Understanding the structure and electronic properties of Th4+-water complexes

2013 ◽  
Vol 91 (9) ◽  
pp. 821-831 ◽  
Author(s):  
Christophe Gourlaouen ◽  
Carine Clavaguéra ◽  
Aude Marjolin ◽  
Jean-Philip Piquemal ◽  
Jean-Pierre Dognon
Keyword(s):  
Quantum Chemistry ◽  
Potential Energy Surfaces ◽  
Topological Analysis ◽  
Minimum Energy ◽  
Aqua Complex ◽  
Energy Curve ◽  
Equilibrium Geometry ◽  
Dissociation Pathway ◽  
Reference Potential ◽  
Dissociation Curves

We present a systematic quantum chemistry study of the [Th(H2O)n]4+ (n = 1 to 10) complexes to gain insight into their electronic structure and properties: the effect of the ligand distribution on the valence shells of the thorium(IV) ion is studied by means of the electron localization function (ELF) topological analysis. Particular care is given to the study of the mono-aqua complex both at its equilibrium geometry, using various tools such as energy decomposition analyses (EDA), and along its dissociation pathway. Indeed, as several electronic states cross the Th4 +-H2O0 ground state along the minimum energy path, we demonstrate that the diabatic representation implemented in MOLPRO is able to generate reference potential energy surfaces that will lead to the evaluation of diabatic dissociation curves. The calculated diabatic interaction energy curve will allow for a consistent parameterization of new generation force fields dedicated to heavy metals based on quantum chemistry.

THEORETICAL TRANSITION PROBABILITIES FOR THE $\tilde{A}^{2}A_{1} -\tilde{X}^{2}B_{1}$ SYSTEM OF H2O+ AND D2O+ AND RELATED FRANCK–CONDON FACTORS BASED ON GLOBAL POTENTIAL ENERGY SURFACES

2005 ◽  
Vol 04 (01) ◽  
pp. 225-245 ◽  
Author(s):  
IKUO TOKUE ◽  
KATSUYOSHI YAMASAKI ◽  
SATOSHI MINAMINO ◽  
SHINKOH NANBU
Keyword(s):  
Potential Energy ◽  
Photoelectron Spectroscopy ◽  
Potential Energy Surfaces ◽  
Least Squares Method ◽  
Transition Probabilities ◽  
Three Dimensional ◽  
Equilibrium Geometry ◽  
Condon Factors ◽  
Energy Surfaces ◽  
Franck Condon

To elucidate the ionization dynamics, in particular the vibrational distribution, of H 2 O +(Ã) produced by photoionization and the Penning ionization of H 2 O and D 2 O with He *(2 3S) atoms, Franck–Condon factors (FCFs) were given for the [Formula: see text] ionization, and the transition probabilities were presented for the [Formula: see text] emission. The FCFs were obtained by quantum vibrational calculations using the three-dimensional potential energy surfaces (PESs) of [Formula: see text] and [Formula: see text] electronic states. The global PESs were determined by the multi-reference configuration interaction calculations with the Davidson correction and the interpolant moving least squares method combined with the Shepard interpolation. The obtained FCFs exhibit that the [Formula: see text] state primarily populates the vibrational ground state, as its equilibrium geometry is almost equal to that of [Formula: see text], while the bending mode (ν2) is strongly enhanced for the H 2 O +(Ã) state; the maximums in the population of H 2 O + and D 2 O + are approximately v2 = 11–12 and 15–17, respectively. These results are consistent with the distributions observed by photoelectron spectroscopy. Transition probabilities for the [Formula: see text] system of H 2 O + and D 2 O + show that the bending progressions consist primarily of the [Formula: see text] emission, with combination bands from the (1, v′2 = 4–8, 0) level being next most important.

scholarly journals Extraction of morphometry and branching angles of porcine coronary arterial tree from CT images

2009 ◽  
Vol 297 (5) ◽  
pp. H1949-H1955 ◽  
Author(s):  
Thomas Wischgoll ◽  
Jenny S. Choy ◽  
Ghassan S. Kassab
Keyword(s):  
Coronary Artery ◽  
Coronary Arteries ◽  
Topological Analysis ◽  
Minimum Energy ◽  
Power Laws ◽  
Ct Images ◽  
Arterial Tree ◽  
Circumflex Artery ◽  
Left Circumflex Artery ◽  
The Right

The morphometry (diameters, length, and angles) of coronary arteries is related to their function. A simple, easy, and accurate image-based method to seamlessly extract the morphometry for coronary arteries is of significant value for understanding the structure-function relation. Here, the morphometry of large (≥1 mm in diameter) coronary arteries was extracted from computed tomography (CT) images using a recently validated segmentation algorithm. The coronary arteries of seven pigs were filled with Microfil, and the cast hearts were imaged with CT. The centerlines of the extracted vessels, the vessel radii, and the vessel lengths were identified for over 700 vessel segments. The extraction algorithm was based on a topological analysis of a vector field generated by normal vectors of the extracted vessel wall. The diameters, lengths, and angles of the right coronary artery, left anterior descending coronary artery, and left circumflex artery of all vessels ≥1 mm in diameter were tabulated for the respective orders. It was found that bifurcations at orders 9–11 are planar (∼90%). The relations between volume and length and area and length were also examined and found to scale as power laws. Furthermore, the bifurcation angles follow the minimum energy hypothesis but with significant scatter. Some of the applications of the semiautomated extraction of morphometric data in applications to coronary physiology and pathophysiology are highlighted.

Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections

2015 ◽  
Vol 177 ◽  
pp. 77-98 ◽  
Author(s):  
Masaaki Nakamura ◽  
Po-Yu Tsai ◽  
Toshio Kasai ◽  
King-Chuen Lin ◽  
Federico Palazzetti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Minimum Energy ◽  
Saddle Points ◽  
Integrated Approach ◽  
Computational Imaging ◽  
Ion Imaging ◽  
Structural Investigations ◽  
Alternative Pathways ◽  
Fragmentation Threshold

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v = 1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v = 0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through “roaming” pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

scholarly journals Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

2016 ◽  
Author(s):  
Pedro J Silva
Keyword(s):  
Electron Transfer ◽  
Active Site ◽  
Quantum Chemical ◽  
Potential Energy Surfaces ◽  
Direct Electron Transfer ◽  
Minimum Energy ◽  
Urate Oxidase ◽  
Redox Potentials ◽  
Deprotonated Form ◽  
Quantum Chemical Computations

Cofactor-less oxygenases perform challenging catalytic reactions between singlet substrates and triplet oxygen, in spite of apparently violating the spin-conservation rule. In bacterial ring-cleaving 2,4-dioxygenase, the active site has been suggested by quantum chemical computations to fine tune triplet oxygen reactivity, allowing it to interact rapidly with its singlet substrate without the need for spin inversion, and in urate oxidase the reaction is thought to proceed through electron transfer from the deprotonated substrate to an aminoacid sidechain, which then feeds the electron to the oxygen molecule. In this work, we perform additional quantum chemical computations on these two systems to elucidate several intriguing features unaddressed by previous workers. These computations establish that in both enzymes the reaction proceeds through direct electron transfer from substrate to O2 followed by radical recombination, instead of minimum-energy crossing points between singlet and triplet potential energy surfaces without formal electron transfer. The active site does not affect the reactivity of oxygen directly but is crucial for the generation of the deprotonated form of the substrates, which have redox potentials far below those of their protonated forms and therefore may transfer electrons to oxygen without sizeable thermodynamic barriers. This mechanism seems to be shared by most cofactor-less oxidases studied so far.

BrHgO• + C2H4 and BrHgO• + HCHO in Atmospheric Oxidation of Mercury: Determining Rate Constants of Reactions with Pre-Reactive Complexes and a Bifurcation

2019 ◽  
Author(s):  
Khoa T. Lam ◽  
Curtis J. Wilhelmsen ◽  
Theodore Dibble
Keyword(s):  
Hydrogen Atom ◽  
Quantum Chemistry ◽  
Transition State ◽  
Rate Constant ◽  
Rate Constants ◽  
Minimum Energy ◽  
Atmospheric Oxidation ◽  
Minimum Energy Path ◽  
Oh Radical ◽  
Hydrogen Atoms

Models suggest BrHgONO to be the major Hg(II) species formed in the global oxidation of Hg(0), and BrHgONO undergoes rapid photolysis to produce the thermally stable radical BrHgO•. We previously used quantum chemistry to demonstrate that BrHgO• can, like OH radical, readily can abstract hydrogen atoms from sp<sup>3</sup>-hybridized carbon atoms as well as add to NO and NO<sub>2</sub>. In the present work, we reveal that BrHgO• can also add to C<sub>2</sub>H<sub>4</sub> to form BrHgOCH<sub>2</sub>CH<sub>2</sub>•, although this addition appears to proceed with a lower rate constant than the analogous addition of •OH to C<sub>2</sub>H<sub>4</sub>. Additionally, BrHgO• can readily react with HCHO in two different ways: either by addition to the carbon or by abstraction of a hydrogen atom. The minimum energy path for the BrHgO• + HCHO reaction bifurcates, forming two pre-reactive complexes, each of which passes over a separate transition state to form a different product.

scholarly journals Variational Quantum Chemistry Programs in JaqalPaq

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 657
Author(s):  
Oliver G. Maupin ◽  
Andrew D. Baczewski ◽  
Peter J. Love ◽  
Andrew J. Landahl
Keyword(s):  
Quantum Chemistry ◽  
Programming Language ◽  
Ground State ◽  
Scientific Computing ◽  
Assembly Language ◽  
Quantum Algorithm ◽  
Meta Programming ◽  
Dissociation Curves ◽  
Ground State Energies ◽  
Python Package

We present example quantum chemistry programs written with JaqalPaq, a python meta-programming language used to code in Jaqal (Just Another Quantum Assembly Language). These JaqalPaq algorithms are intended to be run on the Quantum Scientific Computing Open User Testbed (QSCOUT) platform at Sandia National Laboratories. Our exemplars use the variational quantum eigensolver (VQE) quantum algorithm to compute the ground state energies of the H2, HeH+, and LiH molecules. Since the exemplars focus on how to program in JaqalPaq, the calculations of the second-quantized Hamiltonians are performed with the PySCF python package, and the mappings of the fermions to qubits are obtained from the OpenFermion python package. Using the emulator functionality of JaqalPaq, we emulate how these exemplars would be executed on an error-free QSCOUT platform and compare the emulated computation of the bond-dissociation curves for these molecules with their exact forms within the relevant basis.

Partial Potential Energy Surfaces and Their Application to Reaction Resonances

2017 ◽  
Vol 42 (3) ◽  
pp. 300-305
Author(s):  
Ang-Yang Yu
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Energy Surface ◽  
Minimum Energy ◽  
Reactive Systems ◽  
Resonance State ◽  
Minimum Energy Path ◽  
Feshbach Resonances ◽  
Energy Surfaces ◽  
Elementary Chemical

Feshbach resonances are not restricted to small reactive systems such as F + H2 and I + HI but can be found in many reactive systems. In this paper, the concept of the partial potential energy surface (PPES) is introduced. It is shown that the dynamic “Lake Eyring” explains very well the existence of reactive resonances in elementary chemical reactions. In particular, the PPESs of the Cl + CH3CH2Br and Cl + CH3CH2CH2Br systems, including the minimum energy path and the vibrational potential energy curves, were constructed using quantum chemistry methods. Based on the constructed PPESs, the scattering resonance states of these reactions could be examined and the resonance state lifetimes were estimated.

scholarly journals Topological Analysis of Magnetically Induced Current Densities in Strong Magnetic Fields Using Stagnation Graphs

Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 916-934
Author(s):  
Tom J. P. Irons ◽  
Adam Garner ◽  
Andrew M. Teale
Keyword(s):  
Magnetic Field ◽  
Vector Field ◽  
Magnetic Fields ◽  
Density Functional ◽  
Strong Field ◽  
Topological Analysis ◽  
Equilibrium Geometry ◽  
Strong Magnetic Fields ◽  
Topological Features ◽  
Current Densities

Stagnation graphs provide a useful tool to analyze the main topological features of the often complicated vector field associated with magnetically induced currents. Previously, these graphs have been constructed using response quantities appropriate for modest applied magnetic fields. We present an implementation capable of producing these graphs in arbitrarily strong magnetic fields, using current-density-functional theory. This enables us to study how the topology of the current vector field changes with the strength and orientation of the applied magnetic field. Applications to CH4, C2H2 and C2H4 are presented. In each case, we consider molecular geometries optimized in the presence of the magnetic field. The stagnation graphs reveal subtle changes to this vector field where the symmetry of the molecule remains constant. However, when the electronic state and symmetry of the corresponding equilibrium geometry changes with increasing field strength, the changes to the stagnation graph are extensive. We expect that the approach presented here will be helpful in interpreting changes in molecular structure and bonding in the strong-field regime.

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