Quantum Molecular Calculations Research Articles

Ro-vibrational molecular quantum computing and ro-vibartional entanglement

With the development of quantum computing, kinds of models of quantum computing have been proposed. Recently, more and more attentions have been paid on the quantum computing based on molecular ro-vibrational states. Using this quantum computing model, the multi-qubit quantum computing and a long decoherence time can be achieved conveniently. The numerical simulations have shown that quite high fidelity quantum computing gates can be realized. Ro-vibrational entanglement is a key resource for the ro-vibrational quantum computing. Many researchers have focused on the studies of the dynamics of ro-vibrational entanglements, and such studies could provide suggestions for further researches and applications of the ro-vibrational quantum computing. In this paper, the development of molecular quantum computing and ro-vibrational are briefly reviewed.

Complexity and simplicity of optimal control theory pulses shaped for controlling vibrational qubits

In the context of molecular quantum computation the optimal control theory (OCT) is used to obtain shaped laser pulses for high-fidelity control of vibrational qubits. Optimization is done in time domain and the OCT algorithm varies values of electric field in each time step independently, tuning hundreds of thousands of parameters to find one optimal solution. Such flexibility is not available in experiments, where pulse shaping is done in frequency domain and the number of "tuning knobs" is much smaller. The question of possible experimental interpretations of theoretically found OCT solutions arises. In this work we analyze very accurate optimal pulse that we obtained for implementing quantum gate CNOT for the two-qubit system encoded into the exited vibrational states of thiophosgene molecule. Next, we try to alter this pulse by reducing the number of available frequency channels and intentionally introducing systematic and random errors (in frequency domain, by modifying the values of amplitudes and phases of different frequency components). We conclude that a very limited number of frequency components (only 32 in the model of thiophosgene) are really necessary for accurate control of the vibrational two-qubit system, and such pulses can be readily constructed using OCT. If the amplitude and phase errors of different frequency components do not exceed ±3% of the optimal values, one can still achieve accurate transformations of the vibrational two-qubit system, with gate fidelity of CNOT exceeding 0.99.

Competition between Ascorbate and Glutathione for the Oxidized Form of Methylated Quercetin Metabolites and Analogues: Tamarixetin, 4′O-Methylquercetin, Has the Lowest Thiol Reactivity

Quercetin (Q) is a bioactive compound with excellent antioxidant activity. However, the thiol reactivity of its oxidation product (oxQ) forms a disadvantage. The aim of the present study was to decrease this thiol toxicity. We found that methylated Q metabolites displayed lower thiol reactivity than Q. The most effective was tamarixetin, 4'O-methylquercetin (4'MQ), that has a corresponding oxidation product (ox4'MQ) with thiol reactivity 350 times lower than oxQ. The endogenous metabolism of Q to 4'MQ might be a physiological way to safely benefit from the antioxidant potential of Q in vivo. Our results were explained with Pearson's HSAB concept and corroborated by quantum molecular calculations that revealed a strong correlation between the relative thiol reactivity and the lowest unoccupied molecular orbital (LUMO). The polarity of the molecule and the π-π interaction between the AC- and the B-ring appeared to determine the LUMO and the thiol reactivity of the oxidation product.

Molecular [(Fe3)–(Fe3)] and [(Fe4)–(Fe4)] Coordination Cluster Pairs as Single or Composite Arrays

The synthesis of molecular cluster pairs is a challenge for coordination chemists due to the potential applications of these species in molecular spintronics or quantum computing. The ligand H(4)L, 1,3-bis-(3-oxo-3-(2-hydroxyphenyl)-propionyl)-2-methoxybenzene, has been successfully used to obtain a series of such complexes using the basic Fe(III) trinuclear carboxylates as starting materials. Synthetic control has allowed the isolation of the two molecular cluster pairs that form the composite [Fe(4)O(2)(PhCO(2))(6)(H(2)L)(pz)](2)[Fe(3)O(PhCO(2))(5)(py)(H(2)L)](2) (1). The dimers of trinuclear units, [Fe(3)O(PhCO(2))(5)(H(2)O)(H(2)L)](2) (2) and [Fe(3)O(o-MePhCO(2))(5)(H(2)L)(py)](2) (3), and the dimers of tetranuclear units, [Fe(4)O(2)(PhCO(2))(6)(H(2)L)(pz)](2) (4) and [Fe(4)O(2)(o-MePhCO(2))(6)(H(2)L)(pz)](2) (5), are presented here. The magnetic properties of the reported aggregates show that they are pairs of semi-independent clusters weakly interacting magnetically as required for two-qubit quantum gates.

Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing

In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.

Lycopene coupled ‘trifoliate’ polyaniline nanofibers as multi-functional biomaterial

Bio-conjugation seems to be an unparalleled avenue to tailor the shape-size-bioactivity accord of nanomaterials. In this backdrop, conjugation of tomato peel lycopene through the green chemistry tool of sonication, under statistically optimized parameters led to the morphological alteration of polyaniline (PAni) nanofiber from linear to biomimetic ‘runner’ morphology with trifoliate branching as observed under TEM. X-ray diffractogram was suggestive of alterations in the d-spacing and strain in the polymer backbone post lycopene binding. Post bio-conjugation, the semiconducting-behavior of the PAni nanofibers was retained although lycopene coupling resulted in a decrease in the former's conductivity. DMol3 was employed for the quantum molecular calculations of lycopene interacting with PAni (via non-covalent functionalization involving π–π stacking) and its solvation study. The contribution to HOMO came from the lycopene unit whereas the LUMO had contribution from the aromatic ring of PAni in the conjugated system. The bioactivity of the PAni nanofibers post bio-conjugation was attested by free radical scavenging and anti-lipid peroxidation of liver tissue homogenate. Epiflorescence microscopic imaging demonstrated the cytocompatibility with L929 normal cell line while the nuclear fragmentation and membrane blebbing of apoptotic HeLa cells vouched for the anticancer action of the conjugated system. Furthermore, the reported system exhibited a stimulatory effect on Cucumis sativus seed germination. Thus the study marshals in support of modulated morphology and desirable bio-action of nanoscaled biomaterials via bio-conjugation for advanced applications.

Effect of diatomic molecular properties on binary laser pulse optimizations of quantum gate operations

The importance of the ro-vibrational state energies on the ability to produce high fidelity binary shaped laser pulses for quantum logic gates is investigated. The single frequency 2-qubit ACNOT(1) and double frequency 2-qubit NOT(2) quantum gates are used as test cases to examine this behaviour. A range of diatomics is sampled. The laser pulses are optimized using a genetic algorithm for binary (two amplitude and two phase parameter) variation on a discretized frequency spectrum. The resulting trends in the fidelities were attributed to the intrinsic molecular properties and not the choice of method: a discretized frequency spectrum with genetic algorithm optimization. This is verified by using other common laser pulse optimization methods (including iterative optimal control theory), which result in the same qualitative trends in fidelity. The results differ from other studies that used vibrational state energies only. Moreover, appropriate choice of diatomic (relative ro-vibrational state arrangement) is critical for producing high fidelity optimized quantum logic gates. It is also suggested that global phase alignment imposes a significant restriction on obtaining high fidelity regions within the parameter search space. Overall, this indicates a complexity in the ability to provide appropriate binary laser pulse control of diatomics for molecular quantum computing.

Molecular simulation grid

MoSGrid is the acronym for Molecular Simulation Grid, a BMBF funded joint research project with the aim to offer grid services for the broad field of molecular simulations in the D-Grid infrastructure. Besides tendering various codes ranging from quantum molecular calculations (e.g. Gaussian, Turbomole) via molecular dynamics (e.g. Gromacs) to docking approaches (e.g. FlexX) for high performance computing, one of the main goals is the integration of metadata annotation for data mining and knowledge generation. Molecular simulation codes and computational resources are accessed via the MoSGrid portal (http://www.mosgrid.de), which will offer intuitive access to various tools and will support the users with workflows, for an easy import of molecular data, a simple setup and submission of calculations as well as extraction of relevant results. The portal will hide the complexity of the underlying technology by providing a unified user interface making computational chemistry in general more readily available. MoSGrid’s server-based portal is available as open-access and open-source software. Users are relieved from software installations and do not need to have knowledge about the underlying infrastructure. The portal includes portlets specifically set up for the various simulation programs. Commonly used workflows, simple or complex, can be stored in recipe repositories and are available for every user. Moreover, users can develop, improve, publish, and use workflows for their everyday tasks.

Entropy and complexity analysis of Dirac-delta-like quantum potentials

The Dirac-delta-like quantum-mechanical potentials are frequently used to describe and interpret numerous phenomena in many scientific fields including atomic and molecular physics, condensed matter and quantum computation. The entropy and complexity properties of potentials with one and two Dirac-delta functions are here analytically calculated and numerically discussed in both position and momentum spaces. We have studied the information-theoretic lengths of Fisher, Rényi and Shannon types as well as the Cramér–Rao, Fisher–Shannon and LMC shape complexities of the lowest-lying stationary states of one-delta and twin-delta. They allow us to grasp and quantify different facets of the spreading of the charge and momentum of the system far beyond the celebrated standard deviation.

Fidelity and Mutual Entropy in Mixed States for Fermi-resonance Coupling Vibrations of CS2

The dynamics of four fidelities is studied for mixed coherent states and mixed squeezed states of Fermi-resonance coupling vibrations in molecule CS2. It is demonstrated that those fidelities are dominant-positively correlated with each other, one of which by Wang et al. (Phys. Lett. A 373, 58 (2008)) is the most striking in dominant anti-correlation with quantum mutual entropy. That is useful for molecular quantum computing and quantum information.

Simulating quantum search algorithm using vibronic states of I2 manipulated by optimally designed gate pulses

In this paper, molecular quantum computation is numerically studied with the quantum search algorithm (Grover's algorithm) by means of optimal control simulation. Qubits are implemented in the vibronic states of I2, while gate operations are realized by optimally designed laser pulses. The methodological aspects of the simulation are discussed in detail. We show that the algorithm for solving a gate pulse-design problem has the same mathematical form as a state-to-state control problem in the density matrix formalism, which provides monotonically convergent algorithms as an alternative to the Krotov method. The sequential irradiation of separately designed gate pulses leads to the population distribution predicted by Grover's algorithm. The computational accuracy is reduced by the imperfect quality of the pulse design and by the electronic decoherence processes that are modeled by the non-Markovian master equation. However, as long as we focus on the population distribution of the vibronic qubits, we can search a target state with high probability without introducing error-correction processes during the computation. A generalized gate pulse-design scheme to explicitly include decoherence effects is outlined, in which we propose a new objective functional together with its solution algorithm that guarantees monotonic convergence.

Phase gate and readout with an atom-molecule hybrid platform

We suggest a combined atomic/molecular system for quantum computation, which takes advantage of highly developed techniques to control atoms and recent experimental progress in manipulation of ultracold molecules. We show that two atoms of different species in a given site, {\it e.g.}, in an optical lattice, could be used for qubit encoding, initialization and readout, with one atom carrying the qubit, the other enabling a gate. In particular, we describe how a two-qubit phase gate can be realized by transferring a pair of atoms into the ground rovibrational state of a polar molecule with a large dipole moment, and allowing two molecules to interact via their dipole-dipole interaction. We also discuss how the reverse process of coherently transferring a molecule into a pair of atoms could be used as a readout tool for molecular quantum computers.

Characterization of Cytochrome P450-Mediated Bioactivation of a Compound Containing the Chemical Scaffold, 4,5-Dihydropyrazole-1-carboxylic acid-(4-chlorophenyl amide), to a Chemically Reactive p-Chlorophenyl Isocyanate Intermediate in Human Liver Microsomes

Compound A (Cmpd A) was previously reported to form p-chlorophenyl isocyanate (CPIC), which was trapped by GSH to yield S- (N- [p-chlorophenyl] carbamoyl) glutathione adduct (SCPG) in the presence of human liver microsomes. In this study, P450 3A4 and 2C9 were demonstrated to be the enzymes mediating the activation of Cmpd A to CPIC in human liver microsomes based on inhibitory and correlation studies. Enzyme kinetics studies indicated that P450 3A4 was the primary enzyme involved in the activation of Cmpd A. In silico P450 3A4 active site docking of Cmpd A exhibited a low energy pose that orientated the pyrazole ring proximate to the heme iron atom, in which the distance between the C-3 and potential activated oxygen species was shown to be 3.4 A. Quantum molecular calculations showed that the electron density on C-3 was relatively higher than those on C-4 and C-5. These measurements suggested that the C-3 of Cmpd A was the preferred site of oxidation and hence predisposed Cmpd A in forming CPIC as previously proposed. The in silico prediction was corroborated by studies with the C-3 substituted analogue (methyl at C-3), which showed minimal conversion to CPIC in human liver microsomes. These results demonstrated a pivotal role for P450 3A4 in bioactivating Cmpd A by oxidizing at C-3 of the pyrazoline, hence facilitating the CPIC formation. Evidence of the bioactivation to CPIC in vivo was obtained by liquid chromatography-mass spectrometry (LC/MS) analysis of urine samples from human subjects administered a structural analogue of Cmpd A. The presence of S-(N-[p-chlorophenyl] carbamoyl) N-acetyl l-cysteine (SCPAC) as well as p-chlorophenyl aniline (CPA) was unequivocally demonstrated in the urine samples. The chemical scaffold, 4,5-dihydropyrazole-1-carboxylic acid-[(4-chlorophenyl)-amide], was demonstrated to possess potential metabolic liability in forming a reactive intermediate, CPIC, in humans. Bioactivation to CPIC may cause undesirable side effects through its reactivity and subsequent conversion to CPA, an established rodent carcinogen.

Thermodynamic Role of Glutathione Oxidation by Peroxide and Peroxybicarbonate in the Prevention of Alzheimer’s Disease and Cancer

First principle quantum molecular computations have been carried out at the B3LYP/6-31G(d,p) and G3MP2B3 levels of theory on ethyl mercaptan and diethyl disulfide to study their full conformational space. The consequences of molecular axis chirality for the potential energy hypersurface of diethyl disulfide was fully explored. Thermodynamic functions (U, H, S, and G) have been computed for every conformer of the products as well as the reactants of the redox systems studied. Relative values of the thermodynamic functions were calculated with respect to the reference structures with anti orientation. The energetics of the following Red-Ox reactions Et-SH+HO-OH+HS-Et --> 2H2O+Et-S-S-Et Et-SH+HO-OCOO(-)+HS-Et --> H2O+Et-S-S-Et+HCO3- have been chosen to mimic the biologically important Red-Ox reactions of glutathione G-SH+H2O2+HS-G --> 2H2O+G-S-S-G G-SH+HCO4-+HS-G --> H2O+G-S-S-G+HCO3-. The Red-Ox reaction of Et-SH --> Et-S-S-Et was found to be exothermic by first principle molecular computations and the intramolecular interactions, such as the unusual C-H...H-C noncovalent bondings were studied by Bader's atoms in molecules analysis of the electron density topology. The present paper focuses attention on the thermodynamic aspect of the redox reaction of glutathione. It has been noted previously that on going from a cancerous to a healthy cell, the entropy change is negative, corresponding to information accumulation. Likewise, the dissociation of peptide parallel beta-sheets, that dominate the plaques in Alzheimer's Disease, governs negative entropy change. It may be interesting to note, according to the results obtained in the present paper, a negative entropy change, corresponding to information accumulation.

Silyl Radical Chemistry and Conventional Photoinitiators: A Route for the Design of Efficient Systems

Three new efficient photoinitiators (PI) based on a well-known chromophore skeleton (hydroxyphenylacetophenone, thioxanthone, or benzoin) linked to a silyl-containing moiety are proposed. The ability of these structures to initiate both free radical polymerization and free radical promoted cationic polymerization is investigated. A comparison with parent compounds is provided. High rates of polymerization and high final conversions are obtained. These PI directly generate silyl radicals under light irradiation as characterized by ESR spin-trapping. The analysis of the excited-state processes through laser flash photolysis and quantum molecular calculations allow to explain the observed photochemical behavior. The present results evidence the high potential of these new modified PI.

Entanglement dynamics in Coriolis coupled rovibrational states of formaldehyde

The entanglement dynamics of two vibrational modes of a polyatomic molecule coupled by Coriolis interaction to overall molecular rotation is studied in terms of two negativities, N ( t ) and N s ( t ) , respectively, defined by the minimum of the eigenvalues and by the sum of the negative eigenvalues of the partial transpose of a density matrix. Various initial states are the products of Dicke states and the products of coherent states of vibrations and rotations. Formaldehyde is taken as an example, and the von Neumann entropy s ( t ) is simulated for the comparison with both negativities. It is shown that negativity N s ( t ) is positively correlated with entropy s ( t ) , and the correlated behavior between negativity N ( t ) and entropy s ( t ) strongly depends on initial states. However, these three indicators of entanglement display a dominantly positive correlation for the coherent states with small or large parameters. In addition, for the latter state two quantities N ( t ) and s ( t ) are nearly unchanged for a long time. This time can be further increased by the increasing of vibrational quantum number so that molecular information processing and quantum computing is allowed. These results are useful in quantum information theory.

Entropy and negativity of Fermi-resonance coupling vibrations in a spectroscopic Hamiltonian

The entanglement dynamics of Fermi resonance coupling vibrations in a spectroscopic Hamiltonian for molecules $\mathrm{C}\mathrm{H}{\mathrm{D}}_{3}$, $\mathrm{C}\mathrm{H}{\mathrm{Cl}}_{3}$, and $\mathrm{C}\mathrm{H}{\mathrm{F}}_{3}$ is studied in terms of the von Neumann entropy and negativity with three kinds of initial states that are direct products of coherent states, thermal states, and squeezed states of each mode. It is demonstrated that the increasing rate of entanglement in the early-time evolution is the largest for the squeezed states, while that is the smallest for the coherent states. For small parameters in the coherent and thermal states, entanglement displays a quasiperiodicity with the quasiperiod in $\mathrm{C}\mathrm{H}{\mathrm{F}}_{3}$ being the longest. Furthermore, the dynamical correlation between the von Neumann entropy and negativity shows that positively correlated or anticorrelated behaviors of both measures strongly depend on initial states and molecules. For those states with small parameters, both measures exhibit dominantly positive correlation. These are useful for molecular quantum computing and information processing.

Entropy correlation and entanglement for mixed states in an algebraic model

As an alternative with potential connections to actual experiments, other than the systems more usually used in the field of entanglement, the dynamics of entropy correlation and entanglement between two anharmonic vibrations in a well-established algebraic model, with parameters extracted from fitting to highly excited spectral experimental results for molecules H2O and SO2, is studied in terms of the linear entropy and two negativities for various initial states that are respectively taken to be the mixed density matrices of thermal states and squeezed states on each mode. For a suitable parameter in initial states the entropies in two stretches can show positive correlation or anti-correlation. And the linear entropy of each mode is positively correlated with the negativities just for the mixed-squeezed states with small parameters in H2O while they do not display any correlation in other cases. For the mixed-squeezed states the negativities exhibit dominantly positive correlations with an effective mutual entropy. The differences in the linear entropy and the negativities between H2O and SO2 are discussed as well. Those are useful for molecular quantum computing and quantum information processing.

Molecular electron-spin quantum computers and quantum information processing: pulse-based electron magnetic resonance spin technology applied to matter spin-qubits

Pulse-based Electron–Nuclear and ELectron–electron DOuble Resonance (ENDOR/ELDOR) techniques have been applied to molecular spins in order to implement ensemble electron spin-qubit based quantum computers/computing (QC) and quantum information processing (QIP) in the solid state. Pulsed ENDOR-based QC/QIP experiments for super dense coding (SDC) have for the first time been carried out by the use of molecular electron- and nuclear-spin entities such as the stable malonyl radical as matter spin-qubits. The spin-qubit manipulation technology for quantum gate operations in this work is based on the time-proportional-phase-increment (TPPI) technique, enabling us to distinguish between the phases of spin-qubit based entangled states. The TPPI technique, as firstly applied by Mehring et al. (M. Mehring, J. Mende and W. Scherer, Phys. Rev. Lett., 2003, 90, 153001), has illustrated the establishment of quantum entanglement between electron- and nuclear-spin states and mutual interconversion between the electron–nuclear Bell states. The electron-spin 4π-periodicity in phase shows up in the QC/QIP experiments, explicitly and experimentally illustrating the electron-spin spinor nature for the first time. Tripartite QC experiments have been made, showing the occurrence of separable states. Also, the development of novel electron-spin technology to manipulate multi-electron spin-qubits is described. In this work, the pulsed coherent-dual ELDOR for QC/QIP has for the first time been implemented by invoking a novel microwave dual phase-rotation technique. Thus, applications of the coherent-dual ELDOR to molecular electron spin-qubit systems are also discussed, emphasising designing the molecular two electron-qubit systems appropriate for QC/QIP. g- and/or hyperfine A-tensor engineering approaches give us the two- and multi-electron-qubit systems, which have been a materials challenge to implement matter spin-qubit based QC/QIP. The targeted matter spin-qubits can be used to facilitate selective resonant microwave excitations achieved by the pulsed ELDOR technique. In addition to DiVincenzo's five criteria, general requisites for scalable electron spin-qubit systems as 1D periodic robust spin structures are described. According to the requisites, double- or triple-stranded helicates embedding open-shell metal cations are proposed instead of organic molecular spin-qubits.

Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study

Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations.