Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis

Traditional π-covalent interactions have been proved in the non-metal halogen bond adducts formed by chloride and halogenated triphenylamine-based radical cations. In this study, we have rationally designed two metal-involving halogen bond adducts with π-covalency property, such as [L1-Pd···I-PTZ]⁺ (i.e., 1) and [L2-Pd···I-PTZ]⁺ (i.e., 2), in which the square-planar palladium complexes serve as halogen bond acceptor and 3,7-diiodo-10H-phenothiazine radical cation (i.e., [I-PTZ]^•+) acts as halogen bond donor. Noncovalent interaction analysis and quantum theory of atoms in molecules analysis revealed that there are notable halogen bond interactions along the Pd···I direction without genuine chemical bond formed in both designed adducts. Energy decomposition analysis together with natural orbital for chemical valence calculations were performed to gain insight into their bonding nature, which demonstrated the presence of remarkable π-covalent interactions and σ-covalent interactions in both 1 and 2. We therefore proposed a new strategy for building the metal-involving halogen bonds with π-covalency property, which will help the further development of new types of halogen bonds.     

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.     

分子间弱相互作用的计算——构建氢键、卤键势能面

介绍一个面向大三下学期本科生的计算化学实验。通过量子化学计算对比研究两种分子间弱相互作用——氢键和卤键的势能面,使学生对势能面的概念及两种弱相互作用的区别有一定的直观认识。通过实际上机操作,初步了解Gaussian、Gaussview及Origin等计算化学相关软件的使用,并深入理解结构化学及计算化学课程中所学的理论知识。     

Conceptual Quantum Chemical Analysis of Bonding and Noncovalent Interactions in the Formation of Frustrated Lewis Pairs

The contributions of covalent and noncovalent interactions to the formation of classical adducts of bulky Lewis acids and bases and frustrated Lewis pairs (FLPs) were scrutinized by using various conceptual quantum chemical techniques. Significantly negative complexation energies were calculated for fourteen investigated Lewis pairs containing bases and acids with substituents of various sizes. A Ziegler–Rauk‐type energy decomposition analysis confirmed that two types of Lewis pairs can be distinguished on the basis of the nature of the primary interactions between reactants; dative‐bond formation and concomitant charge transfer from the Lewis base to the acid is the dominant and most stabilizing factor in the formation of Lewis acid–base adducts, whereas weak interactions are the main thermodynamic driving force (>50 %) for FLPs. Moreover, the ease and extent of structural deformation of the monomers appears to be a key component in the formation of the former type of Lewis pairs. A Natural Orbital for Chemical Valence (NOCV) analysis, which was used to visualize and quantify the charge transfer between the base and the acid, clearly showed the importance and lack of this type of interaction for adducts and FLPs, respectively. The Noncovalent Interaction (NCI) method revealed several kinds of weak interactions between the acid and base components, such as dispersion, π–π stacking, C?H ??? π interaction, weak hydrogen bonding, halogen bonding, and weak acid–base interactions, whereas the Quantum Theory of Atoms in Molecules (QTAIM) provided further conceptual insight into strong acid–base interactions.     

“Anti-electrostatic” Halogen Bonding between Ions of Like Charge

Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong “anti-electrostatic” halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of “counter-intuitive” adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.     

Halogen bond versus hydrogen bond: The many‐body interactions approach

The analysis of interrelation between halogen bond and hydrogen bond in the (RX)(HNC)(HCN) complexes (R = CH₃, CF₃ and X = Cl, Br, I) was performed on the basis of DFT calculations. Both two‐body additive contributions and three‐body nonadditive contributions to the total interaction energy were discussed. QTAIM was used for topological analysis of electron density. Additionally, QTAIM analysis of electron density was performed for both two‐ and three‐body complexes. The electron charge transfer in trimers showed the dual character of the fragment with halogen atom involved into the investigated interactions—it acts as Lewis acid and Lewis base, depending on the type of interaction considered. The effect of cooperativity of X‐ and H‐bonding was assessed on the basis of many‐body interaction energy and electron density analysis. Additionally, an alternative two‐body model with the same situation (in the context of intermolecular interactions) is investigated. The anti‐cooperative effect was found also for this model.     

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 Bonds in Adenine-5-Bromouracil Complexes

Ab initio and density functional calculations were employed to investigate the bonding patterns in theadenine-5-bromouracil (AT+) complexes. It is shown that the Br atom in 5-bromouracil (T+) is involved in bonding both with the hydrogen atom of the amino group of adenine (A) and with N7(A) (or N1(A)). With this motif, the Br atom interacts with a nucleophile (H) in a "head-on" fashion and an electrophile(N) in a "side-on" fashion, forming both hydrogen and halogen bonds. Electrostatic attraction between the Br atom in T+ and N7 (or N1) of adenine was found via the electrostatic potential analysis. The existence of the Br···N interactions in the pairs was further conˉrmed by means of Bader's atoms in molecules theory. A bond critical point is identiˉed for the halogen bonds and the topological parameters at the bond critical point indicate the typical closed-shell interactions in the pairs. Natural bond orbital analysis suggests that the charge transfer from the lone pair of the nitrogen atom of adenine is mainly directed to the C-Br antibonding orbital. Finally, halogen bonds in the T+AT+A tetrads were also explored.     

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.     

Nature of MoH···I bonds in Cp2Mo(L)H···I‐C≡C‐R Complexes (L=H,CN, PPh2, C(CH3)3; R=NO2, Cl,Br, H,OH, CH3, NH2)

The nature of the MoH···I bond in Cp₂Mo(L)H···I‐C≡C‐R (L= H, CN, PPh₂, C(CH₃)₃; R=NO₂, Cl, Br, H, OH, CH₃, NH₂) was investigated using electrostatic potential analysis, topological analysis of the electron density, energy decomposition analysis and natural bond orbital analysis. The calculated results show that MoH···I interactions in the title complexes belong to halogen‐hydride bond, which is similar to halogen bonds, not hydrogen bonds. Different to the classical halogen bonds, the directionality of MoH···I bond is low; Although electrostatic interaction is dorminant, the orbital interactions also play important roles in this kind of halogen bond, and steric interactions are weak; the strength of H···I bond can tuned by the most positive electrostatic potential of the I atom. As the electron‐withdrawing ability of the R substituent in the alkyne increases, the electrostatic potential maximum of the I atom increases, which enhances the strength of the H···I halogen bond, as well as the electron transfer.     

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.     

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.     

Ab initio and AIM studies on typical π‐type and pseudo‐π‐type halogen bonds: Comparison with hydrogen bonds

Series of typical π‐type and pseudo‐π‐type halogen‐bonded complexes B ··· ClY and B ··· BrY and hydrogen‐bonded complex B ··· HY (B = C₂H₄, C₂H₂, and C₃H₆; Y = F, Cl, and Br) have been investigated using the MP2/aug‐cc‐pVDZ method. A striking parallelism was found in the geometries, vibrational frequencies, binding energies, and topological properties between B ··· XY and B ··· HY (X = Cl and Br). It has been found that the lengths of the weak bond d(X ··· π)/d(H ··· π), the frequencies of the weak bond ν(X ··· π)/ν(H ··· π), the frequency shifts Δν(X? Y)/Δν(H? Y), the electron densities at the bond critical point of the weak bonds ρ_c(X ··· π)/ρ_c(H ··· π), and the electron density changes Δρ_c(X? Y)/Δρ_c(H? Y) could be used as measures of the strengths of typical π‐type and pseudo‐π‐type halogen/hydrogen bonds. The typical π‐type and pseudo‐π‐type halogen bond and hydrogen bond are noncovalent interactions. For the same Y, the halogen bond strengths are in the order B ··· ClY < B ··· BrY. For the same X, the halogen bond strength decreases according to the sequence F > Cl > Br that is in agreement with the hydrogen bond strengths B ··· HF > B ··· HCl > B ··· HBr. All of these typical π‐type and pseudo‐π‐type hydrogen‐bonded and halogen‐bonded complexes have the “conflict‐type” structure. Contour maps of the Laplacian of π electron density indicate that the formation of B ··· XY halogen‐bonded complex and B ··· HY hydrogen‐bonded complex is very similar. Charge transfer is observed from B to XY/HY and both the dipolar polarization and the volume of the halogen atom or hydrogen atom decrease on B ··· XY/B ··· HY complex formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Halogen Bonding or Hydrogen Bonding between 2,2,6,6-Tetramethyl-piperidine-noxyl Radical and Trihalomethanes CHX3 (X=Cl,Br, I)

The halogen and hydrogen bonding complexes between 2,2,6,6-tetramethylpiperidine-noxyl and trihalomethanes (CHX₃, X=Cl, Br, I) are simulated by computational quantum chem-istry. The molecular electrostatic potentials, geometrical parameters and interaction energy of halogen and hydrogen bonding complexes combined with natural bond orbital analysis are obtained. The results indicate that both halogen and hydrogen bonding interactions obey the order Cl相似文献   

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates

Monohydrates of halogen monoxides ClO·H₂O and BrO·H₂O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug‐cc‐pVnZ basis sets ranging from triple‐ up to quintuple‐ζ. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO…HOH hydrogen bond and OX…OH₂ halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX…O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the O? X…O halogen bond with respect to the O…H? O hydrogen bond. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Co-existing Intermolecular Halogen Bonding and Hydrogen Bonding in the Compound Trans-5,10-bis（1-bromodifluoro-acetyl-1-ethoxycarbonyl-methylidene）thianthrene

Trans-5,10-bis(1-bromodifluoroacetyl-l-ethoxycarbonyl-methylidene)thianthrene (1b) was prepared from the reaction of BrCF2COC(N2)CO2Et with thianthrene. X-ray single crystal diffraction analysis showed that the intermolecular halogen bonding and hydrogen bonding coexisted in this compound. The bromine atom acted as an electron acceptor in the halogen bond and an electron donor in the hydrogen bond. It is the first example that the bromine atom acted as such a dual role in the hydrogen and halogen bond.     

The structure, properties, and nature of HArF-HOX (X = F, Cl, Br) complex: an ab initio study and an unusual short hydrogen bond

The structure and properties (geometric, energetic, electronic, spectroscopic, and thermodynamic properties) of HArF‐HOX (X = F, Cl, Br) complex have been investigated at the MP2/aug‐cc‐pVTZ level. Three types of complexes are formed through a hydrogen bond or a halogen bond. The HArF‐HOX complex is the most stable, followed by the FArH‐OHX complex, and the HArF‐XOH complex is the most unstable. The binding distance in FArH‐OHX complex is very short (1.1–1.7 Å) and is smaller than that in HArF‐HOX complex. However, the interaction strength in the former is weaker than that in the latter. Thus, an unusual short hydrogen bond is present in FArH‐OHX complex. The associated H‐Ar bond exhibits a red shift, whereas the distant one gives a blue shift. A similar result is also found for the O? H and O? X bonds. The isotropic chemical shift is negative for the associated hydrogen atom but is positive for the associated halogen atom. However, a reverse result is found for the anisotropic chemical shift. The analyses of natural bond orbital and atoms in molecules have been performed for these complexes to understand the nature and properties of hydrogen and halogen bonds. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Some measures for making halogen bonds stronger than hydrogen bonds in H2CS-HOX (X = F, Cl, and Br) complexes

The properties and applications of halogen bonds are dependent greatly on their strength. In this paper, we suggested some measures for enhancing the strength of the halogen bond relative to the hydrogen bond in the H(2)CS-HOX (X = F, Cl, and Br) system by means of quantum chemical calculations. It has been shown that with comparison to H(2)CO, the S electron donor in H(2)CS results in a smaller difference in strength for the Cl halogen bond and the corresponding hydrogen bond, and the Br halogen bond is even stronger than the hydrogen bond. The Li atom in LiHCS and methyl group in MeHCS cause an increase in the strength of halogen bonding and hydrogen bonding, but the former makes the halogen bond stronger and the latter makes the hydrogen bond stronger. In solvents, the halogen bond in the Br system is strong enough to compete with the hydrogen bond. The interaction nature and properties in these complexes have been analyzed with the natural bond orbital theory.     

Application of polarizable ellipsoidal force field model to pnicogen bonds

Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono‐ and polysubstituted PH₃–NH₃ complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self‐assembly structures. © 2015 Wiley Periodicals, Inc.     

Ab initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions

Halogen bonding, a specific intermolecular noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This paper presents an ab initio investigation of a series of dimeric complexes formed between bromobenzene and several electron donors. Such small model systems are selected to mimic halogen bonding interactions found within crystal structures as well as within biological molecules. In all cases, the intermolecular distances are shown to be equal to or below sums of van der Waals radii of the atoms involved. Halogen bonding energies, calculated at the MP2/aug-cc-pVDZ level, span over a wide range, from -1.52 to -15.53 kcal/mol. The interactions become comparable to, or even prevail over, classical hydrogen bonding. For charge-assisted halogen bonds, calculations have shown that the strength decreases in the order OH- > F- > HCO2- > Cl- > Br-, while for neutral systems, their relative strengths attenuate in the order H2CS > H2CO > NH3 > H2S > H2O. These results agree with those of the quantum theory of atoms in molecules (QTAIM) since bond critical points (BCPs) are identified for these halogen bonds. The QTAIM analysis also suggests that strong halogen bonds are more covalent in nature, while weak ones are mostly electrostatic interactions. The electron densities at the BCPs are recommended as a good measure of the halogen bond strength. Finally, natural bond orbital (NBO) analysis has been applied to gain more insights into the origin of halogen bonding interactions.