Quantum chemical study of the effect of precursor stereochemistry on dissociative chemisorption and surface redox reactions during the atomic layer deposition of the transition metal copper

Using quantum chemical calculations, we investigate surface reactions of copper precursors and diethylzinc as the reducing agent for effective Atomic Layer Deposition (ALD) of Cu. The adsorption of various commonly used Cu(II) precursors is explored. The precursors vary in the electronegativity and conjugation of the ligands and flexibility of the whole molecule. Our study shows that the overall stereochemistry of the precursor governs the adsorption onto its surface. Formation of different Cu(II)/Cu(I)/Cu(0) intermediate complexes from the respective Cu(II) compounds on the surface is also explored. The surface model is a (111) facet of a Cu55 cluster. Cu(I) compounds are found to cover the surface after the precursor pulse, irrespective of the precursor chosen. We provide new information about the surface chemistry of Cu(II) versus Cu(I) compounds. A pair of CuEt intermediates or the dimer Cu2Et2 reacts in order to deposit a new Cu atom and release gaseous butane. In this reaction, two electrons from the Et anions are donated to copper for reduction to metallic form. This indicates that a ligand exchange between the Cu and Zn is important for the success of this transmetalation reaction. The effect of the ligands in the precursor on the electron density before and after adsorption onto the surface has also been computed through population analysis. In the Cu(I) intermediate, charge is delocalized between the Cu precursor and the bare copper surface, indicating metallic bonding as the precursor densifies to the surface.

A comparison of the reactivity of germylene and dimethylgermylene with some methylgermanes. Direct kinetic and quantum chemical studies

Time-resolved studies of germylene, GeH2, and dimethygermylene, GeMe2, generated by the 193 nm laser flash photolysis of appropriate precursor molecules have been carried out to try to obtain rate coefficients for their bimolecular reactions with dimethylgermane, Me2GeH2, in the gas-phase. GeH2 + Me2GeH2 was studied over the pressure range 1-100 Torr with SF6 as bath gas and at five temperatures in the range 296-553 K. Only slight pressure dependences were found (at 386, 447 and 553 K). RRKM modelling was carried out to fit these pressure dependences. The high pressure rate coefficients gave the Arrhenius parameters: log(A/cm(3) molecule(-1)s(-1)) = -10.99 +/- 0.07 and E-a = -(7.35 +/- 0.48) kJ mol(-1). No reaction could be found between GeMe2 + Me2GeH2 at any temperature up to 549 K, and upper limits of ca. 10(-14) cm(3) molecule(-1)s(-1) were set for the rate coefficients. A rate coefficient of (1.33 +/- 0.04) x 10(-11)cm(3) molecule(-1)s(-1) was also obtained for GeH2 + MeGeH3 at 296 K. No reaction was found between GeMe2 and MeGeH3. Rate coefficient comparisons showed, inter alia, that in the substrate germane Me-for-H substitution increased the magnitudes of rate coefficients significantly, while in the germylene Me-for-H substitution decreased the magnitudes of rate coefficients by at least four orders of magnitude. Quantum chemical calculations (G2(MP2,SVP)// B3LYP level) supported these findings and showed that the lack of reactivity of GeMe2 is caused by a positive energy barrier for rearrangement of the initially formed complexes. Full details of the structures of intermediate complexes and the discussion of their stabilities are given in the paper.

A quantum chemical study on the formation of phosphorus mononitride

The chemical mechanism of the (1)PN formation was successfully studied by using the CCSD(T)/6-311++G(3df,3pd) level of theory. The (1)NH(3) + (3)PH and (4)P + NH(3) reaction paths are not energetically favorable to form the (1)PN molecule. However, the (3)NH + (3)PH, (4)N + (3)PH(3), (4)N + (3)PH, (4)P + (3)NH, and (4)P + (2)NH(2) reaction paths to form the (1)PN molecule are only energetically favorable by taking place through specific transition states to form the (1)PN molecule. The NH(3) + (3)PH, (4)N + (1)PH(3), NH(3) + (4)P, and (4)N + (2)PH(2) reactions are spin-forbidden and the probability of hopping for these reactions was estimated to be 0 by the Landau-Zener theory. This is the first detailed study on the chemical mechanism for the (1)PN formation. (C) 2009 Elsevier B.V. All rights reserved.

A quantum chemical study on the formation of phosphorus mononitride

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A quantum chemical investigation of the metal centres in cytochrome c oxidase

Quantum effects are often of key importance for the function of biological systems at molecular level. Cellular respiration, where energy is extracted from the reduction of molecular oxygen to water, is no exception. In this work, the end station of the electron transport chain in mitochondria, cytochrome c oxidase, is investigated using quantum chemical methodology. Cytochrome c oxidase contains two haems, haem a and haem a3. Haem a3, with its copper companion, CuB, is involved in the final reduction of oxygen into water. This binuclear centre receives the necessary electrons from haem a. Haem a, in turn, receives its electrons from a copper ion pair in the vicinity, called CuA. Density functional theory (DFT) has been used to clarify the charge and spin distributions of haem a, as well as changes in these during redox activity. Upon reduction, the added electron is shown to be evenly distributed over the entire haem structure, important for the accommodation of the prosthetic group within the protein. At the same time, the spin distribution of the open-shell oxidised state is more localised to the central iron. The exact spin density distribution has been disputed in the literature, however, different experiments indicating different distributions of the unpaired electron. The apparent contradiction is shown to be due to the false assumption of a unit amount of unpaired electron density; in fact, the oxidised state has about 1.3 unpaired electrons. The validity of the DFT results have been corroborated by wave function based coupled cluster calculations. Point charges, for use in classical force field based simulations, have been parameterised for the four metal centres, using a newly developed methodology. In the procedure, the subsystem for which point charges are to be obtained, is surrounded by an outer region, with the purpose of stabilising the inner region, both electronically and structurally. Finally, the possibility of vibrational promotion of the electron transfer step between haem a and a3 has been investigated. Calculating the full vibrational spectra, at DFT level, of a combined model of the two haems, revealed several normal modes that do shift electron density between the haems. The magnitude of the shift was found to be moderate, at most. The proposed mechanism could have an assisting role in the electron transfer, which still seems to be dominated by electron tunnelling.

Quantum Chemical Studies on Tropospheric Nucleation Mechanisms Involving Sulfuric Acid

Nucleation is the first step of the process by which gas molecules in the atmosphere condense to form liquid or solid particles. Despite the importance of atmospheric new-particle formation for both climate and health-related issues, little information exists on its precise molecular-level mechanisms. In this thesis, potential nucleation mechanisms involving sulfuric acid together with either water and ammonia or reactive biogenic molecules are studied using quantum chemical methods. Quantum chemistry calculations are based on the numerical solution of Schrödinger's equation for a system of atoms and electrons subject to various sets of approximations, the precise details of which give rise to a large number of model chemistries. A comparison of several different model chemistries indicates that the computational method must be chosen with care if accurate results for sulfuric acid - water - ammonia clusters are desired. Specifically, binding energies are incorrectly predicted by some popular density functionals, and vibrational anharmonicity must be accounted for if quantitatively reliable formation free energies are desired. The calculations reported in this thesis show that a combination of different high-level energy corrections and advanced thermochemical analysis can quantitatively replicate experimental results concerning the hydration of sulfuric acid. The role of ammonia in sulfuric acid - water nucleation was revealed by a series of calculations on molecular clusters of increasing size with respect to all three co-ordinates; sulfuric acid, water and ammonia. As indicated by experimental measurements, ammonia significantly assists the growth of clusters in the sulfuric acid - co-ordinate. The calculations presented in this thesis predict that in atmospheric conditions, this effect becomes important as the number of acid molecules increases from two to three. On the other hand, small molecular clusters are unlikely to contain more than one ammonia molecule per sulfuric acid. This implies that the average NH3:H2SO4 mole ratio of small molecular clusters in atmospheric conditions is likely to be between 1:3 and 1:1. Calculations on charged clusters confirm the experimental result that the HSO4- ion is much more strongly hydrated than neutral sulfuric acid. Preliminary calculations on HSO4- NH3 clusters indicate that ammonia is likely to play at most a minor role in ion-induced nucleation in the sulfuric acid - water system. Calculations of thermodynamic and kinetic parameters for the reaction of stabilized Criegee Intermediates with sulfuric acid demonstrate that quantum chemistry is a powerful tool for investigating chemically complicated nucleation mechanisms. The calculations indicate that if the biogenic Criegee Intermediates have sufficiently long lifetimes in atmospheric conditions, the studied reaction may be an important source of nucleation precursors.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Automatic generation of active coordinates for quantum dynamics calculations: application to the dynamics of benzene photochemistry

A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments

Time-resolved gas-phase kinetic and quantum chemical studies of the reaction of silylene with oxygen

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with O-2. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at five temperatures in the range 297-600 K. The second order rate constants at 10 Torr were fitted to the Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-11.08 +/- 0.04) + (1.57 +/- 0.32 kJ mol(-1))/RT ln10 The decrease in rate constant values with increasing temperature, although systematic is very small. The rate constants showed slight increases in value with pressure at each temperature, but this was scarcely beyond experimental uncertainty. From estimates of Lennard-Jones collision rates, this reaction is occurring at ca. 1 in 20 collisions, almost independent of pressure and temperature. Ab initio calculations at the G3 level backed further by multi-configurational (MC) SCF calculations, augmented by second order perturbation theory (MRMP2), support a mechanism in which the initial adduct, H2SiOO, formed in the triplet state (T), undergoes intersystem crossing to the more stable singlet state (S) prior to further low energy isomerisation processes leading, via a sequence of steps, ultimately to dissociation products of which the lowest energy pair are H2O + SiO. The decomposition of the intermediate cyclo-siladioxirane, via O-O bond fission, plays an important role in the overall process. The bottleneck for the overall process appears to be the T -> S process in H2SiOO. This process has a small spin orbit coupling matrix element, consistent with an estimate of its rate constant of 1 x 10(9) s(-1) obtained with the aid of RRKM theory. This interpretation preserves the idea that, as in its reactions in general, SiH2 initially reacts at the encounter rate with O-2. The low values for the secondary reaction barriers on the potential energy surface account for the lack of an observed pressure dependence. Some comparisons are drawn with the reactions of CH2 + O-2 and SiCl2 + O-2.

Time-resolved gas-phase kinetic and quantum chemical studies of the reaction of silylene with nitric oxide

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with NO. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 299-592 K. The second-order rate constants at 10 Torr fitted the Arrhenius equation log(k/cm(3) molecule(-1) s(-1)) = (- 11.66 +/- 0.01) + (6.20 +/- 0.10 kJ mol(-1))IRT In 10 The rate constants showed a variation with pressure of a factor of ca. 2 over the available range, almost independent of temperature. The data could not be fitted by RRKM calculations to a simple third body assisted association reaction alone. However, a mechanistic model with an additional (pressure independent) side channel gave a reasonable fit to the data. Ab initio calculations at the G3 level supported a mechanism in which the initial adduct, bent H2SiNO, can ring close to form cyclo-H2SiNO, which is partially collisionally stabilized. In addition, bent H2SiNO can undergo a low barrier isomerization reaction leading, via a sequence of steps, ultimately to dissociation products of which the lowest energy pair are NH2 + SiO. The rate controlling barrier for this latter pathway is only 16 kJ mol(-1) below the energy of SiH2 + NO. This is consistent with the kinetic findings. A particular outcome of this work is that, despite the pressure dependence and the effects of the secondary barrier (in the side reaction), the initial encounter of SiH2 with NO occurs at the collision rate. Thus, silylene can be as reactive with odd electron molecules as with many even electron species. Some comparisons are drawn with the reactions of CH2 + NO and SiCl2 + NO.

Time-resolved gas-phase kinetic and quantum chemical studies of reactions of silylene with chlorine-containing species. 1. HCl

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with HCL The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas, at five temperatures in the range of 296-611 K. The second-order rate constants fitted the Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-11.51 +/- 0.06) + (1.92 +/- 0.47 kJ mol(-1))/RTIn10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range of 10-100 Torr, but showed small decreases in value of no more than 20% ( +/- 10%) at I Toff, at both the highest and lowest temperatures. The data are consistent with formation of an initial weakly bound donor-acceptor complex, which reacts by two parallel pathways. The first is by chlorine-to-silicon H-shift to make vibrationally excited chlorosilane, SiH3Cl*, which yields HSiCl by H-2 elimination from silicon. In the second pathway, the complex proceeds via H-2 elimination (4-center process) to make chlorosilylene, HSiCl, directly. This interpretation is supported by ab initio quantum calculations carried out at the G3 level which reveal the direct H-2 elimination route for the first time. RRKM modeling predicts the approximate magnitude of the pressure effect but is unable to determine the proportions of each pathway. The experimental data agree with the only previous measurements at room temperature. Comparisons with other reactions of SiH2 are also drawn.

Time-resolved gas-phase kinetic and quantum chemical studies of reactions of silylene with chlorine-containing species. 2. CH3Cl

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of both silacyclopent-3-ene and phenylsilane, have been carried out to obtain second-order rate constants for its reaction with CH3Cl. The reaction was studied in the gas phase at six temperatures in the range 294-606 K. The second-order rate constants gave a curved Arrhenius plot with a minimum value at T approximate to 370 K. The reaction showed no pressure dependence in the presence of up to 100 Torr SF6. The rate constants, however, showed a weak dependence on laser pulse energy. This suggests an interpretation requiring more than one contributing reaction pathway to SiH2 removal. Apart from a direct reaction of SiH2 with CH3Cl, reaction of SiH2 with CH3 (formed by photodissociation of CH3Cl) seems probable, with contributions of up to 30% to the rates. Ab initio calculations (G3 level) show that the initial step of reaction of SiH2 with CH3Cl is formation of a zwitterionic complex (ylid), but a high-energy barrier rules out the subsequent insertion step. On the other hand, the Cl-abstraction reaction leading to CH3 + ClSiH2 has a low barrier, and therefore, this seems the most likely candidate for the main reaction pathway of SiH2 with CH3Cl. RRKM calculations on the abstraction pathway show that this process alone cannot account for the observed temperature dependence of the rate constants. The data are discussed in light of studies of other silylene reactions with haloalkanes.

Gas phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute rate constants, temperature dependences, RRKM modelling and potential energy surfaces

Time resolved studies of silylene, SiH2, generated by the 193 nm laser. ash photolysis of phenylsilane, have been carried out to obtain rate coefficients for its bimolecular reactions with methyl-, dimethyl- and trimethyl-silanes in the gas phase. The reactions were studied over the pressure range 3 - 100 Torr with SF6 as bath gas and at five temperatures in the range 300 - 625 K. Only slight pressure dependences were found for SiH2 + MeSiH3 ( 485 and 602 K) and for SiH2 + Me2SiH2 ( 600 K). The high pressure rate constants gave the following Arrhenius parameters: [GRAPHICS] These are consistent with fast, near to collision-controlled, association processes. RRKM modelling calculations are consistent with the observed pressure dependences ( and also the lack of them for SiH2 + Me3SiH). Ab initio calculations at both second order perturbation theory (MP2) and coupled cluster (CCSD(T)) levels, showed the presence of weakly-bound complexes along the reaction pathways. In the case of SiH2 + MeSiH3 two complexes, with different geometries, were obtained consistent with earlier studies of SiH2 + SiH4. These complexes were stabilised by methyl substitution in the substrate silane, but all had exceedingly low barriers to rearrangement to product disilanes. Although methyl groups in the substrate silane enhance the intrinsic SiH2 insertion rates, it is doubtful whether the intermediate complexes have a significant effect on the kinetics. A further calculation on the reaction MeSiH + SiH4 shows that the methyl substitution in the silylene should have a much more significant kinetic effect ( as observed in other studies).

Experimental and theoretical evidence for homogeneous catalysis in the gas-phase reaction of SiH2 with H2O (and D2O): a combined kinetic and quantum chemical study

Time-resolved kinetic studies of the reaction of silylene, SiH2, with H2O and with D2O have been carried out in the gas phase at 297 K and at 345 K, using laser flash photolysis to generate and monitor SiH2. The reaction was studied independently as a function of H2O (or D2O) and SF6 (bath gas) pressures. At a fixed pressure of SF6 (5 Torr), [SiH2] decay constants, k(obs), showed a quadratic dependence on [H2O] or [D2O]. At a fixed pressure of H2O or D2O, k(obs) Values were strongly dependent on [SF6]. The combined rate expression is consistent with a mechanism involving the reversible formation of a vibrationally excited zwitterionic donor-acceptor complex, H2Si...OH2 (or H2Si...OD2). This complex can then either be stabilized by SF6 or it reacts with a further molecule of H2O (or D2O) in the rate-determining step. Isotope effects are in the range 1.0-1.5 and are broadly consistent with this mechanism. The mechanism is further supported by RRKM theory, which shows the association reaction to be close to its third-order region of pressure (SF6) dependence. Ab initio quantum calculations, carried out at the G3 level, support the existence of a hydrated zwitterion H2Si...(OH2)(2), which can rearrange to hydrated silanol, with an energy barrier below the reaction energy threshold. This is the first example of a gas-phase-catalyzed silylene reaction.

Time-resolved gas-phase kinetic, quantum chemical and RRKM studies of reactions of silylene with cyclic ethers

Time-resolved kinetic studies of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reactions with oxirane, oxetane, and tetrahydrofuran (THF). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at four or five temperatures in the range 294-605 K. All three reactions showed pressure dependences characteristic of third-body-assisted association reactions with, surprisingly, SiH2 + oxirane showing the least and SiH2 + THF showing the most pressure dependence. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equations where the error limits are single standard deviations: log(k(oxirane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.03 +/- 0.07) + (5.70 +/- 0.51) kJ mol(-1)/RT In 10 log(k(oxetane)(infinity)/cm(3) molecule(-1) s(-1)) = (-11.17 +/- 0.11) + (9.04 +/- 0.78) kJ mol(-1)/RT In 10 log(k(THF)(infinity)/cm(3) molecule(-1) s(-1)) = (-10.59 +/- 0.10) + (5.76 +/- 0.65) kJ mol(-1)/RT In 10 Binding-energy values of 77, 97, and 92 kJ mol(-1) have been obtained for the donor-acceptor complexes of SiH2 with oxirane, oxetane, and THF, respectively, by means of quantum chemical (ab initio) calculations carried Out at the G3 level. The use of these values to model the pressure dependences of these reactions, via RRKM theory, provided a good fit only in the case of SiH2 + THF. The lack of fit in the other two cases is attributed to further reaction pathways for the association complexes of SiH2 with oxirane and oxetane. The finding of ethene as a product of the SiH2 + oxirane reaction supports a pathway leading to H2Si=O + C2H4 predicted by the theoretical calculations of Apeloig and Sklenak.