Structure, spectroscopy and dynamics of halogen molecules interacting with water

Insights into Halogen-Induced Changes in 4-Anilinoquinazoline EGFR Inhibitors: A Computational Spectroscopic Study

The epidermal growth factor receptor (EGFR) is a pivotal target in cancer therapy due to its significance within the tyrosine kinase family. EGFR inhibitors like AG-1478 and PD153035, featuring a 4-anilinoquinazoline moiety, have garnered global attention for their potent therapeutic activities. While pre-clinical studies have highlighted the significant impact of halogen substitution at the C3'-anilino position on drug potency, the underlying mechanism remains unclear. This study investigates the influence of halogen substitution (X = H, F, Cl, Br, I) on the structure, properties, and spectroscopy of halogen-substituted 4-anilinoquinazoline tyrosine kinase inhibitors (TKIs) using time-dependent density functional methods (TD-DFT) with the B3LYP functional. Our calculations revealed that halogen substitution did not induce significant changes in the three-dimensional conformation of the TKIs but led to noticeable alterations in electronic properties, such as dipole moment and spatial extent, impacting interactions at the EGFR binding site. The UV-visible spectra show that more potent TKI-X compounds typically have shorter wavelengths, with bromine's peak wavelength at 326.71 nm and hydrogen, with the lowest IC50 nM, shifting its lambda max to 333.17 nm, indicating a correlation between potency and spectral characteristics. Further analysis of the four lowest-lying conformers of each TKI-X, along with their crystal structures from the EGFR database, confirms that the most potent conformer is often not the global minimum structure but one of the low-lying conformers. The more potent TKI-Cl and TKI-Br exhibit larger deviations (RMSD > 0.65 Å) from their global minimum structures compared to other TKI-X (RMSD < 0.15 Å), indicating that potency is associated with greater flexibility. Dipole moments of TKI-X correlate with drug potency (ln(IC50 nM)), with TKI-Cl and TKI-Br showing significantly higher dipole moments (>8.0 Debye) in both their global minimum and crystal structures. Additionally, optical spectral shifts correlate with potency, as TKI-Cl and TKI-Br exhibit blue shifts from their global minimum structures, in contrast to other TKI-X. This suggests that optical reporting can effectively probe drug potency and conformation changes.

The Iodine/Iodide/Starch Supramolecular Complex

The nature of the blue color in the iodine-starch reaction (or, in most cases, iodine-iodide-starch reaction, i.e., I2 as well as I- are typically present) has for decades elicited debate. The intensity of the color suggests a clear charge-transfer nature of the band at ~600 nm, and there is consensus regarding the fact that the hydrophobic interior of the amylose helix is the location where iodine binds. Three types of possible sources of charge transfer have been proposed: (1) chains of neutral I2 molecules, (2) chains of poly-iodine anions (complicated by the complex speciation of the I2-I- mixture), or (3) mixtures of I2 molecules and iodide or polyiodide anions. An extended literature review of the topic is provided here. According to the most recent data, the best candidate for the "blue complex" is an I2-I5--I2 unit, which is expected to occur in a repetitive manner inside the amylose helix.

Interaction energy of Cl2 and Br2 with H2 O: Exchange, dispersion and density the crucial ingredients

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X₂ -H₂ O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl₂ and Br₂ inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl₂ @5¹² , -5.3 ± 0.3 kcal/mol; Cl₂ @5¹² 6² , -5.5 ± 0.1 kcal/mol; Br₂ @5¹² 6² , -7.6 ± 1.0 kcal/mol; Br₂ @5¹² 6³ , -10.6 ± 1.0 kcal/mol; Br₂ @5¹² 6⁴ , -10.9 ± 0.8 kcal/mol.

Halogen bonds with carbenes acting as Lewis base units: complexes of imidazol-2-ylidene: theoretical analysis and experimental evidence

ωB97XD/aug-cc-pVDZ and ωB97XD/aug-cc-pVTZ calculations were performed on complexes of imidazol-2-ylidene that are linked by halogen bonds. This singlet carbene acts as the Lewis base through a lone electron pair located at the carbon centre. The XCCH, XCN and X₂ units were chosen here as those that interact through the X Lewis acid halogen centre (X = Cl, Br and I); if X = F the complexes are linked by interactions which are not classified as halogen bonds. The properties of interactions that occur in complexes are analyzed using the results of DFT calculations which are supported by parameters derived from the Quantum Theory of Atoms in Molecules, QTAIM, and the Natural Bond Orbital, NBO, approaches. The energy decomposition analysis, EDA, applied here provided additional characteristics of interactions linking complexes analyzed. The majority of complexes are linked by the medium in strength and strong halogen bonds which often possess characteristics typical for covalent bonds. Searches through the Cambridge Structural Database were also performed and structures analogues to complexes analyzed theoretically were found, and these structures are also discussed in this study.

Spectroscopic evidence of a particular intermolecular interaction in iodomethane–ethanol mixtures: the cooperative effect of halogen bonding, hydrogen bonding, and the solvent effect

The particular intermolecular interaction of an iodomethane–ethanol mixture is revealed by NIR, Raman, DFT calculation, and 2D correlation analysis.

Selective Emergence of the Halogen Bond in Ground and Excited States of Noble-Gas-Chlorine Systems

Molecular-beam scattering experiments and theoretical calculations prove the nature, strength, and selectivity of the halogen bonds (XB) in the interaction of halogen molecules with the series of noble gas (Ng) atoms. The XB, accompanied by charge transfer from the Ng to the halogen, is shown to take place in, and measurably stabilize, the collinear conformation of the adducts, which thus becomes (in contrast to what happens for other Ng-molecule systems) approximately as bound as the T-shaped form. It is also shown how and why XB is inhibited when the halogen molecule is in the ³ Π_u excited state. A general potential formulation fitting the experimental observables, based on few physically essential parameters, is proposed to describe the interaction accurately and is validated by ab initio computations.

B-Hb⋯π interactions in benzene–borazine sandwich and multidecker complexes: a DFT study

Multidecker complexes of benzene/borazine can be formed through B-H_b⋯π interactions.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates

Clathrate hydrate phases of Cl₂ and Br₂ guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen–halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen–halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme–substrate compounds. The nature of the halogen–water interactions for the Cl₂ and Br₂ molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl₂ and Br₂ guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Association of phenyldiboronic acids with hydrogen bond acceptors to form hydrogen bonded DD·AA-type complexes: a DFT study

DD·AA-type complexes of phenyldiboronic acids.

Multiple Noncovalent Bonding in Halogen Complexes with Oxygen Organics. I. Tertiary Amides

The present work describes the structure and binding of adducts of N,N'-diacetylpiperazine with halogens and interhalogens based on combination of different experimental methods and quantum chemical calculations. On the basis of conductometric and spectro-photometric experimental results, behavior of complexes in the acetonitrile solution was described. The iodine adduct with N,N'-diacetylpiperazine fully degrades into components. Adducts of interhalogens I-X (X = Cl or Br) with N,N'-diacetylpiperazine in acetonitrile partially dissociate to anionic [X-I-X](-) and cationic species. In the solid state, molecules are connected via C═O···I, C-H···I, and Cl···Cl attractive interactions. N,N'-diacetylpiperazine···dihalogen complex is stabilized by simultaneous C═O···I and C-H···I interactions. Such binding mode allows to explain the problems of the direct halogenation of acetyl-containing compounds with molecular halogens as reagents. We believe that the observed binding pattern can be used as prototypical for future design of halogeno complexes.

Diamagnetic Raman Optical Activity of Chlorine, Bromine, and Iodine Gases

Magnetic Raman optical activity of gases provides unique information about their electric and magnetic properties. Magnetic Raman optical activity has recently been observed in a paramagnetic gas (Angew. Chem. Int. Ed. 2012, 51, 11058; Angew. Chem. 2012, 124, 11220). In diamagnetic molecules, it has been considered too weak to be measurable. However, in chlorine, bromine and iodine vapors, we could detect a significant signal as well. Zeeman splitting of electronic ground-state energy levels cannot rationalize the observed circular intensity difference (CID) values of about 10(-4). These are explicable by participation of paramagnetic excited electronic states. Then a simple model including one electronic excited state provides reasonable spectral intensities. The results suggest that this kind of scattering by diamagnetic molecules is a general event observable under resonance conditions. The phenomenon sheds new light on the role of excited states in the Raman scattering, and may be used to probe molecular geometry and electronic structure.

Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study

The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.

From liquid to thin film: colloidal suspensions for tungsten oxide as an electrode material for Li-ion batteries

Using a colloidal suspension, electrochemically active tungsten oxide thin films (150 nm) have been prepared via ultrasonic spray deposition using two different current collectors, namely TiN and Pt.

Performance of local correlation methods for halogen bonding: The case of Br2-(H2O)n,n = 4,5 clusters and Br2@5(12)6(2) clathrate cage

The performance of local correlation methods is examined for the interactions present in clusters of bromine with water where the combined effect of hydrogen bonding (HB), halogen bonding (XB), and hydrogen-halogen (HX) interactions lead to many interesting properties. Local methods reproduce all the subtleties involved such as many-body effects and dispersion contributions provided that specific methodological steps are followed. Additionally, they predict optimized geometries that are nearly free of basis set superposition error that lead to improved estimates of spectroscopic properties. Taking advantage of the local correlation energy partitioning scheme, we compare the different interaction environments present in small clusters and those inside the 5(12)6(2) clathrate cage. This analysis allows a clear identification of the reasons supporting the use of local methods for large systems where non-covalent interactions play a key role.

Motion of Br2 molecules in clathrate cages. A computational study of the dynamic effects on its spectroscopic behavior

This work looks into the spectroscopic behavior of bromine molecules trapped in clathrate cages combining different methodologies. We developed a semiempirical quantum mechanical model to incorporate through molecular dynamics trajectories, the effect movement of bromine molecules in clathrate cages has on its absorption spectra. A simple electrostatic model simulating the cage environment around bromine predicts a blue shift in the spectra, in good agreement with the experimental evidence.

Solvation dynamics through Raman spectroscopy: hydration of Br2 and Br3(-), and solvation of Br2 in liquid bromine

Raman spectroscopy of bromine in the liquid phase and in water illustrates uncommon principles and yields insights regarding hydration. In liquid Br(2), resonant excitation over the B((3)Π(0u)(+)) ← X((1)Σ(g)(+)) valence transition at 532 nm produces a weak resonant Raman (RR) progression accompanied by a five-fold stronger non-resonant (NR) scattering. The latter is assigned to pre-resonance with the C-state, which in turn must be strongly mixed with inter-molecular charge transfer states. Despite the electronic resonance, RR of Br(2) in water is quenched. At 532 nm, the homogeneously broadened fundamental is observed, as in the NR case at 785 nm. The implications of the quenching of RR scattering are analyzed in a simple, semi-quantitative model, to conclude that the inertial evolution of the Raman packet in aqueous Br(2) occurs along multiple equivalent water-Br(2) coordinates. In distinct contrast with hydrophilic hydration in small clusters and hydrophobic hydration in clathrates, it is concluded that the hydration shell of bromine in water consists of dynamically equivalent fluxional water molecules. At 405 nm, the RR progression of Br(3)(-) is observed, accompanied by difference transitions between the breathing of the hydration shell and the symmetric stretch of the ion. The RR scattering process in this case can be regarded as the coherent photo-induced electron transfer to the solvent and its radiative back-transfer.