bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SAAP force field. A simple approach to a new all‐atom protein force field by using single amino acid potential (SAAP) functions in various solvents*
Authors: Iwaoka Michio , Tomoda Shuji 
Published: June 2003

AbstractA simple strategy to compose a new all‐atom protein force field (named as the SAAP force field), which utilizes the single amino acid potential (SAAP) functions obtained in various solvents by ab initio molecular orbital calculation applying the isodensity polarizable continuum model (IPCM), is presented. We considered that the total energy function of a protein force field (ETOTAL) is divided into three components; a single amino acid potential term (ESAAP), an interamino acid nonbonded interaction term (EINTER), and a miscellaneous term (EOTHERS), which is ignored (or considered to be constant) at the current version of the force field. The EINTER term consists of electrostatic interactions (EES') and van der Waals interactions (ELJ'). Despite simplicity, the SAAP force field implicitly involves the correlation among individual terms of the Lifson's potential function within a single amino acid unit and can treat solvent effects unambiguously by choosing the SAAP function in an appropriate solvent and the dielectric constant (D) of medium. Application of the SAAP force field to the Monte Carlo simulation of ForAla2NH2 in vacuo reasonably reproduced the results of the extensive conformational search by ab initio molecular orbital calculation. In addition, the preliminary Monte Carlo simulations for ForGly10NH2 and ForAla10NH2 showed reversible transitions from the extended to the pseudosecondary structures in water (D = 78.39) as well as in ether (D = 4.335). The result suggested that the new approach is efficient for fast modeling of protein structures in various environments. Decomposition analysis of the total energy function (ETOTAL) by using the SAAP force field suggested that conformational propensities of single amino acids (i.e., the ESAAP term) may play definitive roles on the topologies of protein secondary structures. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1192–1200, 2003
Energy decomposition in molecular complexes: Implications for the treatment of polarization in molecular simulations
Authors: Curutchet Carles , Bofill Josep María , Hernández Begoña , Orozco Modesto , Luque F. Javier 
Published: June 2003

AbstractThis study examines the contribution of electrostatic and polarization to the interaction energy in a variety of molecular complexes. The results obtained from the Kitaura–Morokuma (KM) energy decomposition analysis at the HF/6‐31G(d) level indicate that, for intermolecular distances around the equilibrium geometries, the polarization energy can be determined as the addition of the polarization energies of interacting blocks, as the mixed polarization term is typically negligible. Comparison of KM and QM/MM results shows that the electrostatic energy determined in the KM method is underestimated (in absolute value) by QM/MM methods. The reason of such underestimation can be attributed to the simplified representation of treating the interaction between overlapping charge distribution by the interaction of a QM molecule with a set of point charges. Nevertheless, the polarization energies calculated by KM and QM/MM methods are in close agreement. Finally, a consistent, automated strategy to derive charge distributions that include implicitly polarization effects in pairwise, additive force fields is presented. The strategy relies in the simultaneous fitting of electrostatic and polarization energies computed by placing a suitable perturbing particle at selected points around the molecule. The suitability of these charges to describe molecular interactions is discussed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1263–1275, 2003
Performance of hybrid methods for large‐scale unconstrained optimization as applied to models of proteins
Authors: Das B. , Meirovitch H. , Navon I. M. 
Published: June 2003

AbstractEnergy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large‐scale unconstrained optimization that interlace iterations of the limited‐memory BFGS method (L‐BFGS) and the Hessian‐free Newton method (Computat Opt Appl 2002, 21, 143–154). We test the performance of this approach as compared to those of the L‐BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all‐atom AMBER force field with a dielectric constant ϵ = 1 and a distance‐dependent dielectric function ϵ = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from ϵ = 2r to ϵ = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial‐and‐error calculations for each problem. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1222–1231, 2003
Many‐body effects on structure and dynamics of aqueous ionic solutions
Authors: Loeffler Hannes H. 
Published: June 2003

AbstractWe performed several molecular dynamic studies of metal cations in aqueous solution. The alkali metal ion Li+ and the first‐row transition metal ion Mn2+ have been chosen as model systems. Two different three‐body corrections are proposed to mimic the crucial many‐body effects of electrolyte solutions. The correction function, which includes attractive features of the three‐body potential, performs considerably better than the purely repulsive interaction function. Structural and dynamic results show that this simple enhancement is able to satisfactorily reproduce experimental and higher‐level results for the first hydration shell. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1232–1239, 2003
Assessment of the OLYP and O3LYP density functionals for first‐row transition metals
Authors: Baker Jon , Pulay Peter 
Published: June 2003

AbstractWe have investigated the performance of the OLYP and O3LYP density functionals for predicting atomic excitation energies and ionization potentials, and bond dissociation energies, geometries, and vibrational frequencies for selected first‐row transition metal compounds, including hydrides (MH) and singly charged methylene and methyl cations. The OLYP and O3LYP functionals are similar to the well‐known BLYP and B3LYP functionals, respectively, but use a new optimized exchange functional (OPTX) developed by Handy and Cohen (Mol Phys 2001, 99, 403) in place of the standard B88 exchange. A previous study by us on organic reactions (J Chem Phys 2002, 117, 1331) indicated that both OLYP and O3LYP gave results for heats of reaction and barrier heights that were overall superior to those using the popular B3LYP functional. For transition metals, however, although OLYP is overall superior to BLYP for molecular calculations, it is inferior to B3LYP. O3LYP provides results for molecules of about the same quality as B3LYP. For atomic excitation and 4s ionization energies, unless relativistic effects are included, OLYP and O3LYP are clearly worse than both BLYP and B3LYP. There is thus no real incentive to use either OLYP or O3LYP in place of B3LYP for calculations involving first‐row transition metals. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1184–1191, 2003
A computational study of the LiH dimer
Authors: McDowell Sean A. C. 
Published: June 2003

AbstractA theoretical study of the properties of the linear LiH dimer was undertaken. In this dimer, an unusual type of hydrogen bonding (termed “inverse” hydrogen bonding by some authors), which involves the hydrogen bonded molecule acting as an electron donor (rather than as a proton donor), is exhibited. The optimized geometry, dipole moment, interaction energy, atomic charges, harmonic vibrational frequencies, and frequency shifts for the dimer are computed at the SCF, MP2, and QCISD levels of theory using mainly a 6‐31++G(d,p) basis set. We also examined the relative stability of the mono‐deuterated isotopomers of linear (LiH)2, i.e., LiH … LiD and LiD … LiH. Analysis of the normal vibrational modes, changes in the partial atomic charges, and changes in the vibrational frequencies of LiH on complexation were used to gain insight into the bonding and properties of the linear LiH dimer and its isotopomers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1201–1207, 2003
A QM–MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems
Authors: Loferer Markus J. , Loeffler Hannes H. , Liedl Klaus R. 
Published: June 2003

AbstractThe implementation of a hybrid QM–MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree–Fock and density functional methods and varying QM–MM boundaries. Also, the computationally efficient RI‐J method has been examined for use in QM–MM applications. A B12 cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM–MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1240–1249, 2003
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N‐formyl‐serinamide, a model for polar side‐chain containing peptides
Authors: Perczel András , Füzéry Anna K. , Császár Attila G. 
Published: June 2003

AbstractKnowledge of chemical shift–structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For‐L‐Ser‐NH2, was studied. Using the GIAO‐RHF/6‐31+G(d) and GIAO‐RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen (1HN,1Hα,1Hβ1,1Hβ2), carbon (13Cα,13Cβ,13C′) and nitrogen (15N) atoms have been computed for all 44 stable conformers of For‐L‐Ser‐NH2. An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (ω0, ϕ, ψ, ω1, χ,1and χ2). At both levels of theory a linear correlation can be observed between1Hα/ϕ,13Cα/ϕ, and13Cα/ψ. These results indicate that the backbone and side‐chain structures of For‐L‐Ser‐NH2have a strong influence on its chemical shifts. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1157–1171, 2003
A MCSCF method for ground and excited states based on full optimizations of successive Jacobi rotations
Authors: Ivanic Joseph , Ruedenberg Klaus 
Published: June 2003

AbstractA new multiconfigurational self‐consistent field (MCSCF) method based on successive optimizations of Jacobi rotation angles is presented. For given one‐ and two‐particle density matrices and an initial set of corresponding integrals, a technique is developed for the determination of a Jacobi angle for the mixing of two orbitals, such that the exact energy, written as a function of the angle, is fully minimized. Determination of the energy‐minimizing orbitals for given density matrices is accomplished by successive optimization and updating of Jacobi angles and integrals. The total MCSCF energy is minimized by alternating between CI and orbital optimization steps. Efficiency is realized by optimizing CI and orbital vectors quasi‐simultaneously by not fully optimizing each in each improvement step. On the basis of the Jacobi‐rotation based approach, a novel MCSCF procedure is formulated for excited states, which avoids certain shortcomings of traditional excited‐state MCSCF methods. Applications to specific systems show the practicability of the developed methods. Published 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1250–1262, 2003
Synthesis of tritium‐labelled 3′‐azido‐3′‐deoxythymidine
Authors: Sidorov G.V. , Zverkov Yu.B. , Myasoedov N.F. , Jasko M.V. , Skoblov Yu.S. 
Published: June 2003

AbstractNew approaches to the synthesis of 3′‐azido‐3′‐deoxythymidine labelled with tritium in the heterocyclic base have been developed. With this aim, enzymatic transribosylation with [3H]thymine using the enzyme preparation from rat liver and a three‐step chemical synthesis with use of the tritium labelled precursor were studies. The enzyme preparation did not catalyse the transfer of the 3′‐azido‐3′‐deoxyribosyl fragment to the [3H]thymine residue. 5′‐O‐Benzoyl‐2,3′‐anhydrothymidine was taken as a precursor for the tritium labelling by the chemical methods. The resulting [3H]3′‐azido‐3′‐deoxythymidine was obtained with a specific radioactivity of 18.3 Ci/mmol, the tritium is located in the C‐6 position of the thymine residue. Copyright © 2003 John Wiley & Sons, Ltd.
High‐resolution three‐dimensional MR angiography of rodent tumors: Morphologic characterization of intratumoral vasculature
Authors: Fink Christian , Kiessling Fabian , Bock Michael , Lichy Matthias Philipp , Misselwitz Bernd , Peschke Peter , Fusenig Norbert E. , Grobholz Rainer , Delorme Stefan 
Published: June 2003

AbstractPurposeTo evaluate high‐resolution three‐dimensional MR angiography (MRA) for the visualization and morphologic characterization of intratumoral vasculature.Materials and MethodsTwo subcutaneous rodent tumor models (human skin carcinoma HaCaT‐ras‐A‐5RT3 grown in nude mice and rat prostate carcinoma R3327‐AT1 grown in Copenhagen rats) were examined with a clinical 1.5 T MR‐system. For MRA a dedicated high‐resolution three‐dimensional gradient echo pulse sequence with a voxel size of 166 × 206 × 320 μm3 was performed after injection of Gadomer‐17. The image analysis included a correlation of intratumoral vessels with histology. Signal intensity measurements were performed in the vena cava, the tumor underlying muscle, and in various regions of the tumor. Signal‐to‐noise‐ratios (SNR) and contrast‐to‐noise‐ratios (CNR) were calculated from this measurement.ResultsHigh‐resolution MRA allowed a clear distinction of intratumoral blood vessels. The mouse tumor model tended to be strongly vascularized with several intratumoral blood vessels clearly displayed by MRA. When correlated with histology, these intratumoral blood vessels had a size in the range of 300 to 400 μm. In contrast, rat tumors had only sparse capillary intratumoral blood vessels that could only be demonstrated by histology. In both tumor models, dilated blood vessels were observed in the subcutaneous tissue near the tumor. In general, areas with a strong contrast enhancement correlated with viable, well vascularized tumor regions, whereas non‐enhancing tumor areas correlated with tumor necrosis or hypoxic areas.ConclusionHigh‐resolution three‐dimensional MRA allows the visualization of intratumoral vasculature in rodent models. With minimal hardware and software modifications, high‐resolution MRA could be performed on a clinical 1.5 T MRI scanner. Morphologic characterization of intratumoral blood vessels could add important insights into the process of tumor angiogenesis. J. Magn. Reson. Imaging 2003;18:59–65. © 2003 Wiley‐Liss, Inc.
Accelerated dynamic MR imaging with a parallel imaging technique for hypervascular hepatocellular carcinomas: Usefulness of a test bolus in examination and subtraction imaging
Authors: Takahashi Nobuyuki , Yoshioka Hiroshi , Yamaguchi Masayuki , Saida Yukihisa , Itai Yuji 
Published: June 2003

AbstractPurposeTo assess the impact of the accelerated dynamic MR imaging (ADMRI) approach using parallel imaging for detecting hypervascular hepatocellular carcinomas (HCCs) and to evaluate the usefulness of a test bolus in examination and subtraction imaging in this setting.Materials and MethodsThirty patients with 135 HCCs underwent ADMRI using a two‐dimensional gradient‐recalled echo sequence with parallel imaging. Seventeen patients were evaluated without a test bolus and 13 patients with a test bolus. The detectability of HCCs was calculated between the groups with and without a test bolus. ADMRI was evaluated regarding the signal‐to‐noise ratio (SNR) of the lesion and the liver, the contrast‐to‐noise ratio (CNR) of the lesion vs. the liver, and the feasibility of subtraction images.ResultsADMRI with and without a test bolus had almost equal sensitivity (92.5% and 92.6%). No significant difference was seen in the SNR of lesions and the CNR of lesions vs. livers between both groups. With a test bolus, ADMRI could depict the peak enhancement of nodules on the 2nd or 3rd dynamic phases and optimized the timing of peak lesion enhancement. Subtraction images could be obtained regarding minimal slice misregistration.ConclusionADMRI had high detectability of HCCs with and without a test bolus. J. Magn. Reson. Imaging 2003;18:80–89. © 2003 Wiley‐Liss, Inc.
Imaging of the articular cartilage in osteoarthritis of the knee joint: 3D spatial‐spectral spoiled gradient‐echo vs. fat‐suppressed 3D spoiled gradient–echo MR imaging
Authors: Yoshioka Hiroshi , Alley Marcus , Steines Daniel , Stevens Kathryn , Rubesova Erika , Genovese Mark , Dillingham Michael F. , Lang Philipp 
Published: June 2003

AbstractPurposeTo compare three‐dimensional (3D) spatial‐spectral (SS) spoiled gradient‐recalled acquisition in the steady state (SPGR) imaging with fat‐suppressed 3D SPGR sequences in MR imaging of articular cartilage of the knee joint in patients with osteoarthritis.Materials and MethodsMR images of six patients with osteoarthritis of the knee were prospectively examined with a 1.5T MR scanner. For quantitative analyses, the signal‐to‐noise ratios, contrast‐to‐noise ratios, and contrast of cartilage and adjacent structures including meniscus, synovial fluid, muscle, fat tissue, and bone marrow were measured.ResultsIn patients with osteoarthritis, 3DSS‐SPGR images demonstrated higher spatial resolution and higher mean signal‐to‐noise (S/N) ratios (cartilage, 24.9; synovial fluid, 12.3; muscle, 20.7; meniscus, 21.6), with shorter acquisition times (7 minutes 20 seconds), when compared to fat‐suppressed 3D SPGR images (cartilage, 22.3; synovial fluid, 10.8; muscle, 16.7; meniscus, 13.4).Conclusion3DSS‐SPGR imaging is a promising method for evaluating cartilage pathology in patients with osteoarthritis of the knee and has the potential to replace fat‐suppressed 3D SPGR imaging. J. Magn. Reson. Imaging 2003;18:66–71. © 2003 Wiley‐Liss, Inc.
An inductively‐coupled, detachable receiver coil system for use with magnetic resonance compatible endoscopes
Authors: Gilderdale David J. , Williams Andreanna D. , Dave Umakant , deSouza Nandita M. 
Published: June 2003

AbstractPurposeTo construct an inductively‐coupled receiver coil system for use with a magnetic resonance (MR) compatible endoscope, and to evaluate its use in a pilot group of patients with esophageal cancer.Materials and MethodsAn inductively‐coupled coil system, comprising a saddle geometry cylindrical receiver coil fitted as a sleeve around the endoscope tip and a pick‐up coil housed within a channel of an MR‐compatible endoscope, was designed and developed for use at 0.5 T. Twenty‐three patients with esophageal cancer were recruited for MR endoscopy. In 17 cases, the endoscopic coil system was used in conjunction with an external surface coil in order to obtain information from the surrounding mediastinum. The examination took 40–50 minutes.ResultsMR imaging using the inductively‐coupled endoscopic coil was successful in 21 cases (one failed intubation and one artifact from unrelated external source). Image artifact was largely due to respiration and global patient motion in sedated individuals undergoing endoscopy.ConclusionInductively‐coupled coil systems may be used with endoscopes to allow improved safety through increased patient‐system isolation and detachability of coils and electronics for repair or replacement with coils tuned for different frequencies. J. Magn. Reson. Imaging 2003;18:131–135. © 2003 Wiley‐Liss, Inc.
The need for phase‐encoding flow compensation in high‐resolution intracranial magnetic resonance angiography
Authors: Parker Dennis L. , Goodrich K. Craig , Roberts John A. , Chapman Brian E. , Jeong Eun‐Kee , Kim Seong‐Eun , Tsuruda Jay S. , Katzman Gregory L. 
Published: June 2003

AbstractPurposeTo demonstrate that the time delay between phase and frequency encoding and the presence of pulsatile blood flow in high‐resolution time‐of‐flight (TOF) imaging of the intracranial arteries (especially near the circle of Willis) can distort the appearance of blood vessels and result in a cross‐hatch—appearing artifact in surrounding tissue.Materials and MethodsTwo techniques to reduce the artifact, tri‐directional flow compensation (3DFC) and elliptical‐centric (EC) phase‐encoding order, are investigated in five volunteer studies.Results3DFC eliminates the pulsation‐related artifacts and the vessel distortion. A residual amplitude variation artifact is observed. EC phase encoding nearly eliminates the pulsatile motion‐related artifact, but it does not eliminate vessel distortion.ConclusionThe combination of 3DFC and EC phase encoding appears to provide the greatest artifact reduction in the five volunteer studies performed. J. Magn. Reson. Imaging 2003;18:121–127. © 2003 Wiley‐Liss, Inc.