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.     

Can halogen bond energy be reliably estimated from electron density properties at bond critical point? The case of the (A)nZ—Y•••X− (X,Y = F,Cl, Br) interactions

Relationships between the Y•••X bond critical point (BCP) properties or the Y•••X distance and the halogen bond interaction energy were analyzed in detail by theoretical methods for the series of structures [(A)_nZ—Y•••X]⁻ (X,Y = F, Cl, Br; totally 441 structures). No relationship was found for the whole set of structures or for the series [(A)_nZ—F•••X]⁻, [(A)_nZ—Cl•••X]⁻, and [(A)_nZ—Br•••X]⁻. The interaction energies may be roughly estimated from the BCP properties for the series [(A)_nZ—Y•••F]⁻, [(A)_nZ—Y•••Cl]⁻, and [(A)_nZ—Y•••Br]⁻ as well as for [(A)_nZ—Y•••X]⁻ (when (A)_nZ is variable, X and Y are constant) with the mean absolute deviation values 2.04-4.38 kcal/mol. The corresponding recommended relationships are provided and they are significantly different from the popular dependencies deduced previously for other types of noncovalent interactions. Tremendous effect of the computational method and basis set on the relationships under analysis was discovered. Computational results clearly indicate that, for practical purposes, the E_int(BCP property) dependencies should be established not simply for each global type of interactions (hydrogen bond, halogen bond, chalcogen bond, etc.) but for each combination of the first and second order atoms taking into account also the computational method and basis set.     

Halogen bonding with the halogenabenzene bird structure,halobenzene, and halocyclopentadiene

The ability of the “bird-like” halogenabenzene molecule, referred to as X-bird (XCl to At), to form halogen-bonded complexes with the nucleophiles H₂O and NH₃ was investigated using double-hybrid density functional theory and the aug-cc-pVTZ/aug-cc-pVTZ-PP basis set. The structures and interaction energies were compared with 5-halocyclopenta-1,3-diene (halocyclopentadiene; an isomer of halogenabenzene) and halobenzene, also complexed with H₂O and NH₃. The unusual structure of the X-bird, with the halogen bonded to two carbon atoms, results in two distinct σ-holes, roughly at the extension of the C-X bonds. Based on the behavior of the interaction energy (which increases for heavier halogens) and van der Waals (vdW) ratio (which decreases for heavier halogens), it is concluded that the X-bird forms proper halogen bonds with H₂O and NH₃. The interaction energies are larger than those of the halogen-bonded complexes involving halobenzene and halocyclopentadiene, presumably due to the presence of a secondary interaction. © 2019 Wiley Periodicals, Inc.     

Theoretical study on the interactions of halogen‐bonds and pnicogen‐bonds in phosphine derivatives with Br2, BrCl,and BrF

The MP2 ab initio quantum chemistry methods were utilized to study the halogen‐bond and pnicogen‐bond system formed between PH₂X (X = Br, CH₃, OH, CN, NO₂, CF₃) and BrY (Y = Br, Cl, F). Calculated results show that all substituent can form halogen‐bond complexes while part substituent can form pnicogen‐bond complexes. Traditional, chlorine‐shared and ion‐pair halogen‐bonds complexes have been found with the different substituent X and Y. The halogen‐bonds are stronger than the related pnicogen‐bonds. For halogen‐bonds, strongly electronegative substituents which are connected to the Lewis acid can strengthen the bonds and significantly influenced the structures and properties of the compounds. In contrast, the substituents which connected to the Lewis bases can produce opposite effects. The interaction energies of halogen‐bonds are 2.56 to 32.06 kcal·mol^?1; The strongest halogen‐bond was found in the complex of PH₂OH???BrF. The interaction energies of pnicogen‐bonds are in the range 1.20 to 2.28 kcal·mol^?1; the strongest pnicogen‐bond was found in PH₂Br???Br₂ complex. The charge transfer of lp(P) ? σ*(Br? Y), lp(F) ? σ*(Br? P), and lp(Br) ? σ*(X? P) play important roles in the formation of the halogen‐bonds and pnicogen‐bonds, which lead to polarization of the monomers. The polarization caused by the halogen‐bond is more obvious than that by the pnicogen‐bond, resulting in that some halogen‐bonds having little covalent character. The symmetry adapted perturbation theory (SAPT) energy decomposition analysis showes that the halogen‐bond and pnicogen‐bond interactions are predominantly electrostatic and dispersion, respectively.     

The competition of Y⋯o and X⋯n halogen bonds to enhance the group V σ‐hole interaction in the NCY⋯oPH3⋯NCX and OPH3⋯NCX⋯NCY (X,YF,Cl, and Br) complexes

The positive electrostatic potentials (ESP) outside the σ‐hole along the extension of O? P bond in O?PH₃ and the negative ESP outside the nitrogen atom along the extension of the C? N bond in NCX could form the Group V σ‐hole interaction O?PH₃?NCX. In this work, the complexes NCY?O?PH₃?NCX and O?PH₃?NCX?NCY (X, Y?F, Cl, Br) were designed to investigate the enhancing effects of Y?O and X?N halogen bonds on the P?N Group V σ‐hole interaction. With the addition of Y?O halogen bond, the V _{S, max} values outside the σ‐hole region of O?PH₃ becomes increasingly positive resulting in a stronger and more polarizable P?N interaction. With the addition of X?N halogen bond, the V _{S, min} values outside the nitrogen atom of NCX becomes increasingly negative, also resulting in a stronger and more polarizable P?N interaction. The Y?O halogen bonds affect the σ‐hole region (decreased density region) outside the phosphorus atom more than the P?N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X?N halogen bonds. © 2015 Wiley Periodicals, Inc.     

Competitive interaction between halogen and hydrogen bonds in NH2Br‐HOX (X = F,Cl, and Br) complex

The NH₂Br‐HOX (X = F, Cl, and Br) complexes have been investigated with quantum chemical calculations at the MP2/aug‐cc‐pVTZ level. Five isomers are observed for the Cl and Br complexes, whereas only two isomers are found for the F complex. The geometrical, energetic, and spectroscopic parameters have been analyzed for these complexes. The hydrogen‐bonded complexes are more stable than the halogen‐bonded ones. In most complexes, the associated O? H and O? X bonds are elongated and show a red shift, whereas the distant bonds are contracted and exhibit a blue shift. The complexes have been analyzed with natural bond orbital and atoms in molecules. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Rational Modification of the Hierarchy of Intermolecular Interactions in Molecular Crystal Structures by Using Tunable Halogen Bonds

A family of 16 isomolecular salts (3‐XpyH)₂[MX′₄] (3‐XpyH=3‐halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X′=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X‐ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non‐covalent interactions: N? H???X′? M hydrogen bonds, C? X???X′? M halogen bonds and π–π stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C? X???X′? M halogen bonds, whereas an analogous change of the inorganic halogen (X′) weakens both halogen bonds and N? H???X′? M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C? F???X′? M) halogen bonds are absent. The structure is directed by N? H???X′? M hydrogen bonds and π‐stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X′), long (weak) C? X???X′? M interactions are observed with type I halogen–halogen interaction geometries (C? X???X′ ≈ X???X′? M ≈155°), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X′), stronger halogen bonds are formed with a type II halogen–halogen interaction geometry (C? X???X′ ≈180°; X???X′? M ≈110°) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

Predicting the halogen-n (n = 3–6) synthons to form the “windmill” pattern bonding based on the halogen-bonded interactions

The “windmill” pattern cyclic halogen polymers (XBr)3 (X = Cl, Br, I) and (BrY)n (n = 3–6, Y = Cl, Br, I) have been investigated using the density functional theory. Due to the anisotropic distribution of its electron density, the halogen atom can form halogen-bonded interactions by functioning as both electron donor sites and electron acceptor sites. For (XBr)3 (X = Cl, Br, I) trimers, the Cl···Cl interaction is the weakest, and the I···I interaction is the strongest. For (BrY)n (n = 3–6, Y = Cl, Br, I), the Br···Br halogen bonds are the strongest in (BrY)₄ tetramers. We predict that the iodine-4 synthon may allow creation of a self-assembled island during crystal growth. The angle formed by the electron-depleted sigma-hole, the halogen atom and the electron-rich equatorial belt perpendicular to the bond direction, together with the halogen-bond angle, can be used to explain the geometries and strength of the halogen-bond interactions. © 2018 Wiley Periodicals, Inc.     

Structures and electronic properties of Al7x0,- and Al13 X1,2,12- clusters with X=F, Cl, and Br

The structures, binding energies, and electronic properties for Al7X, Al7X-, Al13X-, Al13X2-, and Al13X12- (X = F, Cl, Br) were studied at the B3LYP/6-311+G(2d,p) level. Among the systems studied, Al7 and Al13 clusters in Al7X and Al13X- reveal alkali-like and halogen-like superatom characters, respectively. Al7 can bind with one halogen atom to form a salt-like compound as Al7+delta-X-delta. Al13- can combine with one halogen atom to form a diatomic halogen anion Al13X-. However, when adding more halogens, the superatom structure would be destroyed, resulting in low-symmetry compounds with the center Al atom moving toward the cluster surface. The structures of Al13X1,2,12- (X = F, Cl, Br) are similar to those of X = I; however, their binding energies and electron structures are much different. In addition, the analyses of the calculated NBO charges show that Cl and Br have similar properties, but much different from F, when interacting with the Al clusters. The Al-Cl and Al-Br bonds have more covalent character in Al7X and Al13X2,12-, in contrast to the corresponding Al-F bond, which has prominent ionic character.     

NCO/NCS自由基与XY（X=H,Cl;Y=F,Cl,Br）间σ-型弱作用的理论研究

NCO和NCS是大气化学中非常引人关注的自由基,它们均有三个原子并且两个端基原子均可作为电子给体形成σ-型氢/卤键.本文在MP2/aug-cc-pVDZ水平上研究了NCO/NCS...XY（X=H,Cl;Y=F,Cl,Br）体系中的弱化学键.计算结果表明,氢/卤原子与N原子相连形成的复合物比与O/S原子相连形成的复合物稳定;氢/卤键的稳定性由分子静电势决定,而非原子电负性;对相同的电子给体B（B=N,O/S）和相同的卤原子来说,化学键的强度按Y=F,Cl,Br的顺序逐渐减弱.在氢/卤键形成过程中,自旋电子密度在电子给体和电子受体间的转移较少,但它在自由基内部发生重排,就本文研究的所有复合物而言,自旋电子密度均转移向XY分子的相反位置.     

Four-Center Nodes: Supramolecular Synthons Based on Cyclic Halogen Bonding

The isocyanide trans-[PdBr₂(CNC₆H₄-4-X′)₂] (X′=Br, I) and nitrile trans-[PtX₂(NCC₆H₄-4-X′)₂] (X/X′=Cl/Cl, Cl/Br, Br/Cl, Br/Br) complexes exhibit similar structural motif in the solid state, which is determined by hitherto unreported four-center nodes formed by cyclic halogen bonding. Each node is built up by four Type II C−X′⋅⋅⋅X−M halogen-bonding contacts and include one Type I M−X⋅⋅⋅X−M interaction, thus giving the rhombic-like structure. These nodes serve as supramolecular synthons to form 2D layers or double chains of molecules linked by a halogen bond. Results of DFT calculations indicate that all contacts within the nodes are typical noncovalent interactions with the estimated strengths in the range 0.6–2.9 kcal mol⁻¹.     

Comparison between Hydrogen and Halogen Bonds in Complexes of 6-OX-Fulvene with Pnicogen and Chalcogen Electron Donors

Quantum chemical calculations are applied to complexes of 6-OX-fulvene (X=H, Cl, Br, I) with ZH₃/H₂Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H-bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order O<S<Se<Te, whereas the pattern is murkier for the pnicogen donors. In terms of competition, most halogen bonds to pnicogen donors are stronger than their H-bond analogues, but there is no clear pattern with respect to chalcogen donors. O prefers a H-bond, while halogen bonds are favored by Te. For S and Se, I-bonds are strongest, followed Br, H, and Cl-bonds in that order.     

一系列水合和非水合铀酰卤族(F,Cl,Br)配合物在水溶液中的结构和紫外吸收光谱性质的密度泛函理论研究

本文考虑相对论效应并应用密度泛函理论(DFT)研究水溶液中UO2Xn(H2O)5-n(X=F,Cl,Br;n=1～4)和UO2Xn(X=F,Cl,Br;n=1～6)一系列水合和非水合铀酰化合物的结构和紫外吸收光谱性质。将这一系列物质命名为Xnm(X为F,Cl,和Br;n为卤素配体个数,m为水分子配体的个数)。在水溶液中,溶剂化效应采用类导体屏蔽模型(COSMO)并采用SAS溶剂接触曲面构造空穴模拟水溶剂对配合物的作用。配合物的紫外光谱性质采用考虑旋-轨耦合相对论效应的含时密度泛函(SO-TD-DFT)进行计算。U=O键随着F配体数目的增加而明显伸长,然而随Cl和Br配体数目的增加变化较小。随X配体数目的增加和水分子参与配位,铀与X的结合能逐渐减弱。配合物的紫外光谱计算表明铀酰氟的各种配合物并不出现特征吸收峰,而铀酰氯和铀酰溴的各种配合物均有特征吸收光谱。通过分子轨道分析可以很好解释光谱所体现的特征。     

Does Fluorine Participate in Halogen Bonding?

When R is sufficiently electron withdrawing, the fluorine in the R?F molecules could interact with electron donors (e.g., ammonia) and form a noncovalent bond (F ??? N). Although these interactions are usually categorized as halogen bonding, our studies show that there are fundamental differences between these interactions and halogen bonds. Although the anisotropic distribution of electronic charge around a halogen is responsible for halogen bond formations, the electronic charge around the fluorine in these molecules is spherical. According to source function analysis, F is the sink of electron density at the F ??? N BCP, whereas other halogens are the source. In contrast to halogen bonds, the F ??? N interactions cannot be regarded as lump–hole interactions; there is no hole in the valence shell charge concentration (VSCC) of fluorine. Although the quadruple moment of Cl and Br is mainly responsible for the existence of σ‐holes, it is negligibly small in the fluorine. Here, the atomic dipole moment of F plays a stabilizing role in the formation of F ??? N bonds. Interacting quantum atoms (IQA) analysis indicates that the interaction between halogen and nitrogen in the halogen bonds is attractive, whereas it is repulsive in the F ??? N interactions. Virial‐based atomic energies show that the fluorine, in contrast to Cl and Br, stabilize upon complex formation. According to these differences, it seems that the F ??? N interactions should be referred to as “fluorine bond” instead of halogen bond.     

Competition between halogen bond and hydrogen bond in complexes of superalkali Li3S and halogenated acetylene XCCH (X = F,Cl, Br,and I)

Complexes of superalkali Li₃S and XCCH (X = F, Cl, Br, and I) have been studied with theoretical calculations at the MP2/aug‐cc‐pVTZ level. Three types of structures are found: (A) the X atom combines with the S atom through a halogen bond; (B) the X atom interacts with the π electron of Li₃S by a π halogen bond; (C) the H atom combines with the S atom through a hydrogen bond. For A and B, a heavier halogen atom makes the interaction stronger, while for C, the change of interaction energy is not obvious, showing a small dependence on the nature of the X atom in HCCX. A is more stable than B and their difference in stability decreases as X varies from Cl to I. For the F and Cl complexes, A is weaker than C, however, the former is stronger than the latter in the Br and I complexes. The above three types of interactions have been analyzed by means of electron localization function, electron density difference, and energy decomposition, and the results show that they have similar nature and features with conventional interactions. © 2014 Wiley Periodicals, Inc.     

Triel Bond Formed by Malondialdehyde and Its Influence on the Intramolecular H-Bond and Proton Transfer

Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX₃ (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX₃ (X = Cl and Br) and MDA-AlX₃ (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH₂ substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH₃ (Tr = B and Al).     

Halogen bonding between substituted chlorobenzene and trimethylamine: Decisive role of σ–hole and C?Cl bond breaking energy

Theoretical studies have been carried out on the halogen bonding interaction between para substituted chlorobenzene (Y C₆H₄Cl, Y = H, NH₂, CH₃, F, CN, NO₂) and N(CH₃)₃ using ab initio MP2/aug‐cc‐pVDZ and DFT based wB97XD/6‐311++G(d,p) methods. The positive electrostatic potential (V_S,max) on the Cl atom and the heterolytic bond breaking enthalpy of the C Cl bond have been calculated and their role on halogen bonding is discussed. The heterolytic bond breaking enthalpy of the C Cl bond is proposed as a measure of the strength of the σ‐hole on Cl atom. The binding strength of the complexes ranging between −6.13 kJ mol⁻¹ and −9.29 kJ mol⁻¹ are linearly related to the V_S,max of the Cl atom and the bond breaking enthalpy of the C Cl bond. In addition, energy decomposition analysis was performed on the halogen bonded complexes via symmetry adapted perturbation theory (SAPT) to predict the dominant energy component and the nature of the N···Cl interaction.     

Structure cristalline de NaSbF3NO3·H2O. Etude de la liaison hydrogene OHX (X = Cl,Br, NO3)

NaSbF₃NO₃·H₂O compound has been isolated in the SbF₃NaNO₃H₂O system. The crystal structure was determined by X-ray diffraction on a single crystal. The final R factor is 0.044. The structure is compared with those of NaSbF₃X·H₂O (X = Cl, Br). The hydrogen bonds OH…X (X = Cl, Br, NO₃) form the subject of a vibrational spectroscopic study.     

Fluorine as a Lewis acid: A symmetry-adapted perturbation theory based on density functional theory and interacting quantum atoms study of noncovalent interactions in the NCF⋯NH3 complex

Different computational methods are used to investigate the nature of interaction in the NCF⋯NH₃ model complex, in which the fluorine atom acts as a Lewis acid and forms a noncovalent bond with the ammonia (Lewis base). Symmetry-adapted perturbation theory based on density functional theory (SAPT(DFT)) indicates that the noncovalent interaction in the NCF⋯NH₃ complex is mainly electrostatics. However, dispersion and induction terms also play important roles. Although fluorine noncovalent interactions are typically classified as halogen bonds, they are somewhat different from the well-known halogen bonds of iodine, bromine, and chlorine. The halogen bonds of NCCl⋯NH₃ and NCBr⋯NH₃ are directional and the C  X  N (X = Cl or Br) angle tends to be linear. In contrast, the fluorine interaction in NCF⋯NH₃ is not directional; the interaction energy shows no sensitivity to the angular (C  F  N ) distortions, and the energy profile is flat over a wide angular range (from 180° to about 140° ). However, for the angles less than 130° , the energy curve shows a clear angular dependence and the interaction between NCF and NH₃ becomes stronger as the C  F  N angle decreases. It seems that at the tighter angles, a tetrel-bonded NCF⋯NH₃ complex is preferred. Moreover, interacting quantum atoms (IQA) analysis shows that the competition between different intra-atomic and interatomic interactions determines the geometry of NCF⋯NH₃ complex.