Nature of nonbonded Se...O interactions characterized by 17O NMR spectroscopy and NBO and AIM analyses

To investigate the nature of nonbonded Se...O interactions, three series of 2-substituted benzeneselenenyl derivatives [2-(CHO)C6H4SeX (1), 2-(CH2OH)C6H4SeX, (2), 2-(CH2OiPr)C6H4SeX (3); X = Cl, Br, CN, SPh, SeAr, Me] were synthesized. The 17O NMR absorption observed for 17O-enriched aldehydes 1 appeared upfield relative to benzaldehyde (PhCHO), while the opposite downfield shifts relative to benzyl alcohol (PhCH2OH) were observed for 17O-enriched alcohols 2 and ethers 3. The magnitude of both the upfield and the downfield shifts became larger as the electron-withdrawing ability of a substituent X increased. Quantum chemical calculations at the B3LYP level revealed that for all model compounds the most stable conformer has an intramolecular nonbonded Se.O interaction. Thus, the relative 17O NMR chemical shifts (DeltadeltaO) for 1-3 would reflect the strengths of the Se...O interactions. The natural bond orbital (NBO) analysis demonstrated that the stabilization energy due to an nO --> sigma Se-X orbital interaction (ESe...O) correlates with the Se...O atomic distance on a single curve irrespective of the type of the O atom. On the other hand, the atoms in molecules (AIM) analysis showed that the nonbonded Se...O interactions can be characterized by the presence of a bond critical point, the total energy density (HSe...O) of which decreases with strengthening of the interaction. The results suggested that Se...O interactions have a dominant covalent character rather than an electrostatic one.     

Fluorinated tetrathiafulvalenes with preserved electron-donor properties and segregated fluorous bilayer structures based on F...F nonbonded interactions

The synthesis of the fluorinated 4,5-(2,2'-difluoropropylenedithio)-1,3-dithiol-2-one heterocycle with DAST allows for the preparation of several symmetrical and unsymmetrical di- and tetrafluoro-substituted tetrathiafulvalenes with accessible oxidation potentials (0.6 < E1(1/2) < 0.85 V vs SCE) despite the presence of the electron-withdrawing CF2 groups. The flexibility of the fluorinated seven-membered ring identified from room-temperature NMR data has been thoroughly investigated by temperature-variable 1H and 19F NMR experiments, allowing for the identification of two independent folding processes, whose coalescence temperatures (Tc) and activation energies (deltaGdouble dagger) were determined (Tc = -15 degrees C, deltaGdouble dagger = 50.2 kJ mol(-1) and Tc = 47 degrees C, deltaGdouble dagger = 51.1 kJ mo(-1)). The analysis of the X-ray crystal structures of three of those fluorinated TTF demonstrates the efficiency of the nonbonded fluorine exclusion interactions for the stabilization of layered structures with fluorous bilayers, together with S...S van der Waals interactions and C-H...F hydrogen bonds.     

Experimental and theoretical studies on the nature of weak nonbonded interactions between divalent selenium and halogen atoms

To investigate the nature of weak nonbonded selenium...halogen interactions (Se...X interactions; X = F, Cl, and Br), three types of model compounds [2-(CH(2)X)C(6)H(4)SeY (1-3), 3-(CH(2)X)-2-C(10)H(6)SeY (4-6), and 2-XC(6)H(4)CH(2)SeY (7-9); Y = CN, Cl, Br, SeAr, and Me] were synthesized, and their (77)Se NMR spectroscopic behaviors were analyzed in CDCl(3). The gradual upfield shifts of (77)Se NMR absorptions observed for series 1-3 and 4-6 suggested that the strength of Se...X interaction decreases in the order of Se...F > Se...Cl > Se...Br. The quantum chemical calculations at the B3LYP/631H level using the polarizable continuum model (PCM) revealed that the most stable conformer for 1-3 is the one with an intramolecular short Se...X atomic contact in CHCl(3) (epsilon = 4.9) and also that the n(X) --> sigma(Se-Y) orbital interaction (E(Se...X)) can reasonably explain the order of strength for the Se...X interactions. On the other hand, the (77)Se NMR absorptions observed for series 7-9 did not shift significantly from the reference compounds (C(6)H(5)CH(2)SeY), indicating the absence of the Se...X interaction for 7-9 presumably due to attenuation of basicity for the halogen atom that is substituted directly to the aromatic ring. These observations suggested that the n(X) --> sigma(Se-Y) orbital interaction is a dominant factor for formation of weak Se...X interactions. Electron correlation was also suggested to be important for the stability.     

Molecular beam rotational spectrum of cyclobutanone-trifluoromethane: nature of weak CH...O=C and CH...F hydrogen bonds

The molecular beam Fourier transform microwave spectrum of cyclobutanone-trifluoromethane has been assigned and measured. The carbon atom of trifluoromethane lies in the plane of the heavy atoms of cyclobutanone. The complex is stabilized by one C-H...O=C and two C-H...F-C weak hydrogen bonds. The C-H...O=C interaction, involving one carbonylic oxygen, is studied for the first time in detail with rotationally resolved spectroscopy. The two C-H...F-C weak hydrogen bonds involve two fluorine atoms of trifluoromethane and two hydrogens of the same methylenic group in the alpha position.     

1,4-asymmetric induction in methoxyselenenylation of double bonds at the nitrogen side of chiral perhydro-1,3-benzoxazines promoted by nonbonded Se...N interactions

Regio- and diastereoselective methoxyselenenylation of cinnamylamines attached to a chiral perhydrobenzoxazine occurs in high yields by reaction with benzeneselenenyl chloride in dichloromethane-methanol. The diastereoselection is dependent on the temperature of the reaction and the structure of the substituent at C-2 and can be rationalized by accepting a 1,4-asymmetric induction process after coordination of the selenium to the nitrogen atom of the allylamine system.     

o-hydroxylmethylphenylchalcogens: synthesis, intramolecular nonbonded chalcogen...OH interactions, and glutathione peroxidase-like activity

[Structure: see text]. The synthesis and characterization of a series of organochalcogen (Se, Te) compounds derived from benzyl alcohol 13 are described. The synthesis of the key precursor dichalcogenides 15, 22, and 29 was achieved by the ortho-lithiation route. Selenide 18 was obtained by the reaction of the dilithiated derivative 14 with Se(dtc)2. Oxidation of 15 and 22 with H2O2 afforded the corresponding cyclic ester derivatives 17 and 24, respectively. Oxidation of selenide 18 with H2O2 affords the spirocyclic compound 19. The presence of intramolecular interactions in dichalcogenides 15 and 22 has been proven by single-crystal X-ray studies. The cyclic compounds 17 and 19 have also been characterized by single-crystal X-ray studies. GP(X)-like antioxidant activity of selenium compounds has been evaluated by the coupled bioassay method. Density functional theory calculations at the mPW1PW91 level on ditelluride 22 have identified a fairly strong nonbonding interaction between the hydroxy oxygen and tellurium atom. The second-order perturbation energy obtained through NBO analysis conveys the involvement of n(O) --> sigma(Te-Te) orbital overlap in nonbonding interaction. Post wave function analysis with the Atoms in Molecules (AIM) method identified distinct bond critical point in 15 and 22 and also indicated that the nonbonding interaction is predominantly covalent. Comparison between diselenide 15 and ditelluride 22 using the extent of orbital interaction as well as the value of electron density at the bond critical points unequivocally established that a ditelluride could be a better acceptor in nonbonding interaction, when the hydroxy group acts as the donor.     

N,N-Dimethylaminopropylsilane: a case study on the nature of weak intramolecular Si...N interactions

N,N-Dimethylaminopropylsilane H(3)Si(CH(2))(3)NMe(2) was synthesised by the reaction of (MeO)(3)Si(CH(2))(3)NMe(2) with lithium aluminium hydride. Its solid-state structure was determined by X-ray diffraction, which revealed a five-membered ring with an SiN distance of 2.712(2) A. Investigation of the structure by gas-phase electron diffraction (GED), ab initio and density functional calculations and IR spectroscopy revealed that the situation in the gas phase is more complicated, with at least four conformers present in appreciable quantities. Infrared spectra indicated a possible SiN interaction in the Si-H stretching region (2000-2200 cm(-1)), as the approach of the nitrogen atom in the five-membered ring weakens the bond to the hydrogen atom in the trans position. Simulated gas-phase IR spectra generated from ab initio calculations (MP2/TZVPP) exhibited good agreement with the experimental spectrum. A method is proposed by which the fraction of the conformer with a five-membered ring can be determined by a least-squares fit of the calculated to experimental absorption intensities. The abundance of this conformer was determined as 23.7(6) %, in good agreement with the GED value of 24(6) %. The equilibrium SiN distance predicted by theory for the gas-phase structure was highly variable, ranging from 2.73 (MP2) to 3.15 A (HF). The value obtained by GED is 2.91(4) A, which could be confirmed by a scan of the potential-energy surface at the DF-LCCSD[T] level of theory. The nature of the weak dative bond in H(3)Si(CH(2))(3)NMe(2) can be described in terms of attractive inter-electronic correlation forces (dispersion) and is also interpreted in terms of the topology of the electron density.     

Highly stereoselective asymmetric Pummerer reactions that incorporate intermolecular and intramolecular nonbonded S...O interactions

New chiral sulfoxides (R(S),S)-3, (S(S),S)-3, (R(S),S)-4, and (S(S),S)-4 and known chiral sulfoxides (R(S))-5, (R(S))-6, and (R(S))-7 were synthesized, and the stereochemistry of the new sulfoxides (R(S),S)-3 and (R(S),S)-4 was determined by X-ray crystallographic analysis. In their crystallographic structures, the intramolecular nonbonded S...O close contacts were recognized. Analyses of several sulfoxide complexes including rac-11 with N,N-dimethylacetamide (DMAC) or N-methyl-2-pyrrolidone (NMP) in a MeOH solution utilizing cold-spray ionization mass spectrometry provided, for the first time, direct information for intermolecular nonbonded S...O interactions between sulfoxides and amide (or lactam) in a solution. Highly diastereoselective and enantioselective Pummerer reactions based on the concept of intermolecular and intramolecular nonbonded S...O interactions were performed by treatment of several chiral sulfoxides (R(S), S)-3, (S(S), S)-3, (R(S), S)-4, (S(S), S)-4, (R(S))-5, (R(S))-6, and (R(S))-7 with acetic anhydride and trimethylsilyl triflate (TMSOTf) in DMAC, NMP, N,N-dimethylformamide, and N-formylpiperidine. Mechanistic studies on these facile stereoselective Pummerer reactions revealed the necessity for the amide/TMSOTf complex, such as 26 or 27, to be an efficient activation reagent for Ac(2)O and a trapping reagent for the released acetate ion, and that DMAC and NMP had a positive effect on this highly stereoselective chiral transfer reaction.     

Interplay of phenyl-perfluorophenyl stacking,C-H...F,C-F...pi and F...F interactions in some crystalline aromatic azines

Analysis of phenyl-perfluorophenyl stacking synthon, C-H...F, C-F...pi interactions, and F...F tetramer in three closely related azine crystal structures shows the dominance of Ar-ArF synthon while other interactions are turned on/off depending on the H/F stoichiometry in the molecule.     

Nature of weak inter- and intramolecular interactions in crystals. 1. The F...O and F...H contacts in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole

The topological analysis of the electron density distribution in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole revealed that the F...H and F...O intermolecular contacts correspond to attractive interactions. The energies of these interactions were estimated from the experimental data and it was shown that these contacts are similar to the C—H...O contacts. Analysis of the deformation electron density revealed that the F...O contacts correspond to transfer of the lone electron pair of a fluorine atom to the antibonding -orbital of the C=O bond.     

Synthesis and antibacterial activity of new 1beta-methylcarbapenems having the potential for intramolecular nonbonded S...O interactions.

Mercaptoacetyliminothiadiazoline derivatives (19, 20) useful for the pendant moiety of 1beta-methylcarbapenem antibiotics were efficiently synthesized. Acetyl derivative (18) of 20 was submitted to X-ray analysis, and a significant nonbonded S...O close contact was recognized in the crystallographic structure. New 1beta-methylcarbapenems (5, 6) were synthesized by exploiting 19 and 20, and exhibited considerable antibacterial activities in vitro.     

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.     

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.     

Effect of weak interactions on the H...H distance in stretched dihydrogen complexes

Computational and experimental results presented in this paper demonstrate that the H-H distance in stretched dihydrogen complexes can be hypersensitive to a variety of weak intra- and intermolecular interactions, including those with bulky ligands and solvent molecules, hydrogen-bonding interactions, or ion-pairing. Particularly, the complex IrH(H...H)Cl(2)(P(i)Pr(3))(2) which contains a stretched dihydrogen ligand in the crystalline form, as shown by neutron diffraction, is a trihydride in solution. The difference is due to the intermolecular Ir-Cl...H-Ir hydrogen bonding in the solid.     

Preparation of the first examples of ansa-spiro substituted fluorophosphazenes and their structural studies: analysis of C-H...F-P weak interactions in substituted fluorophosphazenes

The reactions of fluorophosphazenes, endo ansa FcCH(2)P(S)(CH(2)O)(2)[P(F)N](2)(F(2)PN) (1) (Fc = ferrocenyl) and spiro [RCH(2)P(S)(CH(2)O)(2)PN](F(2)PN)(2) (R = Fc (2), C(6)H(5) (3)], with dilithiated diols have been explored. The study resulted in the formation of the first examples of ansa-spiro substituted fluorinated cyclophosphazenes as well as a bisansa substituted fluorophosphazene. The bisansa compound [1,3-[FcCH(2)P(S)(CH(2)O)(2)]][1,5-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (4) was found to be nongeminaly substituted with both the ansa rings in cis configuration, which is in stark contrast to the observations on cyclic chlorophosphazenes where geminal bisansa formation has been observed. The ansa-spiro compounds (5-7) underwent the ansa to spiro transformation leading to dispiro compounds in the presence of catalytic amounts of CsF at room temperature. Two of the ansa-spiro compounds, endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[CH(2)(CH(2)O)(2)]]N(3)P(3)F(2) (5) and endo-[3,5-[FcCH(2)P(S)(CH(2)O)(2)]][1,1-[FcCH(2)P(S)(CH(2)O)(2)]]N(3)P(3)F(2) (6), were structurally characterized, and the crystal structures indicate boat-chair conformation as well as crown conformation for the eight-membered ansa rings. Weak C-H.F-P interactions observed in the crystal structures of the ansa-spiro substituted fluorophosphazene derivatives have been analyzed and compared with C-H.F-P interactions of other fluorinated phosphazenes and thionyl phosphazenes.     

The nature of intermolecular CuI...CuI interactions: a combined theoretical and structural database analysis

The nature of intermolecular interactions between dicoordinate Cu(I) ions is analyzed by means of combined theoretical and structural database studies. Energetically stable Cu(I).Cu(I) interactions are only found when the two monomers involved in the interaction are neutral or carry opposite charges, thus allowing us to speak of bonding between the components of the bimolecular aggregate. A perturbative evaluation of the components of the intermolecular interaction energies, by means the IMPT scheme of Stone, indicates that both the Coulombic and dispersion forces are important in determining the Cu(I).Cu(I) bonding interactions, because only a small part of that energy is attributable to Cu.Cu interactions, while a large component results from Cu.ligand interactions. The electrostatic component is the dominant one by far in the interaction between charged monomers, while in the interaction between neutral complexes, the electrostatic component is found to be of the same order of magnitude as the dispersion term. Bimolecular aggregates that have like charges are repulsive by themselves, and their presence in the solid state results from anion.cation interactions with ions external to this aggregate. In these cases, the short-contact Cu.Cu interactions here should be more properly called counterion-mediated Cu.Cu bonds.     

Gold liquid crystals displaying luminescence in the mesophase and short F...F interactions in the solid state

Rodlike gold(I) complexes, [Au(C6F4OCmH2m+1)(C(triple bond)NC6H4C6H4OCnH2n+1)] (m=2, n=4, 10; m=6, n=10; m=10, n=6, 10), display interesting features. They are liquid crystals and show photoluminescence in the mesophase, as well as in the solid state and in solution. The single-crystal, X-ray diffraction structure of [Au(C6F4OC2H5)(C(triple bond)NC6H4C6H4OC4H9)] confirms its rodlike structure, with a linear coordination around the gold atom, and reveals the absence of any Au...Au interactions (such interactions are often present in luminescent gold complexes). Well-defined, intermolecular Fortho...Fmeta interactions, with remarkably short intermolecular FF distances (2.66 A), are observed; these interactions seem to be responsible for the crystal packing, which consists of an antiparallel arrangement of molecules. Experiments under different conditions support the explanation that the photoluminescence has an intramolecular origin.     

Intramolecular interactions,orbital nature of electronic states,and lulinescence-spectroscopic properties of the phenoxasiline molecule

The electronic structure of the phenoxasiline (POS) molecule in the ground and electronically excited states has been calculated in the framework of the CNDO/S-CI method in sp and spd basis sets. The orbital nature of the S₁ and T₁ states and some luminescence-spectroscopic properties of POS have been determined theoretically and experimentally, and the influence of the l electrons of the oxygen atom and the d AO's of the silicon atom, as well as the geometry of the molecule, on them has been analyzed.Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 22, No. 5, pp. 626–632, September–October, 1986.