bluuebunny/crossref_metadata_2025 huggingface dataset:
The Hamiltonians of NMR. Part III
Authors: Smith Scott A. , Palke William E. , Gerig J. T.
Published: March 2007

Building on our previous discussions of the Hamiltonian operators that are important in the description of high‐resolution NMR experiments, we use here the same symbolism and approach to develop formulations for time‐dependent operators. These considerations lead to discussions of free precession and the influence of applied radio‐frequency fields. As with the previous articles, the presentations are explicit, the mathematical operations are explained in detail, and all assumptions made are indicated.
Orientational dependence of vicinal proton‐proton NMR coupling constants: The Karplus relationship
Authors: Minch Michael J.
Published: March 2007

Vicinal proton‐proton coupling constants depend on a variety of stereochemical parameters such as bond angle, bond length, substituent electronegativity and orientation, and — most importantly — on the torsion angle between the coupling protons. The sensitivity of vicinal proton‐proton coupling constants 3JHH′, to variations of dihedral angle ϕwas first rationalized in valence bond terms by Karplus, who showed that the coupling constants could be approximately fitted to a cos2ϕ function. The Karplus equation 3JHH′ = Acos2ϕ + Bcosϕ + C (or variants thereof) has been a major tool of the structural chemist for 35 years. Karplus started with the Ramsey formula for Fermi contact contribution, expressed by ground‐state wave functions and a mean excitation energy. More sophisticated molecular orbital (MO) treatments have afforded analogous expressions that may be used to predict trends correctly but are rarely useful for accurate estimations of dihedral angles. Numerous attempts have been made to account for the effect of substituents, bond angles, and lengths — either empirically by the choice of A, B, and C (with different values for each type of compound) or semiempirically, starting with theoretically more sophisticated expressions with statistically adjustable parameters. Theoretical and empirical approaches are reviewed and compared.
Signal‐to‐noise ratio: A calculation from first principle applied to NMR in the earth's field
Authors: Laukien Dirk D. , Weaver David , Tschopp Werner H.
Published: March 2007

NMR in the Earth's field is used as an example for calculating the signal‐to‐noise ratio from first principle. A simple loop is used as a transmitter and a receiver coil. Parameters significant in a signal‐to‐noise calculation are derived for this application. The influence of the receiving electronics is included in the calculations. Example spectra of NMR signals obtained in the Earth's field are given.
ENC, a motor of progress in NMR
Authors: Ernst Richard R.
Published: March 2007

During the course of my scientific career I have accumulated an uncountable number of debts to people, organizations, and fortunate events. I am particularly obliged to a long series of Experimental Nuclear Magnetic Resonance Conferences, the ENC's. Not only have they been an invaluable source of inspiration and an occasion for establishing new friendships, but the yearly ENC had, and still has, the same function as the first warm Sunday afternoon in spring time when people are eagerly promenading and showing their most pretty dress, prepared with much love during the preceding dark winter months. Each ENC is a landmark, an hour of truth where success or failure of the previous twelve months of intense research becomes evident.

Indeed from 1964 to very recently, I was working and living truly from ENC to ENC, having only one thought in mind: to be properly prepared with a new experiment or a new revealing insight to be presented at the next conference. I think it is important in the unstructured life of a scientist to have these regular caesuras to account for ones achievements.

In this article I would like to present, based on a special request by the editors, the abstracts of all my personal and co‐authored abstracts of ENC presentations from 1964 to 1992 as a token of appreciation for the importance the ENC's have played in my scientific life. They will be adorned with remarks on the context of their emergence.
Two‐dimensional 13C, heteroelement correlation spectroscopy
Authors: Fäcke Thomas , Wagner Ronald , Berger Stefan
Published: March 2007

Two‐dimensional heteronuclear correlation spectroscopy between the spin pairs 13C, nX (with n X = 2H, 6Li, 11B, 15N, 19F, 29Si, 31P, 77Se, 119Sn, 125Te, 195Pt, 199Hg, and 207Pb) is discussed. The necessary hardware requirements are explained, and the three most important correlation techniques are compared using product operator formalism. Selected simple examples demonstrate the usefulness of this new method.
Planar surface gradient coil
Authors: Cho Z. H. , Yi J. H.
Published: March 2007

In NMR imaging, spatial information of an object is made possible by the gradient fields. Desirable qualities in a gradient field for conventional imaging include linearity, speed, and strength. Recent developments in high resolution or fast imaging or both require strong gradient fields and fast switching capability. Until recently, most conventional gradient coils available were the Golay‐type, together with Helmholtz‐type coil, mounted on a cylindrical support. Some of the drawbacks of the cylindrically shaped coils include the fixed geometry and relatively weak gradient fields due to the limitation imposed on the object size, which necessitate the large coil diameter. In this article, a novel gradient coil, namely the surface gradient coil (SGC), is described and reviewed. The SGC, an unconventional gradient coil that is constructed on a flat surface, is presented as an alternative to the conventional Golay‐type coil. This flat and arbitrarily sized surface gradient coil could satisfy two important requirements. First, it could provide much larger gradient fields while providing substantially improved switching speed due to its small size. Secondly, the planar structure of the surface gradient coil, in conjunction with a surface radio frequency (RF) coil, provides a movable probe for localized imaging of large objects. The latter, i.e., the possibility of integrating the SGC with the surface RF coil suggests a new direction in NMR imaging similar to the movable probe, widely used in ultrasound imaging. The movable probe would then allow us to carry out fast in vivo high‐resolution imaging of the human body hitherto difficult to carry out with conventional gradient coils. The basic design concepts, together with the improved design, achieved through numerical optimization, and some experimental results obtained with the prototype SGC probes, are given.
Calculation of CIDNP signal intensities
Authors: Goez Martin
Published: March 2007

A quantitative treatment of the radical pair mechanism, which is the predominant mechanism giving rise to chemically induced dynamic nuclear polarization (CIDNP), is presented. Calculation of the spin evolution of radical pairs is performed with the density matrix formalism. Combination of the results with the equations describing the radical pair dynamics leads to general relationships that allow the populations of the nuclear spin states in the reaction products to be obtained. Finally, it is shown how the line intensities observed in pulsed NMR experiments can be extracted from the computed nuclear spin polarizations.
Selection of coherence transfer pathways by pulsed‐field gradients in nmr spectroscopy
Authors: Zhu Jian‐Ming , Smith Ian C. P.
Published: March 2007

The use of pulsed‐field gradients has emerged as a promising approach for the selection of coherence transfer pathways in NMR spectroscopy. Applying field gradient pulses instead of phase cycling can reduce data acquisition time, minimize artifacts, and provide new ways to suppress solvent signals. This paper provides a practical introduction to the technique. The selection of coherence transfer pathways by field gradient pulses is based on the characteristic sensitivities of coherence to field gradients and on the formation of coherence transfer echoes. A general formulation for selection of coherence transfer pathways by field gradient pulses is provided. Examples are used to illustrate the design of field gradient pulse sequences for the selection of specific coherence transfer pathways in multiple‐pulse experiments.
Outcome of patients with Philadelphia chromosome‐positive chronic myelogenous leukemia post‐imatinib mesylate failure
Authors: Kantarjian Hagop , O'Brien Susan , Talpaz Moshe , Borthakur Gautam , Ravandi Farhad , Faderl Stefan , Verstovsek Srdan , Rios Mary Beth , Shan Jianqin , Giles Francis , Cortes Jorge
Published: March 2007

BACKGROUND.

The prognosis of patients with chronic myelogenous leukemia (CML) after failure of imatinib mesylate therapy is not well documented.

METHODS.

The outcome of 420 patients with CML post‐imatinib failure (resistance‐recurrence in 374; toxicities in 46) were reviewed in relation to survival, overall, and by different therapies.

RESULTS.

The estimated 3‐year survival rates were 72% in 88 patients who progressed in chronic phase, 30% in 130 patients who progressed in accelerated phase, 7% in 156 patients who progressed in blastic phase, and 75% in 37 patients in chronic phase with imatinib intolerance. Survival in chronic phase was better when subsequent therapy was nilotinib or dasatinib vs allogeneic stem cell transplant vs others (estimated 2‐year survival rates 100% vs 72% vs 67%; P = .01), but not in accelerated‐blastic phase.

CONCLUSIONS.

Prognosis post‐imatinib failure in chronic phase is reasonable; it is poor if the CML phase post‐imatinib failure is accelerated or blastic. Cancer 2007. © 2007 American Cancer Society.
A role for acetylcholine receptors in their own aggregation on muscle cells
Authors: Milholland Rebecca B.R. , Gordon Herman
Published: March 2007

Both neurotrophic factors and activity regulate synaptogenesis. At neuromuscular synapses, the neural factor agrin released from motor neuron terminals stimulates postsynaptic specialization by way of the muscle specific kinase MuSK. In addition, activity through acetylcholine receptors (AChRs) has been implicated in the stabilization of pre‐ and postsynaptic contacts on muscle at various stages of development. We show here that activation of AChRs with specific concentrations of nicotine is sufficient to induce AChR aggregation and that this induction requires the function of L‐type calcium channels (L‐CaChs). Furthermore, AChR function is required for agrin induced AChR aggregation in C2 muscle cells. The same concentrations of nicotine did not induce observable tyrosine phosphorylation on either MuSK or the AChR β subunit, suggesting significant differences between the mechanisms of agrin and activity induced aggregation. The AChR/L‐CaCh pathway provides a mechanism by which neuromuscular signal transmission can act in concert with the agrin‐MuSK signaling cascade to regulate NMJ formation. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Oxidative stress, nitric oxide, and the mechanisms of cell death in Lurcher Purkinje cells
Authors: McFarland Rebecca , Blokhin Andrei , Sydnor James , Mariani Jean , Vogel Michael W.
Published: March 2007

Oxidative stress is postulated to play a role in cell death in many neurodegenerative diseases. As a model of neonatal neuronal cell death, we have examined the role of oxidative stress in Purkinje cell death in the heterozygous Lurcher mutant (+/Lc). Lurcher is a gain of function mutation in the δ2 glutamate receptor (GluRδ2) that turns the receptor into a leaky membrane channel, resulting in chronic depolarization of +/Lc Purkinje cells starting around the first week of postnatal development. Virtually, all +/Lc Purkinje cells die by the end of the first postnatal month. To investigate the role of oxidative stress in +/Lc Purkinje cell death, we have examined nitric oxide synthase (NOS) activity and the expression of two markers for oxidative stress, nitrotyrosine and manganese super oxide dismutase (MnSOD), in wild type and +/Lc Purkinje cells at P10, P15, and P25. The results show that NOS activity and immunolabeling for nitrotyrosine and MnSOD are increased in +/Lc Purkinje cells. To determine whether peroxynitrite formation is a prerequisite for +/Lc Purkinje cell death, +/Lc mutants were crossed with an α‐nNOS knockout mutant (nNOSα−/−) to reduce the production of NO. Analysis of the double mutants showed that blocking α‐nNOS expression does not rescue +/Lc Purkinje cells. However, we present evidence for sustained NOS activity and nitrotyrosine formation in the GluRδ2+/Lc:nNOS−/− double mutant Purkinje cells, which suggests that the failure to rescue GluRδ2+/Lc:nNOS−/− Purkinje cells may be explained by the induction of alternative nNOS isoforms. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Germline transgenesis and insertional mutagenesis in the ascidianCiona intestinalis
Authors: Sasakura Yasunori
Published: March 2007

Stable transgenesis is a splendid technique that is applicable to the creation of useful marker lines, enhancer/gene traps, and insertional mutagenesis. Recently, transposon‐mediated transformation using a Tc1/marinertransposable elementMinoshas been reported in two ascidians:Ciona intestinalisandC. savignyi. The transposon derived from an insect,Drosophila hydei, has high activity for excision inCionaembryos and transposition in their genome. As much as 37% ofMinos‐injectedC. intestinalistransmitted transposon insertions to the subsequent generation.Minos‐mediated germline transgenesis has also been achieved by means of electroporation method.Minostechniques have been applied to enhancer traps and insertional mutagenesis inCiona. For those reasons,Minosoffers the high potential for use as a powerful tool for future genetic studies. This review specifically addresses recent achievements of transformation techniques inCiona, as exemplified using theMinossystem. Developmental Dynamics 236:1758–1767, 2007. © 2007 Wiley‐Liss, Inc.
The Ditertiary‐Phosphane‐Bridged Heteronuclear Cluster RuOs3(μ‐H)2(CO)9(μ‐CO)2(μ‐dppm): Synthesis and Reactivity with Alkynes
Authors: Tan Yong Leng Kelvin , Leong Weng Kee
Published: March 2007

A high‐yielding alternative synthesis of the dppm‐bridged heteronuclear cluster RuOs3(μ‐H)2(CO)9(μ‐CO)2(μ‐dppm) (1) [dppm = bis(diphenylphosphanyl)methane] has been developed. Thermolysis of 1 resulted in dephenylation of both phosphane groups to afford the butterfly cluster RuOs3(CO)12(μ4,κ2:κ2‐PhPCH2PPh) (2). The reaction of 1 with selected alkynes afforded the products RuOs3(μ‐H)(CO)8(μ‐CO)(μ3,κ2:κ1‐PhPCH2PPh2)(μ3,η1:η2:η1‐L) (3) (L = alkyne) in which the alkyne is aligned parallel to an Os–Os bond(// Os‐Os isomer). The clusters incorporating internal alkynes underwent isomerization to the //Ru‐Os isomer by alkyne and hydride migration. Several other cluster products of these reactions were also identified, including RuOs3(μ‐H)(CO)8(μ‐CO)(μ3,κ2:κ1‐PhPCH2PPh2)(μ3,η1:η2:η1‐tBuC2CHO)(6) in which the methyl group of the alkyne has been oxidized to an aldehyde. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Synthesis and Structural Characterization of Novel Ytterbium(III) Complexes with both a μ‐Oxo Group and Bridged Indenyl Ligands, and Ytterbium(II) Complexes with Bridged Indenyl Ligands
Authors: Cheng Lin , Feng Yan , Wang Shaowu , Luo Wei , Yao Wei , Yu Zeyan , Xi Xiaobing , Huang Zixiang
Published: March 2007

The reactivity of the ytterbium(III) amide [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with different bridged indene compounds in the presence of external donor ligands was studied. Reaction of [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with the corresponding 1,2‐bis(indenyl)ethane [(CH2)2(C9H7)2] or Me2Si(C9H7)2, followed by the addition of excess thf, produced a novel tetranuclear ytterbium complex [{η5:η5‐(CH2)2(C9H6)2}Yb(μ‐Cl)(μ3‐O)Yb(Cl)N(SiMe3)2Li(thf)4]2 (1) or a novel dinuclear ytterbium complex [η5:η5‐(CH3)2Si(C9H6)2Yb]2(μ‐Cl)(μ‐O)Li(thf)2 (2), respectively. Treatment of [(Me3Si)2N]3Yb(μ‐Cl)Li(thf)3 with (CH2)2(C9H6SiMe3)2 (3) or Me2Si(C9H7)2 under different conditions produced ytterbium(II) complexes [η5:η5‐(CH2)2(C9H5SiMe3)2]Yb(thf)2·(C6H14)0.5 (4) and [η5:η5‐(CH2)2(C9H5SiMe3)2]Yb·dme (5) or [η5:η5‐(CH3)2Si(C9H6)2]Yb·tmeda (6), respectively. Interaction of the ytterbium(III) amide [η5:η5‐(CH2)2(C9H6)2]YbN(SiMe3)2 with excess tmeda afforded the ytterbium(II) complex [η5:η5‐(CH2)2(C9H6)2]Yb·tmeda (7). All the compounds were fully characterized by spectroscopic methods and elemental analyses. Complexes 1, 2, and 4 were additionally characterized by single‐crystal X‐ray diffraction analyses. The solvents and temperature effects on the reaction are discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
New Aspects for Modeling Supramolecular Interactions in Vanadium Haloperoxidases: β‐Cyclodextrin Inclusion Compounds of cis‐Dioxovanadium(V) Complexes
Authors: Lippold Ines , Görls Helmar , Plass Winfried
Published: March 2007

The reaction of potassium vanadate and the hydrazone ligand derived from Schiff base condensation of salicylaldehyde and biphenyl‐4‐carboxylic acid hydrazide (H2salhybiph) in the presence of β‐cyclodextrin (β‐CD) in water yields the 1:1 inclusion compound K[VO2(salhybiph)@ β‐CD]. The characterization in solution confirmed the integrity of the inclusion compound in different polar solvents such as DMSO and water. The inclusion compound crystallizes with additional water molecules in the triclinic space group P1. The supramolecular aggregation of the inclusion compound in the solid state is established through hydrogen bonding interactions between adjacent β‐CD hosts and the π–π stacking ability of the ligand side chain of the guest complexes. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Quantitative analysis of thiols in consumer products on a microfluidic CE chip with fluorescence detection
Authors: Revermann Tobias , Götz Sebastian , Karst Uwe
Published: March 2007

A microchip CE‐based method for the quantification of the thiols mercaptoethanoic acid (MAA) and 2‐mercaptopropionic acid (2‐MPA) in depilatory cream and cold wave lotions was developed. The thiols were first derivatized with the fluorogenic reagent ammonium‐7‐fluorobenzo‐2‐oxa‐1,3‐diazole‐4‐sulfonate (SBD‐F). The derivatives were separated within only 20 s by microchip CE and detected by their fluorescence. Conventional CE with diode array detection and LC with fluorescence detection were used for validation. The internal standard 3‐mercaptopropionic acid (3‐MPA) provided RSDs of multiple injections of only 4% or less for the MCE approach. LOD is 2 μM, LOQ 6 μM, and the linear range comprises nearly three decades of concentration starting at the LOQ.
Experimental verification of a wireless sensing and control system for structural control using MR dampers
Authors: Loh Chin‐Hsiung , Lynch Jerome P. , Lu Kung‐Chun , Wang Yang , Chang Chia‐Ming , Lin Pei‐Yang , Yeh Ting‐Hei
Published: March 2007

The performance aspects of a wireless ‘active’ sensor, including the reliability of the wireless communication channel for real‐time data delivery and its application to feedback structural control, are explored in this study. First, the control of magnetorheological (MR) dampers using wireless sensors is examined. Second, the application of the MR‐damper to actively control a half‐scale three‐storey steel building excited at its base by shaking table is studied using a wireless control system assembled from wireless active sensors. With an MR damper installed on each floor (three dampers total), structural responses during seismic excitation are measured by the system's wireless active sensors and wirelessly communicated to each other; upon receipt of response data, the wireless sensor interfaced to each MR damper calculates a desired control action using an LQG controller implemented in the wireless sensor's computational core. In this system, the wireless active sensor is responsible for the reception of response data, determination of optimal control forces, and the issuing of command signals to the MR damper. Various control solutions are formulated in this study and embedded in the wireless control system including centralized and decentralized control algorithms. Copyright © 2007 John Wiley & Sons, Ltd.
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
Authors: Gront Dominik , Kmiecik Sebastian , Kolinski Andrzej
Published: March 2007

In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the α carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near‐native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Can an OH radical form a strong hydrogen bond? A theoretical comparison with H2O
Authors: Lai Chin‐Hung , Chou Pi‐Tai
Published: March 2007

In this study, we apply UCCSD/6‐31++G** to investigate the ability of an OH radical acting as a hydrogen bond acceptor with HF, HCl, and H2O (HO…HX; XF, Cl, OH) or as a hydrogen bond donor with H2O and H2S (OH…XH2; XO and S). We also replace OH with H2O and make a fair comparison between them. Additionally, the counterpoise method (CP) has been used to examine the effect of basis set superposition error (BSSE). Our results reveal that OH is a stronger hydrogen bond donor but a weaker hydrogen bond acceptor than H2O. This conclusion is independent of the correction for BSSE and can be rationalized by the NBO analysis, the results of which indicate that OH radical has a lowernOand σ*O–Hin energy than that of H2O. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods
Authors: Swart Marcel , Solà Miquel , Bickelhaupt F. Matthias
Published: March 2007

We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (SN2) reactions involving, amongst others, nucleophilic attack at carbon, nitrogen, silicon, and sulfur. In particular, we investigate the ability of the local density approximation (LDA), generalized gradient approximation (GGA), meta‐GGA as well as hybrid DFT to reproduce high‐level coupled cluster (CCSD(T)) benchmarks that are close to the basis set limit. The most accurate GGA, meta‐GGA, and hybrid functionals yield mean absolute deviations of about 2 kcal/mol relative to the coupled cluster data, for reactant complexation, central barriers, overall barriers as well as reaction energies. For the three nonlocal DFT classes, the best functionals are found to be OPBE (GGA), OLAP3 (meta‐GGA), and mPBE0KCIS (hybrid DFT). The popular B3LYP functional is not bad but performs significantly worse than the best GGA functionals. Furthermore, we have compared the geometries from several density functionals with the reference CCSD(T) data. The same GGA functionals that perform best for the energies (OPBE, OLYP), also perform best for the geometries with average absolute deviations in bond lengths of 0.06 Å and 0.6°, even better than the best meta‐GGA and hybrid functionals. In view of the reduced computational effort of GGAs with respect to meta‐GGAs and hybrid functionals, let alone coupled cluster, we recommend the use of accurate GGAs such as OPBE or OLYP for the study of SN2 reactions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution
Authors: Fatmi M. Qaiser , Hofer Thomas S. , Randolf Bernhard R. , Rode Bernd M.
Published: March 2007

Structural and dynamical properties of the TiO2+ ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent–solvent interactions. Both first and second hydration shell have been treated at Hartree‐Fock (HF) quantum mechanical level. A TiO bond distance of 1.5 Å was observed for the [TiO]2+ ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 Å and 2.1 Å, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO2+ hydrate can be characterized as [(H2O)0.7(H2O)(H2O)ax]2+. The second shell consists in average of 12 water molecules located at a mean distance of 4.4 Å. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO2+ ion in aqueous solution. For the dynamics of the TiO2+ ion, different sets of dynamical parameters such as Ti=O, TiOeq, and TiOax stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine
Authors: Quapp Wolfgang
Published: March 2007

We report a new, high‐dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one‐dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C7 ax → C5, some TSs of the enantiomerisation of C7 ax from L‐form to quasi‐D‐form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly α‐helix in the Ac(Ala)15NHMe polyalanine (all at the quantum mechanical level B3LYP/6‐31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some α‐ or 310‐hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Vertical excitation energies for ribose and deoxyribose nucleosides
Authors: So Remmick , Alavi Saman
Published: March 2007

Vertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time‐dependent density functional theory (TDDFT) method at the B3LYP/6‐311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug‐cc‐pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest nπ* and ππ* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low‐energy nπ* and πσ* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low‐lying excited state transitions of the binding to phosphate groups at the 5′‐ and 3′,5′‐hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de‐excitation dynamics of nucleic acids are discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.
Clinical MR imaging of degenerative spinal disease: Pulse sequences, gradient‐echo techniques, and contrast agents
Authors: Ross Jeffrey S. , Tkach Jean , VanDyke Carolyn , Modic Michael T.
Published: March 2007

DEGENERATION OF THE INTERVERTEBRAL disk is a ubiquitous process, seen at autopsy in 97% of adults by age 49 years (1). Low back pain is the most expensive health care problem in patients 20–50 years old, with $14 billion spent yearly on treatment and compensation (2). The greatest costs connected with low back pain occur in patients who have pain longer than 3 months and in those with recurrent pain episodes (3). Approximately 5.2 million people are disabled by back pain (3–5).

These statistics indicate that the accurate diagnosis of back pain disease is obviously of great importance. In the diagnosis of disk degeneration and its sequelae, magnetic resonance (MR) imaging has become a key ingredient. The utility of conventional two‐dimensional spin‐echo MR imaging of the spine has been firmly established for extradural disease (6–8). Gradient‐echo techniques have more recently been used to enhance the cerebrospinal fluid (CSF)‐extradural interface in the evaluation of degenerative disease (9–13). Some of the new imaging findings and concepts regarding the use of contrast material and three‐dimensional techniques in the evaluation of degenerative disease of the spine are reviewed.
MR imaging of the vocal tract during vowel production
Authors: Lakshminarayanan A. V. , Lee Sungbok , McCutcheon Martin J.
Published: March 2007

Modeling of vocal tract behavior during speech production requires accurate measurements of the entire vocal tract. To accomplish this, magnetic resonance (MR) imaging was performed on a 0.5‐T system with a custom‐made, double‐loop, wraparound coil. A midsagittal section of the region from the glottis to the lips was imaged during sustained production of five American English vowels. A gradient‐spoiled gradient‐echo sequence was used to achieve a 4‐second imaging time. Images showed clear profiles of the entire vocal tract and exhibited essential articulatory features of vowel production. It was possible to measure midsagittal widths at various points along the vocal tract with 1‐mm resolution. The measurements were used to construct a tube model for prediction of the acoustic output of the vocal tract. It is concluded that risk‐free MR imaging promises to be an important means of acquiring data for vocal tract modeling, with applications to speech pathology, linguistics, and artificial speech.
Modified iterative model based on data extrapolation method to reduce Gibbs ringing
Authors: Amartur Sundar , Haacke E. Mark
Published: March 2007

An iterative algorithm that involves image filtering and data replacement (as suggested by Constable and Henkelman) is investigated for reducing the Gibbs artifact in magnetic resonance imaging. The image is processed with an edge‐preserving filter to estimate the height and location of a set of model elements (ó functions or boxes) for generating the missing high‐frequency information. Filtering was performed in the complex image domain to account for discontinuities in phase as well as magnitude. The process is repeated after each data replacement to handle varying degrees of contrast. The convergence and signal‐to‐noise characteristics of the algorithm are investigated by means of simulated and clinical examples. The results indicate that the algorithm performs reasonably well in reducing ringing artifacts due to nearby edge contrast seen in most of the homogeneous, isointense regions. Nevertheless, it may generate some spurious thickening of structures that do not match the assumed step‐edge models.
Comparison of Fe‐HBED and Fe‐EHPG as hepatobiliary MR contrast agents
Authors: Hoener Betty‐Ann , Engelstad Barry L. , Ramos Emiliano C. , Macapinlac Homer A. , Price David C. , Johnson Thomas R. , White David L.
Published: March 2007

The authors studied the biodisposition and hepatobiliary transport of two potential magnetic resonance imaging contrast agents, the iron (III) chelates of N,N′‐bis(2‐hydroxybenzyl)ethylenediamine‐N,N′‐diacetic acid (HBED) and diastereomeric N,N′‐ethylenebis(2‐hydroxyphenylglycine) (EHPG). Fecal and urinary excretion (mean ± standard deviation), respectively, of FE‐59 over 7 days in rats given tracer doses of the contrast agents were 67% ± 2% and 22% ± 1% for Fe‐59‐HBED and 22% ± 2% and 26% ± 5% for Fe‐59‐EHPG. In bile duct‐cannulated rats given 0.05‐mmol/kg doses labeled with Fe‐59, 52% ± 8% of Fe‐59 from Fe‐59‐HBED but only 17% ± 3% of that from Fe‐59‐EHPG was excreted into the bile within 90 minutes. Bromosulfophtha‐lein, but not taurocbolate or oxyphenonium, was shown to compete with both agents for hepatobiliary transport. Enterohepatic recirculation of both agents was less than 1%.
Simultaneous acquisition of phase‐contrast angiograms and stationary‐tissue images with Hadamard encoding of flow‐induced phase shifts
Authors: Dumoulin Charles L. , Souza Steven P. , Darrow Robert D. , Pelc Norbert J. , Adams William J. , Ash Stephen A.
Published: March 2007

A technique for the simultaneous acquisition of three‐dimensional phase‐contrast angiograms and stationary‐tissue images is described. Hadamard multiplexed encoding of flow information permits image acquisition times that are a third shorter than those of previous phase‐contrast methods. The encoding scheme described also enables differentiation of flow‐induced phase shifts from phase shifts due to resonance offset conditions such as field inhomogeneities and chemical shift. Display strategies that combine this phase information with the flow image are described.
Encoding strategies for three‐direction phase‐contrast MR imaging of flow
Authors: Pelc Norbert J. , Bernstein Matt A. , Shimakawa Ann , Glover Gary H.
Published: March 2007

Three encoding strategies for the measurement of flow velocities in arbitrary directions with phase‐contrast magnetic resonance imaging are presented; their noise and dynamic range performance are compared by means of theoretical analysis and computer simulation. A six‐point measurement strategy is shown to be quite inefficient in terms of velocity variance per unit time. A simple four‐point method exhibits equal dynamic range; its noise depends on flow direction but on average is equal to that of the six‐point method. An alternate, balanced four‐point method has noise that is direction independent and has, depending on implementation, possibly lower noise levels. Either four‐point method is more efficient and is preferred over the six‐point approach.
MR image contrast at high field strength
Authors: Vinitski Simon , Griffey Richard H.
Published: March 2007

The T1 of soft tissues increases with magnetic field strength. Some tissue contrast may be diminished on high‐field‐strength magnetic resonance (MR) images when conventional TRs are used, because of altered T1 effects on the MR signals. This necessitates longer TRs in techniques that use long TRs, which prolongs the examination excessively. Behavior of macroscopic magnetization is governed by the Bloch equations. Therefore, T1 contributions to the MR signal can be modulated by means of both timing intervals and radio‐frequency pulses. The analytic solution to the Bloch equations allowed calculation of white matter/gray matter and gray matter/cerebrospinal fluid contrast in both spin‐echo and inversion‐recovery (IR) imaging. Rabbit brains (normal and tumor‐containing) were then imaged in vivo at 1.5 and 4.7 T. In addition, MR images of a human head were obtained at 4.O T. Experimental results supported the theoretical predictions that brain contrast on long TR spinecho or IR images increases with field strength. However, varying the excitation flip angle allowed optimization of the T1 contribution to the MR signals, improving image contrast and/or reducing examination time. Thus, the dependence of T1 on field strength determines the optimum choice of imaging techniques and parameters in a predictable fashion.
MR imaging of Hippel‐Lindau disease: Value of gadopentetate dimeglumine
Authors: Nelson David R. , Yuh William T. C. , Wazirim Mary H. , Ryals Tony J. , Sato Yutaka , Kao Simon C. S. , Hawes Donald R. , Williams Richard D.
Published: March 2007

Hippel‐Lindau disease is an autosomal dominant disorder characterized by tumors of the central nervous system and abdominal viscera. Frequent multisystem radiologic evaluation of persons at risk is desirable. Twenty‐seven patients with Hippel‐Lindau disease or a family history of the disease were examined with both unenhanced and gadopentetate dimeglumine‐enhanced magnetic resonance (MR) imaging to study the usefulness of the contrast medium in the evaluation of these patients. The MR studies were correlated with computed tomographic (CT) scans in seven patients and cerebral angiograms in five. Twelve patients had hemangioblastomas in the brain, and eight of these patients also had spinal cord lesions (most were multiple), well demonstrated with gadopentetate dimeglumine. Contrast‐enhanced MR imaging enabled detection of more central nervous system lesions and provided better delineation than unenhanced MR imaging, CT, or angiography. In addition, four patients with multiple renal cysts seen on CT scans and unenhanced MR images had enhancing lesions that were later proved to be renal cell carcinoma at angiography and/or surgery. Four patients had cystic lesions in the pancreas that did not enhance and were later proved to be pancreatic cysts. The authors conclude that gadopentetate dimeglumine‐enhanced MR imaging appears to be a useful method for evaluating and following up patients with Hippel‐Lindau disease.
Assessing response to therapy of spinal metastases with gadolinium‐enhanced MR imaging
Authors: Sugimura Kazuro , Kajitani Akiko , Okizuka Hiromi , Sugihara Masaki , Mizutani Masami , Ishida Tetsuya
Published: March 2007

The utility of gadolinium‐enhanced magnetic resonance (MR) imaging in assessing the response of spinal metastases to therapy was evaluated. Fifteen patients (62 affected vertebral bodies) with spinal metastases were evaluated with gadopentetate dimeglumineenhanced imaging before and after irradiation or chemotherapy. Signal intensities of the lesions and of adjacent normal vertebral bodies were compared. Before therapy, metastatic foci enhanced significantly more than did normal vertebral bodies. After therapy, the lesions were divided into 37 responding lesions (group 1) and 25 nonresponding lesions (group 2). In group 1, lesion enhancement diminished considerably and the patients with these lesions remained clinically asymptomatic for 2–6 months. In group 2, lesion enhancement did not diminish much, and the difference between the groups was significant. Gadolinium‐enhanced MR imaging may thus be a useful method for assessing the effectiveness of therapy for spinal me. tastases.
TE interleaving: New multisection imaging technique
Authors: Bishop Jonathan E. , Plewes Donald B.
Published: March 2007

A new pulse sequence that increases the number of sections that can be acquired with a T2‐weighted multisection imaging prescription is presented. The sequence achieves a higher efficiency in section acquisition per unit time by interleaving excitation and data collection for up to three separate sections during the long TE (⩾ 80 msec) of a T2‐weighted spin‐echo pulse sequence. The necessary modifications of the section‐select and readout gradient waveforms for the implementation of TE‐interleaved (TEI) sequences, with and without flow compensation, are described. Secondary‐ and stimulated‐echo artifacts are present on some TEI images, but these can be controlled with appropriate spoiler gradients. The signal‐to‐noise ratio for contiguous sections is slightly reduced compared with that of a standard multisection pulse sequence. These observations indicate that the effects of radio‐frequency section interference are enhanced by the TEI sequence.
MR imaging of poststenotic flow phenomena: Experimental studies
Authors: Krug Barbara , Kugel Harald , Friedmann Gerd , Bunke Juergen , van Dijk Peter , Schmidt Rainer , Hirche Hans Juergen
Published: March 2007

Poststenotic flow patterns were analyzed in a flow phantom with a 1.5‐T magnetic resonance (MR) imager, with use of different MR imaging and MR angiographic pulse sequences. Spin‐echo, fast field‐echo, two‐dimensional inflow (multiple single‐section technique), and flow‐adjusted‐gradient sequences were applied. For the spin‐echo sequences, modulus and phase images were reconstructed from each data set. The length of the region of poststenotic changes in signal amplitude and phase measured at a constant flow rate increased with stenosis grade. Likewise, the length of the region of poststenotic changes measured at a constant stenosis grade increased with flow rate. Moreover, the results depended on the alignment of the flow direction with the readout gradient. Comparison of modulus and phase images allowed discrimination of turbulent and nonturbulent flow, which yields additional information on stenosis grade in clinical MR angiography.
Theoretical aspects of motion sensitivity and compensation in echo‐planar imaging
Authors: Duerk Jeffrey L. , Simonetti Orlando P.
Published: March 2007

Magnetic resonance (MR) imaging can be performed on or below the time scale of most anatomic motion via echo‐planar imaging (EPI) techniques and their derivatives. The goal is to image rapidly and reduce artifacts that typically result from view‐to‐view changes in the spatial distribution of spins due to motion. However, the required time‐dependent magnetic field gradient waveforms remain sensitive to the dephasing effects of motion. Sources of motion artifact are simulated for spins moving along the imaging axes and are shown to be an important source of reduced image quality in EPI. A novel method of EPI is proposed that (a) refocuses single or multiple derivatives of motion at all echoes and (b) prevents accumulation of velocity (or higher derivative)‐induced dephasing along the phase‐encoding axis by moment nulling all phase‐encoding‐step waveforms about a single instant of time. Theoretical EPI sequences with considerable reductions in ghosts, blurring, and signal loss due to motion sensitivity are produced and compared with other EPI methods. Their time efficiency is presented as a function of available (relative) gradient strength for a variety of sequence waveforms.
MR imaging of normal rat brain at 0.35 T and correlated histology
Authors: Fiel Robert J. , Alletto James J. , Severin Charles M. , Nickerson Peter A. , Acara Margaret A. , Pentney Roberta J.
Published: March 2007

A custom‐built small‐animal transceiver was used for in vivo imaging of normal rat brain at 0.35 T, with the objective of identifying anatomic components by comparison of images with corresponding histologic sections. The cerebrum, cerebellum, brain stem, ventricles, hippocampus, and subarachnoid space were identified and cerebrospinal fluid (CSF) was differentiated from gray matter and white matter on coronal and transaxial magnetic resonance (MR) images. These images compare favorably with those obtained by others at higher field strengths in regard to delineating major neuroanatomic structures. It is concluded that this technique will be useful for investigating smallanimal models of human neurologic disease involving morphologic and morphometric changes in gray matter, white matter, and CSF‐filled spaces.
Endorectal surface coil MR imaging of prostatic carcinoma with the inversion‐recovery sequence
Authors: Parivar Farhad , Rajanayagam Vasanthan , Waluch Victor , Eto Ross T. , Jones Lawrence W. , Ross Brian D.
Published: March 2007

The value of inversion‐recovery (IR) sequences in the diagnosis and staging of prostatic carcinoma with magnetic resonance (MR) imaging was studied. Twenty‐six patients with carcinoma of the prostate were imaged at 1.5 T with an endorectal surface coil and with a variety of IR sequences and a set of spin‐echo (SE) sequences for comparison. Ex vivo prostate specimens were imaged again at the same field strength. The two images were correlated with histologic sections. Cancer was identified with MR imaging in 96% of patients. Of the tumors more than 4 mm in diameter, 87% were identified on T2‐weighted SE images, whereas only 26% were identified on IR images. However, IR images may be more useful in local staging of carcinoma. Gross capsular infiltration was present in only two patients; however, it was detectable (and excluded in five other patients) by means of IR images. It was not detectable on SE images. The high quality of images obtained with the endorectal coil was confirmed. The authors conclude that addition of the IR sequence to MR imaging with the endorectal coil may improve the usefulness of this examination.
Quantitation of structural distortion of the cervical neural foramina in gradient‐echo MR imaging
Authors: Tien Robert D. , Buxton Richard B. , Schwaighofer Bernard W. , Chu Pauline K.
Published: March 2007

Quantitative errors (due to magnetic susceptibility artifacts) in the measurement of the cervical spinal neural foramina with fast gradient‐echo (GRE) magnetic resonance imaging were assessed. Cylindric phantoms of different materials were used to demonstrate the nature of magnetic susceptibility artifacts, emphasizing the dependence of the artifact on tissue geometry. Neural foramina diameters measured on thin, sagittal GRE and spin‐echo (SE) images through the neural foramina of a fresh human cervical spine specimen were then compared with direct measurements with calipers. The GRE images showed more apparent narrowing than did the SE images. The absolute distortion of seven neural foramina was rather constant (less than two pixels) on the GRE images; therefore, the relative distortion was inversely proportional to the size of the neural foramen, ranging up to 10% in the upper cervical region at a short TE. The absolute and relative distortion increased as TE increased. At a constant TE, the structural distortion did not change with different TRs or flip angles. The shortest possible TE is recommended in evaluation of the cervical spine.
T2‐weighted three‐dimensional MP‐RAGE MR imaging
Authors: Mugler John P. , Spraggins Thomas A. , Brookeman James R.
Published: March 2007

The application of three‐dimensional (3D) magnetization‐prepared rapid‐gradientecho (MP‐RAGE) imaging to the acquisition of T2‐weighted 3D data sets has been investigated, with a 90x°–180y°−90−x° pulse set (driven equilibrium) for the T2 contrast preparation. A theoretical model was used to study the contrast behavior of brain tissue. The effects of radiofrequency and static‐field inhomogeneities and eddy currents on the T2 contrast preparation and the effects of eddy currents on the gradientecho acquisition resulted in blurring and intensity banding artifacts. With a multistep gradient preparation, these artifacts could be suppressed. With further development, this technique may yield a clinically practical method for obtaining T2‐weighted 3D data sets of relatively large volumes (eg, the whole head) suitable for multiplanar reformatting.