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PubMed2003

Solvent polarity and hydrogen-bonding effects on the nitrogen NMR shieldings of N-nitrosamines and DFT calculations of the shieldings of C-, N-, and O-nitroso systems.

High-precision nitrogen NMR shieldings, bulk susceptibility corrected, are reported for dimethyl-N-nitrosamine (I) and diethyl-N-nitrosamine (II) in a variety of solvents which represent a wide range of solvent properties from the point of view of polarity as well as hydrogen bond donor and acceptor strength. The observed range of solvent-induced nitrogen shielding variations of (I) and (II) is significant for the amino-type nitrogens, up to about 16 ppm, and originates essentially from the deshielding effect of the increasing polarity of solvent. On the other side, the nitroso nitrogen shieldings reveal an even stronger response to solvent effects, within about 20 ppm, but in this case the increasing polarity and hydrogen bond donor strength of solvent produce enhanced shielding. DFT quantum-mechanical calculations using the GIAO/B3PW91/6-311++G** approach and geometry optimizations employing the same basis set and hybrid density functionals show an excellent correlation with the experimental data on C-, N-, and O-nitroso moieties and reproduce not only major changes but also most of the subtle variations in the experimental nitrogen shieldings of the nitroso systems as a whole. A combination of the calculations involving the corresponding N and O-protonated species and the trends observed in the solvent-induced nitrogen shielding variations shows clearly that the prime acceptor site for hydrogen bonding is the nitroso oxygen atom.

Algorithms↗

PubMed2005

Variational grand-canonical electronic structure method for open systems.

An ab initio method is developed for variational grand-canonical molecular electronic structure of open systems based on the Gibbs-Peierls-Boguliobov inequality. We describe the theory and a practical method for performing the calculations within standard quantum chemistry codes using Gaussian basis sets. The computational effort scales similarly to the ground-state Hartree-Fock method. The quality of the approximation is studied on a hydrogen molecule by comparing to the exact Gibbs free energy, computed using full configuration-interaction calculations. We find the approximation quite accurate, with errors similar to those of the Hartree-Fock method for ground-state (zero-temperature) calculations. A further demonstration is given of the temperature effects on the bending potential curve for water. Some future directions and applications of the method are discussed. Several appendices give the mathematical and algorithmic details of the method.

Journal Article↗

PubMed2005

On concomitant gradients in low-field MRI.

Growing interest in magnetic resonance imaging (MRI) at ultra-low magnetic fields (ULF, approximately muT fields) has been motivated by several advantages over its counterparts at higher magnetic fields. These include narrow line widths, the possibility of novel imaging schemes, reduced imaging artifacts from susceptibility variations within a sample, and reduced system cost and complexity. In addition, ULF NMR/MRI with superconducting quantum interference devices is compatible with simultaneous measurements of biomagnetic signals, a capability conventional systems cannot offer. Acquisition of MRI at ULF must, however, account for concomitant gradients that would otherwise result in severe image distortions. In this paper, we introduce the general theoretical framework that describes concomitant gradients, explain why such gradients are more problematic at low field, and present possible approaches to correct for these unavoidable gradients in the context of a non-slice-selective MRI protocol.

Algorithms↗

PubMed2006

Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions.

Simulations of hydride and deuteride transfer catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) are presented. TmDHFR was modeled with its active homodimeric quaternary structure, where each monomer has three subdomains. The potential energy function was a combined quantum mechanical and molecular mechanical potential (69 atoms were treated quantum mechanically, and 35 287, by molecular mechanics). The calculations of the rate constants by ensemble-averaged variational transition state theory with multidimensional tunneling predicted that hydride and deuteride transfer at 278 K proceeded with 81 and 80% by tunneling. These percentages decreased to 50 and 49% at 338 K. The kinetic isotope effect was dominated by contributions of bound vibrations and decreased from 3.0 to 2.2 over the temperature range. The calculated rates for hydride and deuteride transfer catalyzed by the hypothetical monomer were smaller by approximately 2 orders of magnitude. At 298 K tunneling contributed 73 and 66% to hydride and deuteride transfer in the monomer. The decreased catalytic efficiency of the monomer was therefore not the result of a decrease of the tunneling contribution but an increase in the quasi-classical activation free energy. The catalytic effect was associated in the dimer with correlated motions between domains as well as within and between subunits. The intrasubunit correlated motions were decreased in the monomer when compared to both native dimeric TmDHFR and monomeric E. coli enzyme. TmDHFR and its E. coli homologue involve similar patterns of correlated interactions that affect the free energy barrier of hydride transfer despite only 27% sequence identity and different quaternary structures.

Algorithms↗

PubMed2004

Enhanced sensitivity to residual dipolar couplings of elastomers by higher-order multiple-quantum NMR.

The homonuclear and heteronuclear residual dipolar couplings in elastomers reflect changes in the cross-link density, temperature, the uniaxial and biaxial extension or compression as well as the presence of penetrant molecules. It is shown theoretically that for an isolated methyl group the relative changes in the intensity of the homonuclear double-quantum buildup curves in the initial time regime due to variation of the residual dipolar coupling strength is less sensitive than the changes in the triple-quantum filtered NMR signal when considering the same excitation/reconversion time. For a quadrupolar nucleus with spin I=2 the sensitivity enhancement was simulated for four-quantum, triple-quantum, and double-quantum buildup curves. In this case the four-quantum build-up curve shows the highest sensitivity to changes of spin couplings. This enhanced sensitivity to the residual dipolar couplings was tested experimentally by measuring 1H double-quantum, triple-quantum, and four-quantum buildup curves of differently cross-linked natural rubber samples. In the initial excitation/reconversion time regime, where the residual dipolar couplings can be measured model free, the relative changes in the intensity of the four-quantum buildup curves are about five times higher than those of the double-quantum coherences. For the first time proton four-quantum coherences were recorded for cross-linked elastomers.

Algorithms↗

PubMed2005

Method of simulating dose reduction for digital radiographic systems.

The optimisation of image quality vs. radiation dose is an important task in medical imaging. To obtain maximum validity of the optimisation, it must be based on clinical images. Images at different dose levels can then either be obtained by collecting patient images at the different dose levels sought to investigate-including additional exposures and permission from an ethical committee-or by manipulating images to simulate different dose levels. The aim of the present work was to develop a method of simulating dose reduction for digital radiographic systems. The method uses information about the detective quantum efficiency and noise power spectrum at the original and simulated dose levels to create an image containing filtered noise. When added to the original image this results in an image with noise which, in terms of frequency content, agrees with the noise present in an image collected at the simulated dose level. To increase the validity, the method takes local dose variations in the original image into account. The method was tested on a computed radiography system and was shown to produce images with noise behaviour similar to that of images actually collected at the simulated dose levels. The method can, therefore, be used to modify an image collected at one dose level so that it simulates an image of the same object collected at any lower dose level.

Algorithms↗

PubMed2000

Full breast digital mammography with an amorphous silicon-based flat panel detector: physical characteristics of a clinical prototype.

The physical characteristics of a clinical prototype amorphous silicon-based flat panel imager for full-breast digital mammography have been investigated. The imager employs a thin thallium doped CsI scintillator on an amorphous silicon matrix of detector elements with a pixel pitch of 100 microm. Objective criteria such as modulation transfer function (MTF), noise power spectrum, detective quantum efficiency (DQE), and noise equivalent quanta were employed for this evaluation. The presampling MTF was found to be 0.73, 0.42, and 0.28 at 2, 4, and 5 cycles/mm, respectively. The measured DQE of the current prototype utilizing a 28 kVp, Mo-Mo spectrum beam hardened with 4.5 cm Lucite is approximately 55% at close to zero spatial frequency at an exposure of 32.8 mR, and decreases to approximately 40% at a low exposure of 1.3 mR. Detector element nonuniformity and electronic gain variations were not significant after appropriate calibration and software corrections. The response of the imager was linear and did not exhibit signal saturation under tested exposure conditions.

Algorithms↗

PubMed2005

Tracking excited state dynamics with coherent control: automated limiting of population transfer in LDS750.

Closed loop automated pulse shaping experiments are conducted to investigate population transfer in solutions of the laser dye LDS750 in acetonitrile and ethanol. Guided by a genetic algorithm, the optical phases of broadband noncollinear parametric amplifier pulses are modulated by a micromachined deformable mirror to minimize sample fluorescence. The objectives were to test if nonlinearly chirped pulses could reduce population transfer below levels attained by their linearly chirped analogues, and if so, whether the resulting pulse shapes could be rationalized in terms of the photoinduced molecular dynamics. We further aimed to discover how the optimal solutions depend on the pulse fluence, and on the nature of the solvent. Using frequency resolved optical gating, the optimal field is shown to consist of a transform limited blue portion, which promotes population to the excited state, and a negatively chirped red tail, which follows the Stokes shifting of the excited density and dumps it back down to the ground state through stimulated emission. This is verified by comparing the optimal group delay dispersion with multichannel transient absorption data collected in acetonitrile. The optimal pulse shape was not significantly affected by variation of pulse fluence or by the change of solvent for the two polar liquids investigated. These results are discussed in terms of accumulated insights concerning the photophysics of LDS750 and the capabilities of our learning feedback scheme for quantum control.

Journal Article↗

PubMed2005

Exchange methods in Kohn-Sham theory.

Differences between exchange methods in exchange-only Kohn-Sham theory are highlighted by calculations of diatomic molecule total energies, uncoupled isotropic NMR shieldings, and HOMO-LUMO eigenvalue differences. Optimised effective potential (OEP) and Wu-Yang (WY) results are very similar. Localised Hartree-Fock (LHF) and Krieger-Li-Iafrate (KLI) results are close to one another, but are different to OEP and WY. Becke 1988 exchange (B88X) is different again. Shieldings reduce from OEP/WY to LHF/KLI to B88X, which is consistent with an observed reduction in HOMO-LUMO gaps. LHF, KLI, and B88X shieldings and HOMO-LUMO gaps are closer to near-exact, correlated values, than are the OEP values. These variations arise entirely due to differences in the one-electron exchange potentials, which is clearly evident in potential difference plots, relative to OEP, for the N2 molecule. Density difference plots are also presented, which exhibit a spatial correlation with the potential differences. HOMO and LUMO probability density difference plots show a contraction of the LUMO relative to OEP, which is consistent with the NMR and HOMO-LUMO findings. Plots are also presented for near-exact, correlated Kohn-Sham calculations. The features are qualitatively similar to those observed in the LHF, KLI, and B88X plots, highlighting correlated character in these approximate exchange-only calculations.

Algorithms↗

PubMed2004

LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules.

A linear-scaling semiempirical method, LocalSCF, has been proposed for the quantum-chemical calculations of ultralarge molecular systems by treating the large-scale molecular task as a variational problem. The method resolves the self-consistent field task through the finite atomic expansion of weakly nonorthogonal localized molecular orbitals. The inverse overlap matrix arising from the nonorthogonality of the localized orbitals is approximated by preserving the first-order perturbation term and applying the second-order correction by means of a penalty function. This allows for the separation of the orbital expansion procedure from the self-consistent field optimization of linear coefficients, thereby maintaining the localized molecular orbital size unchanged during the refinement of linear coefficients. Orbital normalization is preserved analytically by the variation of virtual degrees of freedom, which are orthogonal to the initial orbitals. Optimization of linear coefficients of localized orbitals is performed by a gradient procedure. The computer program running on a commodity personal computer was applied to the GroEL-GroES chaperonin complex containing 119,273 atoms.

Algorithms↗

PubMed2002

Direct conversion detectors: the effect of incomplete charge collection on detective quantum efficiency.

Direct conversion detectors offer the potential for very high resolution and high quantum efficiency for x-ray imaging, however, variations in signal can arise due to incomplete charge collection. A charge transport model was developed to describe the signal and noise resulting from incomplete charge collection. This signal to noise ratio (SNR) reduction was incorporated into the cascaded systems model for a simple x-ray detector. A new excess noise factor, A(c) (termed the collection noise factor) is introduced to describe the reduction in detective quantum efficiency (DQE). The DQE is proportional to the product of the quantum efficiency and the collection noise factor. If the trapping cross sections for electrons and holes are very different, and if the detector is biased improperly, the collection noise factor can drop to as low as 50%. In addition, the signal loss due to incomplete charge collection will reduce the DQE in the presence of added noise. Because of this, the DQE generally does not continue to improve with greater detector thickness. The collection noise factor and DQE are predicted for CdZnTe, PbI2, and Se. The optimization of detector thickness should be based not only on quantum efficiency but also on the charge collection statistics, which are influenced by bias field and polarity.

Algorithms↗

PubMed1996

A 23Na multiple-quantum-filtered NMR study of the effect of the cytoskeleton conformation on the anisotropic motion of sodium ions in red blood cells.

Recently, it has been shown that 23Na double-quantum-filtered NMR spectroscopy can be used to detect anisotropic motion of bound sodium ions in biological systems. The technique is based on the formation of the second-rank tensor when the quadrupolar interaction is not averaged to zero. Using this method, anisotropic motion of bound sodium in human and dog red blood cells was detected, and the effect was shown to depend on the integrity of the membrane cytoskeleton. In the present study, multiple-quantum-filtered techniques were applied in combination with a quadrupolar echo to measure the transverse-relaxation times, T2f and T2s. Line fitting was performed to obtain the values of the residual quadrupolar interaction, which was measured for sodium in a variety of mammalian erythrocytes of different size, shape, rheological properties, and sodium concentrations. Human unsealed white ghosts were used to study sodium bound at the anisotropic sites on the inner side of the RBC membrane. Modulations of the conformation of the cytoskeleton by the variation of either the ionic strength or pH of the suspending medium caused drastic changes in both the residual quadrupolar interaction and T2f due to changes in the fraction of bound sodium ions as well as changes in the structure of the binding sites. By combining the two spectroscopic parameters, structural change can be followed. The changes in the structure of the sodium anisotropic binding sites deduced by this method were found to correlate with known conformational changes of the membrane cytoskeleton. Variations of the medium pH affected both the fraction of bound sodium ions and the structure of the anisotropic binding sites. Sodium and potassium were shown to bind to the anisotropic binding sites with the same affinity.

Algorithms↗

PubMed1993

Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra.

The three-dimensional solution structure of a trisdecamer DNA duplex sequence, d(AGCTTGCCTTGAG).d(CTCAAGGCAAGCT), from a conserved region of HIV-1 genome's long terminal repeat, has been investigated using NMR spectroscopy and restrained molecular dynamics calculations. Interproton distances derived from two-dimensional nuclear Overhauser enhancement (2D NOE) experiments, using the iterative complete relaxation matrix algorithm MARDIGRAS, and torsion angles for sugar rings, estimated from stimulated fitting of double-quantum-filtered correlation (2QF-COSY) spectra, were obtained [Mujeeb, A., Kerwin, S. M., Egan, W. M., Kenyon, G. L., & James, T. L. (1992) Biochemistry 31, 9325-38]. These structural restraints have now been employed as the basis for structure refinement using restrained molecular dynamics (rMD) to search conformational space for structures consistent with the experimental restraints. Specifically, upper and lower bounds on the restraints were incorporated into the AMBER (version 4.0) total potential energy function of the system, the bounds being used to define the width of a flat-well penalty term in the AMBER force field. Confidence in the time-averaged structure obtained is engendered by convergence to essentially the same structure (root-mean-square deviation approximately 0.9 A) when two quite different DNA models, A-DNA and B-DNA (RMSD approximately 6.5 A), were employed as starting structures and when various initial trajectories were used for the rMD runs. The derived structure is further supported by the total energy calculated, the restraint violation energy, the restraint deviations, and the fit with experimental data. For the latter, the sixth-root residual index indicated a good fit of the determined structure with experimental 2D NOE spectral intensities (R1x < 0.07), and the RMS difference between vicinal proton coupling constants calculated for the derived structure and experimental coupling constants were also in reasonable agreement (JRMS = 0.9 Hz). While the structure of the trisdecamer is basically in the B-DNA family, some structural parameters manifest interesting local variations. The helix parameters indicate that, compared with classical B-DNA, the structure is longitudinally more compressed. Local structural variations at the two TG steps in particular together create bending into the major groove of the duplex. Comparison of the two-CTTG-tetrads in the duplex reveals that they have similar structures, with the TT moieties being almost identical; however, the -CTTG-pur sequence has a larger roll and slide for the -TG- step than for the -CTTG-pyr sequence, in accord with published X-ray crystallographic conclusions.

Base Sequence↗

PubMed1991

Long-term enhancement of CA1 synaptic transmission is due to increased quantal size, not quantal content.

Quantal components of Schaffer collateral synaptic transmission recorded intracellularly from CA1 pyramidal cells were examined using 2 methods: simultaneous recordings of CA3-CA1 cell-pairs, and minimal electrical stimulation in stratum radiatum. Quantal parameters estimated by the method of failures and by a computer algorithm that optimized parameter estimates using deconvolution of background noise were highly correlated. EPSP-amplitude histograms of CA3-CA1 cell pairs (N = 10) and minimal electrical stimulation (N = 33) could be adequately described either by Poisson or binomial statistics, or by both, and exhibited similar estimates of unit quantal size (q) and mean quantal content (m). Paired-pulse stimulation with 50 msec between stimuli resulted in an expected facilitation in the EPSP amplitude and increase in m during the second response, as estimated by noise deconvolution, by the decrease in apparent failures, and by a decrease in the coefficient of variation of the EPSP. Tetanization of the Schaffer collaterals that induced long-term enhancement (LTE/LTP) of the population response was associated with an average increase in q for minimal-stimulation responses, with no significant change in any estimate of m. Taken together, these data indicate that, under the present experimental conditions, LTE is expressed as an increase in quantal size, rather than an increase in the number of quanta released per presynaptic impulse. Although this is not definitive evidence for a postsynaptic mechanism, these findings do further restrict the classes of possible presynaptic mechanisms that may be proposed to account for LTE expression.

Action Potentials↗

PubMed2004

Spurious signals in DQF spectroscopy: two-shot stimulated echoes.

The most widely used technique for double-quantum filtered (DQF) single-voxel spectroscopy (SVS) is based on a symmetric PRESS sequence with two additional spatially unselective pi/2 pulses, one of which is usually frequency selective. The actual filtering, rejecting signals from all uncoupled resonances, can be done by suitable phase cycling of the rf pulses in successive shots, but in practice gradient filtering is always used. Under usual conditions the sequence repetition time is comparable to the spin-lattice relaxation time, and a stimulated echo is formed by five out of the ten rf pulses in two consecutive shots. This echo is not filtered out by the gradients, and additional phase cycling is needed to eliminate it. Its spatial origin is the full transverse slice selected by the last pulse of the PRESS sequence. The SVS shimming procedure may create an important field variation in this slice (outside the volume of interest VOI). Water singlet signals therefore appear in a band of frequencies other than 4.7 ppm, and remain unaffected by water suppression pulses. In practice phase-alternation schemes can reduce these spurious signals by several orders of magnitude, but even then they may mask the weak metabolite signals of interest. We describe a strategy to minimize these spurious signals and propose a 16-step phase cycling scheme that attenuates the stimulated echo in every two-step subcycle.

Algorithms↗

PubMed2007

Molecular properties from variational reduced-density-matrix theory with three-particle N-representability conditions.

Molecular ground-state energies and two-electron reduced density matrices (2-RDMs) have recently been computed without the many-electron wave function by constraining the 2-RDM to satisfy a complete set of three-positivity conditions for N representability [D. A. Mazziotti, Phys. Rev. A 74, 032501 (2006)]. Energies at both equilibrium and nonequilibrium geometries are obtained within 0.3% of the correlation energy. In this paper the authors extend this work to examine the accuracy of molecular properties, including multipole moments and components of the ground-state energy, relative to full configuration interaction (FCI). Comparisons are also made with 2-RDM methods with two-positivity conditions and two-positivity plus the generalized T1T2 conditions as well as several approximate wave function methods. Using the 2-RDM method with three-positivity conditions, the authors obtain dipole, quadrupole, and octupole moments for BeH2, BH, H2O, CO, and NH3 at equilibrium geometries that are within 0.04% of their FCI values. In addition, for the potential energy surface of N2, the 2-RDM method with three-positivity yields not only accurate total ground-state energies but also accurate expectation values of the kinetic energy operator, the electron-nuclei potential, and electron-electron repulsion.

Algorithms↗

PubMed2006

Geometry and solvent dependence of the electronic spectra of the amide group and consequences for peptide circular dichroism.

The influence of geometry variations and solvent environment of N-methylacetamide on its energies and absorption intensities was systematically analyzed with the aid of the time-dependent density functional theory (TD DFT). Selective and often complicated reactions of individual electronic levels on the perturbations were found important for the resultant spectral profile. For example, the n-pi band position varied by tens of nanometers due to the C=O bond length oscillations, while it was rather unaffected by surrounding water. On the contrary, pi-pi type transition energies and intensities were broadly dispersed by the aqueous environment but exhibited a modest coordinate dependence. A simple electrostatic model used previously for absorption in the IR region (J. Chem. Phys. 2005, 122, 144501) explained these changes only partially. Additionally, electronic transfer between the solute and the solvent had to be considered for faithful modeling of the ultraviolet light absorption. The inclusion of the environment and dynamics in the modeling then provided more accurate positions, intensities, and realistic inhomogeneous widths of spectral lines. These factors were found important for absorption and circular dichroism spectra of larger peptides and proteins. This was demonstrated with a combined DFT/coupled oscillator model providing principal features observed in electronic circular dichroism spectra of standard peptide conformations.

Acetamides↗

PubMed2006

A comparison between objective and subjective image quality measurements for a full field digital mammography system.

This paper presents pre-sampling modulation transfer function (MTF), normalized noise power spectrum (NNPS) and detective quantum efficiency (DQE) results for an amorphous selenium (a-Se) full field digital mammography system. MTF was calculated from the image of an angled 0.5 mm thick Cu edge, acquired without additional beam filtration. NNPS data were acquired at detector air-kerma levels ranging from 9.1 microGy to 331 microGy, using a standard mammography x-ray spectrum of 28 kV, Mo/Mo target/filter combination and 4 cm of PMMA additional filtration. Prior to NNPS estimation, the image statistics were assessed using a variance image. This method was able to easily identify a detector artefact and should prove useful in routine quality assurance (QA) measurements. Detector DQE, calculated from the NNPS and MTF data, dropped to 0.3 for low detector air-kerma settings but reached an approximately constant value of 0.6 above 50 microGy at the detector. Subjective image quality data were also obtained at these detector air-kerma settings using the CDMAM contrast-detail (c-d) test object. The c-d data reflected the trend seen in DQE, with threshold contrast increasing at low detector air-kerma values. The c-d data were then compared against predictions made using two established models, the Rose model and a standard signal detection theory model. Using DQE(0), the Rose model gave results within approximately 15% on average for all the detector air-kerma values studied and for detail diameters down to 0.2 mm. Similar agreement was also found between the measured c-d data and the signal detection theory results, which were calculated using an ideal human visual response function and a system magnification of unity. The use of full spatial frequency DQE improved the agreement between the calculated and observer results for detail sizes below 0.13 mm.

Algorithms↗