Study of structures, energies and vibrational frequencies of (O-2)(n)(+) (n=2-5) clusters by GGA and meta-GGA density functional methods

Using Generalized Gradient Approximation (GGA) and meta-GGA density functional methods, structures, binding energies and harmonic vibrational frequencies for the clusters O-4(+), O-6(+), O-8(+) and O-10(+) have been calculated. The stable structures of O-4(+), O-6(+), O-8(+) and O-10(+) have point groups D-2h, D-3h, D-4h, and D-5h optimized on the quartet, sextet, octet and dectet potential energy surfaces, respectively. Rectangular (D-2h) O-4(+) has been found to be more stable compared to trans-planar (C-2h) on the quartet potential energy surface. Cyclic structure (D-3h) of CA cluster ion has been calculated to be more stable than other structures. Binding energy (B.E.) of the cyclic O-6(+) is in good agreement with experimental measurement. The zero-point corrected B.E. of O-8(+) with D4h symmetry on the octet potential energy surface and zero-point corrected B.E. of O-10(+) with D-5h symmetry on the dectet potential energy surface are also in good agreement with experimental values. The B.E. value for O-4(+) is close to the experimental value when single point energy is calculated by Brueckner coupled-cluster method, BD(T). (C) 2014 Elsevier B.V. All rights reserved.

Isotopic fractionation in proteins as a measure of hydrogen bond length

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor (I) is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate (I) as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric 0-H. ``.0 bonds R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the 0-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total (I) as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization (D(R), used previously to determine bond lengths. (C) 2015 AIP Publishing LLC.

Towards an exact factorization of the molecular wave function

An exact single-product factorisation of the molecular wave function for the timedependent Schrodinger equation is investigated by using an ansatz involving a phasefactor. By using the Frenkel variational method, we obtain the Schrodinger equations for the electronic and nuclear wave functions. The concept of a potential energy surface (PES) is retained by introducing a modified Hamiltonian as suggested earlier by Cederbaum. The parameter in the phase factor is chosen such that the equations of motion retain the physically appealing Born- Oppenheimer-like form, and is therefore unique.

Theory of ozone isotopic effects and various electron transfer reactions

Three separate topics, each stimulated by experiments, are treated theoretically in this dessertation: isotopic effects of ozone, electron transfer at interfaces, and intramolecular directional electron transfer in a supramolecular system.

The strange mass-independent isotope effect for the enrichment of ozone, which has been a puzzle in the literature for some 20 years, and the equally puzzling unconventional strong mass-dependent effect of individual reaction rate constants are studied as different aspects of a symmetry-driven behavior. A statistical (RRKM-based) theory with a hindered-rotor transition state is used. The individual rate constant ratios of recombination reactions at low pressures are calculated using the theory involving (1) small deviation from the statistical density of states for symmetric isotopomers, and (2) weak collisions for deactivation of the vibrationally excited ozone molecules. The weak collision and partitioning among exit channels play major roles in producing the large unconventional isotope effect in "unscrambled" systems. The enrichment studies reflect instead the non-statistical effect in "scrambled" systems. The theoretical results of low-pressure ozone enrichments and individual rate constant ratios obtained from these calculations are consistent with the corresponding experimental results. The isotopic exchange rate constant for the reaction ^(16)O + ^(18)O ^(18)O→+ ^(16)O ^(18)O + ^(18)O provides information on the nature of a variationally determined hindered-rotor transition state using experimental data at 130 K and 300 K. Pressure effects on the recombination rate constant, on the individual rate constant ratios and on the enrichments are also investigated. The theoretical results are consistent with the experimental data. The temperature dependence of the enrichment and rate constant ratios is also discussed, and experimental tests are suggested. The desirability of a more accurate potential energy surface for ozone in the transition state region is also noted.

Electron transfer reactions at semiconductor /liquid interfaces are studied using a tight-binding model for the semiconductors. The slab method and a z-transform method are employed in obtaining the tight-binding electronic structures of semiconductors having surfaces. The maximum electron transfer rate constants at Si/viologen^(2-/+) and InP /Me_(2)Fc^(+/O) interfaces are computed using the tight-binding type calculations for the solid and the extended-Huckel for the coupling to the redox agent at the interface. These electron transfer reactions are also studied using a free electron model for the semiconductor and the redox molecule, where Bardeen's method is adapted to calculate the coupling matrix element between the molecular and semiconductor electronic states. The calculated results for maximum rate constant of the electron transfer from the semiconductor bulk states are compared with the experimentally measured values of Lewis and coworkers, and are in reasonable agreement, without adjusting parameters. In the case of InP /liquid interface, the unusual current vs applied potential behavior is additionally interpreted, in part, by the presence of surface states.

Photoinduced electron transfer reactions in small supramolecular systems, such as 4-aminonaphthalimide compounds, are interesting in that there are, in principle, two alternative pathways (directions) for the electron transfer. The electron transfer, however, is unidirectional, as deduced from pH-dependent fluorescence quenching studies on different compounds. The role of electronic coupling matrix element and the charges in protonation are considered to explain the directionality of the electron transfer and other various results. A related mechanism is proposed to interpret the fluorescence behavior of similar molecules as fluorescent sensors of metal ions.

Efficient sampling of atomic configurational spaces.

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

On representing chemical environments

We review some recently published methods to represent atomic neighbourhood environments, and analyse their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms, and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighbourhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbours increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether new approach, called Smooth Overlap of Atomic Positions (SOAP), that sidesteps these difficulties by directly defining the similarity between any two neighbourhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.

Reactive Many-Body Expansion for a Protonated Water Cluster.

We generalize the standard many-body expansion technique that is used to approximate the total energy of a molecular system to enable the treatment of chemical reactions by quantum chemical techniques. By considering all possible assignments of atoms to monomer units of the many-body expansion and associating suitable weights with each, we construct a potential energy surface that is a smooth function of the nuclear positions. We derive expressions for this reactive many-body expansion energy and describe an algorithm for its evaluation, which scales polynomially with system size, and therefore will make the method feasible for future condensed phase simulations. We demonstrate the accuracy and smoothness of the resulting potential energy surface on a molecular dynamics trajectory of the protonated water hexamer, using the Hartree-Fock method for the many-body term and Møller-Plesset theory for the low order terms of the many-body expansion.

Shell-model Hamiltonian from self-consistent mean-field model: N = Z nuclei

We propose a procedure to determine the effective nuclear shell-model Hamiltonian in a truncated space from a self-consistent mean-field model, e.g., the Skyrme model. The parameters of pairing plus quadrupole-quadrupole interaction with monopole force are obtained so that the potential energy surface of the Skyrme Hartree-Fock + BCS calculation is reproduced. We test our method for N = Z nuclei in the fpg- and sd-shell regions. It is shown that the calculated energy spectra with these parameters are in a good agreement with experimental data, in which the importance of the monopole interaction is discussed. This method may represent a practical way of defining the Hamiltonian for general shell-model calculations. (C) 2009 Elsevier B.V. All rights reserved.

High-spin isomeric structures in exotic odd-odd nuclei: Exploration of the proton drip line and beyond

We investigate the role of two-quasiparticle isomeric states along the proton drip line, using configuration-constrained potential-energy-surface calculations. In contrast to even-even nuclei, odd-odd nuclei can have coexisting low-lying two-quasiparticle states. The low excitation energy and high angular momentum can lead to long-lived isomers. Also, because of the hindrance by spin selection, the probabilities of beta and proton decays from high-spin isomers can be reduced significantly. The present calculations reproduce reasonably well the available data for observed isomers in such nuclei. Unobserved high-spin isomers are predicted, which could be useful for future experimental studies of exotic nuclei at and beyond the proton drip line.

beta-delayed proton decays of Sm-133 and Yb-149

Sm-133 was produced via fusion evaporation in the reaction Ca-40+Ru-96. Its P-delayed proton decay was studied by means of "p-gamma" coincidence in combination with a He-jet tape transport system, including half-lives, proton energy spectra, gamma-transitions following the proton emissions, and the branching ratios to the low-lying states in the grand-daughter nuclei. The possible spins and parities of 133Sm were extracted by fitting the experimental data with a statistical model calculation. The configuration-constrained nuclear potential energy surfaces of Sm-133 were calculated by using the Woods-Saxon Strutinsky method. Comparing the experimental and calculated results, the spins and parities Of Sm-133 were assigned to be 5/2(+) and 1/2(-), which is reconciled with our published simple (EC+beta(+)) decay scheme Of Sm-113 in 2001. In addition, our experimental data on the beta-delayed proton decay of Yb-149 reported in Eur. Phys. J., 2001, A12: 1-4 was also analyzed by using the same method. The spin and parity of Yb-149 was assigned to be 1/2-.

beta-delayed proton decays of Tb-140 and Dy-140 as well as the spin and parity of Dy-143

Tb-140 and Dy-141 were produced via fusion evaporation in the reaction Ca-40+Cd-106. Their beta-delayed proton decays were studied by means of "p-gamma" coincidence in combination with a He-jet tape transport system, including half-lives, proton energy spectra, gamma-transitions following the proton emissions, and the branching ratios to the low-lying states in the grand-daughter nuclei. The ground-state spins and parities of Tb-140 and Dy-141 were extracted as 7(+/-) and 9/2(+/-), respectively, by fitting the experimental data with a statistical model calculation. The configuration-constrained nuclear potential energy surfaces (NPES) of Tb-140 and Dy-141 were calculated by using the Woods-Saxon Strutinsky method, which indicate the ground-state spins and parities of Tb-140 and Dy-147 to be 7(+) and 9/2(-), respectively. In addition, the configuration-constrained NPES of Dy-143 was also calculated by using the same method. From the NPES a 1/2(+) ground state and a 11/2(-) isomer with the excitation energy of 198keV were found. The calculated results are consistent with our experimental data on the decay of Dy-143 reported in Eur. Phys. J., 2003, A16: 347-351.

Molecular dynamics and control following excitation with an ultra-short intense laser pulse

Vibronic excitations of the tri-atomic molecule OClO (A(2)A(2)(nu(1), nu(2), nu(3)) <-- (XB1)-B-2 (0, 0, 0)) with weak and strong ultra-short laser fields are studied within full quantum wavepacket dynamics in hyperspherical coordinates. Different dynamics is observed following excitation with laser pulses of different intensities. With a strong laser pulse, many vibrational states are excited and a spatially more localised wavepacket arises. The numerical results show that the population of different vibrational states of the wavepacket on the excited potential energy surface is altered by the intensity of the laser pulse. The numerical results also suggest a related effect on the phase of the wavepacket. These interesting phenomena can be understood by an analysis of the corresponding results for two model diatomic molecules. The possible physical mechanisms of control of chemical processes using strong laser fields are discussed. (C) 2004 Elsevier B.V. All rights reserved.

Theoretical study on the formation mechanism of Iso-CH2I-Cl

The dissociation and isomerization reaction mechanism on the ground-state potential energy surface for CH2ClI are investigated by ab initio calculations. It is found that the isomer iso-CH2I-Cl can be produced from either the recombination of the photodissociation. fragments or the isomerization reaction of CH2ClI, rather than from isomerization reaction of iso-CH2Cl-I. Further explanations of experimental results are also presented. (C) 2003 Wiley Periodicals, Inc.