Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment

Relation between Halogen Bond Strength and IR and NMR Spectroscopic Markers

The relationship between the strength of a halogen bond (XB) and various IR and NMR spectroscopic quantities is assessed through DFT calculations. Three different Lewis acids place a Br or I atom on a phenyl ring; each is paired with a collection of N and O bases of varying electron donor power. The weakest of the XBs display a C-X bond contraction coupled with a blue shift in the associated frequency, whereas the reverse trends occur for the stronger bonds. The best correlations with the XB interaction energy are observed with the NMR shielding of the C atom directly bonded to X and the coupling constants involving the C-X bond and the C-H/F bond that lies ortho to the X substituent, but these correlations are not accurate enough for the quantitative assessment of energy. These correlations tend to improve as the Lewis acid becomes more potent, which makes for a wider range of XB strengths.

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.

Gauging the Strength of the Molecular Halogen Bond via Experimental Electron Density and Spectroscopy

Strong and weak halogen bonds (XBs) in discrete aggregates involving the same acceptor are addressed by experiments in solution and in the solid state. Unsubstituted and perfluorinated iodobenzenes act as halogen donors of tunable strength; in all cases, quinuclidine represents the acceptor. NMR titrations reliably identify the strong intermolecular interactions in solution, with experimental binding energies of approx. 7 kJ/mol. Interaction of the σ hole at the halogen donor iodine leads to a redshift in the symmetric C-I stretching vibration; this shift reflects the interaction energy in the halogen-bonded adducts and may be assessed by Raman spectroscopy in condensed phase even for weak XBs. An experimental picture of the electronic density for the XBs is achieved by high-resolution X-ray diffraction on suitable crystals. Quantum theory of atoms in molecules (QTAIM) analysis affords the electron densities and energy densities in the bond critical points of the halogen bonds and confirms stronger interaction for the shorter contacts. For the first time, the experimental electron density shows a significant effect on the atomic volumes and Bader charges of the quinuclidine N atoms, the halogen-bond acceptor: strong and weak XBs are reflected in the nature of their acceptor atom. Our experimental findings at the acceptor atom match the discussed effects of halogen bonding and thus the proposed concepts in XB activated organocatalysis.

Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach

Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.

Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond

The halogen bond formed by a series of Lewis acids TF₃X (T = C, Si, Ge, Sn, Pb; X = Cl, Br, I) with NH₃ is studied by quantum chemical calculations. The interaction energy is closely mimicked by the depth of the σ-hole on the X atom as well as the full electrostatic energy. There is a first trend by which the hole is deepened if the T atom to which X is attached becomes more electron-withdrawing: C > Si > Ge > Sn > Pb. On the other hand, larger more polarizable T atoms are better able to transmit the electron-withdrawing power of the F substituents. The combination of these two opposing factors leaves PbF₃X forming the strongest XBs, followed by CF₃X, with SiF₃X engaging in the weakest bonds. The charge transfer from the NH₃ lone pair into the σ*(TX) antibonding orbital tends to elongate the covalent TX bond, and this force is largest for the heavier X and T atoms. On the other hand, the contraction of this bond deepens the σ-hole at the X atom, which would enhance both the electrostatic component and the full interaction energy. This bond-shortening effect is greatest for the lighter X atoms. The combination of these two opposing forces leaves the T-X bond contracting for X = Cl and Br, but lengthening for I.

Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives

The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.

Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.

Crystal Structure Survey and Theoretical Analysis of Bifurcated Halogen Bonds

The possibility that two Lewis bases can share a single halogen atom within the context of a bifurcated halogen bond (XB) is explored first by a detailed examination of the CSD. Of the more than 22,000 geometries that fit the definition of an XB (with X = Cl, Br, I), less than 2% are bifurcated. There is a heavy weighting of I in such bifurcated arrangements as opposed to Br, which prefers monofurcated bonds. The conversion from mono to bifurcated is associated with a smaller number of short contact distances, as well as a trend toward lesser linearity. The two XBs within a bifurcated system are somewhat symmetrical: the two lengths generally differ by less than 0.05 Å, and the two XB angles are within several degrees of one another. Quantum calculations of model systems reflect the patterns observed in crystals and reinforce the idea that the negative cooperativity within a bifurcated XB weakens and lengthens each individual bond.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Influence of Substituents in the Benzene Ring on the Halogen Bond of Iodobenzene with Ammonia

The effects on the CI··N halogen bond between iodobenzene and NH3 of placing various substituents on the phenyl ring are monitored by quantum calculations. Substituents R = N(CH3)2, NH2, CH3, OCH3, COCH3, Cl, F, COH, CN, and NO2 were each placed ortho, meta, and para to the I. The depth of the σ-hole on I is deepened as R became more electron-withdrawing which is reflected in a strengthening of the halogen bond, which varied between 3.3 and 5.5 kcal/mol. In most cases, the ortho placement yields the largest perturbation, followed by meta and then para, but this trend is not universal. Parallel to these substituent effects is a progressive lengthening of the covalent C-I bond. Formation of the halogen bond reduces the NMR chemical shielding of all three nuclei directly involved in the C-I··N interaction. The deshielding of the electron donor N is most closely correlated with the strength of the bond, as is the coupling constant between I and N, so both have potential use as spectroscopic measures of halogen bond strength.

Anti-Electrostatic Pi-Hole Bonding: How Covalency Conquers Coulombics

Intermolecular bonding attraction at π-bonded centers is often described as "electrostatically driven" and given quasi-classical rationalization in terms of a "pi hole" depletion region in the electrostatic potential. However, we demonstrate here that such bonding attraction also occurs between closed-shell ions of like charge, thereby yielding locally stable complexes that sharply violate classical electrostatic expectations. Standard DFT and MP2 computational methods are employed to investigate complexation of simple pi-bonded diatomic anions (BO-, CN-) with simple atomic anions (H-, F-) or with one another. Such "anti-electrostatic" anion-anion attractions are shown to lead to robust metastable binding wells (ranging up to 20-30 kcal/mol at DFT level, or still deeper at dynamically correlated MP2 level) that are shielded by broad predissociation barriers (ranging up to 1.5 Å width) from long-range ionic dissociation. Like-charge attraction at pi-centers thereby provides additional evidence for the dominance of 3-center/4-electron (3c/4e) nD-π*AX interactions that are fully analogous to the nD-σ*AH interactions of H-bonding. Using standard keyword options of natural bond orbital (NBO) analysis, we demonstrate that both n-σ* (sigma hole) and n-π* (pi hole) interactions represent simple variants of the essential resonance-type donor-acceptor (Bürgi-Dunitz-type) attraction that apparently underlies all intermolecular association phenomena of chemical interest. We further demonstrate that "deletion" of such π*-based donor-acceptor interaction obliterates the characteristic Bürgi-Dunitz signatures of pi-hole interactions, thereby establishing the unique cause/effect relationship to short-range covalency ("charge transfer") rather than envisioned Coulombic properties of unperturbed monomers.

Spectroscopic Investigation of Chalcogen Bonding: Halide-Carbon Disulfide Complexes

A combined experimental and theoretical approach has been used to study intermolecular chalcogen bonding. Specifically, the chalcogen bonding occurring between halide anions and CS₂ molecules has been investigated using both anion photoelectron spectroscopy and high-level CCSD(T) calculations. The relative strength of the chalcogen bond has been determined computationally using the complex dissociation energies as well as experimentally using the electron stabilisation energies. The anion complexes featured dissociation energies on the order of 47 kJ/mol to 37 kJ/mol, decreasing with increasing halide size. Additionally, the corresponding neutral complexes have been examined computationally, and show three loosely-bound structural motifs and a molecular radical.

Relative Strengths of a Pnicogen and a Tetrel Bond and Their Mutual Effects upon One Another

The ability of the T and Z atoms of TR₃ZR₂ to engage in a noncovalent interaction with NH₃ is assessed by DFT calculations, where the T atom refers to C, Si, and Ge; Z = As, Sb, and P; and substituents R = H and F. In most instances, the tetrel bond (TB) is both stronger and shorter than the pnicogen bond (ZB). These two bond strengths can be equalized, or preference shifted to the ZB, if F substituents are placed on the Z and H on the T atoms. Employing C as the T atom results in a very weak TB, with the ZB clearly favored energetically. The simultaneous formation of both TB and ZB weakens both, particularly the latter, but both bonds survive intact. Geometric and spectroscopic perturbations of the subunits reflect the two types of noncovalent bonds.

Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.

Modeling of Solute-Solvent Interactions Using an External Electric Field-From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute-solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.

Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond

The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl₄, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.

Origins and properties of the tetrel bond

The tetrel bond (TB) recruits an element drawn from the C, Si, Ge, Sn, Pb family as electron acceptor in an interaction with a partner Lewis base. The underlying principles that explain this attractive interaction are described in terms of occupied and vacant orbitals, total electron density, and electrostatic potential. These principles facilitate a delineation of the factors that feed into a strong TB. The geometric deformation that occurs within the tetrel-bearing Lewis acid monomer is a particularly important issue, with both primary and secondary effects. As a first-row atom of low polarizability, C is a reluctant participant in TBs, but its preponderance in organic and biochemistry make it extremely important that its potential in this regard be thoroughly understood. The IR and NMR manifestations of tetrel bonding are explored as spectroscopy offers a bridge to experimental examination of this phenomenon. In addition to the most common σ-hole type TBs, discussion is provided of π-hole interactions which are a result of a common alternate covalent bonding pattern of tetrel atoms.

NBO/NRT Two-State Theory of Bond-Shift Spectral Excitation

We show that natural bond orbital (NBO) and natural resonance theory (NRT) analysis methods provide both optimized Lewis-structural bonding descriptors for ground-state electronic properties as well as suitable building blocks for idealized "diabatic" two-state models of the associated spectroscopic excitations. Specifically, in the framework of single-determinant Hartree-Fock or density functional methods for a resonance-stabilized molecule or supramolecular complex, we employ NBO/NRT descriptors of the ground-state determinant to develop a qualitative picture of the associated charge-transfer excitation that dominates the valence region of the electronic spectrum. We illustrate the procedure for the elementary bond shifts of SN2-type halide exchange reaction as well as the more complex bond shifts in a series of conjugated cyanine dyes. In each case, we show how NBO-based descriptors of resonance-type 3-center, 4-electron (3c/4e) interactions provide simple estimates of spectroscopic excitation energy, bond orders, and other vibronic details of the excited-state PES that anticipate important features of the full multi-configuration description. The deep 3c/4e connections to measurable spectral properties also provide evidence for NBO-based estimates of ground-state donor-acceptor stabilization energies (sometimes criticized as "too large" compared to alternative analysis methods) that are also found to be of proper magnitude to provide useful estimates of excitation energies and structure-dependent spectral shifts.

F-Halogen Bond: Conditions for Its Existence

The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp², or sp³ C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O₂NF, FOF, ClF, BrF, SiF₄, or GeF₄, but F₂ is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a V_s,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.

Self-assembly of reversed bilayer vesicles through pnictogen bonding: water-stable supramolecular nanocontainers for organic solvents

A new air and moisture stable antimony thiolate compound has been prepared that spontaneously forms stable hollow vesicles. Structural data reveals that pnictogen bonding drives the self-assembly of these molecules into a reversed bilayer. The ability to make these hollow, spherical, and chemically and temporally stable vesicles that can be broken and reformed by sonication allows these systems to be used for encapsulation and compartmentalisation in organic media. This was demonstrated through the encapsulation and characterization of several small organic reporter molecules.

Interplay between Polymorphism and Isostructurality in the 2-Fur- and 2-Thenaldehyde Semi- and Thiosemicarbazones

The four compounds, namely: 5-nitro-2-furaldehyde thiosemicarbazone (1); 5-nitro-2-thiophene thiosemicarbazone (2); 5-nitro-2-furaldehyde semicarbazone (3); and 5-nitro-2-thiophene semicarbazone (4) were synthesized and crystallized. The three new crystal structures of 1, 2, and 4 were determined and compared to three already known crystal structures of 3. Additionally, two new polymorphic forms of 1 solvate were synthesized and studied. The influence of the exchange of 2-thiophene to 2-furaldehyde as well as thiosemicarbazone and semicarbazone on the self-assembly of supramolecular nets was elucidated and discussed in terms of the formed synthons and assemblies accompanied by Full Interaction Maps analysis. Changes in the strength of IR oscillators caused by the molecular and crystal packing effects are described and explained in terms of changes of electron density.