Sulfur in different chemical surroundings – S K XANES spectra of sulfur-containing heterocycles and their quantum-chemically supported interpretation

The excited states in the XANES region of 2-mercaptobenzooxazole and 2-mercaptobenzothiazole and of their sulfur-bridged dimeric analogues were investigated at the sulfur 1s-ionization threshold by means of synchrotron radiation. The electronic excitations were treated employing density functional theory calculations. The theoretical results obtained for the planar monomers and the bent dimers are in good accordance with the experimental spectra. They allow the assignment of the spectral structures in the region of the S 1s-electron binding energy to π^* and σ^* resonances involving orbitals of the >C=S and –C–S_x–C– (x=1,2) moieties of the molecules. The results are discussed in terms of antibonding π^* and σ^* interactions between the sulfur and the neighboring carbon atoms and of the symmetric and antisymmetric combinations of the respective σ^* orbitals of the monomeric units.     

Ab initio study of anomeric effect in 2,2-difluoroglycine

The optimized molecular structures of seven conformations of 2,2-difluoroglycine have been obtained from ab initio calculations. For conformers in which the lone pair of electrons on the nitrogen are antiperiplanar to one of the C–F bonds, that C–F bond is longer than the other C–F bond, which is synperiplanar to the lone pair of electrons. Conformers which have these features are the most stable conformers of those examined. This observation is explained in terms of an anomeric effect of the 1p(N)→σ^*(C–F). At the MP2/6-31G^* level of calculation, conformers IV and V are 21.5 and 18.7 kJ/mol, respectively, more stable than the least stable conformer, VI, which does not exhibit an anomeric effect. Conformer VII was found to be exceptionally stable, in addition to an anomeric effect, this conformer also exhibits features of a FH–O hydrogen bond.     

Ab initio structural trends and torsional sensitivity in n-hexane and comparisons with crystallographic structural results

The molecular structures of n-hexane were determined by RHF/4-21G ab initio geometry optimization at 30° grid points in its three-dimensional τ₁(C11–C8–C5–C1), τ₂(C14–C11–C8–C5), τ₃(C17–C14–C11–C8) conformational space. Of the resulting 12×12×12=1728 grid structures, 468 are symmetrically non-equivalent and were optimized constraining the torsions τ₁, τ₂, and τ₃ to the respective grid points, while all other structural parameters were relaxed without any constraints. From the results, complete parameter surfaces were constructed using natural cubic spline functions, which make it possible to calculate parameter gradients, |P|=[(∂P/∂τ_i)²+(∂P/∂τ_j)²]^1/2, where P is a C–C bond length or C–C–C angle. The parameter gradients provide an effective measure of the torsional sensitivity of the system and indicate that dynamic activities in one part of the molecule can significantly affect the density of states, and thus the contributions to vibrational entropy, in another part. This opens the possibility of dynamic entropic conformational steering in complex molecules; i.e. the generation of free energy contributions from dynamic effects of one part of a molecule on another. When the conformational trends in the calculated C–C bond lengths and C–C–C angles are compared with average parameters taken from some 900 crystallographic structures containing n-hexyl fragments or longer C–C bond sequences, some correlation between calculated and experimental trends in angles is found, in contrast to the bond lengths for which the two sets of data are in complete disagreement. The results confirm experiences often made in crystallography. That is, effects of temperature, crystal structure and packing, and molecular volume effects are manifested more clearly in bond lengths than bond angles which depend mainly on intramolecular properties. Frequency analyses of the τ₁, τ₂ and τ₃ torsional angles in the crystal structures show conformational steering in the sense that, if τ₁ is trans peri-planar (170°≤τ₁≤180°; −180°≤τ₁≤−170°), the values of τ₂ and τ₃ are clustered closely around the ideal gauche (±60°) and trans (±180°) positions. In contrast, when τ₁ is in the region (50°≤τ₁≤70°), there is a definite increase in the populations of τ₂ and τ₃ at −90 and −150°.     

On the role of localized molecular orbitals in the formation of bond dipoles

The hypothesis of the classical chemistry about bond dipoles resulting from shifts of separate pairs of electrons is proved using the non-canonical method of molecular orbitals (MOs). To this end, a relation is sought between the total charge distribution inside an individual chemical bond of a polyatomic molecule and the square of the respective single localized MO (LMO). General expressions for these MOs are obtained directly on the basis of the Brillouin theorem without invoking additional localization criteria. The two characteristics under comparison are presented in an explicit algebraic form in terms of meaningful components. Reshaping of square of the ‘own’ LMO of the given bond is shown to play the decisive role in the formation of secondary dipoles of initially homopolar bonds (e.g. of C–C and C–H bonds in substituted alkanes), as well as of bonds of relatively low initial polarity. Thus, representability of these dipoles by shifts of the ‘own’ pairs of electrons of respective bonds is supported. For bonds of a high initial polarity, the secondary dipoles are shown to originate mainly from contributions of LMOs of other bonds extending over the antibonding basis orbital of the given bond. Moreover, the actual secondary bond dipole takes an opposite direction vs. that predicted by the shift of the respective ‘own’ pair of electrons in this case. The latter result serves to account for the known low nucleofugality of highly electronegative heteroatoms in the S_N2 reactions.     

Structure and conformational properties of carbonylbisimidosulfuryl fluoride, O=C(N=S(O)F2)2

The molecular structure and conformational properties of O=C(N=S(O)F₂)₂ (carbonylbisimidosulfuryl fluoride) were determined by gas electron diffraction (GED) and quantumchemical calculations (HF/3-21G* and B3LYP/6-31G*). The analysis of the GED intensities resulted in a mixture of 76(12)% syn–syn and 24(12)% syn–anti conformer (ΔH⁰=H⁰(syn–anti)−H⁰(syn–syn)=1.11(32) kcal mol⁻¹) which is in agreement with the interpretation of the IR spectra (68(5)% syn–syn and 32(5)% syn–anti, ΔH⁰=0.87(11) kcal mol⁻¹). syn and anti describe the orientation of the S=N bonds relative to the C=O bond. In both conformers the S=O bonds of the two N=S(O)F₂ groups are trans to the C–N bonds. According to the theoretical calculations, structures with cis orientation of an S=O bond with respect to a C–N bond do not correspond to minima on the energy hyperface. The HF/3-21G* approximation predicts preference of the syn–anti structure (ΔE=−0.11 kcal mol⁻¹) and the B3LYP/6-31G* method results in an energy difference (ΔE=1.85 kcal mol⁻¹) which is slightly larger than the experimental values. The following geometric parameters for the O=C(N=S)₂ skeleton were derived (r_a values with 3σ uncertainties): C=O 1.193 (9) Å, C–N 1.365 (9) Å, S=N 1.466 (5) Å, O=C–N 125.1 (6)° and C–N=S 125.3 (10)°. The geometric parameters are reproduced satisfactorily by the HF/3-21G* approximation, except for the C–N=S angle which is too large by ca. 6°. The B3LYP method predicts all bonds to be too long by 0.02–0.05 Å and the C–N=S angle to be too small by ca. 4°.     

Structure and stability of thiourea with water, DFT and MP2 calculations

The relative stabilities of thiourea in water are investigated computationally by considering thiourea–water complexes containing up to 1–6 water molecules (CS(NH₂)₂(H₂O)_n=1–6) using density functional theory and MP2 ab initio molecular orbital theory. The results show that the thiourea complex is stable and has an unusually high affinity for incoming water molecules. The clusters are progressively stabilized by the addition of water molecules, as indicated by the increasing of the binding energy. The binding energy of the cluster to each H₂O molecule is about 33 kJ mol⁻¹ for n=1–5.The C–S bond, N–C bond distance, Mulliken populations and binding energy keep approximately constant as the clusters increase in size with an increasing number of H₂O molecules. As the solvation progresses, the C–S distance increases monotonically while the Mulliken populations on the C–S bond reduces monotonically with the addition of each H₂O molecule, indicating that the C–S bond of the thiourea unit in the clusters is de-stabilized with an increasing number of H₂O molecules. Charge transfers for the clusters are mainly found at N, S atoms of the thiourea.     

Theoretical study of the reaction of Cu with OCS

The reactivity of Cu⁺ with OCS on both singlet and triplet potential energy surfaces (PES) has been investigated at the UB3LYP/6-311+G(d) level. The object of this investigation was the elucidation of the reaction mechanism. The calculated results indicated that both the C–S and C–O bond activations proceed via an insertion–elimination mechanism. Intersystem crossing between the singlet and triplet surfaces may occur along both the C–S and C–O bond activation branches. The ground states of CuS⁺ and CuO⁺ were found to be triplets, whereas CuCO⁺ and CuCS⁺ have singlet ground states. The C–S bond activation is energetically much more favorable than the C–O bond activation. All theoretical results are in line with early experiments.     

Theoretical study on the structure and UV–visible spectrum of pyridine–chloranil charge-transfer complex

The ground-state structure of the charge-transfer complex formed by pyridine (Py) as electron donor and chloranil (CA) as acceptor has been studied by full geometry optimization at the MP2 and DFT levels of theory. Binding energies were calculated and counterpoise corrections were used to correct the BSSE. Both MP2 and DFT indicate that the pyridine binds with chloranil to form an inclined T-shape structure, with the pyridine plane perpendicular to the chloranil. The CP and ZPE corrected binding energies were calculated to be 14.21 kJ/mol by PBEPBE/6-31G(d) and 23.21 kJ/mol by MP2/6-31G(d). The charge distribution of the ground state Py–CA complex was evaluated with the natural population analysis, showing a net charge transfer from Py to CA. Analysis of the frontier molecular orbitals reveals a σ–π interaction between CA and Py, and the binding is reinforced by the attraction of the O₇ atom of CA with the H₂₃ atom of Py. TD-DFT calculations have been performed to analyze the UV–visible spectrum of Py–CA complex, revealing both the charge transfer transitions and the weak symmetry-relieved chloranil π–π^* transition in the UV–visible region.     

A computational study of bond dissociation enthalpies in haloethenes

Carbon–hydrogen bond dissociation enthalpies (BDEs) were computed for all haloethenes, C₂H_4−nX_n (n=0–3, X=F, Cl, Br, I), at the B3LYP/6-311+G(3df,2p) level using isodesmic reactions. It was found that C–H bond strengths in the monohaloethenes varied substantially, by as much as 18 kJ mol⁻¹, dependent upon the bond's stereochemical position relative to the halogen. BDEs in the dihaloethanes varied in the order CX₂CH–H>(E)-CHXCX–H>(Z)-CHXCX–H. Trends in the computed bond enthalpies were discussed and explained on the basis of relative steric repulsions and hyperconjugative delocalization interactions, as determined from Natural Bond Orbital analysis.     

An ab initio study on the vibrational and electronic spectra of the molybdenum–sulfur clusters with Mo2OnS4−n(n=0–4) core

Using the ab initio method, the vibrational and electronic spectra of binuclear molybdenum clusters which contain Mo₂O_nS_4−n(n=0–4) core were investigated. The main absorption bands in the IR spectra of these clusters are assigned and compared with each other, especially for the case of the trans isomers. The electronic spectra were studied by performing the CIS calculations. The ground state and the first excited state of the clusters were discussed by using the natural bond orbital method. It is shown that the band corresponding to the longest wavelength can be assigned to three kinds of transition types. Two transitions, σ(Mo–Mo)→π*(Mo–X_t)(X=S,O) and σ(Mo–Mo)→σ*(Mo–Mo), can be seen in most cases.     

Co-adsorption NO and organic molecules on Cu sites in zeolites: Quantum chemical DFT calculations

The co-adsorption of organic molecules: acetone, formaldehyde, ethene and acetylene together with NO on the same Cu⁺ site in zeolite CuZSM-5 was investigated by DFT calculations. The aim of this study was to follow the effect of NO on activation of multiple bonds in organic molecules and the effect of organic molecules on the activation of NO bond. The extent of activation of CO, CC, CC as well as of NO bonds was characterized by the result of calculation as the elongation of the multiple bonds, decrease of bond order as the decrease of stretching frequency, while population analysis gave information on the mechanism of activation. It has been found that the presence of NO co-adsorbed on the same Cu⁺ site as organic molecule resulted in more effective activation of CO bond in acetone and formaldehyde, but resulted in a less effective activation of CC and CC bond in ethane and acetylene. On the other hand, the presence of organic molecule resulted in more effective activation of NO bond (more important bond weakening) in NO molecule. The most significant NO bond weakening took place if NO was co-adsorbed with acetone or formaldehyde. Both acetone and formaldehyde transmit the most negative charge to the Cu⁺-zeolite system if adsorbed “solo” in Cu-zeolite. This negative charge may be next transmitted to antibonding NO orbitals resulting in so important NO bond weakening.     

Synthesis, electrochemistry and structural characterization of luminescent rhenium(I) monoynyl complexes and their homo- and hetero-metallic binuclear complexes

A series of luminescent rhenium(I) monoynyl complexes, [Re(N---N)(CO)₃(CC---R)] (N---N=bpy, ^tBu₂bpy; R=C₆H₅, C₆H₄---Cl-4, C₆H₄---OCH₃-4, C₆H₄---C₈H₁₇-4, C₆H₄---C₆H₅, C₈H₁₇, C₄H₃S, C₄H₂S---C₄H₃S, C₅H₄N), together with their homo- and hetero-metallic binuclear complexes, {Re(N---N)(CO)₃(CC---C₅H₄N)[M]} (N---N=bpy, ^tBu₂bpy; [M]=[Re{(CF₃)₂-bpy}(CO)₃]ClO₄, [Re(NO₂-phen)(CO)₃]ClO₄, W(CO)₅) have been synthesized and their electrochemical and photoluminescence behaviors determined. The structural characterization and electronic structures of selected complexes have also been studied. The luminescence origin of the rhenium(I) alkynyl complexes has been assigned as derived states of a [dπ(Re)→π*(N---N)] metal-to-ligand charge transfer (MLCT) origin mixed with a [π(CCR)→π*(N---N)] ligand-to-ligand charge transfer (LLCT) character. The assignments are further supported by extended Hückel molecular orbital (EHMO) calculations, which show that the LUMO mainly consists of π*(N---N) character while the HOMO is dominated by the antibonding character of the Re---CCR moiety resulted from the overlap of the dπ(Re) and π(CCR) orbitals.     

Quantum mechanical study of tautomerism of methimazole and the stability of methimazole–I2 complexes

DFT and ab initio theoretical methods were used to calculate the relative stability of tautomers in the methimazole (MMI). The calculations show that the thione form of MMI 1 is more stable than the thiol tautomer in good agreement with the experimental results. The DFT and ab initio calculations were also used to determine the stability of MMI–I₂ complexes. All methods suggest that the methimazole in the MMI–I₂ complex exists almost exclusively as the thione tautomer. The Gibbs free energy difference between planar and perpendicular forms of thione tautomer of MMI–I₂ complex indicates that the planar form is the predominant complex. The counterpoise corrected Gibbs free energy also shows that the MMI–I₂(plan.) complex is more stable than the MMI–I₂(perp.) complex. These predictions are in good agreement with the experimental results. By using the natural bond orbital (NBO) approach, the effects of charge transfer interactions on the stability of MMI–I₂ complexes were investigated. The LP₃(S)→σ*(I–I) and LP₃(I)→σ*(N–H) charge transfer interactions may be very important in the stability of the planar form. The results show that the LP₃(S)→σ*(I–I) charge transfer interaction causes a greater increase in the σ*(I–I) antibond occupation number, and concomitantly, a greater increase in the corresponding I–I bond length in the planar complex with respect to the perpendicular complex. The LP₃(S)→σ*(I–I) charge transfer interaction is assisted by NHI intermolecular hydrogen bonding. The atom in molecule (AIM) analysis shows that the charge density and its Laplacian at the SI bond critical point of the planar complex is greater than the perpendicular complex.     

Synthesis and crystal structure of 9,10-dihydro-9,10-etheno-1,8-dichloro-11-diphenylphosphinyl-12-(diphenylphosphinylethynyl)anthracene

The title compound, 9,10-dihydro-9,10-etheno-1,8-dichloro-11-diphenylphosphinyl-12-(diphenylphosphinylethynyl)anthracene (1), has been synthesized and its crystal structure has been determined. The compound 1 crystallized into the triclinic space group P-1 with =74.837(4)°, β=88.156(4)°, γ=65.398(4)°, Z=2, D_c=1.352 gcm⁻³. In the crystal structure of 1a, one chloroform molecule was included by the compound 1 with a 1:1 ratio and the existence of non-classical intermolecular C–HO hydrogen bonds, intramolecular C–HCl and C–HO hydrogen bonds and π–π stacking were observed.     

Theoretical study of the reaction of Sc with SCO in gas phase

In order to elucidate the mechanism of reaction M⁺ + SCO, both triplet and singlet potential energy surfaces (PESs) for the reaction of Sc⁺ + SCO have been theoretically investigated using the DFT (B3LYP/6-311+G*) level of theory. The geometries for reactants, intermediates, transition states and products were completely optimized. All the transition states were verified by the vibrational analysis and the intrinsic reaction coordinate calculations. The involving potential energy curve-crossing dramatically affects reaction mechanism, reaction rate has been discussed, and the crossing points (CPs) have been localized by the approach suggested by Yoshizawa et al. The present results show that the reaction mechanism are insertion–elimination mechanism both along the C–S and C–O bond activation branches, but the C–S bond activation is much more favorable in energy than the C–O bond activation. All theoretical results not only support the existing conclusions inferred from early experiment, but also complement the pathway and mechanism for this reaction.     

Molecular structure and conformational stability of allylisocyanate—post-Hartree–Fock and density functional theory studies

The molecular structure and conformational stability of allylisocyanate (CH₂CHCH₂NCO) molecule was studied using the ab initio and DFT methods. The geometries of possible conformers, C-gauche (δ=120°, θ=0°) (δ=C=C–C–N and θ=C–C–N=C) and C-cis N-trans (δ=0° and θ=180°) were optimized employing HF/6-31G^*, MP2/6-31G^* levels of theory of ab initio and BLYP, B3LYP, BPW91 and B3PW91 methods of DFT implementing the atomic basis set 6-311+G(d,p). The structural and physical parameters of the above conformers were discussed with the experimental and theoretical values of the related molecules, methylisocyanate and 3-fluoropropene. It has been found that the N=C=O bond angle is not linear as the experimental result for both the conformers and the theoretical bond angle is 173°. The rotational potential energy surfaces have been performed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The Fourier decomposition potentials were analysed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The HF/6-31G^* level of theory predicted that the C-gauche conformer is more stable than the C-cis N-trans conformer by 0.41 kJ/mol, but the MP2 and DFT methods predicted the C-cis N-trans conformer is found to be more stable than the C-gauche conformer. The calculated chemical hardness value at the HF/6-31G^* level of theory predicted the C-cis N-trans form is more stable than C-gauche form, whereas the chemical hardness value at the MP2/6-31G^* level of theory favours the slight preference towards the C-gauge conformer.     

Effect of the nature of mendiaxon–X interactions (X= Na, Cu, H) and the hydrogen bonding on the ν(C=O) behavior: theoretical and spectroscopic study

Theoretical and spectroscopic (IR and Raman) study of different 7-hydroxy-4-methylcoumarin (mendiaxon) systems (mend⁻, mendNa, mendCu, mendH and mendH · 2H₂O) were performed at B3LYP/6-31G(d) and B3LYP/6-31++G(d,p) levels of theory. The geometric and electronic structures as well as the vibrational behavior of the systems studied were discussed: (1) as to the changes that occurred in the anion coumarin ring upon the mend⁻–X⁺ (X⁺ =Na⁺, Cu⁺, H⁺) interactions and (2) as to the changes that occurred in mendH due to hydrogen bondings in mendH · 2H₂O. The largest bond length changes in the anion coumarin ring were obtained for mendH and the smallest ones for mendNa. The bond length changes were mainly produced from the electrostatic effect of the positive charge of X. The induced polarization of the C=O bond upon the mend⁻–X⁺ interactions was found to be opposite to the basic one and it led to shorter C=O bond lengths (higher ν(C=O) frequencies) in the order: mendNa, mendCu and mendH. Conversely, upon the hydrogen bonding the induced polarization of the C=O bond was found in the same direction as the basic one and it produced elongation to the C=O bond length (lower ν(C=O) frequency). On the basis of the correlations found, the ν(C=O) positions in mendNa, mendCu, mendH and mendH · 2H₂O were explained.     

DFT study on the reaction mechanisms of polyfluorosulfonate ester with F

Gas-phase reaction of C(1)F₃S(2)O₂O(3)C(4)H₂C(5)F₃ and F⁻(16) is investigated using DFT method. The geometries of various stationary points and their relative energies are obtained from 6-31+G*, 6-311G**, and 6-311++G** levels. In the S_N2(C) reaction leading to the cleavage of the C(4)–O(3) bond, the reaction complex results from attacking of F⁻ at a hydrogen atom H11 attached to carbon atom C(4). Afterward, F⁻ is attacking the atom C(4) from the backside of the atom O(3) with the help of the neighboring effect, and meanwhile a multi-membered ring, F(16)–H(11)–C(4)–C(5)–F(16), is being formed. The S_N2(C) reaction is irreversible. On the contrary, the S_N2(S) reaction leading to the cleavage of the S(2)–O(3) bond is reversible, and it is initiated by attacking of F⁻ at the atom S(2) from the backside of the atom O(3). The products of the reaction CF₃SO₃CH₂CF₃ +F⁻ should be, thermodynamically, controlled due to the reversibility of the S_N2(S) reaction, and those result, chemospecifically, from the cleavage of the C–O bond. At last, the SCRF calculations confirm that the solvent effect is preferable to the S_N2(C) reaction.     

Theoretical investigation of two-photon absorption properties for a series of bifluorene molecules

The two-photon absorption (TPA) cross-sections of a series of bifluorene molecules with different substituents (constructing three types of structures D–π–D, A–π–A and D–π–A) were calculated using ZINDO/SOS program. The results showed that the A–π–A structure with strong substituent-nitro had the largest TPA cross-section for these molecules. To verify the results, we analyzed the charge quantity of the ground and the main excited states as well as the frontier orbitals of the investigated molecules. The equilibrium geometries were obtained with AM1 method, and using ZINDO-SOS to calculate the third-order nonlinearities of the molecules, then gained the TPA cross-sections. We found that for the compounds with bifluorene as π center, the donor and acceptor strength are the important factor for the enhancement of the TPA properties, and compared with molecules with fluorene as π center, the large TPA cross-sections of bifluorene are caused by coupling effects between the two monomers.