Body composition studies by means of superconducting quantum interference device biomagnetometry.
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Body Composition↗
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Unified mechanistic concept of electrophilic aromatic nitration: convergence of computational results and experimental data.
The mechanism of electrophilic aromatic nitration was revisited. Based on the available experimental data and new high-level quantum chemical calculations, a modification of the previous reaction mechanism is proposed involving three separate intermediates on the potential energy diagram of the reaction. The first, originally considered an unoriented pi-complex or electron donor acceptor complex (EDA), involves high electrostatic and charge-transfer interactions between the nitronium ion and the pi-aromatics. It explains the observed low substrate selectivity in nitration with nitronium salts while maintaining high positional selectivity, as well as observed oxygen transfer reactions in the gas phase. The subsequent second intermediate originally considered an oriented "pi-complex" is now best represented by an intimate radical cation-molecule pair, C(6)H(6)(+)(*)()/NO(2), that is, a SET complex, indicative of single-electron transfer from the aromatic pi-system to NO(2)(+). Subsequently, it collapses to afford the final sigma-complex intermediate, that is, an arenium ion. The proposed three discrete intermediates in electrophilic aromatic nitration unify previous mechanistic proposals and also contribute to a better understanding of this fundamentally important reaction. The previously obtained ICR data of oxygen transfer from NO(2)(+) to the aromatic ring are also accommodated by the proposed mechanism. The most stable intermediate of this reaction on its potential energy surface is a complex between phenol and NO(+). The phenol.NO(+) complex decomposes affording C(6)H(6)O(+)(*)/PhOH(+) and NO, in agreement with the ICR results.
Benzene↗
Computational study of the reaction of fluorine atom with acetone.
The reaction of F(2P) with acetone has been studied theoretically using ab initio quantum chemistry methods and transition state theory. The potential energy surface was calculated at the G3MP2 level using the MP2/6-311G(d,p) optimized structures. Additionally, to ensure the accuracy of the calculations, optimizations with either larger basis set (e.g., MP2/G3MP2Large) or higher level electron correlation [e.g., CCSD/ 6-311G(d,p)] were also performed. It has been revealed that the F + CH3C(O)CH3 reaction proceeds via two pathways: (1) the direct hydrogen abstraction of acetone by F gives the major products HF + CH3C(O)CH2; (2) the addition of F atom to the >C=O double bond of acetone and the subsequent C-C bond cleavage gives the minor products CH3 + CH3C(O)F. All other product channels are of no importance due to the occurrence of significant barriers. Both abstraction and addition appear to be barrierless processes. Variational transition state model and multichannel RRKM theory were employed to calculate the temperature- and pressure-dependent rate constants and branching ratios. The predicted rate constants for the abstraction channel and the yields of HF + CH3C(O)CH3 and CH3 + CH3C(O)F are both in good agreement with the experimental data at 295 K and 700 Torr. A negative temperature dependence of the overall rate constants was predicted at temperatures below 500 K.
Journal Article↗
Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study.
The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.
Absorption↗
Quantum leap. Interview by Terry Monahan.
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Attitude to Computers↗
Hydrogen bonding in the LaNi3BH3 hydride.
The electronic structure of the intermetallic LaNi3B as well as the novel hydride LaNi3BH3 have been theoretically investigated by means of quantum chemistry methods. We employed a mixed approach to investigate the electronic structure of these compounds: state-of-the-art energy band calculations and molecular cluster computations. We computed the energy bands and the total and partial density of states using both the linear-augmented plane waves and projector-augmented wave methods. In addition the electronic structure of three representative clusters of the local environment of Ni atoms was investigated by quantum chemistry ab initio molecular calculations. In this report, we discuss the chemical bonding and we investigated the H site occupancy energies and correlate this estimate with the occupancy fraction and metal-hydrogen distances experimentally observed.
Journal Article↗
Software tools and databases for bacterial systematics and their dissemination via global networks.
The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic 'Authority Files' are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.
Amino Acid Sequence↗
Ab-initio molecular geometry and normal coordinate analysis of tetrahydrothiophene molecule.
The molecular geometry of tetrahydrothiophene (THT) was quantum mechanically calculated using the split valence 6-31G** basis set. Electron correlation energy has been computed employing MP2 method. The molecule showed a twist form puckered structure with a twist torsion angle of 13 degrees and has a total energy of -347,877.514 kcal/mol of which a 436.715 kcal/mol electron correlation energy. The envelope form of the molecule showed an inter-plane angle of 22 degrees and has a total energy of -347,874.430 kcal/mol involving -436.558 kcal/mol electron correlation energy. The normal coordinates of the molecule were theoretically analyzed and the fundamental vibrational frequencies were calculated. The IR and laser Raman spectra of THT molecule was measured. All the observed vibrational bands including combination bands and overtones were assigned to normal modes with the aid of the potential energy distribution values obtained from normal coordinate calculations. The molecular force field was determined by refining the initial set of force constants using the least square fit method instead of using the less accurate scaling factor methods. The determined molecular force field has produced simulated frequencies which best match the observed values. The lowest-energy modes of vibration were two molecular out-of-plane deformations, observed at 114 and 166 cm(-1). The barrier of ring twisting estimated from the observed ring out-of-plane vibrational mode at 114 cm(-1) was estimated.
Models, Chemical↗
Ab-initio molecular geometry and normal coordinate analysis of pyrrolidine molecule.
The molecular geometry of pyrrolidine was quantum mechanically calculated using the split valence 6-31G** basis set. Electron correlation energy has been computed employing MP2 method. The molecule showed an envelope form puckered structure with inter-plane angle of 36.4 degrees and has a total energy of -132976.80 kcal mol(-1) of which a -464.86 kcal mol(-1) electron correlation energy. The twist form of the molecule showed a twist angle of 10.2 degrees from planarity and has a total energy of -132976.05 kcal mol(-1) involving -464.097 kcal mol(-1) electron correlation energy. The normal coordinates of the molecule were theoretically analyzed on the basis of the Cs point symmetry of the envelope form. Using initial set of force constants obtained from the ab-initio calculations the fundamental vibrational frequencies were computed. The IR and laser Raman spectra of Pyrrolidine molecules were measured. All the observed vibrational bands including combination bands and overtones were assigned to normal modes with the aid of the potential energy distribution values obtained from normal coordinate calculations. The molecular force field was obtained by refining the initial set of force constants using the least square fit method. The molecular force field was determined by refining the initial set of force constants using the least square fit method instead of using the less accurate scaling factor methods. The determined molecular force field has produced simulated frequencies best match to the observed values. The low frequency molecular out-of-plane deformation modes were observed in both infrared and Raman spectra at 298 and 163 cm(-1). The barrier of ring twisting estimated from the observed ring out-of-plane vibrational mode at 163 cm(-1) was found 3.1 kcal mol(-1).
Mathematical Computing↗
Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications.
Reactive oxygen species present in the cell generate DNA damage. One of the major oxidation products of guanine in DNA, 8-oxo-7,8-dihydroguanine, formed by loss of two electrons, is among the most extensively studied base lesions. The further removal of two electrons from this product can yield spiroiminodihydantoin (Sp) R and S stereoisomers. Both in vitro and in vivo experiments have shown that the Sp stereoisomers are highly mutagenic, causing G --> T and G --> C transversions. Hence, they are of interest as examples of endogenous DNA damage that may initiate cancer. To interpret the mutagenic properties of the Sp lesions, an understanding of their structural properties is needed. To elucidate these structural effects, we have carried out computational investigations at the level of the Sp-modified base and nucleoside. At the base level, quantum mechanical geometry optimization studies have revealed exact mirror image symmetry of the R and S stereoisomers, with a near-perpendicular geometry of the two rings. At the nucleoside level, an extensive survey of the potential energy surface by molecular mechanics calculations using AMBER has provided three-dimensional potential energy maps. These maps reveal that the range and flexibility of the glycosidic torsion angles are significantly more restricted in both stereoisomeric adducts than in unmodified 2'-deoxyguanosine. The structural and energetic results suggest that the unusual geometric, steric, and hydrogen bonding properties of these lesions underlie their mutagenicity. In addition, stereoisomer-specific differences indicate the possibility that their processing by cellular replication and repair enzymes may be differentially affected by their absolute configuration.
8-Hydroxy-2'-Deoxyguanosine↗
Construction of a perfectly N-representable two-electron density matrix carrying full information on an interacting system.
The two-particle density matrix contains all information, which is "readable" by one- and two-particle operators. The report discusses the building of a two-electron density matrix, which is perfectly N-representable by construction. The 2-matrix of a pure quantum state is obtained without the intermediate determination of the wave function. The procedure is illustrated by computations on atomic and small molecular systems.
Journal Article↗
Singlet-triplet splittings and their relevance to the spin-dependent exciton formation in light-emitting polymers: an EOM/CCSD study.
By employing the coupled-cluster equation of motion method (EOM/CCSD) for excited-state structures, we have investigated the structure dependence of the singlet and triplet exciton splittings, through extensive calculations for polythiophene (PT), poly(3,4-ethylenedioxythiophene) (PEDOT), poly(thienylenevinylene) (PTV), polyparaphenylene vinylene (PPV), MEHPPV, polyparaphenylene ethylene (PPE), polyfluorene (PFO), and ladder-type polyparaphenylene (mLPPP). The results for the polymer are extrapolated through computations for the oligomers with increasing length. Recent investigations have been quite controversial about whether the internal quantum efficiency of electroluminescence could be higher than the 25% spin statistics limit or not in polymeric materials. Using a simple relationship between the exciton formation rate and the excitation energy level, we have discussed the material-dependent ratios of singlet and triplet exciton formation, which are in good agreement with the magnetic-field resonance detected transient spectroscopy measurement by Wohlgenannt et al. for a series of electronic polymers. This provides another piece of evidence to support the view that the internal quantum efficiency for conjugated polymers can exceed the 25% limit.
Journal Article↗
Quantum statistical and wave packet studies of insertion reactions of S(1D) with H2, HD, and D2.
A thorough theoretical investigation of the reactions between S(1D) and various hydrogen isotopomers (H2, D2, and HD) has been carried out using a recent ab initio potential energy surface. State-resolved integral and differential cross sections, thermal rate constants, and their dependence on energy or temperature were obtained from quantum mechanical capture probabilities within a statistical model. For comparison, the J=0 reaction probabilities were also computed using an exact wave packet method. The statistical results are in excellent agreement with available exact differential and integral cross sections. The comparison with experimental results shows that the agreement is reasonably good in general, but some significant differences exist, particularly for the SD/SH branching ratio in the S(1D)+HD reaction.
Journal Article↗
Conductance through two dots coupled in series: application of the exact solution.
Using the exact Bethe-ansatz solution, we study the conductance through symmetric and asymmetric double-dot (DD) systems in the Kondo regime, where two quantum dots are coupled in series. The application of the Ward-Takahashi identity enables us to compute the conductance at low temperatures. For strong inter- and intra-dot Coulomb repulsions with weak inter-dot tunneling, we discuss how the Kondo effect evolves for an asymmetric DD system as well as a symmetric DD system in a magnetic field. In particular, we clarify that the conductance is decreased (increased) in the asymmetric DD (symmetric DD in a field), reflecting that the Kondo effect due to inter-dot charge fluctuations is suppressed (enhanced).
Journal Article↗
Universal ratios in the 2D tricritical ising model
We consider the universality class of the two-dimensional tricritical Ising model. The scaling form of the free energy leads to the definition of universal ratios of critical amplitudes which may have experimental relevance. We compute these universal ratios by a combined use of results coming from perturbed conformal field theory, integrable quantum field theory, and numerical methods.
Journal Article↗
Néel and Spin-Peierls ground states of two-dimensional SU(N) quantum antiferromagnets.
The two-dimensional SU(N) quantum antiferromagnet, a generalization of the quantum Heisenberg model, is investigated by quantum Monte Carlo simulations. The ground state for N or=5 with broken lattice translational invariance. Our computation of the magnetization and the dimerization order parameter shows the absence of the intermediate spin-liquid phase.
Journal Article↗
Deutsch-jozsa algorithm using triggered single photons from a single quantum dot.
We demonstrate a two-qubit Deutsch-Jozsa algorithm with single photons from a single InP quantum dot. The qubits are implemented via the spatial mode and the polarization of a single photon. Our photon source is operated both under continuous and pulsed excitation, the latter allowing deterministic quantum logic by generating photons on demand with a strong suppression of two-photon events. The computation reached a success probability of up to 79%. We also exploit the concept of decoherence-free subspaces that helps to make our experimental setup robust against sources of phase noise.
Journal Article↗
Structure of Cu6PbO8
First-principles quantum mechanical calculations based on density functional theory were performed for Cu6PbO8, hexacopper lead octaoxide, murdochite. The computed lattice parameter, density and bond lengths at ambient pressure are in good agreement with experimental data for murdochite. At about 18 GPa a phase transition is predicted, when a polymorph with a Suzuki-type structure, i.e. a close-packed structure with ordered vacancies, is proposed to become stable. The pressure dependence of the structural parameters has been calculated for the two polymorphs and their bulk moduli have been predicted. It is argued that the incorporation of halogen atoms is not a precondition for the stability of murdochite.
Journal Article↗