Unique Use of Dibromo-L-Tyrosine Ligand in Building of Cu(II) Coordination Polymer-Experimental and Theoretical Investigations.

Although the crystals of coordination polymer {[CuCl(µ-O,O'-L-Br2Tyr)]}n (1) (L-Br2Tyr = 3,5-dibromo-L-tyrosine) were formed under basic conditions, crystallographic studies revealed that the OH group of the ligand remained protonated. Two adjacent [CuCl(L-Br2Tyr)] monomers, bridged by the carboxylate group of the ligand in the syn-anti bidentate bridging mode, are differently oriented to form a polymeric chain; this specific bridging was detected also by FT-IR and EPR spectroscopy. Each Cu(II) ion in polymeric compound 1 is coordinated in the xy plane by the amino nitrogen and carboxyl oxygen of the parent ligand and the oxygen of the carboxyl group from the symmetry related ligand of the adjacent [Cu(L-Br2Tyr)Cl] monomer, as well as an independent chlorine ion. In addition, the Cu(II) ion in the polymer chain participates in long-distance intermolecular contacts with the oxygen and bromine atoms of the ligands located in the adjacent chains; these intramolecular contacts were also supported by NCI and NBO quantum chemical calculations and Hirshfeld surface analysis. The resulting elongated octahedral geometry based on the [CuCl(L-Br2Tyr)] monomer has a lower than axial symmetry, which is also reflected in the symmetry of the calculated molecular EPR g tensor. Consequently, the components of the d-d band obtained by analysis of the NIR-VIS-UV spectrum were assigned to the corresponding electronic transitions.

Trapping of Small Molecules within Single or Double Cyclo[18]carbon Rings.

The encapsulation of a set of small molecules, H2, CO, CO2, SO2, and SO3, by a circular C18 ring is investigated by quantum calculations. These ligands lie near the center of the ring but, with the exception of H2, are disposed roughly perpendicular to the ring plane. Their binding energies with the C18 vary from 1.5 kcal/mol for H2 up to 5.7 kcal/mol for SO2, and the bonding is dominated by dispersive interactions spread over the entire ring. The binding of these ligands on the outside of the ring is weaker but allows the opportunity for each to bond covalently with the ring. A pair of C18 units lie parallel to one another. This pair can bind each of these ligands in the area between them with only small perturbations of the double ring geometry. The binding energies of these ligands to this double ring configuration are amplified by some 50% compared to the single ring systems. The presented data concerning the trapping of small molecules may have larger implications regarding hydrogen storage or air pollution reduction.

Anion⋯anion interaction within Ch(CH3)X4- (Ch = S, Se, Te; X = Cl, Br, I) dimers stabilized by chalcogen bonds.

In a crystal, a pair of homoanions (Te(C6H5)Cl4-) are arranged in a parallel manner, close enough to interact with each other. Quantum chemical analysis indicates the existence of two strong noncovalent chalcogen bonds engaging the σ-hole of the chalcogen atoms from one unit and electron density accumulated on the Cl atom of the neighboring unit. In a solid, chalcogen bonds are supported by a multitude of HBs between interacting (Te(C6H5)Cl4-) anions and the C5H5NBr+ counterions. These studies are extended to the model homodimers [(Ch(CH3)X4)-]2, where Ch represents an atom of group 16 (S, Se, and Te) while X = Cl, Br, and I. In these model systems, the aromatic ring was replaced by a methyl group and the counterions were not included. The consequence of this is a different noncovalent bond network in comparison to the system in a solid (the absence of intermolecular HBs and the presence of dihalogen bonds). The tendency for more exoenergetic complexation increases in the Cl < Br < I series. The chalcogen size effect is much smaller. However, critical to the stability of this system is overcoming the Coulomb repulsion between the two monoanions. This is possible because of the polarizable environment that exists in the crystal due to the presence of counter ions.

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.

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.

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.

Experimental and theoretical evidence of attractive interactions between dianions: [PdCl4]2-⋯[PdCl4]2.

Inspection of the arrangement of tetrachloridopalladate(II) centers in a crystalline solid places the Cl of one [PdCl4]2- directly above the Pd center of its neighbor. A survey of the CSD provides 22 more examples of such MX42-⋯MX42- complexes, with M being a Group 10 metal and X = Cl, Br, or I. Quantum calculations attribute this arrangement to a π-hole bond wherein Cl lone pairs of one unit transfer charge to vacant orbitals above the Pd center of its neighbor. The stabilizing effect of this bond must overcome the strong Coulombic repulsion between the two dianions, which is facilitated by a polarizable environment as would be present in a crystal, but much more so when the effects of the neighboring counterions are factored in. These conclusions are extended to other [MX4]2- homodimers, where M represents other members of Group 10, namely Ni and Pt.

Triel bonds within anion···anion complexes.

The ability of two anions to interact with one another is tested in the context of pairs of TrX4- homodimers, where Tr represents any of the triel atoms B, Al, Ga, In, or Tl, and X refers to a halogen substituent F, Cl, or Br. None of these pairs engage in a stable complex in the gas phase, but the situation reverses in water where the two monomers are held together by Tr⋯X triel bonds, complemented by stabilizing interactions between X atoms. Some of these bonds are quite strong, notably those involving TrF4-, with interaction energies surpassing 30 kcal mol-1. Others are very much weaker, with scarcely exothermic binding energies. The highly repulsive electrostatic interactions are counteracted by large polarization energies.

Anionanion (MX3-)2 dimers (M = Zn, Cd, Hg; X = Cl, Br, I) in different environments.

The possibility that MX3- anions can interact with one another is assessed via ab initio calculations in gas phase as well as in aqueous and ethanol solution. A pair of such anions can engage in two different dimer types. In the bridged configuration, two X atoms engage with two M atoms in a rhomboid structure with four equal M-X bond lengths. The two monomers retain their identity in the stacked geometry which contains a pair of noncovalent MX interactions. The relative stabilities of these two structures depend on the nature of the central M atom, the halogen substituent, and the presence of solvent. The interaction and binding energies are fairly small, generally no more than 10 kcal mol-1. The large electrostatic repulsion is balanced by a strong attractive polarization energy.

Crystallographic and Theoretical Evidences of Anion⋠⋠⋠Anion Interaction.

Planar (HgCl3 )- anions are stacked fairly closely together in a slipped parallel arrangement within several crystal structures. Quantum chemical analysis shows evidence of strong noncovalent spodium bonds between the Hg π-hole of one unit and the Cl atom of an adjacent unit. Anion⋅⋅⋅anion spodium bonds work in tandem with crystal packing forces.

Anion-anion and anion-neutral triel bonds.

The ability of a TrCl4- anion (Tr = Al, Ga, In, Tl) to engage in a triel bond with both a neutral NH3 and CN- anion is assessed by ab initio quantum calculations in both the gas phase and in aqueous medium. Despite the absence of a positive σ or π-hole on the Lewis acid, strong triel bonds can be formed with either base. The complexation involves an internal restructuring of the tetrahedral TrCl4- monomer into a trigonal bipyramid shape, where the base can occupy either an axial or equatorial position. Although this rearrangement requires a substantial investment of energy, it aids the complexation by imparting a much more positive MEP to the site that is to be occupied by the base. Complexation with the neutral base is exothermic in the gas phase and even more so in water where interaction energies can exceed 30 kcal mol-1. Despite the long-range coulombic repulsion between any pair of anions, CN- can also engage in a strong triel bond with TrCl4-. In the gas phase, complexation is endothermic, but dissociation of the metastable dimer is obstructed by an energy barrier. The situation is entirely different in solution, with large negative interaction energies of as much as -50 kcal mol-1. The complexation remains an exothermic process even after the large monomer deformation energy is factored in.

Pnicogen Bonds Pairing Anionic Lewis Acid with Neutral and Anionic Bases.

The complexation process between anionic ZCl4- (Z = P, As, Sb) and neutral NCH and pyridine, as well as the CN- anion, is studied in both the gas phase and aqueous solution by high-level ab initio calculations. Despite the absence of a positively charged σ-hole on ZCl4-, a pnicogen bond (ZB) holds all of these complexes together. The dimerization induces the ZCl4- to rearrange internally from a see-saw to a square geometry. The complexation process is endothermic for both HCN and CN- in the gas phase but for different reasons. The approach of CN- to ZCl4- must overcome anion-anion Coulomb repulsion, while HCN is a much weaker base. The intermediate nucleophilicity of pyridine leads to an exothermic dimerization reaction despite the deformation of the ZCl4- structure. The dimers must traverse an energy barrier in order to dissociate. Formation of the dianionic -NC···ZCl4- complex becomes exothermic in aqueous solution. Complexation with HCN remains endothermic in water, although less so, and the exothermicity of ZB formation with pyridine is enhanced by solvation.

Anion⋠⋠⋠Anion Attraction in Complexes of MCl3- (M=Zn, Cd, Hg) with CN.

High-level ab initio calculations show that the MCl3- anions comprising Group 2B M atoms Zn, Cd, and Hg form a stable complex with the CN- anion, despite the like charge of the two ions. The complexation occurs despite a negative π-hole region above the M atom of MCl3- . The dimerization distorts the planar geometry of MCl3- into a pyramidal shape which reduces the negative potential above the M atom, facilitating a close approach of the two anions, with R(M⋅⋅⋅C)∼2 Å, and an overall attractive electrostatic attraction within the dimer. In the gas phase, this dimer is less stable than the pair of separated ions by some 30 kcal/mol. However, the dissociation must surmount an energy barrier of roughly 25 kcal/mol which occurs at an intermolecular distance of 4 Å. In aqueous solution, the dimerization process is exothermic and barrier-free, with a binding energy in the 11-18 kcal/mol range.

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.

How Many Pnicogen Bonds can be Formed to a Central Atom Simultaneously?

A central ZF3 molecule (Z = P, As, Sb, Bi) is allowed to interact with a number of nucleophiles exemplified by NCH, NH3, and NC- anion. The Z···N pnicogen bond (ZB) to a single base grows stronger for heavier Z atom: P < A < Sb < Bi and follows the NCH < NH3 < NC- order for the three bases. The maximum number of ZBs depends on both the nature of the base and pnicogen atom. PF3 and AsF3 can pnicogen bond with only a single CN-; SbF3 and BiF3 can interact with two anions but only weakly. The weak NCH nucleophile can engage in a maximum of two ZBs, while three ZBs occur for NH3. The latter NH3 maximum can be extended to four ZBs but only for BiF3. The fourth ZB is somewhat longer and weaker than the others, and the entire (H3N)4···BiF3 complex relies partially on secondary interactions for its stability.

Chalcogen bonding of two ligands to hypervalent YF4 (Y = S, Se, Te, Po).

The ability of two NH3 ligands to engage in simultaneous chalcogen bonds to a hypervalent YF4 molecule, with Y = S, Se, Te, Po, is assessed via quantum calculations. The complex can take on one of two different geometries. The cis structure places the two ligands adjacent to one another in a pseudo-octahedral geometry, held there by a pair of σ-hole chalcogen bonds. The bases can also lie nearly opposite one another, in a distorted octahedron containing one π-hole and one strained σ-hole bond. The cis geometry is favored for Y = S, while Te, and Po tend toward the trans structure; they are nearly equally stable for Se. In either case, the binding energy rises rapidly with the size of the Y atom, exceeding 30 kcal mol-1 for PoF4.

Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment.

Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A-F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X-H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.

Influence of monomer deformation on the competition between two types of σ-holes in tetrel bonds.

One of several tetrel (T) atoms was covalently attached to three F atoms and a substituted phenyl ring. A NH3 base can form a tetrel bond with TF3C6H2R3 (T = Si, Ge, Sn, Pb; R = H, F, CH3) in a position opposite either an F atom or the ring. The σ-hole opposite the highly electron-withdrawing F (T-F) is more intense than that opposite the ring (T-C). However, when the Lewis base deforms from a tetrahedral to a trigonal bipyramidal shape so as to accommodate the base, it is the T-C σ-hole that is more intense. Accordingly, it is the T-C tetrel-bonded complex for which there is a larger interaction energy with NH3, as high as 34 kcal mol-1. Countering this trend, it requires more energy for the TF3C6H2R3 to deform into the geometry it adopts within the T-C complex than within its T-F counterpart. There is consequently a balance between the overall binding energies of the two competing sites. The smaller tetrel atoms Si and Ge, with their larger deformation energies, show a preference for T-F tetrel binding, while the T-C site is preferred by Pb which suffers from a smaller degree of deformation energy. There is a near balance for T = Sn and the two sites show comparable binding energies.

On the ability of pnicogen atoms to engage in both σ and π-hole complexes. Heterodimers of ZF2C6H5 (Z = P, As, Sb, Bi) and NH3.

When bound to a pair of F atoms and a phenyl ring, a pyramidal pnicogen (Z) atom can form a pnicogen bond wherein an NH3 base lies opposite one F atom. In addition to this σ-hole complex, the ZF2C6H5 molecule can distort in such a way that the NH3 approaches on the opposite side to the lone pair on Z, where there is a so-called π-hole. The interaction energies of these π-hole dimers are roughly 30 kcal/mol, much larger than the equivalent quantities for the σ-hole complexes, which are only 4-13 kcal/mol. On the other hand, this large interaction energy is countered by the considerable deformation energy required for the Lewis acid to adopt the geometry necessary to form the π-hole complex. The overall energetics of the complexation reaction are thus more exothermic for the σ-hole dimers than for the π-hole dimers.

Hexacoordinated Tetrel-Bonded Complexes between TF4 (T=Si, Ge, Sn, Pb) and NCH: Competition between σ- and π-Holes.

In order to accommodate the approach of two NCH bases, a tetrahedral TF4 molecule (T=Si, Ge, Sn, Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geometry of TF4 , associated with the trans arrangement of the bases, is higher in energy than its see-saw structure that corresponds to the cis trimer. On the other hand, the square geometry offers an unobstructed path of the bases to the π-holes above and below the tetrel atom and hence enjoys a higher interaction energy than is the case for the σ-holes approached by the bases in the cis arrangement. When these two effects are combined, the total binding energies are more exothermic for the cis than for the trans complexes. This preference amounts to some 3 kcal mol-1 for Sn and Pb, but is amplified for the smaller tetrel atoms.