Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.     

Competition between Inter and Intramolecular Tetrel Bonds: Theoretical Studies Complemented by CSD Survey

Crystal structures document the ability of a TF₃ group (T=Si, Ge, Sn, Pb) situated on a naphthalene system to engage in an intramolecular tetrel bond (TB) with an amino group on the adjoining ring. Ab initio calculations evaluate the strength of this bond and evaluate whether it can influence the ability of the T atom to engage in a second, intermolecular TB with another nucleophile. A very strong CN⁻ anionic base can approach the T either along the extension of a T−C or T−F bond and form a strong TB with an interaction energy approaching 100 kcal/mol, although this bond is weakened a bit by the presence of the internal T⋅⋅⋅N bond. The much less potent NCH base engages in a correspondingly longer and weaker TB, less than 10 kcal/mol. Such an intermolecular TB is weakened by the presence of the internal TB, to the point that it only occurs for the two heavier tetrel atoms Sn and Pb.     

Triel Bonds with Au Atoms as Electron Donors

The novel triel bonds of BX₃ (X=H, F, Cl, Br, and I) and C₅H₅B as electron acceptors and AuR₂ (R=Cl and CH₃) as an electron donor were explored. The triel bond is a primary driving force for most complexes, while the contribution from a halogen-chlorine interaction in BX₃−AuCl₂ (X=Cl, Br, and I) and an iodine-Au interaction in BI₃−Au(CH₃)₃ is also very important. Interestingly, the positively charged Au atom of AuCl₂ can attractively bind with the holes of BX₃ and C₅H₅B. The interaction energy lies in the range of 1 and 80 kcal/mol, in the order X=F<H<Cl<Br<I. In most cases, the triel bond of C₅H₅B is stronger than the triel bond of BX₃. In the formation of B−Au triel bond, electrostatic energy is not dominant, while polarization energy including orbital interaction has the largest contribution for the strongly bonded complexes and dispersion energy for the weak triel bond.     

Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments

Molecules of the type XYT = Ch (T = C, Si, Ge; Ch = S, Se; X,Y = H, CH₃, Cl, Br, I) contain a σ-hole along the T = Ch bond extension. This hole can engage with the N lone pair of NCH and NCCH₃ so as to form a chalcogen bond. In the case of T = C, these bonds are rather weak, less than 3 kcal/mol, and are slightly weakened in acetone or water. They owe their stability to attractive electrostatic energy, supplemented by dispersion, and a much smaller polarization term. Immersion in solvent reverses the electrostatic interaction to repulsive, while amplifying the polarization energy. The σ-holes are smaller for T = Si and Ge, even negative in many cases. These Lewis acids can nonetheless engage in a weak chalcogen bond. This bond owes its stability to dispersion in the gas phase, but it is polarization that dominates in solution.     

The Role of Hydrogen Bonds in Interactions between [PdCl4]2− Dianions in Crystal

[PdCl₄]²⁻ dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. The placement of neutral ligands in their vicinity reduces the repulsion, but the interaction remains highly endothermic. When the ligands acquire a unit positive charge, the electrostatic component and the full interaction energy become quite negative, signalling an exothermic association. Raising the charge on these counterions to +2 has little further stabilizing effect, and in fact reduces the electrostatic attraction. The ability of the counterions to promote the interaction is attributed in part to the H-bonds which they form with both dianions, acting as a sort of glue.     

Competition between Intra and Intermolecular Pnicogen Bonds: Complexes between Naphthalene Derivatives and Neutral or Anionic Bases

The PnF₂ (Pn=P,As,Sb,Bi) on a naphthalene scaffold can engage in an internal pnicogen Pn⋅⋅⋅N bond (PnB) with an NH₂ group placed close to it on the adjoining ring. An approaching neutral NH₃ molecule can engage in a second PnB with the central Pn, which tends to weaken the intramolecular bond. The presence of the latter in turn weakens the intermolecular PnB with respect to that formed in its absence. Replacement of the external NH₃ by a CN⁻ anion causes a fundamental change in the bonding pattern, producing a fourth covalent bond with Pn, which rearranges into a trigonal bipyramidal motif. This addition disrupts the internal Pn⋅⋅⋅N pnicogen bond, recasting the PnF₂⋅⋅⋅NH₂ interaction into an NH⋅⋅⋅F H-bond.     

Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond

A computational study of the complexes formed by TF₃OH (T=C, Si, Ge) with three nitrogen-containing bases NCH, NH₃, and imidazole (IM) is carried out at the MP2/aug-cc-pVTZ level. TF₃OH can participate in two different types of noncovalent interactions: a hydrogen bond (HB) involving the hydroxyl proton and a tetrel bond (TB) with the tetel atom T. The strength of the HB is largely unaffected by the identity of T while the TB is enhanced as T grows larger. The HB is preferred over the TB for most systems, with the exception of GeF₃OH with either NH₃ or IM. MgCl₂ engages in a Mg⋅⋅⋅O Magnesium bond (Mg-bond) with the TF₃OH O atom, which cooperatively enhances both the HB and TB. The HB strengthening is particularly large for the NH₃ or IM bases, and especially for CF₃OH, but is slowly reduced as the T atom grows larger. The TB enhancement, on the other hand, behaves in the opposite fashion, accelerating for the larger T atoms. As a bottom line, the Mg-bond generally reinforces and accentuates the preference for the HB or TB that is already present in the dimer. The Mg-bond is also responsible for a proton transfer in the HB configurations with NH₃ and IM.     

Complexes of HArF and AuX (X = F,Cl, Br,I). Comparison of H-bonds,halogen bonds,F-shared bonds and covalent bonds

The various sorts of complexes in which HArF and AuX (X = F, Cl, Br, I) can engage are probed by MP2/aug-cc-pVTZ calculations. The most weakly bound are those containing a halogen bond (XB) of the AuX⋯FArH sort, with binding energies less than 8 kcal/mol. H-bonded dimers FArH⋯XAu are a little stronger, held together by some 12 kcal/mol. Being the most strongly bound places the F atom of HArF roughly midway between Ar and Au in an F-shaped structure, bound by some 43–54 kcal/mol. The last sort of product involves atomic rearrangements wherein the H atom migrates from Ar to Au, followed by formation of a covalent Ar–Au bond. The resulting molecular unit is stabilized by 30–40 kcal/mol relative to the original HArF and AuX reactants. The H-bonded dimers are held together by an unusually large polarization component, surpassing electrostatic attraction, while dispersion predominates for the halogen bonds. Perturbations of the geometries and stretching frequencies offer a ready means of distinguishing the different types of complexes by spectroscopic techniques.     

Anion–Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment

Ab initio calculations are applied to the question as to whether a AeX₅⁻ anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F⁻, Cl⁻, or CN⁻. The latter approaches the central Ae atom from above the molecular plane, along its C₅ axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.     

H2XP…SHY复合物中磷键与硫键的理论研究

用从头算量子化学方法MP2 与CCSD(T)研究了H₂XP和SHY (X, Y=H, F, Cl, Br)分子的P与S之间形成的磷键X―P…S与硫键Y―S…P的本质与规律以及取代基X与Y对成键的影响. 计算结果表明, 硫键比磷键强, 连接在Lewis 酸上的取代基的电负性增大导致形成的磷键或硫键增强, 键能增大, 对单体的结构和性质的影响也增大; 而连接在Lewis 碱上的取代基效应则相反. 硫键键能为8.37-23.45 kJ·mol^-1, 最强的硫键结构是Y 电负性最大而X 电负性最小的HFS…PH₃, CCSD(T)计算的键能是16.04 kJ·mol^-1; 磷键键能为7.54-14.65 kJ·mol^-1, 最强的磷键结构是X 电负性最大而Y 电负性最小的H₂FP…SH₂, CCSD(T)计算的键能是12.52 kJ·mol^-1. 对磷键与硫键能量贡献较大的是交换与静电作用. 分子间超共轭lp(S)-σ^*(PX)与lp(P)-σ^*(SY)对磷键与硫键的形成起着重要作用, 它导致单体的极化, 其中硫键的极化效应较大, 从而有一定的共价特征.     

Halogen and Chalcogen Bond Energies Evaluated Using Electron Density Properties

Halogen (X-bond) and chalcogen bond (Ch−bond) energies for 36 complexes have been obtained at the RI-MP2/def2−TZVP level of theory, involving the heavier halogen and chalcogen atoms (Br, I, Se, Te). We have explored the existence of linear relationships between the interaction energies and the local kinetic energy densities at the bond critical points that characterize the σ-hole interactions (both electronic G(r) and potential V(r) energy densities). Interestingly, we have found strong relationships for halogen and chalcogen bonding energies, especially for the V(r) energy density, thus allowing to estimate the interaction energy without computing the separate monomers. This is also useful to estimate the interaction in monomeric systems (intramolecular X/Ch-bonds), as illustrated using several examples. Remarkably, we have also found a good relationship when in the same representation both halogen and chalcogen atoms are included, thus allowing to use the same empirical correlation for both interactions.     

The Balance between Hydrogen Bonds,Halogen Bonds,and Chalcogen Bonds in the Crystal Structures of a Series of 1,3,4-Chalcogenadiazoles

In order to explore how specific atom-to-atom replacements change the electrostatic potentials on 1,3,4-chalcogenadiazole derivatives, and to deliberately alter the balance between intermolecular interactions, four target molecules were synthesized and characterized. DFT calculations indicated that the atom-to-atom substitution of Br with I, and S with Se enhanced the σ-hole potentials, thus increasing the structure directing ability of halogen bonds and chalcogen bonds as compared to intermolecular hydrogen bonding. The delicate balance between these intermolecular forces was further underlined by the formation of two polymorphs of 5-(4-iodophenyl)-1,3,4-thiadiazol-2-amine; Form I displayed all three interactions while Form II only showed hydrogen and chalcogen bonding. The results emphasize that the deliberate alterations of the electrostatic potential on polarizable atoms can cause specific and deliberate changes to the main synthons and subsequent assemblies in the structures of this family of compounds.     

On the Stability of Interactions between Pairs of Anions – Complexes of MCl3− (M=Be,Mg, Ca,Sr, Ba) with Pyridine and CN−

The ability of the central M atom of the MCl₃⁻ anion, with M=Be, Mg, Ca, Sr, Ba, to engage in a noncovalent bond with an approaching nucleophile is gauged by ab initio methods. The N atom of pyridine forms a M⋅⋅⋅N bond with an interaction energy between 12 and 21 kcal mol⁻¹, even though the π-hole above the M atom is not necessarily positive in sign. Despite a strong Coulombic repulsion between two anions, CN⁻ is also able to approach the M atom so as to engage in a metastable complex that is higher in energy than the individual anions. The energy barrier separating this complex from its constituent anion pair is roughly 20 kcal mol⁻¹. Despite the endothermic formation reaction energy of the CN⁻⋅⋅⋅MCl₃⁻ complex, the electron topology signals a strong interaction, more so than in pyridine⋅⋅⋅MCl₃⁻ with its exothermic binding energy. The dianionic complex is held together largely on the strength of interorbital interactions, thereby overcoming a repulsive electrostatic component. The latter is partially alleviated by the pyramidalization of the MCl₃ unit which makes its π-hole more positive. The complex sinks below the separate monomers in energy when the system is immersed in an aqueous medium, with a binding energy that varies from as much as 20 kcal mol⁻¹ for Be down to 1.2 kcal mol⁻¹ for Ba.     

PH2X与五元杂环体系磷键相互作用的理论研究

用MP2/aug-cc-pVDZ方法计算了PH2X(X=H,F,Cl,Br)与五元杂环化合物(吡咯、呋喃、噻吩)的相互作用,经完全均衡校正法校正基组重叠误差.在MP2/aug-cc-pVDZ优化基础上采用Gaussian 03程序包中的NBO程序计算了二级微扰稳定化能(ΔE2),并运用AIM 2000程序对其AIM性质进行了计算.为了进一步加强对该类相互作用的认识,应用约化密度梯度(RDG)填色等值面图和电子密度差图对代表性的体系进行了图形化分析.研究表明:PH3与三个五元杂环化合物形成的是P—H…π氢键相互作用;PH2X(X=F,Cl,Br)与五元杂环化合物形成磷键相互作用,这些磷键体系存在π型和n型两种形式的磷键相互作用,前者形成复合物的稳定性高于后者,并且相互作用大小与磷原子到杂环质心的矢量和P—X方向矢量的夹角密切相关.作为比较,我们对PCl3与这三种杂环化合物之间的相互作用也进行了研究,结果发现,PCl3分子中沿Cl—P键的P端出现了三个正的静电势区域或称作"σ-hole",因此其与杂环化合物形成的是分子间多磷键复合物.AIM拓扑分析表明磷键相互作用的本质属于闭壳层静电相互作用,且电子密度与复合物稳定性呈正相关.RDG图形化分析揭示了磷键相互作用所在的空间位置以及相对强度.DDF分析表明,磷键相互作用的存在使磷原子端基的电子密度减少,而沿着P—X轴以及五元杂环分子的电子密度增加,从而直观地体现了形成复合物后电子密度的重排情况.     

Detailed comparison of the pnicogen bond with chalcogen,halogen, and hydrogen bonds

The characteristics of the pnicogen bond are explored using a variety of quantum chemical techniques. In particular, this interaction is compared with its halogen and chalcogen bond cousins, as well as with the more common H‐bond. In general, these bonds are all of comparable strength. More specifically, they are strengthened by the presence of an electronegative substituent on the electron‐acceptor atom, and each gains strength as one moves down the appropriate column of the periodic table, for example, from N to P to As. These noncovalent bonds owe their stability to a mixture in nearly equal parts of electrostatic attraction and charge transfer, along with a smaller dispersion component. The charge transfer arises from the overlap between the lone pair of the electron donor and a σ* antibond of the acceptor. The angular characteristics of the equilibrium geometry result primarily from a compromise between electrostatic and induction forces. Angular distortions of the H‐bond are typically less energetically demanding than comparable bends of the other noncovalent bonds. © 2012 Wiley Periodicals, Inc.     

Anionic CH⋅⋅⋅X− Hydrogen Bonds: Origin of Their Strength,Geometry, and Other Properties

CF₃H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug‐cc‐pVDZ calculations. The binding energy of monoanions halide, NO₃^?, formate, acetate, HSO₄^?, and H₂PO₄^? lie in the 12–17 kcal mol^?1 range, although F^? is more strongly bound, by 26 kcal mol^?1. Dianions SO₄^2? and HPO₄^2? are bound by 27 kcal mol^?1, and trianion PO₄^3? by 45 kcal mol^?1. When two O atoms are available on the anion, the CH???O^? H‐bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.     

(CH3)2S与HOCl分子间的卤键和氢键相互作用

在DFT-B3LYP/6-311++G**水平上分别求得(CH3)2S…ClOH卤键复合物和(CH3)2S…HOCl氢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, 10Cl—11O和12H—11O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-11.69和-24.16 kJ·mol-1. 自然键轨道理论(NBO)分析表明, 在(CH3)2S…ClOH卤键复合物中, 引起10Cl—11O键变长的因素包括两种电荷转移: (i) 孤对电子LP(1S)1→σ*(10Cl—11O); (ii) 孤对电子LP(1S)2→σ*(10Cl—11O), 其中孤对电子LP(1S)2→σ*(10Cl—11O)转移占主要作用, 总的结果是使σ*(10Cl—11O)的自然布居数增加0.14035e, 同时11O原子的再杂化使其与10Cl成键时s成分增加, 即具有与电荷转移作用同样的“拉长效应”; 在(CH3)2S…HOCl氢键复合物中也存在类似的电荷转移, 但是11O原子的再杂化不同于前者. 自然键共振理论(NRT)进行键序分析表明, 在卤键复合物和氢键复合物中, 10Cl—11O和12H—11O键的键序都减小. 通过分子中原子理论(AIM)分析了复合物中卤键和氢键的电子密度拓扑性质.     

Interactions between temozolomide and guanine and its S and Se‐substituted analogues

Temozolomide was paired with guanine, 6‐selenoguanine, and 6‐thioguanine, as well as the SH tautomer of the latter. The potential energy surface of each heterodimer was searched for all minima, using Dispersion‐Corrected Density Functional Theory and MP2 methods. Among the dozens of minima, three categories were observed. Stacked geometries place the aromatic systems of the two molecules parallel to one another, while the two systems are roughly perpendicular to one another in a second category. Also found are coplanar structures held together by H‐bonds. Dispersion proves to be a dominating attractive force for the stacked structures, less so for perpendicular, and smallest for the coplanar dimers. Geometries and energetics are relatively insensitive to S and Se substitution, but tautomerization reverses relative stabilities of different geometries.     

Theoretical Studies on the Hydrogen Bonds of Different Position Action Mechanisms of Thymine with Uracil

In this research, the hydrogen bonds Y···H-X(X = C, N; Y = N, O) of thymine and uracil have been theoretically studied. The results show that hydrogen bond leads to bond length elongation and stretches the frequency red-shift of N-H···Y. Meanwhile, the C-H···O bonds shorten and stretch the frequency blue-shift. They all belong to traditional hydrogen bonds. The intermolecular charge transfer caused by the intermolecular hyperconjugation ρ*(N–H) →n(Y) and intramolecular charge redistribution by intramolecular hyperconjugation ρ(C-H)→ρ*(C-N) play important roles in the formation of hydrogen bonds. According to the judgment standards proposed by Bader and Popelier, these hydrogen bonds have typical electron density topological properties. Electrostatic surface potential(ESP) is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as the prediction of likely sites of electrophilic and nucleophilic metabolic attack.