Pnicogen bonds between X═PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases

Involvement of Arsenic Atom of AsF3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models

Bonding within the AsF3 crystal is analyzed via quantum chemical methods so as to identify and quantify the pnicogen bonds that are present. The structure of a finite crystal segment containing nine molecules is compared with that of a fully optimized cluster of the same size. The geometries are qualitatively different, with a much larger binding energy within the optimized nonamer. Although the total interaction energy of a central unit with the remaining peripheral molecules is comparable for the two structures, the binding of the peripherals with one another is far larger in the optimized cluster. This distinction of much stronger total binding within the optimized cluster is not limited to the nonamer but repeats itself for smaller aggregates as well. The average binding energy of the cluster rises quickly with size, asymptotically approaching a value nearly triple that of the dimer.

On the Importance of Pnictogen and Chalcogen Bonding Interactions in Supramolecular Catalysis

In this review, several examples of the application of pnictogen (Pn) (group 15) and chalcogen (Ch) bonding (group 16) interactions in organocatalytic processes are gathered, backed up with Molecular Electrostatic Potential surfaces of model systems. Despite the fact that the use of catalysts based on pnictogen and chalcogen bonding interactions is taking its first steps, it should be considered and used by the scientific community as a novel, promising tool in the field of organocatalysis.

On the Importance of σ–Hole Interactions in Crystal Structures

Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.

Group 12 Carbonates and their Binary Complexes with Nitrogen Bases and FH2 Z Molecules (Z=P, As, Sb): Synergism in Forming Ternary Complexes

MCO₃ (M=Zn, Cd, Hg) forms a spodium bond with nitrogen-containing bases (HCN, NHCH₂ , NH₃ ) and a pnicogen bond with FH₂ Z (Z=P, As, Sb). The spodium bond is very strong with the interaction energy ranging from -31 kcal/mol to -56 kcal/mol. Both NHCH₂ and NH₃ have an equal electrostatic potential on the N atom, but the corresponding interaction energy is differentiated by 1.5-4 kcal/mol due to the existence of spodium and hydrogen bonds in the complex with NHCH₂ as the electron donor. The spodium bond is weakest in the HCN complex, which is not consistent with the change of the binding distance. The spodium bond becomes stronger in the CdCO₃ <ZnCO₃ <HgCO₃ sequence although the positive electrostatic potential on the Hg atom is smallest. This is because the electrostatic interaction is dominant in the spodium-bonded complexes of CdCO₃ and ZnCO₃ but the polarization interaction in that of HgCO₃ . The pnicogen bond is much weaker than the spodium bond and the former has a larger enhancement than the latter in the FH₂ Z⋅⋅⋅OCO₂ M⋅⋅⋅N-base ternary complexes.

Plausible Pnicogen Bonding of epi-Cinchonidine as a Chiral Scaffold in Catalysis

As a non-covalent interaction of a chiral scaffold in catalysis, pnicogen bonding of epi-cinchonidine (epi-CD), a cinchona alkaloid, was simulated to consider whether the interaction can have the potential controlling enantiotopic face like hydrogen bonding. Among five reactive functional groups in epi-CD, two stable complexes of the hydroxyl group (X-epi-CD1) at C₁₇ and of the quinoline ring (X-epi-CD2) at N₁₆ with pnictide family analytes [X = substituted phosphine (PX), i.e., F, Br, Cl, CF₃, CN, HO, NO₂, and CH₃, and pnictide family analytes, i.e., PBr₃, BiI₃, SbI₃, and AsI₃] were predicted with intermolecular interaction energies, charge transfer (Q_Mulliken and Q_NBO), and band gap energies of HOMO-LUMO (Eg) at the B3LYP/6-31G(d,p) level of density functional theory. It was found that the dominant site of pnicogen bonding in epi-CD is the quinoline ring (N₁₆ atom) rather than the hydroxyl group (O₃₆ atom). In addition, the UV-Vis spectra of the complex were calculated by time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level and compared with experimental measurements. Through these calculations, two intermolecular interactions (H-bond vs. pnicogen bond) of epi-CD were compared.

Formation of phosphine imide (HN[double bond, length as m-dash]PH3) and its phosphinous amide (H2N-PH2) isomer

We present the first formation of the previously elusive phosphine imide (HN[double bond, length as m-dash]PH3) along with its phosphinous amide (H2N-PH2) isomer via exposure of phosphine (PH3) and ammonia (NH3) ices to ionizing radiation. Our approach may be extended to prepare, separate, and detect highly reactive compounds such as intermediates of Wittig reactions.

Unusual blue to red shifting of C-H stretching frequency of CHCl3 in co-operatively P⋯Cl phosphorus bonded POCl3-CHCl3 heterodimers at low temperature inert matrixes

Heterodimers of POCl₃-CHCl₃ were generated in Ne, Ar, and Kr matrixes at low temperatures and were studied using infrared spectroscopy. The remarkable role of co-operative pentavalent phosphorus bonding in the stabilization of the structure dictated by hydrogen bonding is deciphered. The complete potential energy surface of the heterodimer was scanned by ab initio and density functional theory computational methodologies. The hydrogen bond between the phosphoryl oxygen of POCl₃ and C-H group of CHCl₃ in heterodimers induces a blue-shift in the C-H stretching frequency within the Ne matrix. However, in Ar and Kr matrixes, the C-H stretching frequency is exceptionally red-shifted in stark contrast with Ne. The plausibility of the Fermi resonance by the C-H stretching vibrational mode with higher order modes in the heterodimers has been eliminated as a possible cause within Ar and Kr matrixes by isotopic substitution (CDCl₃) experiments. To evaluate the influence of matrixes as a possible cause of red-shift, self-consistent Iso-density polarized continuum reaction field model was applied. This conveyed the important role of the dielectric matrixes in inducing the fascinating vibrational shift from blue (Ne) to red (Ar and Kr) due to the matrix specific transmutation of the POCl₃-CHCl₃ structure. The heterodimer produced in the Ne matrix possesses a cyclic structure stabilized by hydrogen bonding with co-operative phosphorus bonding, while in Ar and Kr the generation of an acyclic open structure stabilized solely by hydrogen bonding is promoted. Compelling justification regarding the dispersion force based influence of matrix environments in addition to the well-known dielectric influence is presented.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

F-Halogen Bond: Conditions for Its Existence

The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp², or sp³ C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O₂NF, FOF, ClF, BrF, SiF₄, or GeF₄, but F₂ is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a V_s,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.

Calculated coupling constants 1 J(X-Y) and 1 K(X-Y), and fundamental relationships among the reduced coupling constants for molecules Hm X-YHn , with X, Y ═ 1 H, 7 Li, 9 Be, 11 B, 13 C, 15 N, 17 O, 19 F, 31 P, 33 S, and 35 Cl

Equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) calculations have been performed to determine coupling constants ¹ J(X-Y) for 65 molecules H_m X-YH_n , with X,Y ═ ¹ H, ⁷ Li, ⁹ Be, ¹¹ B, ¹³ C, ¹⁵ N, ¹⁷ O, ¹⁹ F, ³¹ P, ³³ S, and ³⁵ Cl. The computed ¹ J(X-Y) values are in good agreement with available experimental data. The reduced coupling constants ¹ K(X-Y) have been derived from ¹ J(X-Y) by removing the dependence on the magnetogyric ratios of X and Y. Patterns are found for the reduced coupling constants on a ¹ K(X-Y) surface that are related to the positions of X and Y in the periodic table.

On Transannulation in Azaphosphatranes: Synthesis and Theoretical Analysis

A combined synthetic-theoretical study has been undertaken to determine the factors that influence transannulation in azaphosphatranes. The commonly used proazaphosphatrane P(i-BuNCH₂CH₂)₃N and several of its oxidized congeners are used as model systems. The haloazaphosphatranes of P(i-BuNCH₂CH₂)₃N were synthesized, including a rare fluoroazaphopshatrane, and used as references for computational investigations. Comparisons of the experimental and theoretical observations highlight the flexibility observed in transannulated atranes and the potential for multiple local energetic minima depending on the identity of the equatorial substituents for a given azaphosphatrane. Theoretical calculations also identify the role of the ethylene linker in azaphosphatrane bonding, the influence of transannulation on P-electrophile interactions, and the contribution of electrostatic interactions to transannulation.

Insight into the Effects of Electrostatic Potentials on the Conversion Mechanism of the Hydrogen-Bonded Complexes and Carbon-Bonded Complexes: An Ab Initio and Quantum Theory of "Atoms in Molecules" Investigation

Carbon bond and hydrogen bond are common noncovalent interactions; although recent advances on these interactions have been achieved in both the experimental and computational aspects, little is known about the conversion mechanism between them. Here, MP2 calculations with aug-cc-pVDZ basis set (aug-cc-pVDZ-pp for element Sn) were used to optimize the geometric configurations of the hydrogen-bonded complexes MH₃F···HCN (M = C, Si, Ge, and Sn), carbon-bonded complexes HCN···MH₃F (M = C, Si, Ge, and Sn), and transition states; the conversion mechanism between these two types of interactions has been carried out. The molecular electrostatic potential, especially the σ-hole, is directly related to the flatten degree of intrinsic reaction coordinate (IRC) curve. The energy barriers from the hydrogen-bonded complexes to the carbon-bonded complexes are 6.99, 7.73, 10.56, and 13.59 kJ·mol^-1. The energy barriers from the carbon-bonded complexes to the hydrogen-bonded complexes are 4.65, 7.81, 9.10, and 13.04 kJ·mol^-1. The breakage and formation of the bonds along the reaction paths have been discussed by the topological analysis of electronic density. The energy barriers are obviously related to the width of the structure transition region (STR). For the first derivative curve of IRC energy surface versus reaction coordinate, there is a maximum peak and a minimum peak, reflecting the structural transition states in the ring STRs.

Elusive hypervalent phosphorus⋯π interactions: evidence for paradigm transformation from hydrogen to phosphorus bonding at low temperatures

A paradigm transformation from hydrogen to phosphorus bonding is found to depend on the proton affinity of the interacting π-systems.

Comparison of pnicogen and tetrel bonds in complexes containing CX2 carbenes (X = F, Cl, Br, OH, OMe, NH2, and NMe2)

The similarities and differences of pnicogen and tetrel bonds formed by carbenes CX₂ with H₃AsO and H₃SiCN were investigated by carrying out ab initio calculations in association with topological analysis of electron density.

Competition between tetrel bond and pnicogen bond in complexes of TX3-ZX2 and NH3

The complexes formed between TX₃-ZX₂ (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH₃ were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX₃-ZX₂, two types of complex were obtained. For CX₃-ZX₂, NH₃ is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX₃-ZX₂ (T = Si and Ge), however, the base favors engaging in a tetrel bond with the σ-hole on the T atom although the corresponding pnicogen-bonded complex is also stable. When NH₃ approaches the CX₃ terminal of CX₃-ZX₂, weak interactions are observed that may be classified as van der Waals interactions. The relative stability of both types of complexes is not affected by the substituent X. The tetrel bond is very strong and the largest interaction energy is up to -144 kJ mol^-1. Dispersion is dominant in the weak van der Waals complexes, while tetrel- and pnicogen-bonded complexes are dominated by electrostatic interactions, with comparable contributions from polarization.

Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer

HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH₃ , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY₂ forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.

The potential of pnicogen bonding for catalysis - a computational study

Pnicogen bonding is a noncovalent interaction between the electrophilic region of a phosphorus atom and a Lewis base. Although this interaction can be comparable in strength to other noncovalent interactions, no systematic application in organic synthesis or catalysis is known so far. To identify the potential of this interaction for organocatalysis, we have now analysed different pnicogen-bond donors as catalysts for the activation of three different model reactions employing density functional theory. Our calculations suggest rate accelerations of several orders of magnitude for all cases indicating that synthetic applications should be feasible. Furthermore, our results indicate that pnicogen-bond donors can be comparable to halogen-bond-based catalysts in these reactions.

Aerogen bonds formed between AeOF2 (Ae = Kr, Xe) and diazines: comparisons between σ-hole and π-hole complexes

The interaction between KrOF₂ or XeOF₂ and the 1,2, 1,3, and 1,4 diazines is characterized chiefly by a Kr/XeN aerogen bond, as deduced from ab initio calculations. The most stable dimers take advantage of the σ-hole on the aerogen atom, wherein the two molecules lie in the same plane. The interaction is quite strong, as much as 18 kcal mol^-1. A second class of dimer geometry utilizes the π-hole above the aerogen atom in an approximate perpendicular arrangement of the two monomers; these structures are not as strongly bound: 6-8 kcal mol^-1. Both sorts of dimers contain auxiliary CHF H-bonds which contribute to their stability, but even with their removal, the aerogen bond energy remains as high as 14 kcal mol^-1. The nature and strength of each specific interaction is confirmed and quantified by AIM, NCI, NBO, and electron density shift patterns. There is not a great deal of sensitivity to the identity of either the aerogen atom or the position of the two N atoms in the diazine.

Pentavalent phosphorus as a unique phosphorus donor in POCl3 homodimer and POCl3–H2O heterodimer: matrix isolation infrared spectroscopic and computational studies

Phosphorus, an important element among the pnicogen group, opens up avenues for experimental and computational explorations of its interaction in a variety of compounds.

Modulating of the pnicogen-bonding by a H⋯π interaction: An ab initio study

An ab initio study of the cooperativity in XH₂P⋯NCH⋯Z and XH₂P⋯CNH⋯Z complexes (X=F, Cl, Br, CN, NC; Z=C₂H₂,C₆H₆) connected by pnicogen-bonding and H⋯π interactions is carried out by means of MP2 computational method. A detailed analysis of the structures, interaction energies and bonding properties is performed on these systems. For each set of the complexes considered, a favorable cooperativity is observed, especially in X=F and CN complexes. However, for a given X or Z, the amount of cooperativity effects in XH₂P⋯CNH⋯Z complexes are more important than XH₂P⋯NCH⋯Z counterparts. Besides, the influence of a H⋯π interaction on a P⋯N (C) bond is more pronounced than that of a P⋯N (C) bond on a H⋯π bond. The quantum theory of atoms in molecules shows that ternary complexes have increased electron densities at their bond critical points relative to the corresponding binary systems. The results also indicate that the strength of the P⋯N(C) and H⋯π interactions increases in the presence of the solvent.

Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR

The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.

Modulating intramolecular P⋯N pnictogen interactions

The strength of P⋯N intramolecular pnictogen interactions can be modulated, enhanced or diminished upon substitution of different electron withdrawing or donor groups.

PCl3–C6H6 heterodimers: evidence for P⋯π phosphorus bonding at low temperatures

A phosphorous trichloride (PCl₃)–benzene (C₆H₆) heterodimer was generated in a low temperature N₂ matrix and was characterized using infrared spectroscopy.

NMR Investigations of Noncovalent Carbon Tetrel Bonds. Computational Assessment and Initial Experimental Observation

Group IV tetrel elements may act as tetrel bond donors, whereby a region of positive electrostatic potential (σ-hole) interacts with a Lewis base. The results of calculations of NMR parameters are reported for a series of model compounds exhibiting tetrel bonding from a methyl carbon to the oxygen or nitrogen atoms in various functional groups. The (13)C chemical shift (δiso) and the (1c)J((13)C,Y) coupling (Y = (17)O, (15)N) across the tetrel bond are recorded as a function of geometry. The sensitivity of the NMR parameters to the noncovalent interaction is demonstrated via an increase in δiso and in |(1c)J((13)C,Y)| as the tetrel bond shortens. Gauge-including projector-augmented wave density functional theory (DFT) calculations of δiso are reported for crystals that exhibit tetrel bonding in the solid state. Experimental δiso values for solid sarcosine and its tetrel-bonded salts corroborate the computational findings. This work offers new insights into tetrel bonding and facilitates the incorporation of tetrel bonds as restraints in NMR crystallographic structure refinement.

An ab initio study on tunability of σ-hole interactions in XHS:PH2Y and XH2P:SHY complexes (X = F, Cl, Br; Y = H, OH, OCH3, CH3, C2H5, and NH2)

Quantum chemical calculations are performed to investigate the tunability of σ-hole interactions in chalcogen-bonded XHS:PH2Y and pnicogen-bonded XH2P:SHY complexes, where X  =  F, Cl, Br and Y  =  H, OH, OCH3, CH3, C2H5, NH2. The formation of these binary complexes can be understood in terms of molecular electrostatic potentials (MEPs), considering the P and S atoms as an electron acceptor or an electron donor in the chalcogen and pnicogen bonds. The strength of the XHS:PH2Y and XH2P:SHY complexes for a given Y increases as follows: X = Br < Cl < F. In addition, an acceptable linear relationship is found between the interaction energies and the magnitudes of the product of most positive and negative MEPs. This finding along with the electron density difference maps provides a clear picture of the electrostatic nature of the interactions in the XHS:PH2Y and XH2P:SHY complexes. The calculated spin-spin coupling constants across the chalcogen bond interactions in the XHS:PH2Y complexes display a quadratic dependence with the P···S binding distance.