Halogen bonding in mono- and dihydrated halobenzene

Density functional theory calculations were performed on halogen-bonded and hydrogen-bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06-2X density functional with the 6-31+G(d) (for C, H, F, Cl, and Br) and aug-cc-pVDZ-PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh-H₂O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••O_w internuclear separation (where O_w is the water oxygen). For all XPh-H₂O systems hydrogen-bonded systems exist, containing a combination of CH•••O_w and O_wH_w•••X hydrogen bonds. For all systems except X = At the X•••H_w hydrogen-bonding interaction is stronger than the X•••O_w halogen bond. In the XPh-(H₂O)₂ system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the C H bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as C H•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.     

Halogen bonds with benzene: An assessment of DFT functionals

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes. © 2013 Wiley Periodicals, Inc.     

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.     

Halogen versus halide electronic structure

Halide anions X-are known to show a decreasing proton affinity(PA),as X descends in the periodic table along series F,Cl,Br and I.But it is also well-known that,along this series,the halogen atom X becomes less electronegative(or more electropositive).This corresponds to an increasing energy of the valence np atomic orbital(AO) which,somewhat contradictorily,suggests that the electron donor capability and thus the PA of the halides should increase along the series F,Cl,Br,I.To reconcile these contradictory ...     

A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene

Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from −27.80 to −37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇²ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C₆H₆⋯ClF, C₆H₆⋯ICl, C₆H₆⋯BrF and C₆H₆⋯IF, and the dispersion interaction is the main part in the complexes of C₆H₆⋯BrCl, C₆H₆⋯IBr.     

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4?O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4?O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4?O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4?O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.     

Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, E_int, using relationships between E_int and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between E_int and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]⁻ and [Z–Hal···I]⁻ types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol.     

Halogen Bonding Interactions of Polychlorinated Biphenyls and the Potential for Thyroid Disruption

Polychlorinated biphenyl (PCB) flame retardants are persistent pollutants and inhibit neurodevelopment, particularly in the early stages of life. Halogen bonding (XB) to the iodothyronine deiodinases (Dio) that modulate thyroid hormones (THs) is a potential mechanism for endocrine disruption. Cl⋅⋅⋅Se XB interactions of PCBs with SeMe⁻, a small model of the Dio active site selenocysteine, are compared with previous results on polybrominated diphenylethers (PBDEs) and THs using density functional theory. PCBs generally display weaker XB interactions compared to PBDEs and THs, consistent with the dependence of XB strength on the size of the halogen (I>Br>Cl). PCBs also do not meet a proposed energy threshold for substrates to undergo dehalogenation, suggesting they may behave as competitive inhibitors of Dio in addition to other mechanisms of endocrine disruption. XB interactions in PCBs are position-dependent, with ortho interactions slightly more favorable than meta and para interactions, suggesting that PCBs may have a greater effect on certain classes of Dio. Flexibility of PCBs around the biphenyl C−C bond is limited by ortho substitutions relative to the biphenyl linkage, which may contribute to the ability to inhibit Dio and other TH-related proteins.     

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A⁻ and the analogous hydrogen-bonded complexes DH⋅⋅⋅A⁻ (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A⁻ arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A⁻ and the σ* orbital of D–X.     

Partition potential for hydrogen bonding in formic acid dimers

The ground-state energy and density of 4 low-energy conformations of the formic acid dimer were calculated via partition density functional theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds (HBs) among all 4 dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than 1 HB. We also provide numerical confirmation of the intuitive (but unproven) observation that fragment deformation energies are larger for systems with larger binding energies.     

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future.     

3,4,5-三羟基苯甲酸二聚体氢键结构性质

分子间相互作用在生物和材料等科学中发挥着关键作用,研究分子间相互作用的本质意义重大。氢键是分子间相互作用的一种主要形式,在确定分子构象和晶体结构以及生物分子尤其是核酸和蛋白质的结构功能中起着重要作用[1-3]。苯甲酸衍生物广泛存在于生物大分子内,与生物活性离子通过氢键作用等改变生物活性分子的活性功能,研究苯甲酸衍生物分子间氢键相互作用对于了解生物体内的化学现象具有重要意义。研究表明菱角的抗肿瘤作用明显,实验上已经从菱角中成功提取了活性单体化合物:3,4,5-三羟基苯甲酸二聚体[4],理论研究标题化合物的氢键结构与氢…     

Structure and property of the hydrogen bonding complex between triazines and water

The study of the intermolecular interactions that drive the solvation of six-membered nitrogenated aromatic rings is of particular importance since they are known to constitute key building blocks of pro- teins and nucleotides[1―5]. The investigation of the 1:1 adduct of these molecules with water will be the first step in the understanding of such interactions. These molecules possess two different proton-acceptor sites: the ring π cloud and the lone pairs of electrons on the nitrogen atoms…     

Orbital overlap and chemical bonding

The chemical bonds in the diatomic molecules Li(2)-F(2) and Na(2)-Cl(2) at different bond lengths have been analyzed by the energy decomposition analysis (EDA) method using DFT calculations at the BP86/TZ2P level. The interatomic interactions are discussed in terms of quasiclassical electrostatic interactions DeltaE(elstat), Pauli repulsion DeltaE(Pauli) and attractive orbital interactions DeltaE(orb). The energy terms are compared with the orbital overlaps at different interatomic distances. The quasiclassical electrostatic interactions between two electrons occupying 1s, 2s, 2p(sigma), and 2p(pi) orbitals have been calculated and the results are analyzed and discussed. It is shown that the equilibrium distances of the covalent bonds are not determined by the maximum overlap of the sigma valence orbitals, which nearly always has its largest value at clearly shorter distances than the equilibrium bond length. The crucial interaction that prevents shorter bonds is not the loss of attractive interactions, but a sharp increase in the Pauli repulsion between electrons in valence orbitals. The attractive interactions of DeltaE(orb) and the repulsive interactions of DeltaE(Pauli) are both determined by the orbital overlap. The net effect of the two terms depends on the occupation of the valence orbitals, but the onset of attractive orbital interactions occurs at longer distances than Pauli repulsion, because overlap of occupied orbitals with vacant orbitals starts earlier than overlap between occupied orbitals. The contribution of DeltaE(elstat) in most nonpolar covalent bonds is strongly attractive. This comes from the deviation of quasiclassical electron-electron repulsion and nuclear-electron attraction from Coulomb's law for point charges. The actual strength of DeltaE(elstat) depends on the size and shape of the occupied valence orbitals. The attractive electrostatic contributions in the diatomic molecules Li(2)-F(2) come from the s and p(sigma) electrons, while the p(pi) electrons do not compensate for nuclear-nuclear repulsion. It is the interplay of the three terms DeltaE(orb), DeltaE(Pauli), and DeltaE(elstat) that determines the bond energies and equilibrium distances of covalently bonded molecules. Molecules like N(2) and O(2), which are usually considered as covalently bonded, would not be bonded without the quasiclassical attraction DeltaE(elstat).     

CH3SH与HOCl分子间氢键和卤键的结构与性质

在DFT-B3LYP及MP2/6-311＋＋G**水平上分别求得CH3SH…HOCl氢键复合物和CH3SH…ClOH卤键复合物势能面上的稳定构型. 频率分析表明, 与单体HOCl相比, 在两种复合物中, Cl(9)—O(7)和H(8)—O(7)键伸缩振动频率发生显著的红移. 经MP2/6-311＋＋G**水平计算的含基组重叠误差(BSSE)校正的气相中相互作用能分别为－19.23和－6.85 kJ&#8226;mol－1. 自然键轨道理论(NBO)分析表明, 在CH3SH…ClOH卤键复合物中, 引起Cl(9)—O(7)键变长的因素包括2种电荷转移: (i)孤对电子LP[S(1)]1→σ*[Cl(9)—O(7)]; (ii)孤对电子LP[S(1)]2→σ*[Cl(9)—O(7)], 其中孤对电子LP[S(1)]2→σ*[Cl(9)—O(7)]转移占主要作用, 总的结果是使σ*[Cl(10)—O(11)]的自然布居数增加, 同时O(7)和Cl(9)原子s成分均增加的杂化重优具有与电荷转移作用相同的“拉长效应”; 在CH3SH…HOCl氢键复合物中也存在类似的电荷转移, 但是O(7)原子的再杂化效应不同于前者. 自然键共振理论(NRT)进行键序分析表明, 在氢键复合物和卤键复合物中, H(8)—O(7)和Cl(9)—O(7)键的键序都减小. 通过分子中原子理论(AIM)分析了复合物中氢键和卤键的电子密度拓扑性质.     

The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength

In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me₃PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond.     

Effect of excess electron on structure,bonding, and spectral properties of sulfur/selenium based dichalcogen systems

First principle based quantum chemical methods are employed to characterize structure, bonding, and spectral properties of sulfur and selenium based dichalcogen systems in presence of an excess electron. Inter molecular two-center three-electron (2c-3e) bonding between two chalcogen (X) atoms is described in the systems of the type (R-X)₂^•- (R = Ph, PhCH₂ X = S, Se). In addition, effect of electron withdrawing (-NO₂) and electron donating (-CH₃) groups in phenyl ring on the stability of these 2c-3e bonded systems is also studied in water medium applying a macroscopic hydration model. Molecular parameters and binding energy of the neutral, (R-X)₂ and reduced, (R-X)₂^•- dichalcogen systems are compared. Search for minimum energy structures of these open shell doublet systems are carried out applying various density functionals with dispersion corrections and MP2 method considering 6-311++G (d,p) set of basis functions for all atoms. Effect of water medium is introduced through a macroscopic solvation model based on density (SMD). Frontier molecular orbitals based analysis is carried out for showing the definite presence of 2c-3e bond between two chalcogen atoms in these radical anions of sulfur and selenium based aromatic dichalcogen systems. Excited state calculations are performed on all these systems using Time Dependent Density Functional Theory (TDDFT). UV-Vis spectra are simulated and effect of solvent water on the absorption maximum of these radical anions is discussed. This study illustrates that the combination of electronic effect and geometrical flexibility decides the strength of two-center three-electron bond in these systems.     

Mechanistic Aspects of the Gas‐Phase Reactions of Halobenzenes with Bare Lanthanide Cations: A Combined Experimental/Theoretical Investigation

The gas‐phase reactions of chlorobenzene with all atomic lanthanide cations Ln⁺ (except Pm⁺) have been investigated by using Fourier transform ion cyclotron resonance mass spectrometry in conjunction with density functional theory calculations. According to the latter, a direct chlorine transfer to the lanthanide cation, which has been observed previously for fluorine abstraction from fluorobenzene, is not operative for the C₆H₅Cl/Ln⁺ couples; rather, chlorine transfer proceeds through an initial coordination of the lanthanide cation to the aromatic ring of the substrate. Both, the product distribution and the chlorine abstraction efficiencies are affected by the bond dissociation energy (BDE(Ln⁺?Cl)) as well as the promotion energies of Ln⁺ to attain a 4fⁿ 5d¹ 6s¹ configuration. In addition, mechanistic aspects of some C?H and C?C bond activations are presented. Where appropriate, comparison with the previously studied C₆H₅F/Ln⁺ systems is made.     

Three for the Price of One: Concomitant I⋯N,I⋯O,and I⋯π Halogen Bonds in the Same Crystal Structure

The ditopic molecule 3-(1,3,5-trimethyl-1H-4-pyrazolyl)pentane-2,4-dione (HacacMePz) combines two different Lewis basic sites. It forms a crystalline adduct with the popular halogen bond (XB) donor 2,3,5,6-tetrafluoro-1,4-diiodobenzene (TFDIB) with a HacacMePz:TFDIB ratio of 2:3. In a simplified picture, the topology of the adduct corresponds to a hcb net. In addition to the expected acetylacetone keto O and pyrazole N acceptor sites, a third and less common short contact to a TFDIB iodine is observed: The acceptor site is again the most electron-rich site of the pyrazole π-system. This iminic N atom is thus engaged as the acceptor in two orthogonal halogen bonds. Evaluation of the geometric results and of a single-point calculation agree with respect to the strength of the intermolecular contacts: The conventional N⋯I XB is the shortest (2.909(4) Å) and associated with the highest electron density (0.150 eÅ−3) in the bond critical point (BCP), followed by the O⋯I contact (2.929(3) Å, 0.109 eÅ−3), and the π contact (3.2157(3) Å, 0.075 eÅ−3). If one accepts the idea of deducing interaction energies from energy densities at the BCP, the short contacts also follow this sequence. Two more criteria identify the short N⋯I contact as the most relevant: The associated C–I bond is significantly longer than the database average, and it is the only intermolecular interaction with a negative total energy density in the BCP.