Strength of the [Z-I···Hal]- and [Z-Hal···I]- Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy.
Ontology highlight
ABSTRACT:
SUBMITTER: Kuznetsov ML
PROVIDER: S-EPMC8038634 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Experimental electron-density studies based on high-resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl...Cl contacts vary smoothly as a function of the interaction distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitrogen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge-density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron-rich nucleophiles and heavy halogen atoms resemble three-centre-four-electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow intermediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,-1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated interaction. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen-carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen-bond strength. We find exceptionally long C-I distances for tetrafluorodiiodobenzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations.
| S-EPMC6727171 | biostudies-literature
Project description:The formation of a halogen-bond (XB) complex in the excited state was recently reported with a quadrupolar acceptor-donor-acceptor dye in two iodine-based liquids (J. Phys. Chem. Lett.2017, 8, 3927-3932). The ultrafast decay of this excited complex to the ground state was ascribed to an electron transfer quenching by the XB donors. We examined the mechanism of this process by investigating the quenching dynamics of the dye in the S1 state using the same two iodo-compounds diluted in inert solvents. The results were compared with those obtained with a non-halogenated electron acceptor, fumaronitrile. Whereas quenching by fumaronitrile was found to be diffusion controlled, that by the two XB compounds is slower, despite a larger driving force for electron transfer. A Smoluchowski-Collins-Kimball analysis of the excited-state population decays reveals that both the intrinsic quenching rate constant and the quenching radius are significantly smaller with the XB compounds. These results point to much stronger orientational constraint for quenching with the XB compounds, indicating that electron transfer occurs upon formation of the halogen bond.
| S-EPMC6930453 | biostudies-literature
Project description:The construction of more stable proteins is important in biomolecular engineering, particularly in the design of biologics-based therapeutics. We show here that replacing the tyrosine at position 18 (Y18) of T4 lysozyme with the unnatural amino acid m-chlorotyrosine ( mClY) increases both the thermal stability (increasing the melting temperature by ∼1 °C and the melting enthalpy by 3 kcal/mol) and the enzymatic activity at elevated temperatures (15% higher than that of the parent enzyme at 40 °C) of this classic enzyme. The chlorine of mClY forms a halogen bond (XB) to the carbonyl oxygen of the peptide bond at glycine 28 (G28) in a tight loop near the active site. In this case, the XB potential of the typically weak XB donor Cl is shown from quantum chemical calculations to be significantly enhanced by polarization via an intramolecular hydrogen bond (HB) from the adjacent hydroxyl substituent of the tyrosyl side chain, resulting in a distinctive synergistic HB-enhanced XB (or HeX-B for short) interaction. The larger halogens (bromine and iodine) are not well accommodated within this same loop and, consequently, do not exhibit the effects on protein stability or function associated with the HeX-B interaction. Thus, we have for the first time demonstrated that an XB can be engineered to stabilize and increase the activity of an enzyme, with the increased stabilizing potential of the HeX-B further extending the application of halogenated amino acids in the design of more stable protein therapeutics.
| S-EPMC6052408 | biostudies-literature
Project description:Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely -F, -Cl, -Br, -CF3, -N(CH3)2, -OCH3, -NHCOCH3 on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions.
| S-EPMC8303970 | biostudies-literature
Project description:Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.
| S-EPMC6695802 | biostudies-literature
Project description:Local nature of the boron-nitrogen (BN) bonding with different formal multiplicities (B≡N, B=N, B-N) have been investigated for 25 experimentally established organoboron molecules in both real and the Hilbert space, using topological analysis of electron localization function (ELF), electron density (AIM), and natural bond orbital (NBO) method. Each BN bond has been represented (ELF) by the bonding disynaptic attractor V(B,N), with the basin electron population between 5.72e and 1.83e, confirming possible existence of all the three bond types. A covalent character of bonding can be associated with the dative mechanism due to the V(B,N) bonding basin formed mainly (91-96%) by the N electron density. Similarly, the NBO method shows 2-center natural orbitals, consisting largely of the hybrids from the N atom. The AIM analysis yields the features typical for shared (H(3,-1)(r) < 0) and closed-shell (∇2ρ(3,-1)(r) > 0) interactions. The delocalization indices, describing electron exchanges between B and N quantum atoms, are smaller than 1.5, even for formally very short triple B≡N bonds. Graphical abstract .
| S-EPMC7220893 | biostudies-literature
Project description:The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
| S-EPMC4768247 | biostudies-other
Project description:Energy profiles of seven halogen-bonded complexes were analysed with the topological energy partitioning called Interacting Quantum Atoms (IQA) at MP4(SDQ)/6-31+G(2d,2p) level of theory. Explicit interatomic electron correlation energies are included in the analysis. Four complexes combine X2 (X = Cl or F) with HCN or NH3, while the remaining three combine ClF with HCN, NH3 or N2. Each complex was systematically deformed by translating the constituent molecules along its central axis linking X and N, and reoptimising its remaining geometry. The Relative Energy Gradient (REG) method (Theor. Chem. Acc. 2017, 136, 86) then computes which IQA energies most correlate with the total energy during the process of complex formation and further compression beyond the respective equilibrium geometries. It turns out that the covalent energy (i.e., exchange) of the halogen bond, X…N, itself drives the complex formation. When the complexes are compressed from their equilibrium to shorter X…N distance then the intra-atomic energy of N is in charge. When the REG analysis is restricted to electron correlation then the interatomic correlation energy between X and N again drives the complex formation, and the complex compression is best described by the destabilisation of the through-space correlation energy between N and the "outer" halogen.
| S-EPMC7321288 | biostudies-literature
Project description:Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C-X...O-Y interaction (C-X is a carbon-bonded chlorine, bromine, or iodine, and O-Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X...O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl...O, 3.37 A for Br...O, and 3.50 A for I...O) and can conform to the geometry seen in small molecules, with the C-X...O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X...O-Y angle approximately 120 degrees . Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.
| S-EPMC529416 | biostudies-literature
Project description:As an important intermolecular interaction, halogen bonding has been studied extensively, but its nature still suffers from controversy without one uniform essence. Electrostatics, charge transfer, polarization and dispersion are emphasized, but the covalent nature is usually overlooked except for the strong halogen bonding species I3 -, which is widely accepted as a result of a three-center four-electron (3c-4e) interaction. In our study, the potential energy surface of I3 - has been evaluated to explore the dissociation from I3 - to I2⋯I-. We found that different from an equivalent 3c-4e bond in I3 -, I2⋯I- can be rationalized by a polarized one. In addition, when the orbitals are polarized, it is exactly what traditional charge transfer or the popular σ-hole picture describes. I3 - can be described by the Lewis theory model with the middle I+ cation serving as the Lewis acid and two terminal I- anions acting as Lewis base. Therefore, we further extended this model to a series of I-containing species with chemical composition of L-I+-L, F--I+-L and H3P-I+-L (L = OH-, F-, Cl-, Br-, I-, PH3, NH3, H2S, HI, H2O, HBr and HCl) to explore the nature of halogen bonding. When the forces of two bases around I+ are the same, it corresponds to an equivalent 3c-4e bond, such as I3 -. Otherwise, it is a polarized multicenter bond, such as I2⋯I-. This work gives a new insight into the nature of halogen bonding compounds: besides the well-known I3 -, the nature of the other species is also a multicenter bond, existing as equivalent and polarized 3c-4e bonds, respectively.
| S-EPMC9042191 | biostudies-literature