Proton and deuteron position preferences in water clusters: an ab initio study

In order to explore the effect of H-to-D substitution on the zero-point energy (ZPE) of water clusters, Hessians were computed for a database of 53 optimized (H2O)n clusters, 5 < or = n < or = 21, at the B3LYP6-311 + + G** level. The 53 clusters contained 1524 protons, which were sorted into 18 categories according to the type of their donor O and (if not free) acceptor O. Letting deltaZPE[H]* denote the change in ZPE when the proton H* is replaced by D, mean values for deltaZPE[H*] for the H-bonded categories ranged from -2172 cal mol(-1) for H* in a DDAA-DDAA bond to -2118 for H* in a DAA-DDA bond. Mean value for H* free on DAA (respectively, DA) was -2018 (respectively, -1969). For DAA-DDA bonds, and for short H bonds in general, there was a strong inverse correlation between /deltaZPE[H*]/ and the O-H* distance. deltaZPE for multiple H-to-D substitutions was additive, except for a cooperativity effect of -13.7 to -19.7 cal mol(-1) when two substituted protons were in the same H2O unit and a much smaller cooperativity when one proton's donor was the other's acceptor. Implications of these data include a relative preference for D to occupy H bonded rather than free positions in finite water clusters, a value of 3.82 for the disproportionation equilibrium constant of mixed ice at 150 K, increased occupation by H at surface positions of mixed ice, and a larger average coordination number for liquid D2O than for liquid H2O.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

Pseudorotation motion in tetrahydrofuran: an ab initio study

The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

HF(H2O)n clusters with an excess electron: ab initio study

The structures of electron-bound and neutral clusters of HF(H2O)n (n=1-3) were optimized at the level of second-order Moller-Plesset perturbation theory (MP2). Then, the energies were studied using the coupled cluster singles, doubles, and perturbative triples correction [CCSD(T)] method. The vertical detachment energies of the electron-bound clusters for n=1-3 are 60, 180, and approximately 300 meV, respectively. In the case of the n=3, two structures are competing energetically. The electron-bound clusters for n=1 and 2 are 1.5 and 1.8 kcal/mol more stable than the neutral, while that for n=3 is 0.6-0.9 kcal/mol less stable. The excess electron is stabilized in the surface-bound state of the dipole oriented structures of the hydrated acid clusters. Vibrational spectra of the electron-bound clusters are discussed.     

Towards SiC surface functionalization: an ab initio study

We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular-dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for biocompatible devices.     

Thermal decomposition of decalin: an ab initio study

Density functional theory calculations (B3LYP and BH&HLYP functionals) of the potential energy surface have been performed to investigate the mechanisms of decalin breakdown, and the Rice-Ramsperger-Kassel-Marcus and transition state theory methods have been used to compute the high-pressure limit thermal rate constants for the new reaction pathways. The new pathways connect decalin to five primary monoaromatic species: benzene, toluene, styrene, ethylbenzene, and xylene. The reactions used for the new routes are carbon-carbon bond cleavage reaction, dissociation reaction, and hydrogen abstraction and addition reactions. A kinetic analysis was performed for pyrolytic conditions, and benzene, toluene, and xylene were identified as major products.     

Wheland intermediates: an ab initio valence bond study

The traditional resonance model for electrophilic attacks on substituted aromatic rings is revisited using high level valence bond (VB) calculations. A large π-donation is found in the X = NH(2) case and a weaker one for the X = Cl case, not only for ortho and para isomers but also for the meta case, which can be explained by considering five (not three) fundamental VB structures. No substantial π-effect is found in the X = NO(2) case, generally viewed as π-attractive.     

O-H stretch modes of dodecahedral water clusters: a statistical ab initio study

Infrared frequencies calculations were carried out for 20 (H2O)20 water clusters obeying the 5(12) dodecahedral geometry, optimized at the B3LYP/6-311++G** level. Their combined spectra contained 800 O-H stretch modes, ranging from 2181 to 3867 cm(-1) (unscaled), which were treated and studied as a database. Of these, 752 modes (94%) could be assigned to a single dominant O-H stretch. These 752 were classified into five subdatabases depending on the local H-bond type of the dominant stretch. The frequency (nu) was correlated with the O-H distance (b(OH)), with H-bond length (R(OO)) where applicable, and with other variables. The parameter b(OH) alone accounted for 96-99% of the variance in nu for stretches in H-bonds. The correlation with R(OO) is substantially weaker. Normal modes were classified as "high ratio" or "low ratio" depending upon the mode's distribution of kinetic energy among the O-H bonds. High-ratio modes (389 modes, or 49% of our sample) are modeled well as a single oscillator undergoing small perturbations by weak coupling from other oscillators. Low-ratio modes involve strong coupling with at least one other O-H stretch for which b(OH2) is close to b(OH). The IR intensities of modes vary widely but can be explained in terms of a single equation giving dipole moment derivatives as a function of b(OH). For the lowest-energy (H2O)20 clusters, their IR stretch spectra contained eight distinguishable absorption bands. An explanation for eight bands in terms of the theory of polyhedral water clusters is offered.     

Structure, electronic, and optical properties of TiO2 atomic clusters: an ab initio study

Atomic clusters of TiO(2) are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO(2) clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in photocatalysis and photovoltaics. In this work, we prove that clusters with anatase symmetry are energetically stable and can be considered as the starting seeds to growth much larger and complex nanostructures. The electronic gap of these inorganic molecules is investigated, and shown to be larger than the optical gap by almost 4 eV. Therefore, strong excitonic effects appear in these systems, much more than in the corresponding bulk phase. Moreover, the use of various levels of theory demonstrates that charge transfer effects play an important role under photon absorption, and therefore the use of adiabatic functionals in time dependent density functional theory has to be carefully evaluated.     

Electron attachment to HCl clusters

Negatively charged cluster ions of hydrogen chloride are formed by electron attachment to HCl clusters, which are produced in a seeded supersonic beam traversing a sustained gas discharge. Cluster ions of (HCl) _n ^? , withn=2, and tentatively withn=3 and 4 are observed. Cluster ions like Cl _n ^? , Cl _n ^? (HCl) _m , and withAr attached to them are also seen. The relevance to radiation chemistry of HCl if briefly discussed. Atoms evaporating from the hot, thoriated tungsten filament of the glow discharge lead to clusters such as Th _n ^? and its oxides.     

Electron donor-acceptor interactions in ethanol-CO2 mixtures: an ab initio molecular dynamics study of supercritical carbon dioxide

The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello molecular dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercritical carbon dioxide-ethanol mixtures. The probability density distribution of CO2 molecules around ethanol in the supercritical state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 molecules themselves leads to significant deviations from linearity in the geometry of the CO2 molecule. The vibrational spectra of carbon dioxide obtained from the atomic velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the nu2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concentration in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixture when compared to its gas-phase value, in agreement with experiments.     

Current rectification by asymmetric molecules: an ab initio study

Current rectification effect in an asymmetric molecule HCOO-C6H4-(CH2)n sandwiched between two aluminum electrodes has been studied using an ab initio nonequilibrium Green's function method. The conductance of the system decreases exponentially with the increasing number n of CH2. The phenomenon of current rectification is observed such that a very small current appears at negative bias and a sharp negative differential resistance at a critical positive bias when n>or=2. The rectification effect arises from the asymmetric structure of the molecule and the molecule-electrode couplings. A significant rectification ratio of approximately 38 can be achieved when n=5.     

Glycine interaction with carbon nanotubes: an ab initio study

The interaction of the glycine radical on the side walls of both armchair and zigzag single walled carbon nanotubes is investigated by density functional theory. It is found that the interaction potential of the N-centered glycine radical with the tubes has a minimum of 16.9 (armchair) and 20.2 (zigzag) kcal/mol with respect to the dissociation products. In contrast, the C-centered radical, which is 22.7 kcal/mol lower in energy than the N-centered radical, does not form stable complexes with both types of carbon nanotubes.     

Cooperativity in intramolecular bifurcated hydrogen bonds: an ab initio study

Molecular orbital and density functional theory calculations are performed on some di- and tetrasubstituted derivatives of anthraquinone, dihydrophenazine, and acridone to investigate cooperativity in a pair of bifurcated hydrogen bonds occurring in the same molecule. The various structures were selected as convenient model systems for three-center hydrogen bonding of both H...A...H and A...H...A types. In the former type, the C=O moieties in anthraquinone and acridone act as bifurcated hydrogen bond acceptors, and substituted OH groups act as hydrogen bond donors. In the latter type, the N-H moieties in dihydrophenazine, acridones act as bifurcated hydrogen bond donors, and the carbonyl oxygens of substituted CHO groups act as hydrogen bond acceptors. Different indicators of cooperativity reveal that two intramolecular bifurcated hydrogen bonds simultaneously present in the same molecule significantly reinforce each other.     

Electron attachment to SO2 clusters

Electron attachment to SO₂ clusters formed by nozzle expansion was investigated (n up to 8) in a molecular-beam electron-ionization mass-spectrometer system. Electron ionization of SO₂ clusters was also studied (n up to 18) showing no pronounced structure in the mass spectra and no strong dependence on electron energy, the dominant positive ion being the (SO₂) _n ⁺ series. Also present but less abundant are the fragment ion series (SO₂) _n SO⁺, (SO₂) _n S⁺ and (SO₂) _n O⁺ with decreasing intensities in that order. The dominant negative ion is (SO₂) _n ^? . The homologous series (SO₂) _n O^? and (SO₂) _n SO^? are less abundant, the series (SO₂) _n S^? has not been observed at all (except SO₂·S^? produced in the background gas via secondary processes). The negative ion mass spectra show a strong dependence on electron energy due to a rich resonance like structure of the attachment cross sections involved. These attachment cross sections have been determined (up to 40 eV) and they show significant differences for the different homologous series. The most striking feature is that for instance (SO₂) _n SO^? ions do not show any signal at the first main resonance of SO^? from SO₂. Likewise (SO₂) _n O^? ions only show a strongly diminished signal at the first main resonance of O^? from SO₂. This is in contrast to results in O₂, CO₂ and N₂O. Conversely, (SO₂) _n ^? ions show — besides peaks at the position of the first and second O^? resonance — additional resonances below and above these peaks. In addition, (SO₂) ₅ ^? and larger ones show a zero energy peak consisting of stoichiometric SO₂ cluster ions similar to observations in O₂, CO₂ and H₂O. The attachment cross section of S^? from SO₂ has been found to show an additional previously undetected peak at ～1 eV. Moreover, the present study revealed the existence of a S _n ^? (n up to 8) series being produced with nearly zero energy electrons via volume and surface processes in and around the ion source.     

Gold adatoms and clusters on PPV: An ab initio investigation

We have performed an ab initio investigation of the energetic, structural, electronic, and vibrational properties of Au atoms and clusters adsorbed on poly-p-phenylene vinylene (PPV) chains, Au(n)/PPV (with n =?1, 2, 6, 7, 10, and 12). We find that the Au(n)/PPV systems are energetically stable by 0.5 eV, compared with the isolated systems, viz., PPV chain and Au(n) clusters, thus supporting the formation of Au(n)/PPV nanocomposites. Further support to the formation of Au(n)/PPV has been provided by examining the vibrational properties of pristine PPV and Au(n)/PPV systems. In agreement with experimental measurements, we find a reduction on the in-plane vibrational frequency of C-C bonds of Au(n)/PPV, when compared with the same vibrational modes of pristine PPV. The electronic properties of isolated Au(n) clusters are modified when adsorbed on PPV. The highest occupied states of Au(n)/PPV are mostly concentrated on the Au(n) cluster, while the lowest unoccupied states are mainly localized along the PPV chain. The HOMO-LUMO energy gap of the Au(n)/PPV systems are smaller than the energy gap of the isolated systems, Au(n) clusters, and pristime PPV chains.     

Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,     

Addition of anions to carbonyl compounds: an ab initio study

Energies for the addition of anionic nucleophiles, Z(-), to carbonyl compounds, XYCO, are calculated at the G2(MP2) level of theory. The substituents X, Y, and Z are taken from the set {H, CH3, NH2, OH, F, CF3, CHCH2, CHO, CCH, and CN}. The basicity and, to a lesser extent, ionization potential of Z(-) were found to correlate with the enthalpy of addition of Z(-) to H2CO. The enthalpy of addition of Z(-) to XYCO relative to H2CO is largely independent of Z. The ordering of the enthalpies of addition for the series of XYCO's is rationalized. By using a thermodynamic cycle, the independence of this ordering from Z is attributed to the additivity of the inductive stabilization of XYZCO(-) by X and Y versus H2ZCO(-). A method for estimating the enthalpy of addition for nucleophile/carbonyl combinations not studied above is described and shown to give good results on a model system.     

First ultraviolet absorption band of methane: an ab initio study

Quantum mechanical calculations of the cross sections for photodissociation of CH4 and CD4 in the 1t2-->3s band are presented. The potential energy surfaces for the three states correlating with the 1 1T2 state at tetrahedral geometries are calculated. The elements of the (3x3) matrix representing the electronic Hamiltonian in the diabatic basis are expanded in powers of nuclear coordinates, up to the second order. The expansion coefficients are based on accurate multireference configuration interaction calculations. The electronically nonadiabatic dynamics is treated with the multiconfiguration time-dependent Hartree approach. All nine internal degrees of methane are included in the quantum dynamics simulations. The calculated cross section agrees well with experiment. Semiclassical calculations using the reflection principle suggest that the peaks in the spectrum correspond to the three adiabatic electronic states correlating with the 1 1T2 state at Td geometries. However, the non-Born-Oppenheimer terms in the Hamiltonian have a strong effect on the positions of the peaks in the absorption spectrum. The results of semiclassical calculations, which neglect these terms, are therefore quite different from the accurate quantum results and experiment.