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At least 1,369 records · Page 76Linked to original sources
PubMed2007

Blue-shifting hydrogen bond in the benzene-benzene and benzene-naphthalene complexes.

Ab initio complete optimizations at MP2/6-31++G** level have been performed in the T-shaped geometry of the benzene-benzene and benzene-naphthalene complexes. To check the effect of the basis set superposition error (BSSE), optimizations have been done in the BSSE corrected and BSSE uncorrected potential energy surfaces. The BSSE effect in the calculation of the Hessian has also been evaluated to check its influence in the frequency values. Quantum theory atoms in molecules (QTAIM) calculations have also been performed on both dimers. Intermolecular energies differ around a 25% when the optimization is performed with or without counterpoise corrected gradients. The influence of BSSE is also noticeable in the distances. Frequency shifts show big changes because of the BSSE. Thus, uncorrected values are up 350% larger than corrected ones. The hypotheses given in the literature to explain the origin of the blue-shifting hydrogen bond do not seem to give a suitable explanation for all characteristics of the behavior found in the studied systems.

Benzene↗
PubMed2005

Quantum phase slips in the presence of finite-range disorder.

To study the effect of disorder on quantum phase slips (QPSs) in superconducting wires, we consider the plasmon-only model where disorder can be incorporated into a first-principles instanton calculation. We consider weak but general finite-range disorder and compute the form factor in the QPS rate associated with momentum transfer. We find that the system maps onto dissipative quantum mechanics, with the dissipative coefficient controlled by the wave (plasmon) impedance Z of the wire and with a superconductor-insulator transition at Z = 6.5 k. We speculate that the system will remain in this universality class after resistive effects at the QPS core are taken into account.

Journal Article↗
PubMed1997

Optimal phosphor thickness for portal imaging.

A theoretical approach known as quantum accounting diagram (QAD) analysis has been used to calculate the spatial-frequency-dependent detective quantum efficiency (DQE) of two portal imaging systems: one based on a video camera and another based on an amorphous silicon array. The spatial frequency-dependent DQEs have then been used to determine indices of displayed and perceived image quality. These indices are figures of merit that can be used to optimize the design of linear imaging systems. We have used this approach to determine which of eight phosphor screen thicknesses (ranging between 67 and 947 mg/cm2) is optimal for the two designs of portal imaging systems. The physical characteristics (i.e., detection efficiencies, gains, and MTFs) of each of the eight x-ray detectors have been measured and combined with the physical characteristics of the remaining components to calculate the theoretical DQEs. In turn, the DQEs have been used to calculate theoretical indices of displayed and perceived image quality for two types of objects: a pelvis object and a pointlike object. The maximal indices of displayed and perceived image quality were obtained with screen thickness ranging between 358 and 947 mg/cm2, depending upon the imaging system design and the object being imaged. Importantly, the results showed that there is no single optimal screen thickness. The optimal thickness depended upon imaging task (e.g., detecting large, low-contrast structures, or detecting edges and small structures). Nevertheless, the results showed that there were only modest improvements in the indices of image quality for phosphor screens thicker than 350-400 mg/cm2.

Biophysical Phenomena↗
PubMed2006

An X-ray computed tomography imaging agent based on long-circulating bismuth sulphide nanoparticles.

Nanomaterials have become increasingly important in the development of new molecular probes for in vivo imaging, both experimentally and clinically. Nanoparticulate imaging probes have included semiconductor quantum dots, magnetic and magnetofluorescent nanoparticles, gold nanoparticles and nanoshells, among others. However, the use of nanomaterials for one of the most common imaging techniques, computed tomography (CT), has remained unexplored. Current CT contrast agents are based on small iodinated molecules. They are effective in absorbing X-rays, but non-specific distribution and rapid pharmacokinetics have rather limited their microvascular and targeting performance. Here we propose the use of a polymer-coated Bi(2)S(3) nanoparticle preparation as an injectable CT imaging agent. This preparation demonstrates excellent stability at high concentrations (0.25 M Bi(3+)), high X-ray absorption (fivefold better than iodine), very long circulation times (>2 h) in vivo and an efficacy/safety profile comparable to or better than iodinated imaging agents. We show the utility of these polymer-coated Bi(2)S(3) nanoparticles for enhanced in vivo imaging of the vasculature, the liver and lymph nodes in mice. These nanoparticles and their bioconjugates are expected to become an important adjunct to in vivo imaging of molecular targets and pathological conditions.

Animals↗
PubMed1999

[Computed tomography of the abdomen with multidetector-array CT].

BACKGROUND: The advent of multidetector CT (MDCT) constitutes a quantum leap creating a wealth of new opportunities in medical imaging. However, while the basic principles of spiral CT still apply, we are now challenged to rethink our strategies in planning a CT study to take full advantage of the increased capabilities of MDCT. MATERIALS AND METHODS: We report here our preliminary experiences with MDCT for abdominal CT imaging within a 5-month period. During this time, suitable protocols for investigation of the abdomen using MDCT were developed. The capabilities of MDCT allow for tailoring dedicated CT protocols for routine applications as well as for biphasic liver studies and CT angiography of the aorta and abdominal vessels. RESULTS: The speed of MDCT can either be used to reduce the time needed to cover a given volume, or to use narrower beam collimations to increase the resolution of detail along the z-axis and reduce volume averaging. Higher scan speed allows reduction of the amount of contrast material in vascular applications and suppression of motion artifacts. Higher spatial resolution with thinner collimations reduces volume averaging and improves the detection of small hepatic and pancreatic lesions. Detailed analysis of vascular structures and high-quality three-dimensional reformations become feasible. New problems arise from the large amount of data generated by MDCT. CONCLUSIONS: MDCT offers a wealth of new opportunities that help us to come to a fast and accurate diagnosis in suspected abdominal disease. Traditional indications for performing CT are reemphasized and new clinical applications can be exploited.

Abdomen↗
PubMed1994

Dual-energy digital mammography utilizing stimulated phosphor computed radiography.

Dual-energy subtraction is a radiographic technique for the acquisition of a material selective image by the weighted subtraction of low- and high-energy digital X-ray images. This is achieved by exploiting the energy dependence of the X-ray attenuation components in the image. This can allow the removal of background morphology to enhance the presentation of otherwise obscured details. The detection of microcalcifications in a mammogram by dual-energy techniques has previously been investigated. These investigations indicated that, using dual-energy techniques, small microcalcifications could be extracted from the background breast morphology with sufficient signal to noise ratio (SNR) to be full visualized. The authors present the extension of a theoretical dual-energy model to incorporate practical considerations and then compare the results with experimentally derived data using a commercially available computed radiography system. In particular the extended model now takes into account the energy dependent detective quantum efficiency of a system. This is thought to be a major factor in reducing the efficiency of dual-energy mammography. The theoretical model predicts that dual-exposure dual-energy mammography, utilizing HRIII image plates, could not provide a detail SNR of five for calcifications smaller than 470 mu m. The experimental results verify this and indicate that dual-energy subtraction mammography, utilizing computed radiography, is currently not a viable technique for the detection of clinically significant microcalcifications. Further advances in X-ray image detector efficiency will be required if the full potential of this technique is to be achieved.

Breast Diseases↗
PubMed2005

Breakdown of weak-field magnetotransport at a metallic quantum critical point.

We show how the collapse of an energy scale in a quantum critical metal can lead to physics beyond the weak-field limit usually used to compute transport quantities. For a density-wave transition we show that the presence of a finite magnetic field at the critical point leads to discontinuities in the transport coefficients as temperature tends to zero. The origin of these discontinuities lies in the breakdown of the weak-field Jones-Zener expansion which has previously been used to argue that magnetotransport coefficients are continuous at simple quantum critical points. The presence of potential scattering and magnetic breakdown rounds the discontinuities over a window determined by tauDelta < 1 where Delta is the order parameter and tau is the quasiparticle elastic lifetime.

Journal Article↗
PubMed2004

Virtual brain states and non-locality of the ERP.

It has been previously proposed that conscious process involves the collapse of quantum, dynamical brain states through conscious observation. It has been further proposed that the brain process has an active role in selecting the status of uncertain stimuli. On the basis of these proposals it was predicted that event-related potentials (ERPs) would differ under unobserved versus pre-observed conditions. This has been found to be the case. Here we describe our most recent data, which shows that the difference between the pre-observed (inactive) and unobserved (active) conditions in ERPs is replicable, and seems to involve a selective process of matching stimulus and virtual brain state under the two conditions. Maximization of entropy by congruence of stimulus and brain potential through a quantum entropy operator is the proposed physical mechanism for this finding. The prefrontal lobe inhibition of perseverative brain states under the active condition is proposed to be the neurological mechanism of the findings.

Acoustic Stimulation↗
PubMed2004

QSim, a program for NMR simulations.

We present QSim, a program for simulation of NMR experiments. Pulse sequences are implemented and analyzed in QSim using a mouse driven interface. QSim can handle almost any modern NMR experiment, using multiple channels, shaped pulses, mixing, decoupling, phase-cycling and pulsed field gradients. Any number of spins with any spin quantum number can, in theory, be used in simulations. Relaxation is accounted for during all steps of pulse sequences and relaxation interference effects are supported. Chemical kinetics between any numbers of states can be simulated. Both classical and quantum mechanical calculations can be performed. The result of a simulation can be presented either as magnetization as a function of time or as a processed spectrum.

Computer Graphics↗
PubMed2007

QSAR models for predicting the activity of non-peptide luteinizing hormone-releasing hormone (LHRH) antagonists derived from erythromycin A using quantum chemical properties.

Multiple linear regression (MLR) combined with genetic algorithm (GA) and Bayesian-regularized Genetic Neural Networks (BRGNNs) were used to model the binding affinity (pK(I)) of 38 11,12-cyclic carbamate derivatives of 6-O-methylerythromycin A for the Human Luteinizing Hormone-Releasing Hormone (LHRH) receptor using quantum chemical descriptors. A multiparametric MLR equation with good statistical quality was obtained that describes the features relevant for antagonistic activity when the substituent at the position 3 of the erythronolide core was varied. In addition, four-descriptor linear and nonlinear models were established for the whole dataset. Such models showed high statistical quality. However, the BRGNN model was better than the linear model according to the external validation process. In general, our linear and nonlinear models reveal that the binding affinity of the compounds studied for the LHRH receptor is modulated by electron-related terms.

Animals↗
PubMed2006

Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: constrained MD simulation studies.

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P(II)), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure.

Alanine↗
PubMed1991

Interaction energy studies on antibiotics nucleoside analogs 2-azaadenine.

The 2-azaadenine antibiotic is known to be a potent cytotoxic nucleoside analog. Evaluation of the interaction energy of this molecule with nucleic acid bases and base pairs has been performed using a quantum-mechanical perturbation technique. Both in-plane and stacking energies have been computed. These energy values along with their sites of association have been compared with the standard energy values and spatial positions for the nucleic acid bases during transcription. The results have been examined in the light of their biological significance.

Adenine↗
PubMedDate not supplied

Prediction of cellular toxicity of halocarbons from computed chemodescriptors: a hierarchical QSAR approach.

A hierarchical quantitative structure-activity relationship (HiQSAR) approach was used to estimate toxicity and genetic toxicity for a set of 55 halocarbons using computed chemodescriptors. The descriptors consisted of topostructural (TS), topochemical (TC), geometrical, semiempirical (AM1) quantum chemical, and ab initio (STO-3G, 6-31G(d), 6-311G, 6-311G(d), and aug-cc-pVTZ) quantum chemical indices. For the two toxicity endpoints investigated, ARR and D(37), the TC indices gave the best cross-validated R(2) values. The 3-D indices also performed either as well as or slightly superior to the TC indices. For the four categories of quantum chemical indices used for the development of predictive models, the AM1 parameters gave the worst performance, and the most advanced ab initio (B3LYP/aug-CC-pVTZ) parameters gave the best results when used alone. This was also the case when the quantum chemical indices were used in the hierarchical QSAR approach for both of the toxicity endpoints, ARR and D(37). The models resulting from HiQSAR are of sufficiently good quality to estimate toxicity of halocarbons from structure.

Aspergillus niger↗
PubMedDate not supplied

Many-body optimization using an ab initio monte carlo method.

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Journal Article↗
PubMed2002

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions.

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.

Journal Article↗
PubMed2006

Hydrogen transfer between sulfuric acid and hydroxyl radical in the gas phase: competition among hydrogen atom transfer, proton-coupled electron-transfer, and double proton transfer.

In an attempt to assess the potential role of the hydroxyl radical in the atmospheric degradation of sulfuric acid, the hydrogen transfer between H2SO4 and HO* in the gas phase has been investigated by means of DFT and quantum-mechanical electronic-structure calculations, as well as classical transition state theory computations. The first step of the H2SO4 + HO* reaction is the barrierless formation of a prereactive hydrogen-bonded complex (Cr1) lying 8.1 kcal mol(-1) below the sum of the (298 K) enthalpies of the reactants. After forming Cr1, a single hydrogen transfer from H2SO4 to HO* and a degenerate double hydrogen-exchange between H2SO4 and HO* may occur. The single hydrogen transfer, yielding HSO4* and H2O, can take place through three different transition structures, the two lowest energy ones (TS1 and TS2) corresponding to a proton-coupled electron-transfer mechanism, whereas the higher energy one (TS3) is associated with a hydrogen atom transfer mechanism. The double hydrogen-exchange, affording products identical to reactants, takes place through a transition structure (TS4) involving a double proton-transfer mechanism and is predicted to be the dominant pathway. A rate constant of 1.50 x 10(-14) cm(3) molecule(-1) s(-1) at 298 K is obtained for the overall reaction H2SO4 + HO*. The single hydrogen transfer through TS1, TS2, and TS3 contributes to the overall rate constant at 298 K with a 43.4%. It is concluded that the single hydrogen transfer from H2SO4 to HO* yielding HSO4* and H2O might well be a significant sink for gaseous sulfuric acid in the atmosphere.

Journal Article↗
PubMed2006

Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-bond conformations in gaseous and liquid water.

The vibrational IR spectra in the O-H stretching region are computed for water clusters containing 6-22, 28, and 30 molecules using quantum-chemical calculations (B3LYP and an augmented basis set). For the cluster with 20 molecules, several different structures were studied. The vibrational spectrum was partitioned into contributions from different molecules according to their coordination properties. The frequency shifts depend on the number of donated/accepted H-bonds primarily of the two molecules participating in the H-bond, but also of the surrounding molecules H-bonding to these molecules. The frequencies of H-bonds between two molecules of the same coordination type are spread over a broad interval. The most downshifted hydrogen-bond vibrations are those donated by a single-donor 3-coordinated molecule where the H-bond is accepted by a single-acceptor molecule. The H-bonded neighbors influence the downshift, and their contribution can be rationalized in the same way as for the central dimer. Single donors/acceptors cause larger downshifts than 4-coordinated molecules, and the least downshift is obtained for double donors/acceptors. This result is at variance with the conception that experimental liquid water spectra may be divided into components for which larger downshifts imply higher H-bond coordination. A mean spectral contribution for each coordination type for the donor molecule was derived and fitted to the experimental liquid water IR spectrum, which enabled an estimation of the distribution of H-bond types and average number of H-bonds (3.0 +/- 0.2) in the liquid.

Journal Article↗