluoro-1,4-diiodobenzene and 4-(dimethylamino)pyridine co-crystallize in 1:2 stoichiometry. A diffraction experiment at standard resolution was already conducted in 2010 and revealed one of the shortest N···I contacts ever reported. We collected X-ray intensities at 100 K up to a very high resolution of 1.23 Å−1. These experimental data allowed to refine a structure model based on atom-centered multipoles according to the Hansen-Coppens approach and provided an experimental electron density. A subsequent analysis with the help of Bader’s atoms in molecules theory showed a strong interaction between the pyridine N atom and the σ hole of its closest iodine neighbor on the halogenated benzene. This contact is characterized by a distance of 2.6622(4) Å and associated with a remarkably large electron density of 0.359(5) e⋅Å−3 in the (3, −1) critical point, unprecedented for a secondary interaction. This bona fide shortest halogen bond ever investigated by an experimental charge density study is associated with a significantly negative total energy density in the bond critical point and thus can reliably be classified as strong. Both the electron density and the position of the bond critical point suggest to compare the short N···I contact to coordinative or covalent bonds rather than to σ hole interactions.

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Halogen bonding (or X bonding) has attracted increasing interest due to its significant role in molecular recognition in biological systems. Trypsin-like serine proteases have many physiological and pathophysiological functions. There is therefore extensive interest in generating specific inhibitors for pharmacological intervention in their enzymatic activity. We study here if it is possible to use halogenated compounds as the P1 group to bind to the S1 specificity pocket of trypsin-like serine proteases to avoid the low bioavailability of the amidine or guanidine P1 group that is typically used in many inhibitors. We used 4-chlorobenzylamine (ClBA), 4-bromobenzylamine (BrBA) and 4-iodobenzylamine (IBA) as probes to test their binding modes to a trypsin-like serine protease, urokinase-type plasminogen activator (uPA), which has been recognized as a marker for breast cancer and an important target for inhibitor development. The results showed that these compounds inhibited uPA with stronger efficacies compared with their non-halogenated analogues. We also determined the high-resolution crystal structures of uPA in complex with BrBA and IBA, respectively. The structures revealed that BrBA bound to the S1 pocket of uPA via halogen bonds, but IBA did not make halogen bonds with uPA, demonstrating that the iodine may not be the best choice as a target moiety for serine proteases. These results advocate halogen bonding, especially bromine bonding, as an efficient strategy for the future design of novel inhibitors against trypsin-like serine proteases to provide strong potency and promote bioavailability.

Quantum Crystallography: Current Developments and Future Perspectives

Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.