Donor-acceptor nature of specific nonbonded interactions of sulfur and halogen atoms. Influence on the geometry and packing of molecules

Chemistry Faculty, Moscow State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 3, pp. 105–118, May–June 1, 1992.     

The nature of halogen...halogen synthons: crystallographic and theoretical studies

A study of the halogen...halogen contacts in organic compounds using ab initio calculations and the results of previously reported crystallographic studies show that these interactions are controlled by electrostatics. These contacts can be represented by the geometric parameters of the C--X1...X2--C moieties (where theta1=C--X1...X2 and theta2=X1...X2--C; ri=X1...X2 distance). The distributions of the contacts within the sum of van der Waals radii (rvdW) versus thetai (theta1=theta2) show a maximum at theta approximately 150 degrees for X=Cl, Br, and I. This maximum is not seen in the distribution of F...F contacts. These results are in good agreement with our ab initio calculations. The theoretical results show that the position of the maximum depends on three factors: 1) The type of halogen atom, 2) the hybridization of the ipso carbon atom, and 3) the nature of the other atoms that are bonded to the ipso carbon atom apart from the halogen atom. Calculations show that the strength of these contacts decreases in the following order: I...I>Br...Br>Cl...Cl. Their relative strengths decrease as a function of the hybridization of the ipso carbon atom in the following order: sp2>sp>sp3. Attaching an electronegative atom to the carbon atom strengthens the halogen...halogen contacts. An electrostatic model is proposed based on two assumptions: 1) The presence of a positive electrostatic end cap on the halogen atom (except for fluorine) and 2) the electronic charge is anisotropically distributed around the halogen atom.     

Quantitative evaluation of weak nonbonded Se...F interactions and their remarkable nature as orbital interactions

To evaluate weak intramolecular nonbonded Se...F interactions recently characterized for a series of o-selenobenzyl fluoride derivatives (Iwaoka et al., Chem. Lett. 1998, 969-970), the temperature dependence of the nuclear spin coupling between Se and F (J(Se...F)) was investigated for 2-(fluoromethyl)phenylselenenyl cyanate (1a) and bis[2-(fluoromethyl)phenyl] diselenide (1e) in CD2Cl2 and CD3CN. A significant increase in the magnitude of J(Se...F) was observed for both 1a and 1e upon lowering temperature, whereas the values of J(Se...F) for the corresponding trifluoromethyl compounds slightly reduced or remained unchanged at low temperatures. Application of the rapid equilibrium model between two possible conformers revealed that conformer A with an intramolecular Se...F interaction is more stable in enthalpy (DeltaH) by 1.23 kcal/mol for 1a (in CD2Cl2) and by 0.85 and 0.83 kcal/mol for 1e (in CD2Cl2 and CD3CN, respectively) than conformer B, which does not have close Se...F contact. The negligible solvent effects for 1e suggested marginal electrostatic nature of the Se...F interactions. Instead, importance of the n(F) -->sigma*(Se-X) orbital interaction was suggested by quantum chemical (QC) calculations and the natural bond orbital (NBO) analysis.     

The nature of halogen...halide synthons: theoretical and crystallographic studies

Two types of halogen...halide synthons are investigated on the basis of theoretical and crystallographic studies; the simple halogen...halide synthons and the charge assisted halogen...halide synthons. The former interactions were investigated theoretically (ab initio) by studying the energy of interaction of a halide anion with a halocarbon species as a function of Y...X- separation distance and the C-Y...X- angle in a series of complexes (R-Y...X-, R=methyl, phenyl, acetyl or pyridyl; Y=F, Cl, Br, or I; X-=F-, Cl-, Br-, or I-). The theoretical study of the latter interaction type was investigated in only one system, the [(4BP)Cl]2 dimer, (4BP=4-bromopyrdinium cation). Crystal structure determinations, to complement the latter theoretical calculations, were performed on 13 n-chloropyridinium and n-bromopyridinium halide salts (n=2-4). The theoretical and crystallographic studies indicate that these interactions are controlled by electrostatics and are characterized by linear C-Y...X- angles and separation distances less than the sum of van der Waals radius (rvdW) of the halogen atom and the ionic radii of the halide anion. The strength of these contacts from calculations varies from weak or absent, e.g., H3C-Cl...I-, to very strong, e.g., HCC-I...F- (energy of interaction ca. -153 kJ/mol). The strengths of these contacts are influenced by four factors: (a) the type of the halide anion; (b) the type of the halogen atom; (c) the hybridization of the ipso carbon; (d) the nature of the functional groups. The calculations also show that charge assisted halogen...halide synthons have a comparable strength to simple halogen...halide synthons. The nature of these contacts is explained on the basis of an electrostatic model.     

Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions

In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A? (PLA?), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.     

Experimental and theoretical studies of 45Sc NMR interactions in solids

Solid-state 45Sc NMR spectroscopy, ab initio calculations, and X-ray crystallography are applied to examine the relationships between 45Sc NMR interactions and molecular structure and symmetry. Solid-state 45Sc (I = 7/2) magic-angle spinning (MAS) and static NMR spectra of powdered samples of Sc(acac)3, Sc(TMHD)3, Sc(NO3)3.5H2O, Sc(OAc)3, ScCl3.6H2O, ScCl3.3THF, and ScCp3 have been acquired. These systems provide a variety of scandium coordination environments yielding an array of distinct 45Sc chemical shielding (CS) and electric field gradient (EFG) tensor parameters. Acquisition of spectra at two distinct magnetic fields allows for the first observations of scandium chemical shielding anisotropy (CSA). 45Sc quadrupolar coupling constants (CQ) range from 3.9 to 13.1 MHz and correlate directly with the symmetry of the scandium coordination environment. Single-crystal X-ray structures were determined for Sc(TMHD)3, ScCl3.6H2O, and Sc(NO3)3.5H2O to establish the hitherto unknown scandium coordination environments. A comprehensive series of ab initio calculations of EFG and CS tensor parameters are in excellent agreement with the observed parameters. Theoretically determined orientations of the NMR interaction tensors allow for correlations between NMR tensor characteristics and scandium environments. Solid-state 45Sc, 13C, and 19F NMR experiments are also applied to characterize the structures of the microcrystalline Lewis acid catalyst Sc(OTf)3 (for which the crystal structure is unknown) and a noncrystalline, microencapsulated, polystyrene-supported form of the compound.     

Theoretical investigations on heteronuclear chalcogen-chalcogen interactions: on the nature of weak bonds between chalcogen centers

To understand the intermolecular interactions between chalcogen centers (O, S, Se, Te), quantum chemical calculations on model systems were carried out. These model systems were pairs of monomers of the composition (CH3)2X1 (X1 = O, S, Se, Te) as the donors and CH3X2Z (with X2 = O, S, Se, Te and Z = Me, CN) as the acceptors. The variation of X1, X2, and Z leads to 32 pairs with 8 homonuclear cases (X1 = X2 = O, S, Se, Te) and 24 heteronuclear cases (X1 not equal X2). The MP2/SDB-cc-pVTZ, 6-311G* level of theory was used to derive the geometrical parameters and the interaction energies of the model systems. The pairs with Z = CN (17-32) show a considerably higher interaction energy than the pairs with CH3 groups only (1-16). Natural bond orbital (NBO) analysis revealed that the interaction of the dimers 1, 2, 5, 6, 9, 10, 13, 14, 17, 21, 25, and 29 is mainly due to weak hydrogen bonding between methyl groups and chalcogen centers. These systems all contain hard chalcogen atoms as acceptors. For all other systems, the chalcogen-chalcogen interaction dominates. The one-electron picture of an interaction between the lone pair of the donor chalcogen atom and the chalcogen-carbon antibonding sigma* orbital serves as a model to qualitatively rationalize trends found in many of these systems. However, it has to be applied with some amount of skepticism. A detailed analysis based on symmetry-adapted perturbation theory (SAPT) reveals that induction and dispersion forces dominate and contribute to the bonding in each case. Hydrogen-bonded compounds involve bonding electrostatic contributions. Compounds dominated by chalcogen-chalcogen interactions exhibit bonding due to electrostatic interactions only if one of the chalcogen atoms involved is sulfur or oxygen.     

Properties of halogen atoms for representing intermolecular electrostatic interactions related to halogen bonding and their substituent effects

The electrostatic properties of halogen atoms are studied theoretically in relation to their ability of halogen bonding, which is an attractive intermolecular interaction of a covalently bonded halogen atom with a negatively charged atom of a neighboring molecule. The electric quadrupole (of electronic origin) with a positive zz component Θ_zz of a covalently bonded halogen atom, where the z axis is taken along the covalent bond involving the halogen atom, is mainly responsible for the attractive electrostatic interaction with a negatively charged atom. This positive Θ_zz is an intrinsic property of halogen atoms with the p_x²p_y²p_z configuration of the valence electronic shell, as shown by ab initio molecular orbital calculations for isolated halogen atoms with this electronic configuration, and increases in the order of F < Cl < Br < I, in parallel with the known general sequence of the strength of halogen bonding. For halogen‐containing aromatic compounds, the substituent effects on the electrostatic properties are also studied. It is shown that the magnitude of Θ_zz and the electric field originating from it are rather insensitive to the substituent effect, whereas the electric field originating from atomic partial charges has a large substituent effect. The latter electric field tends to partially cancel the former. The extent of this partial cancellation is reduced in the order of Cl < Br < I and is also reducible by proper substitution on or within the six‐membered ring of halobenzene. Perspectives on the development of potential function parameters applicable to halogen‐bonding systems are also briefly discussed. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Isostructurality, polymorphism and mechanical properties of some hexahalogenated benzenes: the nature of halogen...halogen interactions

The nature of intermolecular interactions between halogen atoms, X...X (X = Cl, Br, I), continues to be of topical interest because these interactions may be used as design elements in crystal engineering. Hexahalogenated benzenes (C6Cl(6-n)Br(n), C6Cl(6-n)I(n), C6Br(6-n)I(n)) crystallise in two main packing modes, which take the monoclinic space group P2(1)/n and the triclinic space group P1. The former, which is isostructural to C6Cl6, is more common. For molecules that lack inversion symmetry, adoption of this monoclinic structure would necessarily lead to crystallographic disorder. In C6Cl6, the planar molecules form Cl...Cl contacts and also pi...pi stacking interactions. When crystals of C6Cl6 are compressed mechanically along their needle length, that is, [010], a bending deformation takes place, because of the stronger interactions in the stacking direction. Further compression propagates consecutively in a snakelike motion through the crystal, similar to what has been suggested for the motion of dislocations. The bending of C6Cl6 crystals is related to the weakness of the Cl...Cl interactions compared with the stronger pi...pi stacking interactions. The triclinic packing is less common and is restricted to molecules that have a symmetrical (1,3,5- and 2,4,6-) halogen substitution pattern. This packing type is characterised by specific, polarisation-induced X...X interactions that result in threefold-symmetrical X3 synthons, especially when X = I; this leads to a layered pseudohexagonal structure in which successive planar layers are inversion related and stacked so that bumps in one layer fit into the hollows of the next in a space-filling manner. The triclinic crystals shear on application of a mechanical stress only along the plane of deformation. This shearing arises from the sliding of layers against one another. Nonspecificity of the weak interlayer interactions here is demonstrated by the structure of twinned crystals of these compounds. One of the compounds studied (1,3,5-tribromo-2,4,6-triiodobenzene) is dimorphic, adopting both the monoclinic and triclinic structures, and the reasons for polymorphism are suggested. To summarise, both chemical and geometrical models need to be considered for X...X interactions in hexahalogenated benzenes. The X...X interactions in the monoclinic group are nonspecific, whereas in the triclinic group some X...X interactions are anisotropic, chemically specific and crystal-structure directing.     

Experimental studies on selenium cluster structures

In this paper, we report properties of selenium clusters produced by vapor condensation technique. Impact electronic ionization is performed on clusters in the size range from 2 to 36 atoms. The measured ionization potentials exhibit small oscillation corresponding to the wiggles observed on the mass distribution. An attempt to connect these experimental observations with the geometrical structure of the molecules is made in the discussion.     

On the nature of bonds between carbon atoms

The combined effect of conjugation and van der Waals' interaction has been calculated for carbon sp²-sp² single bonds of different lengths and for different molecular conformations. The bond shortening effect of conjugation is found to be comparable to that of hybridization. The attractive van der Waals' interaction, on the other hand, is always found to be small. It seems thus most improbable that this interaction should be the cause of the planarity of butadiene.     

Long-range interactions between atoms and molecules

The refractive index data for various gases are fitted to analytical formulae from which may be calculated the coefficient of the leading term of the long-range two-body interactions and the coefficient of the leading term of the long-range non-additive three-body interactions. Coefficients are obtained for mixtures of the gases He, Ne, A, Kr, Xe, H₂, N₂ and CH₄, the probable error being 5%.     

Experimental and theoretical studies of the structures and interactions of vancomycin antibiotics with cell wall analogues

Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy-resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Molecular dynamics simulations of the vancomycin, peptide, and vancomycin-peptide complex were carried out to explore the low energy conformations. Density functional theory (DFT) calculations of the geometries, proton affinities, and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala, and noncovalent complexes of VA with N-acetyl-D-Ala-D-Ala and V with N(alpha),N(epsilon)-diacetyl-L-Lys-D-Ala-D-Ala. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the primary amine of the disaccharide group. The experimental binding energy of 30.9 +/- 1.8 kcal/mol is in good agreement with the binding energy of 36.3-42.0 kcal/mol calculated for the model system representing the preferred structure of the complex.     

Statistical and theoretical investigations on the directionality of nonbonded S...O interactions. Implications for molecular design and protein engineering

Weak nonbonded interactions between a divalent sulfur (S) atom and a main-chain carbonyl oxygen (O) atom have recently been characterized in proteins. However, they have shown distinctly different directional propensities around the O atom from the S...O interactions in small organic compounds, although the linearity of the C-S...O or S-S...O atomic alignment was commonly observed. To elucidate the observed discrepancy, a comprehensive search for nonbonded S.O interactions in the Cambridge Structural Database (CSD) and MP2 calculations on the model complexes between dimethyl disulfide (CH(3)SSCH(3)) and various carbonyl compounds were performed. It was found that the O atom showed a strong intrinsic tendency to approach the S atom from the backside of the S-C or S-S bond (in the sigma(S) direction). On the other hand, the S atom had both possibilities of approach to the carbonyl O atom within the same plane (in the n(O) direction) and out of the plane (in the pi(O) direction). In the case of S...O(amide) interactions, the pi(O) direction was significantly preferred as observed in proteins. Thus, structural features of S...O interactions depend on the type of carbonyl groups involved. The results suggested that S.O interactions may control protein structures to some extent and that the unique directional properties of S...O interactions could be applied to molecular design.     

A computational study on the nature of the halogen bond between sulfides and dihalogen molecules

The characteristics and nature of the halogen bonding in a series of B···XY (B = H₂S, H₂CS, (CH₂)₂S; XY = ClF, Cl₂, BrF, BrCl, Br₂) complexes were analyzed by means of the quantum theory of “atoms in molecules” (QTAIM) and “natural bond orbital” (NBO) methodology at the second-order Møller-Plesset (MP2) level. Electrostatic potential, bond length, interaction energy, topological properties of the electron density, the dipole moment, and the charge transfer were investigated systematically. For the same electron donor, the interaction energies follows the B···BrF > B···ClF > B···BrCl > B···Br₂ > B···Cl₂ > B···ClBr order. For the same electron acceptor, the interaction energies increase in the sequence of H₂S, H₂CS, and (CH₂)₂S. Topological analyses show these halogen bonding interactions belong to weak interactions with an electrostatic nature. It was found that the strength of the halogen-bonding interaction correlates well with the electrostatic potential associated with halogen atom and the amount of charge transfer from sulfides to dihalogen molecules, indicating that electrostatic interaction plays an important role in these halogen bonds. Charge transfer is also an important factor in the halogen bonds involved with dihalogen molecules.     

Experimental and theoretical studies on the radical-cation-mediated imino-Diels-Alder reaction

The feasibility of an electron transfer imino-Diels-Alder reaction between N-benzylideneaniline and arylalkenes in the presence of a pyrylium salt as a photosensitizer has been demonstrated by a combination of product studies, laser flash photolysis (LFP), and DFT theoretical calculations. A stepwise mechanism involving two intermediates and two transition states is proposed.     

Influence of the d orbital occupation on the nature and strength of copper cation-pi interactions: threshold collision-induced dissociation and theoretical studies

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies of a wide variety of copper cation-pi complexes, Cu(+)(pi-ligand), where pi-ligand = benzene, flurobenzene, chlorobenzene, bromobenzene, iodobenzene, phenol, toluene, anisole, pyrrole, N-methylpyrrole, indole, naphthalene, aniline, N-methylaniline, and N,N-dimethylaniline. The primary and lowest energy dissociation pathway corresponds to the endothermic loss of the intact neutral pi-ligand for all complexes except those to N-methylpyrrole, indole, aniline, N-methylaniline, and N,N-dimethylaniline. In the latter complexes, the primary dissociation pathway corresponds to loss of the intact ligand accompanied by charge transfer, thereby producing a neutral copper atom and ionized pi-ligand. Fragmentation of the pi-ligands is also observed at elevated energies in several cases. Theoretical calculations at the B3LYP/6-311G(d,p) level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Multiple low-energy conformers are found for all of the copper cation-pi complexes. Theoretical bond dissociation energies are determined from single point energy calculations at the B3LYP/6-311+G(3df,2p) level of theory using the B3LYP/6-311G(d,p) optimized geometries. The agreement between theory and experiment is very good for most complexes. The nature and strength of the binding in these copper cation-pi complexes are studied and compared with the corresponding cation-pi complexes to Na(+). Natural bond orbital analyses are carried out to examine the influence of the d orbital occupation on copper cation-pi interactions.     

Some theoretical studies on hydrogen molecule capture by platinum atoms

Pseudopotential SCF-LCAO-MO and variational and perturbative Cl calculations were carried out for H₂ molecule capture by a single Pt atom with C_2v symmetry. A pseudopotential for the platinum atom including relativistic effects was used. Singlet and triplet states of the Pt-H₂ interaction having different representations of the mentioned C_2v symmetry were studied. The triplet ground state of Pt leads to two A₁ and B₂ states in which the metal atom cannot capture H₂; i.e., both have repulsive interaction energies. The electronic state responsible for the capture of H₂ is the closed-shell, singlet A₁ excited state. The equilibrium geometry of the system is reached with a broken H? H bond at a HPtH angle of about 100°. Additionally another shallower minimum for a singlet A₁ linear structure is observed. Specific predictions for the thermal and photochemical Pt + H₂ reactions that can be carried out under matrix isolation conditions are made.