Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue

Conformation of N-acetyl-(E)-dehydrophenylalanine N', N'-dimethylamide (Ac-(E)-ΔPhe-NMe(2)) in solution, a member of (E)-α, β-dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the Φ, Ψ potential energy surfaces were calculated at the MP2/6-31 + G(d,p) level of theory in chloroform solution modeled by the self-consistent reaction field-polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds and dipole interactions between carbonyl groups. The obtained NMR spectral features were compared with theoretical nuclear magnetic shieldings, calculated using Gauge Independent Atomic Orbitals (GIAO) approach and rescaled to theoretical chemical shifts using benzene as reference. The calculated indirect nuclear spin-spin coupling constants were compared with available experimental parameters.

From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations

It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n complete basis set calculations the prediction of nuclear shieldings at the CCSD(T) level of nearly similar accuracy as those, obtained by fitting results obtained from computationally demanding pcS-n calculations at the CCSD(T) limit. A significant saving of computational efforts can thus be achieved by scaling inexpensive CCSD(T)/aug-cc-pVTZ-J calculations of nuclear isotropic shieldings with affordable DFT complete basis set limit corrections.

Extrapolation of water and formaldehyde harmonic and anharmonic frequencies to the B3LYP/CBS limit using polarization consistent basis sets

The harmonic and anharmonic frequencies of fundamental vibrations in formaldehyde and water were successfully estimated using the B3LYP Kohn-Sham limit. The results obtained with polarization- and correlation-consistent basis sets were fitted with a two-parameter formula. Anharmonic corrections were obtained by a second order perturbation treatment (PT2). We compared the performance of the PT2 scheme on the two title molecules using SCF, MP2 and DFT (BLYP, B3LYP, PBE and B3PW91 functionals) methods combined with polarization consistent pc-n (n = 0, 1, 2, 3, 4) basis sets, Dunning’s basis sets (aug)-cc-pVXZ where X = D, T, Q, 5, 6 and Pople’s basis sets up to 6-311++G(3df,2pd). The influence of SCF convergence level and density grid size on the root mean square of harmonic and anharmonic frequency deviations from experimental values was tested. The wavenumber of formaldehyde CH₂ anharmonic asymmetric stretching mode is very sensitive to grid size for large basis sets; this effect is not observed for harmonic modes. BLYP-calculated anharmonic frequencies consistently underestimate observed wavenumbers. On the basis of formaldehyde anharmonic frequencies, we show that increasing the Pople basis set size does not always lead to improved agreement between anharmonic frequencies and experimental values.

Figure

Convergence of Nuclear Magnetic Shieldings in the Kohn-Sham Limit for Several Small Molecules

Convergence patterns and limiting values of isotropic nuclear magnetic shieldings were studied for several small molecules (N2, CO, CO2, NH3, CH4, C2H2, C2H4, C2H6, and C6H6) in the Kohn-Sham limit. Individual results of calculations using dedicated families of Jensen's basis sets (pcS-n and pcJ-n) were fitted toward the complete basis set limit (CBS) using a simple two-parameter formula. Several density functionals were used; calculated vibrational corrections (ZPV) applied; and, for comparison purposes, similar calculations performed using RHF, MP2, SOPPA, SOPPA(CCSD), and CCSD(T) methods and additionally, the aug-cc-pVTZ-J basis set. Finally, the CBS estimated results were critically compared with earlier reported literature data and experimental results. Among 42 studied DFT methods, the KTn and "pure" functionals produced the most accurate heavy atom isotropic nuclear shieldings.

Towards noise immune detection of fetal QRS complexes

The noninvasive fetal electrocardiography is a source of more precise information on the fetal heart activity than the measurements based on Doppler ultrasound signals. However, the clinical diagnostic applications of this technique are limited by difficulty with successful detection of small amplitude fetal QRS complexes. In this study, we investigate the influence of different stages of fetal signals processing on the detection performance. The main propositions of the paper are: application of normalized matched filtering to fetal QRS complexes enhancement and a new approach to the final detection of the complexes. Compared to the classical detectors, the proposed new one allows a significant increase of the detection performance for signals of very different quality.

H2O, H2, HF, F2 and F2O nuclear magnetic shielding constants and indirect nuclear spin-spin coupling constants (SSCCs) in the BHandH/pcJ-n and BHandH/XZP Kohn-Sham limits

Good performance of segmented contracted basis sets XZP, where X = D, T, Q and 5, for obtaining H(2)O, H(2), HF, F(2) and F(2)O nuclear isotropic shielding constants in the BHandH Kohn-Sham basis set limit was shown. The results of two- and three-parameter complete basis set limit extrapolation schemes were compared with experimental results, earlier literature data and benchmark ab initio results. Similar convergence patterns of shieldings obtained from calculations using general purpose XZP basis sets and from polarization-consistent basis sets pcS-n and pcJ-n, where n = 0, 1, 2, 3 and 4, designed to accurately predict magnetic properties were observed. On the contrary, the SSCCs were more sensitive to the XZP basis set size and generally less accurate than those estimated using pcJ-n basis set family. The BHandH density functional markedly outperforms B3LYP method in predicting heavy atom shieldings and SSCCs values in the studied systems.

Complete basis set prediction of methanol isotropic nuclear magnetic shieldings and indirect nuclear spin-spin coupling constants (SSCC) using polarization-consistent and XZP basis sets and B3LYP and BHandH density functionals

Efficient B3LYP and BHandH density functionals were used to estimate methanol's nuclear magnetic isotropic shieldings and spin-spin coupling constants in the basis set limit. Polarization-consistent pcS-n and pcJ-n (n = 0, 1, 2, 3 and 4), and segmented contracted XZP, where X = D, T, Q and 5, basis sets were used and the results fitted with simple mathematical formulas. The performance of the methods was assessed from comparison with experiment and higher level calculations. 1J(CH) and 3J(HH) values were determined from very diluted solutions in deuterochloroform and compared with theoretical predictions. The agreement between complete basis set (CBS) density functional theory (DFT) predicted isotropic shieldings and spin-spin values and experiment was good. The BHandH/pcS-n methanol shieldings obtained using structures optimized at the same level of theory are approaching the accuracy of the advanced coupled-cluster-singles-doubles-approximate triples (CCSD(T)) calculations.

Prediction of water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) using correlation-consistent and polarization-consistent basis sets in the Kohn-Sham basis set limit

Density functional theory (DFT) was used to estimate water's isotropic nuclear shieldings and indirect nuclear spin-spin coupling constants (SSCCs) in the Kohn-Sham (KS) complete basis set (CBS) limit. Correlation-consistent cc-pVxZ and cc-pCVxZ (x = D, T, Q, 5, and 6), and their modified versions (ccJ-pVxZ, unc-ccJ-pVxZ, and aug-cc-pVTZ-J) and polarization-consistent pc-n and pcJ-n (n = 0, 1, 2, 3, and 4) basis sets were used, and the results fitted with a simple mathematical formula. The performance of over 20 studied density functionals was assessed from comparison with the experiment. The agreement between the CBS DFT-predicted isotropic shieldings, spin-spin values, and the experimental values was good and similar for the modified correlation-consistent and polarization-consistent basis sets. The BHandH method predicted the most accurate (1)H, (17)O isotropic shieldings and (1)J(OH) coupling constant (deviations from experiment of about -0.2 and -1 ppm and 0.6 Hz, respectively). The performance of BHandH for predicting water isotropic shieldings and (1)J(OH) is similar to the more advanced methods, second-order polarization propagator approximation (SOPPA) and SOPPA(CCSD), in the basis set limit.

Complete basis set B3LYP NMR calculations of CDCl3 solvent's water fine spectral details

The assignment of singlet at 1.55 ppm and the 1:1:1 triplet at 1.519 ppm to H(2)O and HOD in the 400 MHz (1)H NMR spectrum of CDCl(3) solvent were supported by complete basis set (CBS) GIAO-B3LYP calculated chemical shift and the CBS B3LYP estimated (2)J(D,H) spin-spin coupling constant (SSCC). The CBS fitting of B3LYP/cc-pCVxZ and B3LYP/pcJ-n predicted SSCC values, the accurate value of (2)J(D,H) = -1.082 +/- 0.030 Hz of HOD in chloroform-d(1) and the H/D isotopic shift of 0.0307(1) ppm were reported for the first time. The agreement between CBS B3LYP predicted chemical shift, spin-spin values and experiment was good.

Evaluation of fetal heart rate baseline estimation method using testing signals based on a statistical model

Computer-aided fetal monitoring is based on automated analysis of the fetal heart rate (FHR) variability. The first and the main step in the automated signal interpretation is the estimation of the so called FHR baseline. There are various algorithms for baseline estimation, of different efficiency. For its evaluation, the method of modeling of FHR signal based on the preset baseline component has been developed. The best algorithm is expected to provide the same baseline as the component baseline used to model the FHR signal. Generated signals were used to compare the baselines that have been estimated by two algorithms: the first one relying on artificial neural networks and the classical one using nonlinear filtering of FHR signal.

Polarization-Consistent versus Correlation-Consistent Basis Sets in Predicting Molecular and Spectroscopic Properties

Compared to the correlation-consistent basis sets, it is not known if polarization-consistent pc-n basis sets, which were initially developed for HF and DFT calculations, can provide a monotonic and faster convergence toward the basis-set limit for results at correlated levels as well as better accuracy for a similar number of basis functions. It is also not known whether the pc-n basis sets can compute second derivatives of energy, such as nuclear magnetic shielding tensors, efficiently. To address these questions, the pc-n (n = 1-4), cc-pVxZ, and/or aug-cc-pVxZ (x = D, T, Q, 5, and 6) basis sets were used to compute the molecular and/or spectroscopic parameters of H2, H2O, and NH3 at the RHF, B3-LYP, MP2, and/or CCSD(T) levels of theory. The results show that compared to the cc-pVxZ and/or aug-cc-pVxZ basis sets the pc-n basis sets yield faster convergence toward the basis-set limit but equivalent molecular and/or spectroscopic parameters in the basis-set limit at the RHF, DFT, MP2, and CCSD(T) levels. Because the pc-n basis sets show faster convergence, fewer basis-set functions are needed to reach the accuracy obtained with the aug-cc-pVxZ basis sets, enabling faster calculations and less computer storage space. The results also show that the pc-n basis sets, in conjunction with the "locally dense" basis-set approach, could be applied to predict accurate parameters; thus, they could be used to estimate accurate molecular or spectroscopic properties (e.g., NMR parameters) for larger systems such as the active site of enzymes.

[A web-based e-learning tool in academic teaching of trauma surgery. First experiences and evaluation results]

There are lots of possibilities for universities to offer contents of teaching to students by the Internet. Often the students can download slides or a special lecture note from the intranet of the university. Another way is to make a movie of the lecture and post this lecture movie on the Internet. In the Hanover Medical School we employed an alternative. It was developed by the Trauma Surgery Clinic and the Institute of Medical Informatics at the Hanover Medical School. Our goal was to use just one web-based content resource for the lecture and for the work at home. The Institute of Medical Informatics used a web-based content management system (CMS) Schoolbook to implement this e-learning application.Since October 2005 the Trauma Surgery Schoolbook has been used in the lecture on trauma surgery in all terms, and we evaluated the academic year 2005/2006. The results of the evaluation showed us that the students were very interested in using this e-learning application. The possibility to reinforce the learning material at home is a good chance for the students. Also the organisation of lectures was improved because the materials were all in one place. The lecturer needs to learn several new tasks, but we also got a positive response. Our experiences of the last academic year showed that it was a good way to use one web-based content resource for teaching and learning in the context of a lecture.

Instrumentation for fetal cardiac performance analysis during the antepartum period

Cardiotocography as a simultaneous recording of fetal heart rate (FHR) and uterine contraction activity is a basic method for evaluation of fetal condition. Continuous variability of the fetal heart rate is an indirect sign of adequate oxygenation of a fetus. Unfortunately, the reverse case is not always true, signs suggesting pathological changes can also appear in recording when the fetal is not at risk. The cardiotocography shall then be recognized as a more screening than diagnostic method. It will be interesting to develop a noninvasive method being complementary to routine cardiotocography. This method should allow the adequate prediction of a bad clinical outcome when the test is abnormal. The paper presents the system that makes possible cardiotocograms analysis in parallel with the assessment of additional parameters determined from comparison of mechanical and electrical fetal heart activity signals. The studies are aimed at development of set of parameters that are high correlated with fetal outcome.

Timing events in Doppler ultrasound signal of fetal heart activity

Among various methods of monitoring fetal heart activity a Doppler ultrasound technique is the most often used. Complexity and variability of Doppler signal make difficult the precise measurement of timing dependences defining individual phases of cardiac cycle. Aim of the work was to carry out detailed comparative analysis of Doppler echo coming from movement of two different objects within fetal heart: valve and wall. Joint time frequency analysis were applied. Fetal monitor performed a role of input device in our measurement station based on LabView environment. Doppler signal was acquired from analog outputs with a help of dedicated data acquisition card. Average recording time in a group of 15 patients was 20 minutes. Analysis comprised determination and comparison of spectrograms and power density spectrums corresponding to individual phases of cardiac cycle.

eLearning in education and advanced training in neuroradiology: introduction of a web-based teaching and learning application

INTRODUCTION

New information technologies offer the possibility of major improvements in the professional education and advanced training of physicians. The web-based, multimedia teaching and learning application Schoolbook has been created and utilized for neuroradiology.

METHODS

Schoolbook is technically based as a content management system and is realized in a LAMP environment. The content is generated with the help of the developed system and stored in a database. The layout is defined by a PHP application, and the webpages are generated from the system.

RESULTS

Schoolbook is realized as an authoring tool so that it can be integrated into daily practice. This enables the teacher to autonomously process the content into the web-based application which is used for lectures, seminars and self-study. A multimedia case library is the central building block of Schoolbook for neuroradiology, whereby the learner is provided with original diagnostic and therapeutic data from numerous individual cases. The user can put individual emphasis on key learning points as there are various ways to work with the case histories. Besides the case-based way of teaching and learning, a systematically structured way of dealing with the content is available.

CONCLUSION

eLearning offers various opportunities for teaching and learning in academic and scientific as well as in economic contexts. Web-based applications such as Schoolbook may be beneficial not only for basic university education but also for the realization of international educational programmes such as the European Master of Medical Science with a major in neuroradiology.

Cross-relaxation bottleneck in water–lysozyme proton magnetization exchange

The proton spin-lattice relaxation parameters in natural and deuterated lysozyme solutions have been measured as a function of temperature (0-50 degrees C). The variation of the apparent magnitudes of the water proton magnetizations in the solutions with temperature indicates that magnetic coupling mixes protein and water proton magnetizations. The results are consistent with an exchange cross-relaxation model (Hills, B. P., Mol Phys 1992, 76, 489-508) in which the cross-relaxation acts between the labile and nonlabile protons, rather than between water and protein protons. Although this cross-relaxation pathway clearly affects the observed magnetization fractions in this protein solution, its influence on the relaxation rates is less apparent.

Spectroscopic characterization of natural corals

The FTIR, micro-Raman, NMR, and XPS spectra of 25 different natural corals have been compared. Reflectance and transmission absorbance IR and Raman data have been used as rapid and efficient means of classification of natural corals containing aragonite (non-precious white species), calcite (red, pink, precious white species), and organic material (black protein polymer). The combination of reflectance IR and infrared microscopy could serve as a rapid, non-destructive method for distinguishing natural corals from artificial, fake jewels.

Hartree-Fock and density functional complete basis-set (CBS) predicted nuclear shielding anisotropy and shielding tensor components

The nuclear shielding anisotropy and shielding tensor components calculated using the hybrid density functional B3PW91 are reported for a model set of compounds comprised of N2, NH3, CH4, C2H4, HCN and CH3CN. An estimation of density functional theory (DFT) and Hartree-Fock complete basis-set limit (CBS) parameters from a 2 (3) point exact fit vs. least-squares fit was obtained with the cc-pVxZ and aug-cc-pVxZ basis sets (x=D, T, Q, 5, 6). Both Hartree-Fock- and DFT-predicted CBS shielding anisotropies and shielding tensor components of the model molecules were in reasonable agreement with available experimental data. The utility of using a limited CBS approach for calculating accurate anisotropic shielding parameters of larger molecules as complementary methods to solid-state NMR is proposed.

beta-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations. Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

IR studies were preformed to determine possible transition metal ion binding sites of penicillin, the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M-L complexes with engagement of -COO- and/or -CONH- functional groups. The small shift of vC=O towards higher frequencies rules out direct M-L interaction via beta-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic beta-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the beta-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.

NMR studies on penicillins: hydrogen bonding, self-association and micellar solutions of cloxacillin Na-salt in D2O

Self-association and formation of micellar solutions of cloxacillin sodium salt (CLO-Na) dissolved in heavy water have been investigated by NMR-spectroscopy. Concentration and temperature dependence of proton and carbon chemical shifts of cloxacillin-Na in D2O is presented and certain 1H and 13C NMR line assignments have been substantiated.

Copper-D-penicillamine complex as potential contrast agent for MRI

In vitro and in vivo proton T1 data are reported that demonstrate that the paramagnetic copper-D-penicillamine complex can be applied as a potential contrast agent to magnetic resonance imaging.

Failure of prediction of liver function test abnormalities with the urine urobilinogen and urine bilirubin assays

A prospective observational study of 229 cases was conducted in a busy ambulatory care setting to evaluate the sensitivity, specificity, predictive values, and accuracy of spot urine urobilinogen and urine bilirubin assays as screening tests for serum liver function test (LFT) abnormalities. Both urine tests exhibited remarkably similar characteristics overall once they were adjusted to maximize accuracy and predictive values (occurring at a normal or abnormal "threshold," respectively, of 3.4 or 5.07 mumol/d for urobilinogen and 0 or 1+ for urine bilirubin). The percentage of cases correctly identified were 81% to 83% for serum bilirubin assays, 68% to 72% for other LFTs, but only 62% to 63% for screens for cases with at least one abnormal LFT finding. Poor sensitivities (47% to 49%) limited the detection of abnormal findings by the screen; both screens were reasonably specific (79% to 89%), but negative predictive values were suitable (89%) for serum bilirubin results only and were prohibitively lower (49% to 50%) in predicting all patients without LFT abnormalities. We conclude that spot urine urobilinogen and urine bilirubin determinations, although good screens for isolated serum bilirubin elevations, have unacceptable statistical properties as predictors of other LFT results due to a high proportion of false-negative results.

Abnormalities of urine urobilinogen and urine bilirubin assays and their relation to abnormal results of serum liver function tests

A prospective observational study of 324 cases was conducted in a busy ambulatory care setting to evaluate the sensitivity, specificity, predictive values, and accuracy of spot urine urobilinogen and urine bilirubin assays as screening tests for serum liver function test (LFT) abnormalities. High positive predictive values (88% for at least one abnormal LFT) make the evaluation of positive urine screens detected during routine health care maintenance examinations imperative. Because extraneous factors may influence both urine and serum test results, however, urine assays obtained as a screening parameter in clinical presentations (abdominal pain, jaundice, constitutional symptoms, etc) have only limited clinical utility. The high proportion of false-negative results for both urine assays renders their statistical properties unacceptable as screens in these clinical situations.

Accuracy of urine urobilinogen and bilirubin assays in predicting liver function test abnormalities

Components of the dipstick urinalysis (urine urobilinogen and urine bilirubin) are often used by emergency physicians to screen for the need to obtain liver function tests in many clinical situations. A prospective observational study was conducted to evaluate the sensitivity, specificity, and predictive properties of spot urine bilirubin and urobilinogen assays in the emergency department as screening test for serum liver function test (LFT) abnormalities. Of 122 patients, abdominal pain was the indication for laboratory evaluation in 54%; jaundice and constitutional symptoms were the indication in 29%. Overall sensitivities for both urine assays were 70% to 74% for serum bilirubin, but 43% to 53% for other LFTs; specificities were 77% to 87% for both urine screens. Positive predictive values show that the urine assays were 83% to 86% reliable for detecting at least one LFT abnormality. Negative predictive values were 85% for both urine assays for serum bilirubin elevations, but lower for other LFTs. Urine urobilinogen has its greatest clinical utility as a screen when a normal/abnormal threshold of 2.0/4.0 mg/dL is used.