Effect of intermolecular O-H ⋯ O hydrogen bonding on the molecular structure of phenol: An ab initio molecular orbital study

The effect of intermolecular O-H O hydrogen bonding on the molecular structure of phenol has been studied by SCF ab initio MO calculations at the HF/6-31G * level. The systems investigated are eight phenol-water complexes and the dimer and trimer of phenol. Optimized geometries show that hydrogen bond formation causes a consistent pattern of changes in the structure of the molecule. When phenol acts as a proton donor, the expected increase ofr (O-H) is accompanied by a slight decrease ofr(C-O) and of the internal ring angles at theipso andpara positions, and by an increase ofr(C _ipso © _ortho ). These changes suggest that the relative contribution of polar canonical forms to the electronic structure of the molecule increases upon hydrogen bond formation, since this enhances the strength of the interaction. The opposite changes occur when phenol acts as a proton acceptor, except forr(O-H), which is the same as in the free molecule. If phenol acts as a proton donorand as a proton acceptor, the two hydrogen bonds become stronger due to a synergic effect. In this case, however, the structural deformation of the molecule is less pronounced than in the previous cases, due to the opposite effect of the two hydrogen bonds. The available experimental evidence on gas-crystal structural differences for phenol is critically reviewed, also in the light of the present results on gas-phase complexes.     

Crystal and molecular structure analysis of flutamide. Bifurcated helicoidal C-H ⋯ O hydrogen bonds

Crystal structure determination and semiempirical AM1 and PM3 calculations were performed on flutamide {2-methyl-N[4 nitro-3-(trifluoromethyl) phenyl] propamide}, a powerful nonsteroidal androgen antagonist. The molecule is almost planar apart from CF₃, NO₂, and CH₃ groups. The NO₂ plane makes an angle of 36.3(4) with the least-square plane of the phenyl ring. The molecules are intermolecularly linked by one N-H O and one C-H O hydrogen bonds. A bifurcated helicoidal hydrogen bond network is formed by the intermolecular C-H O hydrogen bond together with another intramolecular C-H O hydrogen bond. The calculated structures are in good agreement with the crystallographic conformations. AM1 is more accurate for predicting the intramolecular C-H O hydrogen bond while PM3 gives a better geometry for the crowded nitro group. AM1 and PM3 charges of benzenic hydrogens are used to predict the propensity of these atoms to form hydrogen bonds. The noncentrosymmetric space group of the crystal (Pna2₁), the calculated dipole moment (8.88 D), and the calculated angle between molecular dipoles and the twofold axis (–49) close to the optimal value (54.7) indicate that flutamide might be a possible candidate for nonlinear optical material.     

Synthesis,molecular structure and reactivity of new π-conjugated diyne with ferrocenyl and phenyl units

New π-conjugated butadiynyl ligand FcC(CH₃)₂Fc′–CC–CC–Ph (L₁) has been synthesized and its reaction with Co₂(CO)₈ has been studied. New clusters [FcC(CH₃)₂Fc′–CC–CC–Ph][Co₂(CO)₆]_n [(1): n = 1; (2): n = 2] and [Fc–CC–CC–Ph][Co₂(CO)₆]_n [(3): n =  1; (4): n = 2] were obtained by the reaction of ligands FcC(CH₃)₂Fc′–CC–CC–Ph (L₁) and Fc–CC–CC–Ph (L₂) with Co₂(CO)₈ respectively and the composition and structure of the clusters and ligands have been characterized by elemental analysis, FTIR, ¹H and ¹³C NMR and MS. The crystal structures of compounds L₁, L₂, 2 and 4 have been determined by X-ray single crystal analysis.     

Intramolecular π-complexes based on nitroaryl derivatives of furotroponimine: structure and stereodynamics

Neutral aromatic electrophiles, such as trinitrobenzene and dinitrobenzofuroxane, covalently bound to the furotroponimine moiety form intramolecular through-space charge-transfer π-complexes both in solution and in the crystalline state. The kinetic and activation parameters of stereodynamic processes were determined by dynamic NMR spectroscopy. These parameters provide quantitative estimates of the kinetic stability of the p-complexes. The electronic and geometric characteristics of the π-complexes were calculated by the B3LYP/6-31G** method.     

Synthesis of complex Si–O–N–H derivatives by molecular bombardment of silicon and silicon dioxide

Bombardment of a silicon target in a high vacuum with a molecular beam (mixture of high energy H₂+N₂, obtained by charge exchange) and a thermal beam of O₂ produces on the target a variety of compounds. The target is then bombarded by the same molecular beams which produce, extracted by an electrostatic field at an energy of about 10 keV, molecular ions due to the compounds thus formed. These ions are analysed (electromagnet) to give a primary spectrum of ions according to their mass, which are individually selected and dissociated in a collision cell (same H₂+N₂ mixture). Mass analysis of the dissociation fragments leads to the identification of silicon clusters (Si)_n and of Si–O–N–H derivatives, the fragmentations of which permit a definitive determination of their molecular complexity. Dissociation spectra have thus been obtained for some of the most intense peaks of the primary spectrum, on the one hand, and on the other hand for some peaks of lower intensity but of special interest to us (see below). The composition of the fragments is confirmed by the study of the satellite ions derived from the natural 28, 29 and 30 isotopes of silicon, and by the use of deuterium instead of hydrogen. None of the Si–O–N–H derivatives obtained was apparently known earlier. It is shown that some of these molecules (those ‘of special interest to us’) may be identical with sila-analogues of standard amino acids and of nucleic bases: the fact that their fragmentations are identical with those of the corresponding carbon analogues speaks in favour of a structural identity. However, one cannot yet distinguish between the various possible isomeric arrangements, as none of them has been independently prepared, which excludes a direct comparison with reference samples, and as these isomers might give identical fragments; we hope to be able to resolve this ambiguity later. Anyhow, the substances formed are the most complex molecular silicon derivatives so far produced: e.g. Si₂O₂NH₅, Si₃O₂NH₇, Si₄O₃NH₉, Si₄O₂N₂H₄, Si₄ON₃H₅, Si₅O₃N₂H₁₀, Si₅O₂NH₁₁, corresponding to sila-glycine, sila-alanine, sila-threonine, sila-uracile, sila-cytosine, sila-valine, sila-glutamine, – or isomers. Similar results have been obtained using a silicon dioxide target and high energy molecular beams of hydrogen and of nitrogen, without thermal oxygen, or with a carborundum target. © 2000 Académie des sciences / Éditions scientifiques et médicales Elsevier SASmolecular impact / silicon derivatives / amino-acid silicon analogues     

Synthesis, bioactivity and DFT structure–activity relationship study of novel 1,2,3-thiadiazole derivatives

A series of novel 1,2,3-thiadiazole derivatives were designed and synthesized. Their structures were characterized by ¹H NMR, MS and HRMS. The bioactivity tests indicated that compound 9b exhibits a favorable KARI inhibition rate, and some of these novel compounds also showed moderate herbicidal activity against Brassica campestris.     

Hydration effects on the molecular structure of silica-supported vanadium oxide catalysts: A combined IR,Raman, UV–vis and EXAFS study

The effect of hydration on the molecular structure of silica-supported vanadium oxide catalysts with loadings of 1–16 wt.% V has been systematically investigated by infrared, Raman, UV–vis and EXAFS spectroscopy. IR and Raman spectra recorded during hydration revealed the formation of V–OH groups, characterized by a band at 3660 cm⁻¹. Hydroxylation was found to start instantaneously upon exposure to traces of water, reflecting a very high sensitivity of the supported vanadium oxide catalysts for H₂O. Further hydration resulted in the appearance of a V–O–V vibration band located around 700 cm⁻¹ pointing to the formation of di- or polymeric species. EXAFS analysis at 77 K indicated structural changes as the oxygen coordination changed from four to five. Moreover, a V⋯V contribution was detected for the hydrated species. The IR, Raman and UV–vis data suggested a pyramidal anchoring of the dehydrated VO_x species, whereas, the EXAFS data pointed to the presence of single V–O–Si bonded VO_x species. This difference is attributed to water condensation effects at 77 K during EXAFS acquisition, resulting in a partial re-hydroxylation of the dehydrated samples, as confirmed by complementary IR and Raman analysis. Combining the results of this study with data from our previous studies [D.E. Keller, F.M.F. de Groot, D.C. Koningsberger, B.M. Weckhuysen, J. Phys. Chem. B 109 (2005) 10223; D.E. Keller, D.C. Koningsberger, B.M. Weckhuysen, J. Phys. Chem. B 110 (2006) 14313] as well as literature led to a reaction scheme in which a monomeric VO_x species anchored by three Si–O–V bonds to the silica support (pyramidal-type structure) is transformed into a monomeric VO_x species anchored by one Si–O–V bond (umbrella-type structure) by partial hydration of the catalyst material. This results in the formation of both V–O–H and Si–O–H bonds. At higher water pressures, larger vanadium oxide clusters are formed due to full hydration of the catalyst surface and a de-attachment of the vanadium oxide from the support surface. The results of this study provide evidence, that an umbrella-type structure (i.e., Si–O–VO(OH)₂) could be present under catalytic conditions where H₂O is a reaction product (e.g., partial oxidation of methanol to formaldehyde and oxidative dehydrogenation of alkanes). In other words, both the pyramidal ((Si–O)₃–VO) and the umbrella (Si–O–VO(OH)₂) model can exist at a support surface, their relative ratio depending on the hydration degree of the catalyst material. This study also illustrates that a corroborative characterization requires the use of multiple spectroscopic techniques applied at the same samples under almost identical measuring conditions.     

Amide,urea and thiourea‐containing triphenylene derivatives: influence of H‐bonding on mesomorphic properties

The synthesis and thermotropic properties are reported for a series of hexaalkoxytriphenylenes that contain an amide, urea or thiourea group in one of their alkoxy tails. The intermolecular hydrogen bonding abilities of these molecules have a disturbing influence on the formation and stability of the columnar liquid crystalline phases. The stronger the hydrogen bonding the more the liquid crystallinity is suppressed, probably due to disturbance of the π–π stacking of the triphenylene discs. As a direct result, urea‐ and amide‐containing triphenylene derivatives are not liquid crystalline, but several thiourea derivatives show hexagonal columnar mesophases.     

Theoretical Study on the Structures and Stability of Isomers and Complex of [Si, C, O, O] System

Introduction[Si,C ,O ,O]systemhasattractedmuchattentioninthefieldsofchemistryandmaterials1 3becauseofthefollow ingseveralcauses .First,theinterestisthepotentialimpor tanceininterstellarspace .Heretofore ,SiC ,SiOandCOhavebeendetectedwithintheinterstellarmediumformanyyears,butno [Si,C ,O ,O]isomerswereobservedinthenebulae .FormanySi containingsystemshavebeenstudiedexperimentallyandtheoretically ,4 8andinviewofthepossibleexistenceofthe [Si,C ,O ,O]radicalininterstellarspace ,weselectthe…     

Theoretical Study on the Structures and Stability of Isomers and Complex of[Si,C,O,O] Sytem

A detailed singlet potential energy surface(PES) of [Si,C,O,O] system including a van der Waals (vdW) comples SiO……CO2,eight isomers,and twelve transiton states is investigated by MP2 and QCISD(T) (single-point)methods.At the final QCISD(T)/6-311 G(2df)//MP2/6-311G(d) level with zero-point energy included,the complex SiO……CO is found to be thermodynamically and kinetically the most stable species.Although eight ismoers are located as local energy minima,they are rather unstable toward isomerization to the dissociation fragments or comples.For the reaction of silocon atoms with carbon dioxide,two competitive reaction channels are found,and the primary pathway,which leads to the products of SiO and CO fragments,is the direct oxygen-abstraction process from carbon dioxide by silicon atom with a41.16 kJ/mol reaction barrier height.Our predications are in good agreement with previous experimental and theoretical studies.     

Vibrational circular dichroism of 2,6-di-sec-butyl-4-methylpyridine and 2,6-di-sec-butyl-4-methylpyridine-N-oxide: theoretical evidence on the existence of multiple –CH, –CH2, and –CH3⋯O intramolecular hydrogen bonds on the nitroxide oxygen

Enantiopure (±)-2,6-di-sec-butyl-4-methylpyridine and its oxidized form (±)-2,6-di-sec-butyl-4-methylpyridine-N-oxide were prepared and then separated by chiral HPLC. Their stereochemical structures and their conformational distribution in solution were investigated using vibrational circular dichroism (VCD) and infrared spectroscopy (IR) combined with density functional theory (DFT). The experimental spectra have been compared with theoretical data. This comparison indicated that (−)-2,6-di-sec-butyl-4-methylpyridine and its oxidized form (+)-2,6-di-sec-butyl-4-methylpyridine-N-oxide have an (S,S)-configuration and exist in several conformations. The good fit confirms the reliability of the conformational analysis. Our results indicated that going from the reduced form to the oxidized one strongly influences the type of conformers in solution. Moreover, DFT calculations showed that for all of the conformers of (S,S)-2,6-di-sec-butyl-4-methylpyridine-N-oxide, the formation of four centered intramolecular hydrogen bonds between the hydrogen of the –CH, –CH₂, and –CH₃ groups and the nitroxide oxygen is possible. Moreover the stability of the conformers of both compounds is influenced by the all-trans structure of the sec-butyl moieties.     

Effect of pH and α-, β- and γ-cyclodextrin on the spectral properties of etoricoxib: spectroscopic and molecular dynamics study

The spectral properties of etoricoxib (ETR) at pH 2.0, 6.0 and 10.0 in the presence of cyclodextrins (CDs) were investigated. The absorption spectrum of ETR in acidic medium exhibited two bands centered at 236 and 273 nm, while in basic medium it exhibited two bands centered at 236 and 285 nm. No change in the spectrum was observed in the presence of CDs. The fluorescence emission spectra of ETR in acidic and basic media exhibited one band at 380 nm and another one at 484 nm. The emission band at 484 nm was enhanced when ETR was complexed with β-CD and γ-CD at pH 2.0, 6.0 and 10.0, while the band at 380 nm was enhanced selectively when ETR was complexed with α-CD at pH 2.0. Molecular dynamics simulations computations revealed that at pH 2.0, the sulfonyl moiety of H₂ETR²⁺ is preferentially included within the α-CD cavity, which is believed to cause the enhancement of the band at 380 nm. Moreover, at pH 6.0 and 10.0, the enhancement of the band at 484 nm was related to the inclusion of the chloropyridinyl and methylpyridinyl groups of the bipyridine moiety of HETR⁺ and ETR within β-CD and γ-CD cavities. Benesi–Hildebrand analysis showed that the ETR/β-CD complex adopts a 1:1 stoichiometry with association constant of K ₁₁?=?64.8 at pH 2.0, K ₁₁?=?105.4 at pH 6.0 and K ₁₁?=?520.5 at pH 10.0.     

Formation and structure of Co₂O₄: a combined IR matrix isolation and theoretical study

The formation and structure of dicobalt tetroxide (Co?O?) has been investigated using matrix isolation in solid neon and argon coupled to infrared spectroscopy and quantum chemical methods. It is found that Co?O? can be formed by dimerization of cobalt dioxide without activation energy by diffusion of ground state CoO? molecules at 9 K in the dark. The IR data on eight fundamentals, isotopic effects and quantum chemical calculations are both consistent with a centro-symmetrical structure with two pairs of equivalent oxygen atoms, engaged in a stronger terminal Co-O bond and in a weaker bridging Co-O-Co position. Evidence for other, metastable states is also presented, but the data are not conclusive. The electronic structure and formation pathway has been investigated using the Tao-Perdew-Staroverov-Scuseria/triple-zeta valence polarived basis set (TPSS/TZVP) and broken symmetry unrestricted density functional theory (BS-UDFT) approach and the ground electronic state is predicted to be an open shell 1Ag singlet with the quintet, triplet, septet, and nonet states above by 3.3, 4.9, 9.3, and 27.7 kcal/mol, respectively, but certainly has a complex multireference character that hinders the use of more precise multireference approaches. Different formation pathways have been considered, and the 2(O═Co═O) → Co?O? dimerization reaction is found to be the only barrierless channel and to be strongly exothermic. Comparisons with another transition metal (TM) oxide system (V?O?) suggests that the difference in predicted ground state geometries in TM?O? systems might be due in HOMO-LUMO shapes of the isolated dioxide subunits and optimal overlap configurations.     

Theoretical study on the molecular structures of X-, α-, and β-types of lithium phthalocyanine dimer

We report here the results from theoretical calculations of the potential energy curves, the geometry optimizations, and the electronic structures for three dimers of lithium phthalocyanine (LiPc) by using three types of functional systems: PBE1PBE, B3LYP, and M06. The results were discussed in comparison with those obtained for the dimers of magnesium phthalocyanine (MgPc). The long-range dispersive interactions were considered in part using these functional systems in the increasing order of PBE1PBE, B3LYP, and M06. The mechanism whereby the dispersive interactions affect the geometric and electronic structures of the LiPc and MgPc dimers is discussed. The calculated results provide insight into the computational methods for both open- and closed-shell metal phthalocyanine (MPc) dimers: Although the PBE1PBE and B3LYP functional systems cannot evaluate a weak dispersion interaction appropriately, the M06 functional can estimate a weak dispersion interaction well in both open- and closed-shell MPc dimers. Basis set superposition error (BSSE) corrections play an important role for the quantitative analysis; however, the calculation results without BSSE corrections may be sufficient for the qualitative discussion on the properties of these dimers such as geometries, stabilities, electronic structures, and so on.