Orbital connections for perturbation-dependent basis sets

Summary The use of perturbation-dependent basis sets is analysed with emphasis on the connection between the basis sets at different values of the perturbation strength. A particular connection, the natural connection, that minimizes the change of the basis set orbitals is devised and the second quantization realization of this connection is introduced. It is shown that the natural connection is important for the efficient evaluation of molecular properties and for the physical interpretation of the terms entering the calculated properties. For example, in molecular Hessian calculations the natural connection reduces the size of the relaxation term, leading to faster convergence of the response equations. The physical separation of the terms also means that first-order non-adiabatic coupling matrix elements can be obtained in a very simple way from a molecular Hessian calculation.     

Synthetic nucleic acid secondary structures containing the four stereoisomers of 1,4-bis(thymine-1-yl)butane-2,3-diol

The four stereoisomers of the double-headed acyclic nucleoside 1,4-bis(thymine-1-yl)butane-2,3-diol were incorporated in the central position of four 13-mer oligonucleotides. The phosphoramidite building blocks were synthesized in four or six steps from either D- or L-2,3-O-isopropylidenethreitol. Two epimeric and fully deprotected double-headed nucleosides were analyzed by X-ray crystallography. The incorporation into oligonucleotides was hampered by steric hindrance and formation of a cyclic phosphate. The use of pyridinium chloride as the activator and a kinetic analysis based on 31P NMR of the coupling and detritylation processes led to improved yields of the oligonucleotides. In comparison with the (S)-GNA monomer, one of the four stereoisomers was found to show a similar destabilization of a DNA duplex, indicating that the additional base can be introduced without a thermal penalty. Another stereoisomer was found to induce a thermal stabilization of a DNA:RNA three-way junction. Thus, the stereochemistry of this acyclic double-headed nucleoside motif is important, indicating potential for the design of artificial nucleic acid secondary structures.     

Bioactivities and chemical constituents of a Vietnamese medicinal plant Che Vang, Jasminum subtriplinerve Blume (Oleaceae)

Five crude extracts were made from leaves and stems of Jasminum subtriplinerve Blume (Oleaceae) and investigated for antimicrobial, antioxidant and cytotoxic activities. The extractions were done with petroleum ether, ethyl acetate, ethanol, methanol or water. All extracts exhibited anti-bacterial activity except the water fraction. On the other hand, all extracts exhibit antioxidant activity except the petroleum ether fraction using the DPPH radical scavenging assay. Only the petroleum ether fraction showed a cytotoxicity activity against tested cell-lines, Hep-G2 and RD with IC(50) values of 19.2 and 20 microg mL(-1), respectively. From the petroleum ether and ethyl acetate extracts, two triterpenes namely 3beta-acetyl-oleanolic acid and lup-20-en-3beta-ol and a sterol, stigmast-5-en-3beta-ol were isolated. The structure of those compounds were elucidated by spectrometric methods IR, MS, 1D-NMR, 2D-NMR and simulated ACD/NMR spectra. The data presented here indicate that J. subtriplinerve do contain compounds with interesting biological activity.     

Intramolecular hydrogen bonding of novel o-hydroxythioacetophenones and related compounds evaluated by deuterium isotope effects on 13C chemical shifts

A new class of compounds, the 2-hydroxythioacetophenones, and related compounds have recently been synthesized. The hydrogen-bond system has been characterized by NMR chemical shifts and deuterium isotope effects on these as well as by DFT calculations. Use of solid-state (13)C NMR has enabled measurements of the intrinsic deuterium isotope effects of the most abundant tautomer of beta-thioxoketones. The compounds show very interesting long-range deuterium isotope effects on the thiocarbonyl carbon. The intramolecular hydrogen bonds of o-hydroxythioacetophenones are found to be slightly stronger than those of the corresponding acetophenones. The reactivity and stability of the compounds can be related to hydrogen bonding and to the presence of electron donating substituents.     

Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.     

Linear-scaling implementation of molecular electronic self-consistent field theory

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field (SCF) theories is presented and illustrated with applications to molecules consisting of more than 1000 atoms. The diagonalization bottleneck of traditional SCF methods is avoided by carrying out a minimization of the Roothaan-Hall (RH) energy function and solving the Newton equations using the preconditioned conjugate-gradient (PCG) method. For rapid PCG convergence, the Lowdin orthogonal atomic orbital basis is used. The resulting linear-scaling trust-region Roothaan-Hall (LS-TRRH) method works by the introduction of a level-shift parameter in the RH Newton equations. A great advantage of the LS-TRRH method is that the optimal level shift can be determined at no extra cost, ensuring fast and robust convergence of both the SCF iterations and the level-shifted Newton equations. For density averaging, the authors use the trust-region density-subspace minimization (TRDSM) method, which, unlike the traditional direct inversion in the iterative subspace (DIIS) scheme, is firmly based on the principle of energy minimization. When combined with a linear-scaling evaluation of the Fock/Kohn-Sham matrix (including a boxed fitting of the electron density), LS-TRRH and TRDSM methods constitute the linear-scaling trust-region SCF (LS-TRSCF) method. The LS-TRSCF method compares favorably with the traditional SCF/DIIS scheme, converging smoothly and reliably in cases where the latter method fails. In one case where the LS-TRSCF method converges smoothly to a minimum, the SCF/DIIS method converges to a saddle point.     

Long-range deuterium isotope effects on (13)C chemical shifts of intramolecularly hydrogen-bonded N-substituted 3-(cycloamine)thiopropionamides or amides: a case of electric field effects

A series of intramolecularly hydrogen-bonded N-substituted 3-(piperidine, morpholine, N-methylpiperazine)thiopropionamides and some corresponding amides have been studied with special emphasis on hydrogen bonding. The compounds have been selected in order to vary and to minimize the N...N distance. Geometries, charge distributions, and chemical shifts of these compounds are obtained from DFT-type BP3LYP calculations. 1H and 13C 1D and 2D NMR experiments were performed to obtain H,H coupling constants, 13C chemical shifts assignments, and deuterium isotope effects on13C chemical shifts. Variable-temperature NMR studies and 2D exchange NMR spectra have been used to describe the rather complicated conformational behavior mainly governed by the ring flipping of the piperidine (morpholine) rings and intramolecular hydrogen bonding. Unusual long-range deuterium isotope effects on 13C chemical shifts are observed over as far as eight bonds away from the site of deuteriation. The isotope effects are related to the N...N distances, thus being related to the hydrogen bonding and polarization of the N-H bond. Arguments are presented showing that the deuterium isotope effects on 13C chemical shifts originate in electric field effects.     

Collision-induced dissociation of cytidine and its derivatives

The collision-induced dissociation of adenosine, uridine and guanosine, and their corresponding nucleobases has been published previously.1-3 Here we report the collision-induced dissociation of cytidine and the elucidation of its fragmentation pathways using stable isotope-labeled cytidines, through a quadrupole ion trap for tandem mass spectrometry up to MS(4). Furthermore, we investigated the collision-induced dissociation of five cytidine derivatives: 3-methylcytidine, N(4)-methyl-2'-deoxycytidine, 5-methylcytidine, 2-thiocytidine and N(4)-acetylcytidine. The primary fragmentation pathway was the neutral loss of ribose. MS(3) on the retained nucleobase generally resulted in an intense signal from the elimination of ammonia, but also in fragment ions characteristic of the different cytosine derivatives. On the basis of the MS(n) data, fragmentation pathways and plausible mechanisms are suggested.     

Quantum control of the hyperfine spin of a Cs atom ensemble

We demonstrate quantum control of a large spin angular momentum associated with the F=3 hyperfine ground state of 133Cs. Time-dependent magnetic fields and a static tensor light shift are used to implement near-optimal controls and map a fiducial state to a broad range of target states, with yields in the range 0.8-0.9. Squeezed states are produced also by an adiabatic scheme that is more robust against errors. Universal control facilitates the encoding and manipulation of qubits and qudits in atomic ground states and may lead to the improvement of some precision measurements.     

Prototropic processes in benzaurins. <Superscript>19</Superscript>F and <Superscript>1</Superscript>H NMR spectra of fluoro- and methylsubstituted 4-hydroxyphenyl-diphenylcarbinols,related fuchsones and benzaurins

Tautomerism of benzaurins and hydration are studied. ¹H and ¹⁹F chemical shifts have been determined for a number of substituted 4-hydroxyphenyl-diphenyl carbinols containing fluorine in a 3-, 3*- or 4*-position, and for similar compounds containing additional methyl groups in a position of 3, 3** or 4**. The same data have been obtained for the fuchsones prepared by dehydration of the above carbinols. On this basis chemical shifts of fluorine in different positions have been evaluated as a monitor of the transformation of 4-hydroxyphenyl group to the semiquinone moiety. The ¹⁹F NMR can be used to monitor the transformation of 4**-fluorobenzaurin and the related 3,3*-disubstituted and 3,3*,5,5*-tetramethylsubstituted compounds to the corresponding carbinols due to the addition of a water molecule and to study the tautomerism of the two latter benzaurins as well as that of 3,3*,4**trifluorobenzaurin. Furthermore, fluorine and methyl group chemical shifts are sensitive to syn-anti-isomerism in substituted fuchsones.