An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Verification of DFT-predicted hydrogen storage capacity of VC3H3 complex using molecular dynamics simulations

Density functional theory (DFT) and Fourth‐order Möller–Plesset (MP4) perturbation theory calculations are performed to examine the possibility of hydrogen storage in V‐capped VC₃H₃ complex. Stability of bare and H₂ molecules adsorbed V‐capped VC₃H₃ complex is verified using DFT and MP4 method. Thermo‐chemistry calculations are carried out to estimate the Gibbs free corrected averaged H₂ adsorption energy which reveals whether H₂ adsorption on V‐capped VC₃H₃ complex is energetically favorable, at different temperatures. We use different exchange and correlation functionals employed in DFT to see their effect on H₂ adsorption energy. Molecular dynamic (MD) simulations are performed to confirm whether this complex adsorbs H₂ molecules at a finite temperature. We elucidate the correlation between H₂ adsorption energy obtained from density functional calculations and retaining number of H₂ molecules on VC₃H₃ complex during MDs simulations at various temperatures. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Positive chemical ionization triple‐quadrupole mass spectrometry and ab initio computational studies of the multi‐pathway fragmentation of phthalates

We report the first positive chemical ionization (PCI) fragmentation mechanisms of phthalates using triple‐quadrupole mass spectrometry and ab initio computational studies using density functional theories (DFT). Methane PCI spectra showed abundant [M + H]⁺, together with [M + C₂H₅]⁺ and [M + C₃H₅]⁺. Fragmentation of [M + H]⁺, [M + C₂H₅]⁺ and [M + C₃H₅]⁺ involved characteristic ions at m/z 149, 177 and 189, assigned as protonated phthalic anhydride and an adduct of phthalic anhydride with C₂H₅⁺ and C₃H₅⁺, respectively. Fragmentation of these ions provided more structural information from the PCI spectra. A multi‐pathway fragmentation was proposed for these ions leading to the protonated phthalic anhydride. DFT methods were used to calculate relative free energies and to determine structures of intermediate ions for these pathways. The first step of the fragmentation of [M + C₂H₅]⁺ and [M + C₃H₅]⁺ is the elimination of [R? H] from an ester group. The second ester group undergoes either a McLafferty rearrangement route or a neutral loss elimination of ROH. DFT calculations (B3LYP, B3PW91 and BPW91) using 6‐311G(d,p) basis sets showed that McLafferty rearrangement of dibutyl, di(‐n‐octyl) and di(2‐ethyl‐n‐hexyl) phthalates is an energetically more favorable pathway than loss of an alcohol moiety. Prominent ions in these pathways were confirmed with deuterium labeled phthalates. Copyright © 2010 John Wiley & Sons, Ltd.     

Post‐Synthetic Reversible Incorporation of Organic Linkers into Porous Metal–Organic Frameworks through Single‐Crystal‐to‐Single‐Crystal Transformations and Modification of Gas‐Sorption Properties

The porous metal–organic framework (MOF) {[Zn₂(TCPBDA)(H₂O)₂]?30 DMF?6 H₂O}_n ( SNU‐30 ; DMF=N,N‐dimethylformamide) has been prepared by the solvothermal reaction of N,N,N′,N′‐tetrakis(4‐carboxyphenyl)biphenyl‐4,4′‐diamine (H₄TCPBDA) and Zn(NO₃)₂?6 H₂O in DMF/tBuOH. The post‐synthetic modification of SNU‐30 by the insertion of 3,6‐di(4‐pyridyl)‐1,2,4,5‐tetrazine (bpta) affords single‐crystalline {[Zn₂(TCPBDA)(bpta)]?23 DMF?4 H₂O}_n ( SNU‐31 SC ), in which channels are divided by the bpta linkers. Interestingly, unlike its pristine form, the bridging bpta ligand in the MOF is bent due to steric constraints. SNU‐31 can be also prepared through a one‐pot solvothermal synthesis from Zn^II, TCPBDA^4?, and bpta. The bpta linker can be liberated from this MOF by immersion in N,N‐diethylformamide (DEF) to afford the single‐crystalline SNU‐30 SC , which is structurally similar to SNU‐30 . This phenomenon of reversible insertion and removal of the bridging ligand while preserving the single crystallinity is unprecedented in MOFs. Desolvated solid SNU‐30′ adsorbs N₂, O₂, H₂, CO₂, and CH₄ gases, whereas desolvated SNU‐31′ exhibits selective adsorption of CO₂ over N₂, O₂, H₂, and CH₄, thus demonstrating that the gas adsorption properties of MOF can be modified by post‐synthetic insertion/removal of a bridging ligand.     

Oxidative Dehydrogenation of Propane over a VO2‐Exchanged MCM‐22 Zeolite: A DFT Study

The adsorption and the mechanism of the oxidative dehydrogenation (ODH) of propane over VO₂‐exchanged MCM‐22 are investigated by DFT calculations using the M06‐L functional, which takes into account dispersion contributions to the energy. The adsorption energies of propane are in good agreement with those from computationally much more demanding MP2 calculations and with experimental results. In contrast, B3LYP binding energies are too small. The reaction begins with the movement of a methylene hydrogen atom to the oxygen atom of the VO₂ group, which leads to an isopropyl radical bound to a HO? V? O intermediate. This step is rate determining with the apparent activation energy of 30.9 kcal mol^?1, a value within the range of experimental results for ODH over other silica supports. In the propene formation step, the hydroxyl group is the more reactive group requiring an apparent activation energy of 27.7 kcal mol^?1 compared to that of the oxy group of 40.8 kcal mol^?1. To take the effect of the extended framework into account, single‐point calculations on 120T structures at the same level of theory are performed. The apparent activation energy is reduced to 28.5 kcal mol^?1 by a stabilizing effect caused by the framework. Reoxidation of the catalyst is found to be important for the product release at the end of the reaction.     

Six‐coordinate Co2+ with imidazole,NH3, and H2O ligands: Approaching spin crossover

Octahedral, six‐coordinate Co²⁺ can exist in two spin states: S = 3/2 and S = 1/2. The difference in energy between high spin (S = 3/2) and low spin (S = 1/2) is dependent on both the ligand mix and coordination stereochemistry. B3LYP calculations on combinations of neutral imidazole, NH₃, and H₂O ligands show that low‐spin isomers are stabilized by axial H₂O ligands and in structures that also include trans pairs of equatorial NH₃ and protonated imidazole ligands, spin crossover structures are predicted from spin state energy differences. Occupied Co d orbitals from the DFT calculations provide a means of estimating effective ligand strength for homoleptic and mixed ligand combinations. These calculations suggest that in a labile biological system, a spin crossover environment can be created. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Scorpionate‐Type Coordination in MFU‐4l Metal–Organic Frameworks: Small‐Molecule Binding and Activation upon the Thermally Activated Formation of Open Metal Sites

Postsynthetic metal and ligand exchange is a versatile approach towards functionalized MFU‐4l frameworks. Upon thermal treatment of MFU‐4l formates, coordinatively strongly unsaturated metal centers, such as zinc(II) hydride or copper(I) species, are generated selectively. Cu^I‐MFU‐4l prepared in this way was stable under ambient conditions and showed fully reversible chemisorption of small molecules, such as O₂, N₂, and H₂, with corresponding isosteric heats of adsorption of 53, 42, and 32 kJ mol^?1, respectively, as determined by gas‐sorption measurements and confirmed by DFT calculations. Moreover, Cu^I‐MFU‐4l formed stable complexes with C₂H₄ and CO. These complexes were characterized by FTIR spectroscopy. The demonstrated hydride transfer to electrophiles and strong binding of small gas molecules suggests these novel, yet robust, metal–organic frameworks with open metal sites as promising catalytic materials comprising earth‐abundant metal elements.     

Less Is More: Three‐Coordinate C,N‐Chelated Distannynes and Digermynes

We report here the synthesis of new C,N‐chelated chlorostannylenes and germylenes L³MCl (M=Sn( 1 ), Ge ( 2 )) and L⁴MCl (M=Sn( 3 ), Ge ( 4 )) containing sterically demanding C,N‐chelating ligands L^{3, 4} (L³=[2,4‐di‐tBu‐6‐(Et₂NCH₂)C₆H₂]^?_; L⁴=[2,4‐di‐tBu‐6‐{(C₆H₃‐2′,6′‐iPr₂)N=CH}C₆H₂]^?). Reductions of 1 – 4 yielded three‐coordinate C,N‐chelated distannynes and digermynes [L^{3, 4}M ]₂ for the first time ( 5 : L³, M=Sn, 6 : L³, M=Ge, 7 : L⁴, M=Sn, 8 : L⁴, M=Ge). For comparison, the four‐coordinate distannyne [L⁵Sn]₂ ( 10 ) stabilized by N,C,N‐chelate L⁵ (L⁵=[2,6‐{(C₆H₃‐2′,6′‐Me₂)N?CH}₂C₆H₃]^?) was prepared by the reduction of chlorostannylene L⁵SnCl ( 9 ). Hence, we highlight the role of donor‐driven stabilization of tetrynes. Compounds 1 – 10 were characterized by means of elemental analysis, NMR spectroscopy, and in the case of 1 , 2 , 5 – 7 , and 10 , also by single‐crystal X‐ray diffraction analysis. The bonding situation in either three‐ or four‐coordinate distannynes 5 , 7 , and 10 was evaluated by DFT calculations. DFT calculations were also used to compare the nature of the metal–metal bond in three‐coordinate C,N‐chelating distannyne [L³Sn]₂ ( 5 ) and related digermyme [L³Ge]₂ ( 6 ).     

Theoretical study of reactions between MH (M=B,Al) and the H2S molecule

Reaction mechanisms between MH (M=B, Al) and the H₂S molecule have been theoretically studied. The G3 ab initio and DFT calculations demonstrate that only one stable addition complex (HM:SH₂, M=B, Al) can be formed, and that, starting from the addition complex (HM:SH₂) two parallel reaction channels have been found: one is an addition reaction to give H₂MSH via the three‐membered ring transition state (TS), and the other is a dehydrogenation reaction to give MSH+H₂ via the four‐membered ring TS. Thermodynamics and Eyring transition state theory (TST) with the Wigner correction are also used to compute the thermodynamic functions, the equilibrium constants, A factors, and the rate constants of these reaction channels at 300–1500 K. The calculated results predict that the product H₂BSH in the system of BH+H₂S and the product AlSH+H₂ in the system of AlH+H₂S will be mainly observed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

QM/MM study of the interaction between zigzag SnC nanotube and small toxic gas molecules

Adsorptions of small toxic molecules such as CO, N₂, HCN, SO₂, H₂CO, and NH₃ on a single‐walled (6,0) SnC nanotube (SnCNT) are investigated using Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The calculations are carried out at the B3LYP/6‐311++G(d,p)//LANL2DZ:UFF level of theory. The high layer of the model consists of a pyrene‐type ring on the nanotube surface as the adsorption site, where one gas molecule is allowed to interact. Conversely, for the adsorption of the two molecules, a larger site like a coronene ring is used for the high layer. Adsorption energy, Gibbs free energy change, Mulliken charge transfer, and total electron‐density maps are computed in each case. The adsorption strength of the gas molecule on the SnCNT surface is also analyzed from the density of states projected to different atoms (PDOS) of the nanotube–adsorbate complexes. The adsorptions of CO and N₂ on the (6,0) SnCNT surface require to cross potential barriers, and the corresponding transition structures are identified by ONIOM‐IRC calculations. For the remaining four molecules, the processes of adsorption are predicted to be barrier‐less. The calculations for the adsorption of H₂CO on (5,0) and (7,0) SnCNT surfaces are extended to study the effect of the size of the nanotube. Results for the adsorption of a single molecule on (6,0) SnCNT using B3LYP functional are compared with those obtained from a dispersion corrected functional such as M06‐2X. © 2015 Wiley Periodicals, Inc.     

Mechanistic Insight into the Copper‐Catalyzed Regiodivergent Silacarboxylation of Allenes with CO2

DFT calculations were performed to investigate the detailed reaction mechanisms in the copper‐catalyzed regiodivergent silacarboxylation of allenes. According to our calculations, the catalysis would bifurcate at the allene silylcupration step, followed by CO₂ insertion, eventually leading to the carboxylated vinylsilane or allylsilane products. The gaps between the two silylcupration barriers were predicted to be ?2.3, ?0.4, and 2.2 kcal mol^?1 when using (rac)‐Me‐DuPhos, dcpe, and PCy₃ (+H₂O) as the ligands, which nicely accounted for the experimental vinylsilane/allylsilane ratios of 93:7, 50:50, and 15:85, respectively. By means of transition‐state‐energy decomposition, we found that the energy penalty of catalyst deformation into its transition‐state geometry was the key factor in determining the direction of the reaction. The switchable regioselectivity by using different P ligands could be ascribed to structural changes of the Cu?Si and Cu?P bonds during the silylcupration process.     

Accurate ab initio potential energy surface and vibration‐rotation energy levels of hydrogen peroxide

The accurate ground‐state potential energy surface of hydrogen peroxide, H₂O₂, has been determined from ab initio calculations using the coupled‐cluster approach in conjunction with the correlation‐consistent basis sets up to septuple‐zeta quality. Results obtained with the conventional and explicitly correlated coupled‐cluster methods were compared. The core–electron correlation, scalar relativistic, and higher‐order valence–electron correlation effects were taken into account. The adiabatic effects were also discussed. The vibration–rotation energy levels of the H₂O₂, D₂O₂, and HOOD isotopologues were predicted, and the experimental vibrational fundamental wavenumbers were reproduced to 1 cm^?1 (“spectroscopic”) accuracy. © 2012 Wiley Periodicals, Inc.     

Synthesis of End‐Functionalized Polyacetylenes that Contain Polar Groups by Employing Well‐Defined Palladium Catalysts

A series of [(dppf)PdBr(R)]‐type complexes (dppf=1,1′‐bis(diphenylphosphino)ferrocene; R=p‐cyanophenyl ( 1 a ), o‐hydroxymethylphenyl ( 1 b ), and triphenylvinyl ( 1 c )), in combination with silver trifluoromethanesulfonate (AgOTf), were demonstrated to be active for the polymerization of monosubstituted polar acetylene monomers HC?CCONHC₄H₉ ( 2 ), HC?CCO₂C₈H₁₇ ( 3 ), HC?CCH₂OCONHC₆H₁₃ ( 4 ), HC?CCH₂OCO₂C₆H₁₃ ( 5 ), and HC?CCH(CH₃)OH ( 6 ). The yields and molecular weights of the polymers depended on the combination of the Pd catalyst and monomer that was employed. Matrix‐assisted laser‐desorption/ionization–time of flight (MALDI‐TOF) mass spectrometric analysis indicated the formation of polymers that contained the “R” and “H” groups at the chain ends. IR spectroscopic analysis supported the R‐end‐functionalization of the polymers. NMR spectroscopy and MS identified the presence of species that were formed by single, double, and triple insertion of the monomers into the Pd‐C₆H₄‐p‐CN bond, thereby giving solid evidence for an insertion mechanism for the present system. Density functional theory (DFT) calculations suggested the preference for 1,2‐insertion of the monomer compared to 2,1‐insertion.     

On the dynamics of H2 adsorption on the Pt(111) surface

The dynamics and kinetics of the dissociation of hydrogen over the hexagonal close packed platinum (Pt(111)) surface are investigated using Car–Parrinello molecular dynamics and static density functional theory calculations of the potential energy surfaces. The calculations model the reference energy‐resolved molecular beam experiments, considering the degrees of freedom of the catalytic surface. Two‐dimensional potential energy surfaces above the main sites on Pt(111) are determined. Combined with Car–Parrinello trajectories, they confirm the dissociative adsorption of H₂ as the only adsorption pathway on this surface at H₂ incindence energies above 5 kJ/mol. A direct determination of energy‐resolved sticking coefficients from molecular dynamics is also performed, showing an excellent agreement with the experimental data at incidence energies in the 5–30 kJ/mol range. Application of dispersion corrections does not lead to an improvement in the prediction of the H₂ sticking coefficient. The adsorption reaction rate obtained from the calculated sticking coefficients is consistent with experimentally derived literature values.     

An ONIOM and DFT study of water adsorption on rutile TiO2 (110) cluster

Density functional theory (DFT) calculations performed at ONIOM DFT B3LYP/6‐31G**‐MD/UFF level are employed to study molecular and dissociative water adsorption on rutile TiO₂ (110) surface represented by partially relaxed Ti₂₅O₃₇ ONIOM cluster. DFT calculations indicate that dissociative water adsorption is not favorable because of high activation barrier (23.2 kcal/mol). The adsorption energy and vibration frequency of both molecularly and dissociatively adsorbed water molecule on rutile TiO₂ (110) surface compare well with the values reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

MoS<Subscript>2</Subscript> single slab as a model for active component of hydrodesulfuration catalyst: a quantum chemical study 1. Molecular and electronic structure of Mo<Subscript>12</Subscript>S<Subscript>24</Subscript> macromolecule and its adsorption complex with H<Subscript>2</Subscript>S

The molecular and electronic structure of Mo₁₂S₂₄ macromolecule as the MoS₂ single slab structure was calculated by the density functional theory (DFT) method with the B3P86 hybrid exchange-correlation functional. The results of calculations point to slight relaxation of coordinatively unsaturated Mo and S atoms, which is consistent with the published data. The calculated width of the forbidden band (0.85–0.98 eV) is comparable with the experimental value (1.30 eV) and similar to that obtained from DFT calculations with periodic boundary conditions (0.89 eV). The surface Mo centers in the Mo₁₂S₂₄ macromolecule are more reduced than the internal (Mo^IV) atoms. In order to characterize the adsorption capacity of coordinatively unsaturated Mo centers, a Mo₁₂S₂₄·6H₂S adsorption complex was calculated. The structure and energy characteristics of the adsorption complex point to a weak donor-acceptor interaction of the π-lone pair of H₂S molecule with the surface (reduced) Mo centers. The active center of thiophene hydrodesulfuration catalysts is formed as a result of the oxidative addition of hydrogen followed by occlusion of hydrogen into the MoS₂ matrix. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2189–2193, October, 2005.     

Synthesis,crystal structure and conformational analysis of an unexpected [1,5]dithiocine product of aminopyridine and thiovanillin

The condensation reaction of 2‐mercapto‐3‐methoxybenzaldehyde with 3‐aminopyridine afforded an unexpected N‐alkylated [1,5]dithiocine instead of the N‐salicylideneaniline. The proposed mechanism for this condensation involves a strong intramolecular hydrogen bond between the thiol and the amine groups, leading to a second condensation. The corresponding product, i.e. 4,10‐dimethoxy‐13‐(pyridin‐3‐yl)‐6H,12H‐6,12‐epiminodibenzo[b,f][1,5]dithiocine methanol 0.463‐solvate, C₂₁H₁₈N₂O₂S₂·0.463CH₃OH, was characterized by single‐crystal X‐ray diffraction analysis. The supramolecular structure shows π–π stacking and S…S interactions in the crystal packing. Within the asymmetric unit, two geometries of the N atom are observed. Although a planar geometry should be expected, a pyramidal one is observed due to the crystal packing. The presence of the two geometries was further supported by density functional theory (DFT) calculations that show an electronic energy difference of less than 2 kJ mol^?1 between the two conformers.     

Singlet methylene insertion into polar O?H and N?H bonds of water and ammonia—Ab initio and DFT study

Correlated ab initio molecular orbital, DFT, QCISD, G3MP2, and QCISD(T) calculations have been used to investigate the geometries, energetics, and mechanisms governing the insertion reactions of ¹CH₂ into O H and N H bonds of water and ammonia, respectively, in gas phase adopting 6‐311++g(d, p) basis set. It is found that ¹CH₂ reacts with water and ammonia to produce the ylide‐like intermediates H₂C OH₂ and H₂C NH₃, which in turn undergo 1,2‐hydrogen shift to produce methanol and methylamine, respectively. Results obtained indicate that in the gas phase, the ylides and the transition states are located below the reactants' energy levels. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Spontaneous Double Hydrometallation Induced by N→M Coordination in Organometallic Hydrides of Group 14 Elements

Our attempts to synthesise N→M intramolecularly coordinated diorganometallic hydrides L₂MH₂ [M=Si ( 4 ), Ge ( 5 ), Sn ( 6 )] containing the CH=N imine group (in which L is C,N‐chelating ligand {2‐[(2,6‐iPr₂C₆H₃)N=CH]C₆H₄}^?) yielded 1,1′‐bis(2,6‐diisopropylphenyl)‐2,2′‐spriobi[benzo[c][1,2]azasilole] ( 7 ), 1,1′‐bis(2,6‐diisopropylphenyl)‐2,2′‐spriobi[benzo[c][1,2]azagermole] ( 8 ) and C,N‐chelated homoleptic stannylene L₂Sn ( 10 ), respectively. Compounds 7 and 8 are an outcome of a spontaneous double hydrometallation of the two CH=N imine moieties induced by N→M intramolecular coordination (M=Si, Ge) in the absence of any catalyst. In contrast, the diorganotin hydride L₂SnH₂ ( 6 ) is redox‐unstable and the reduction of the tin centre with the elimination of H₂ provided the C,N‐chelated homoleptic stannylene L₂Sn ( 10 ). Compounds 7 and 8 were characterised by NMR spectroscopy and X‐ray diffraction analysis. Because the proposed N→M intramolecularly coordinated diorganometallic hydrides L₂MH₂ [M=Si ( 4 ), Ge ( 5 ), Sn ( 6 )] revealed two different types of reduction reactions, DFT calculations were performed to gain an insight into the structures and bonding of the non‐isolable diorganometallic hydrides as well as the products of their subsequent reactions. Furthermore, the thermodynamic profiles of the different reaction pathways with respect to the central metal atom were also investigated.