bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunocytochemical detection of milk proteins in tracheal aspirates of ventilated infants: A pilot study
Authors: Miller Jamey , Colasurdo Giuseppe N. , Khan Amir M. , Jajoo Charu , Patel Tarak J. , Fan Leland L. , Elidemir Okan
Published: October 2002

In this study, we evaluated immunocytochemical staining for milk proteins (α‐lactalbumin and β‐lactoglobulin) in tracheal aspirates of mechanically ventilated infants, and assessed whether this staining technique supported a clinical diagnosis of aspiration in infants receiving orogastric feedings. All newborns requiring mechanical ventilation in the neonatal intensive care unit of a major tertiary care hospital were potential subjects for this study. Tracheal aspirates were obtained prior to the introduction of enteral feeding and at various time points thereafter in newborns requiring mechanical ventilation. Cells were obtained and processed for immunocytochemical staining of α‐lactalbumin and β‐lactoglobulin.

In total, 88 specimens recovered from 34 infants were adequate for staining. Alveolar macrophages recovered from most of the infants who were never fed (true negative controls) did not display immunoreactivity for milk proteins: 4/34 or 12% of infants' aspirates demonstrated presence of milk proteins before enteral feeding was commenced. Tracheal aspirates obtained from 12 infants after introduction of enteral feedings appeared to support clinical and radiological findings suggestive of aspiration events, with positive immunostaining on several occasions.

These observations support our work in a murine model and demonstrate that immunocytochemical staining of tracheal aspirates for milk proteins may enhance the ability to diagnose pulmonary aspiration. Further studies are needed to define the clinical significance of our findings and the effects of single and repeated aspiration events on respiratory status. Pediatr Pulmonol. 2002; 34:369–374. © 2002 Wiley‐Liss, Inc.
Role of the 14‐3‐3 C‐terminal loop in ligand interaction
Authors: Truong Amy B. , Masters Shane C. , Yang Hongzhu , Fu Haian
Published: October 2002

14‐3‐3 proteins are a family of conserved dimeric molecules that interact with a broad range of target proteins, most of which contain phosphoserine/threonine. The amphipathic groove of 14‐3‐3 is the main structural feature involved in mediating its associations. We have studied another domain of 14‐3‐3, the C‐terminal loop, to determine what role it plays in ligand interaction. A truncated form of 14‐3‐3ζ lacking this C‐terminal loop was generated and found to bind with higher affinity than the wild‐type 14‐3‐3ζ protein to the ligands Raf‐1 and Bad. Interestingly, the truncated 14‐3‐3ζ also showed increased association with the 14‐3‐3 binding‐deficient Bad/S136A mutant. Taken together, these data support a role for the C‐terminal loop as a general inhibitor of 14‐3‐3/ligand interactions. This may provide a mechanism by which inappropriate associations with 14‐3‐3 are prevented. Proteins 2002;49:321–325. © 2002 Wiley‐Liss, Inc.
MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading
Authors: Lu Long , Lu Hui , Skolnick Jeffrey
Published: October 2002

In this postgenomic era, the ability to identify protein–protein interactions on a genomic scale is very important to assist in the assignment of physiological function. Because of the increasing number of solved structures involving protein complexes, the time is ripe to extend threading to the prediction of quaternary structure. In this spirit, a multimeric threading approach has been developed. The approach is comprised of two phases. In the first phase, traditional threading on a single chain is applied to generate a set of potential structures for the query sequences. In particular, we use our recently developed threading algorithm, PROSPECTOR. Then, for those proteins whose template structures are part of a known complex, we rethread on both partners in the complex and now include a protein–protein interfacial energy. To perform this analysis, a database of multimeric protein structures has been constructed, the necessary interfacial pairwise potentials have been derived, and a set of empirical indicators to identify true multimers based on the threading Z‐score and the magnitude of the interfacial energy have been established. The algorithm has been tested on a benchmark set comprised of 40 homodimers, 15 heterodimers, and 69 monomers that were scanned against a protein library of 2478 structures that comprise a representative set of structures in the Protein Data Bank. Of these, the method correctly recognized and assigned 36 homodimers, 15 heterodimers, and 65 monomers. This protocol was applied to identify partners and assign quaternary structures of proteins found in the yeast database of interacting proteins. Our multimeric threading algorithm correctly predicts 144 interacting proteins, compared to the 56 (26) cases assigned by PSI‐BLAST using a (less) permissive E‐value of 1 (0.01). Next, all possible pairs of yeast proteins have been examined. Predictions (n = 2865) of protein–protein interactions are made; 1138 of these 2865 interactions have counterparts in the Database of Interacting Proteins. In contrast, PSI‐BLAST made 1781 predictions, and 1215 have counterparts in DIP. An estimation of the false‐negative rate for yeast‐predicted interactions has also been provided. Thus, a promising approach to help assist in the assignment of protein–protein interactions on a genomic scale has been developed. Proteins 2002;49:350–364. © 2002 Wiley‐Liss, Inc.
Investigating the ultrastructure of fibrous long spacing collagen by parallel atomic force and transmission electron microscopy
Authors: Lin Alvin C. , Goh M. Cynthia
Published: October 2002

The ultrastructure of fibrous long spacing (FLS) collagen fibrils has been investigated by performing both atomic force microscopy (AFM) and transmission electron microscopy (TEM) on exactly the same area of FLS collagen fibril samples. These FLS collagen fibrils were formed in vitro from type I collagen and α1‐acid glycoprotein (AAG) solutions. On the basis of the correlated AFM and TEM images obtained before and after negative staining, the periodic dark bands observed in TEM images along the longitudinal axis of the FLS collagen fibril correspond directly to periodic protrusions seen by AFM. This observation is in agreement with the original surmise made by Gross, Highberger, and Schmitt (Gross J, Highberger JH, Schmitt FO, Proc Natl Acad Sci USA 1954;40:679‐688) that the major repeating dark bands of FLS collagen fibrils observed under TEM are thick relative to the interband region. Although these results do not refute the idea of negative stain penetration into gap regions proposed by Hodge and Petruska (Petruska JA, Hodge AJ. Aspects of protein structure. Ramachandran GN, editor. New York: Academic Press; 1963. p. 289–300), there is no need to invoke the presence of gap regions to explain the periodic dark bands observed in TEM images of FLS collagen fibrils. Proteins 2002;49:378–384. © 2002 Wiley‐Liss, Inc.
Molten globule of bovine α‐lactalbumin at neutral pH induced by heat, trifluoroethanol, and oleic acid: A comparative analysis by circular dichroism spectroscopy and limited proteolysis
Authors: Polverino de Laureto Patrizia , Frare Erica , Gottardo Rossella , Fontana Angelo
Published: October 2002

The calcium‐depleted form of α‐lactalbumin (α‐LA) at neutral pH can be induced to adopt a partly folded state or molten globule upon moderate heating, by dissolving the protein in aqueous TFE or by adding oleic acid. This last folding variant of the protein, named HAMLET, can induce apoptosis in tumor cells. The aim of the present work was to unravel from circular dichroism (CD) measurements and proteolysis experiments structural features of the molten globule of apo‐α‐LA at neutral pH. CD spectra revealed that the molten globule of apo‐α‐LA can be obtained upon mild heating at 45°C, as well as at room temperature in the presence of 15% TFE or by adding to the protein solution 7.5 equivalents of oleic acid. Under these various conditions the far‐ and near‐UV CD spectra of apo‐α‐LA are essentially identical to those of the most studied molten globule of α‐LA at pH 2.0 (A‐state). Proteolysis of the 123‐residue chain of apo‐α‐LA by proteinase K at 4°C occurs slowly as an all‐or‐none process leading to small peptides only. At 37°C, proteinase K preferentially cleaves apo‐α‐LA at peptide bonds Ser34‐Gly35, Gln39‐Ala40, Gln43‐Asn44, Phe53‐Gln54, and Asn56‐Asn57. All these peptide bonds are located at level of the β‐subdomain of the protein (chain region 34–57). Similar sites of preferential cleavage have been observed with the TFE‐ and oleic acid‐induced molten globule of apo‐α‐LA. A protein species given by the N‐terminal fragment 1–34 linked via the four disulfide bridges to the C‐terminal fragment 54–123 or 57–123 can be isolated from the proteolytic mixture. The results of this study indicate that the same molten globule state of apo‐α‐LA can be obtained at neutral pH under mildly denaturing conditions, as indicated by using a classical spectroscopic technique such as CD and a simple biochemical approach as limited proteolysis. We conclude that the molten globule of α‐LA maintains a native‐like tertiary fold characterized by a rather well‐structured α‐domain and a disordered chain region encompassing the β‐subdomain 34–57 of the protein. Proteins 2002;49:385–397. © 2002 Wiley‐Liss, Inc.
Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix
Authors: Li Hao , Tang Chao , Wingreen Ned S.
Published: October 2002

We study the designability of all compact 3 × 3 × 3 and 6 × 6 lattice‐protein structures using the Miyazawa–Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e., sequences that have that structure as their unique lowest‐energy state. Previous studies of hydrophobic‐polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a two‐letter (HP) code in such studies. Here, we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix) and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model—and vice versa—with the associated sequences having enhanced thermodynamic stability. Proteins 2002;49:403–412. © 2002 Wiley‐Liss, Inc.
Treatment of melasma with Pycnogenol®
Authors: Ni Z. , Mu Y. , Gulati O.
Published: October 2002

Melasma (or chloasma) is a common disorder of cutaneous hyperpigmentation predominantly affecting sun‐exposed areas in women. The pathogenesis of melasma is not fully understood and treatments are frequently disappointing and often associated with side effects.

Pycnogenol® is a standardized extract of the bark of the French maritime pine (Pinus pinaster), a well‐known, potent antioxidant. Studies in vitro show that Pycnogenol® is several times more powerful than vitamin E and vitamin C. In addition, it recycles vitamin C, regenerates vitamin E and increases the endogenous antioxidant enzyme system. Pycnogenol® protects against ultraviolet (UV) radiation. Therefore its efficacy in the treatment of melasma was investigated.

Thirty women with melasma completed a 30‐day clinical trial in which they took one 25 mg tablet of Pycnogenol® with meals three times daily, i.e. 75 mg Pycnogenol® per day. These patients were evaluated clinically by parameters such as the melasma area index, pigmentary intensity index and by routine blood and urine tests.

After a 30‐day treatment, the average melasma area of the patients decreased by 25.86 ± 20.39 mm2 (p < 0.001) and the average pigmentary intensity decreased by 0.47 ± 0.51 unit (p < 0.001). The general effective rate was 80%. No side effect was observed. The results of the blood and urine test parameters at baseline and at day 30 were within the normal range. Moreover, several other associated symptoms such as fatigue, constipation, pains in the body and anxiety were also improved.

To conclude, Pycnogenol® was shown to be therapeutically effective and safe in patients suffering from melasma. Copyright © 2002 John Wiley & Sons, Ltd.
Action of  Rubus coreanus extract on systemic and local anaphylaxis
Authors: Shin Tae‐Yong , Kim Sang‐Hyun , Lee Eun‐Soon , Eom Dong‐Ok , Kim Hyung‐Min
Published: October 2002

The effect was investigated of the aqueous extract of Rubus coreanus Miq. (Rosaceae) fruits (RCAE) on systemic and local anaphylaxis. RCAE (0.01–1 g/kg) dose‐dependently inhibited systemic anaphylaxis induced by compound 48/80 in mice. RCAE (1 g/kg) also significantly inhibited local anaphylaxis activated by anti‐DNP IgE. Pretreatment with RCAE at the same concentration before systemic anaphylaxis reduced the plasma histamine levels in a dose‐dependent manner. RCAE (0.001–1 mg/mL) dose‐dependently inhibited the histamine release from rat peritoneal mast cells (RPMC) activated by compound 48/80 or anti‐DNP IgE. The level of cAMP in RPMC, when RCAE was added, significantly increased, compared with that of the normal control. Moreover, RCAE (0.01–1 mg/mL) had a significant inhibitory effect on anti‐DNP IgE‐induced tumour necrosis factor‐α production from RPMC. These results indicate that RCAE may possess antianaphylactic action. Copyright © 2002 John Wiley & Sons, Ltd.
Effect of the alcohol extract of the seeds of Mucuna pruriens on free radicals and oxidative stress in albino rats
Authors: Tripathi Yamini B. , Upadhyay Anil K.
Published: October 2002

In vitro and in vivo studies were made with an alcohol extract of the seeds of Mucuna pruriens (Fabaceae) to investigate its antioxidant property. In vitro studies were carried out in rat liver homogenate to investigate the chemical interaction of various phytochemicals with different species of free radicals. The effect was also checked on iron‐induced lipid peroxidation, oxidation of GSH content, and its interaction with hydroxyl and superoxide radicals. There was no change on the rate of aerial oxidation of GSH content but it significantly inhibited FeSO4 induced lipid peroxidation. It also inhibited the specific chemical reactions induced by superoxides and hydroxyl radicals. The removal of these species was through direct chemical interaction. An in vivo study on albino rats for 30 days showed no toxic effect up to a dose of 600 mg/kg body weight, on oral administration. There was no change in the level of TBA‐reactive substances, reduced glutathione content and SOD activity in the liver. The activity of serum GOT, GPT and alkaline phosphatase was also unchanged. Thus it could be concluded that the alcohol extract of the seeds of M. pruriens has an antilipid peroxidation property, which is mediated through the removal of superoxides and hydroxyl radicals. Copyright © 2002 John Wiley & Sons, Ltd.
Glucose lowering efficacy of Ficus racemosa bark extract in normal and alloxan diabetic rats
Authors: Bhaskara Rao R. , Murugesan T. , Sinha Sanghamitra , Saha B. P. , Pal M. , Mandal Subhash C.
Published: October 2002

The glucose‐lowering efficacy of a methanol extract of the stem bark of Ficus racemosa Linn. (MEBFR) (Family Moraceae) was evaluated both in normal and alloxan‐induced diabetic rats. The MEBFR at the doses examined (200 and 400 mg/kg p.o.) exhibited significant hypoglycaemic activity in both experimental animal models when compared with the control group. The activity was also comparable to that of the effect produced by a standard antidiabetic agent, glibenclamide 10 mg/kg. The present investigation established pharmacological evidence to support the folklore claim that it is an antidiabetic agent. Copyright © 2002 John Wiley & Sons, Ltd.
In vitro Immunomodulatory activity of verbascoside from Nepeta ucrainica L.
Authors: Akbay Pinar , Calis Ihsan , Ündeger Ülkü , Basaran Nursen , Basaran A. Ahmet
Published: October 2002

Nepeta ucrainica L. is used as a herbal tea in Kazakhistan. Phytochemical investigations of the aerial parts of the plant resulted in the isolation of verbascoside (1) and 1,5,9‐epi‐deoxyloganic acid (2). The structures of the compounds were elucidated by spectral (UV, IR, 1H‐NMR and 13C‐NMR) methods and HPLC analysis. The in vitro immunomodulatory activity of verbascoside was investigated by assessing neutrophil function; chemotaxis and intracellular killing activity. Verbascoside showed an increased chemotactic activity in all doses applied compared with the medium used as a negative control and had a positive effect on respiratory burst of neutrophils, but there was an opposite effect with increasing doses, pointing to a possible suppression of neutrophil intracellular killing activity. Copyright © 2002 John Wiley & Sons, Ltd.
Process capability indices for skewed populations
Authors: Chang Young Soon , Choi In Su , Bai Do Sun
Published: October 2002

This paper proposes a new method of constructing process capability indices (PCIs) for skewed populations. It is based on a weighted standard deviation method which decomposes the standard deviation of a quality characteristic into upper and lower deviations and adjusts the value of the PCI using decomposed deviations in accordance with the skewness estimated from sample data. For symmetric populations, the proposed PCIs reduce to standard PCIs. The performance of the proposed PCIs is compared with those of standard and other PCIs, and finite sample properties of the estimates are investigated using Monte Carlo simulation. Numerical studies indicate that considerable improvements over existing methods can be achieved by the use of the weighted standard deviation method when the underlying distribution is skewed. Copyright © 2002 John Wiley & Sons, Ltd.
Systematic trends in E2 transitions along the sodium isoelectronic sequence
Authors: Charro E. , Martín I.
Published: October 2002

Oscillator strengths for E2‐forbidden spectral lines of sodium‐isoelectronic ions, from K IX (Z=19) to Cs XLV (Z=55), have been calculated in the LS‐coupling scheme using the relativistic quantum defect orbital (RQDO) method. The study of many of these sodiumlike ions is relevant to processes in fusion devices and in astrophysical objects. Our data are compared with the very few results available, and their systematic trend is analyzed for np 2P0–n′f 2F0 transitions. The influence of relativistic effects in E2 transitions along this sequence is also discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Improved point‐charge model within the INDO/S‐CI method for describing the ligand excited states of lanthanide coordination compounds
Authors: Batista Hélcio J. , Longo Ricardo L.
Published: October 2002

Due to the spatial extent of the 5s and 5p filled orbitals of lanthanide ions, the shielding of the nuclear charge is not perfect at close distances to the ion. Thus, ligand atoms should experience different effective charge depending upon their distance to the central ion. Using electrostatic arguments and ab initio calculations for Eu3+, we have proposed an improved model that describes the ion as an effective charge, q(r), whose value has the following radial dependence, q(r)=3+14e. This functional form of the point charge has been implemented into the ZINDO program and INDO/S‐CI calculations have been performed for the Eu(btfa)3bipy, Eu(btfa)3⋅2H2O, Eu(bzac)3bipy, and Eu(bzac)3⋅2H2O compounds. The comparison with the experimental absorption spectrum was used to optimize the exponent A parameter. Application of this model to several other Eu3+ coordination compounds yielded better results for the calculated absorption spectra than the fixed 3+ point‐charge model. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Hierarchical construction of finite diabatic sets by Mathieu functions
Authors: Englman R. , Yahalom A. , Baer M.
Published: October 2002

An extension is given for the standard two component model of adiabatic, Born–Oppenheimer (BO) electronic states in a polyatonic molecule, by use of Mathieu functions of arbitrary order. The curl or compatibility conditions for the construction of a diabatic set of states based on a finite‐dimensional subset of BO states are not satisfied exactly. It is shown, however, that, by successively adding higher order Mathieu functions to the BO set, the compatibility conditions are satisfied with increasingly better accuracy. We then generalize to situations in which the nonadiabatic couplings (the dynamic corrections to the BO approximation) are small (though not necessarily zero) between a finite‐dimensional BO subset and the rest of the BO states. We prove that approximate diabatic sets exist, with an error that is of the order of the square of the neglected nonadiabatic couplings. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001
Highly accurate Gaussian basis sets for some 14‐electron diatomic systems*
Authors: Neto A. Canal , Jorge F. E. , Centoducatte R.
Published: October 2002

A molecular improved generator coordinate Hartree–Fock (HF) method is used to generate highly accurate Gaussian basis sets for N2, BF, CO, NO+, and CN−. For these molecular systems, sequences of basis sets of atom‐centred Gaussian‐type functions are employed to explore the accuracy achieved with this method. Our ground state HF total energies are lower than the corresponding ones calculated with other basis sets of primitive Gaussian‐type functions reported in the literature. For the molecular systems here studied, the differences between the HF total energy results obtained with our largest basis sets and with a numerical HF method are equals to 38.2, 13.9, 33.0, 76.7, and 55.7 μhartree for N2, BF, CO, NO+, and CN−, respectively. We have also calculated the multipole electric moments and compare them with the corresponding experimental values and with results computed by other approaches. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Sulfur‐containing mesoionic compounds: Theoretical study on structure and properties
Authors: Fabian Jürgen , Hess B. Andes
Published: October 2002

The structure of the mesoionic 1,3‐dithiolylium‐4‐olate (2) and thiopyrylium‐3‐olate (3) and of their derivatives were calculated by first‐principles methods. The compounds are considered as cylic derivatives of open‐chain thione S‐ylides. The extent of cyclic electron delocalization was discussed in terms of the molecular charge distribution and nucleus‐independent chemical shift values (NICs). The calculated CS bond of SCO of 2 was found to be exceedingly long (>1.80 Å). This result suggests a facile CS ring opening of 2 to S‐ketenyl dithiomethylester. The transition structure of this reaction is nearly isoenergetic with the product of the reaction. The calculated reaction barrier amounts to about 12 kcal/mol and the ring‐to‐chain valence isomerization should therefore occur under thermal conditions. This result is in line with the chemical reactivity of diphenyl‐2. According to time‐dependent density functional theory calculations (TD‐DFT) the sulfur‐containing mesoionic compounds 2 and 3 should be colored. The intense long wavelength absorption of diphenyl‐2 at about 550 nm is well reproduced. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Ab initio study of bending modes in water cage clusters, (H2O)n, n6–10
Authors: Sadlej Joanna
Published: October 2002

Theoretical investigation, employing MP2 level ab initio calculations, is presented of HOH bending modes in water cage clusters, (H2O)n, n6–10. The vibrational bending frequencies are blue‐shifted by 40–170 cm−1 with respect to H2O(g). The magnitude of bending frequency shift depends on the type of water molecules. The three coordinated water molecules with dangling H atoms (DAA) tend to have lower frequencies than do the three coordinated water molecules with dangling oxygen atom (DDA). In contrast to OH stretch, there is no evidence for strong changes in molecular dipole derivatives with respect to bending as a result of hydrogen bonding in the clusters. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Improved model core potentials: Application to the thermochemistry of organoxenon complexes
Authors: Lovallo Christopher C. , Klobukowski Mariusz
Published: October 2002

We recently developed new pseudopotentials for the main group elements, incorporating the L‐shell structure in the basis sets and reoptimizing the parameters. These improved model core potentials were used to study the energetics of reactions leading to compounds with XeIIC bonds. We found that many compounds are thermodynamically stable with respect to the reactants, and consequently they could possibly be formed under the right kinetic conditions. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Energies and widths of the resonance states of the He ion
Authors: Orlikowski Tadeusz
Published: October 2002

Resonance energies and widths are calculated for He in the X1 Σ electronic state using the lifetime matrix method. Nonadiabatic couplings with the first excited state are taken into account. The obtained energies are compared with some previous results. We found that for the considered system the nonadiabatic effects are small and lower the adiabatic energies by less than 0.5 cm−1. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Quantum mechanical and experimental infrared and Raman studies of 1‐methyluracil and its hydrogen‐bonded dimer
Authors: Person Willis B. , Szczepaniak Krystyna , Kwiatkowski Jozef S.
Published: October 2002

Density functional theory at the B3LYP/6‐31G(d,p) level has been used to calculate the structure, force field, and vibrational [infrared (IR) and Raman] spectra of the 1‐methyluracil monomer and its dimer with the cyclic N3H … OC4 hydrogen bonds. The experimental IR spectrum of the 1‐methyluracil monomer isolated in a low‐temperature Ar matrix and the IR and Raman spectra of its polycrystalline solid have been reinvestigated. The cyclic hydrogen bond for the calculated dimer is the same as that in the 1‐methyluracil crystal. It appears that calculation at this level of theory does provide IR and Raman spectra closely resembling the corresponding experimental spectra. We were amazed to find that the agreement between the calculated spectrum of the dimer and the experimental spectrum of the crystalline solid is not worse than the agreement between the calculated spectrum of the monomer and the experimental spectrum of 1‐methyluracil isolated in an Ar matrix. The results of calculation appear to be useful in the interpretation of the experimental spectra of the monomer and crystal. The close agreement found between the calculated and experimental spectra suggests that force constants and geometries of the monomer and dimer are also predicted well by the calculation at this level. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Normal mode analysis of the vibrational spectrum of tropolone—A molecule with seven‐membered ring
Authors: Rostkowska Hanna , Lapinski Leszek , Nowak Maciej J. , Adamowicz Ludwik
Published: October 2002

Infrared spectra of tropolone (2‐hydroxy‐2,4,6‐cycloheptatriene‐1‐one) isolated in Ar and N2 matrices are compared with the spectra theoretically calculated at the DFT (density functional theory) Becke, Lee, Yang, Paar (B3LYP)/6‐31++G** and Møller–Plesset of the second order (MP2)/6‐31+G* levels. The good agreement between experimental spectrum and DFT results allowed assignment of the bands observed in the IR spectrum to the theoretically predicted normal modes described in terms of potential energy distribution (PED). Internal coordinates describing in‐plane and out‐of‐plane deformations of the seven‐membered ring of D7h symmetry (and for eight‐membered ring of D8h symmetry) were designed for the purpose of normal mode analysis. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
New complete orthonormal sets of exponential‐type orbitals and their application to translation of Slater orbitals
Authors: Guseinov I. I.
Published: October 2002

The new complete orthonormal sets of exponential‐type orbitals (ETOs) are introduced in closed form as functions of the exponential, the complex or real regular solid spherical harmonic, and the generalized Laguerre polynomials,

where α=1,0,−1,−2,−3,… . These Ψα‐ETOs are represented as finite linear combinations of Slater‐type orbitals (STOs). The Coulomb Sturmian and Lambda ETOs are the special classes of Ψα‐ETOs for α=1 and α=0, respectively. By the use of Ψα‐ETOs the simpler expansion formulas for translation of STOs are derived. The translation coefficients are presented by a linear combination of overlap integrals. The final results are especially useful for machine computations of arbitrary multielectron multicenter molecular integrals over STOs that arise in the Hartree–Fock–Roothaan approximation and also in the Hylleraas correlated wave function method which play a significant role in theory and application to quantum mechanics of atoms, molecules, and solids. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Structural symmetry study of some bis‐adduct of an acceptor with two donors
Authors: Liao Hsin‐Yi , Chu San‐Yan
Published: October 2002

The protonated water dimer has a symmetric structure 1 in contrast to the asymmetric structure of protonated ammonia dimer 2. To make a general understanding of structural symmetry difference for these D–A–D systems, we carried out a systematic theoretical study with the B3LYP/6‐31+G** method. We considered the electron donors (D) of the lone pair on either side of BF, CO, and N2 molecules, as well as the electron acceptors (A) like Li+, CH3+, SiH3+, and PH2+ beside the proton. We found the magnitude of the first bonding energy between D and A [BE(1)] is decisive for the symmetry of the D–A–D system. A larger BE(1) leads to a smaller BE(2), the bonding energy of D–A with the second donor. This gives rise to a stronger tendency toward asymmetry. The magnitude of BE(1) correlates well with the difference in ionization potential (ΔIP) of the orbitals involved in the D–A interaction. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Ab initio and density functional theory calculations of the dipole polarizability and the second dipole hyperpolarizability of benzene
Authors: Soscún Humberto , Hernández Javier , Escobar Ramón , Toro‐Mendoza Carlos , Alvarado Ysaías , Hinchliffe Alan
Published: October 2002

The linear dipole polarizability α and nonlinear second dipole hyperpolarizability γ of benzene were calculated using the ab initio SCF–MO restricted Hartree–Fock (HF) method. The coupled perturbed HF and time‐dependent HF (TDHF) methods were used for the evaluation of the static and dynamic properties, respectively. The TDHF approach was applied at different optical frequencies, and the second hyperpolarizability γ was evaluated for different optical processes. Electron correlation was taken into account by using the Møller–Plesset perturbation theory (MP2) and the density functional theory B3LYP hybrid approach, with a finite field method, with electric fields of ±0.01, ±0.02, ±0.03, and ±0.04 a.u. used. Benzene was assumed to have a D6h geometry, and the standard STO/6‐31+G(d,p) (A) and optimized STO/6‐31+G(d*,p) (B) basis sets were employed for the calculations. In the optimized basis set, the d exponent of the C atomic function was varied in order to obtain a maximum static benzene γ at the TDHF level of theory. This optimized basis set was able to gives values for the (hyper)polarizabilities of benzene that agree excellently with experimental results and previous calculations. The calculated properties were analyzed in terms of the Laplacian of the electron density calculated using the atoms in molecules method due to Bader. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Quantum dynamical manifolds: Applications to excitonic coupled high temperature superconductivity
Authors: Scofield D. F. , Collins T. C.
Published: October 2002

The physical rationale supporting the introduction of many‐body differential geometric methods for self‐consistently calculating the properties of quantum systems is given. The methods are then used to determine new self‐consistent, self‐gauge field quantum dynamical manifold equations describing a high temperature superconductor. This includes itinerant electron screening of Coulomb repulsion and local electron, exciton‐mediated attraction. The article includes new quantum geometric equations for the paired electrons or holes (potential cooperons) of a superconductor. It is shown how other mechanisms can easily be incorporated into the calculation of the quasi‐particle geometry of the quantum dynamical manifold. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Quantum electrodynamical density‐matrix functional theory and group theoretical consideration of its solution
Authors: Ohsaku Tadafumi , Yamanaka Shusuke , Yamaki Daisuke , Yamaguchi Kizashi
Published: October 2002

For studying the group theoretical classification of the solutions of the density functional theory in relativistic framework, we propose quantum electrodynamical density‐matrix functional theory (QED–DMFT). QED–DMFT gives the energy as a functional of a local one‐body 4×4 matrix \documentclass{article}\pagestyle{empty}\begin{document}$Q(x)\equiv-\langle\psi(x)\bar{\psi}(x)\rangle$\end{document}, where \documentclass{article}\pagestyle{empty}\begin{document}$\psi$\end{document} and \documentclass{article}\pagestyle{empty}\begin{document}$\bar{\psi}$\end{document} are a 4‐component Dirac field and its Dirac conjugate, respectively. We examine some characters of QED–DMFT. After these preparations, by using Q(x), we classify the solutions of QED–DMFT under O(3) rotation, time reversal, and spatial inversion. The behavior of Q(x) under nonrelativistic and ultrarelativistic limits is also presented. Finally, we give plans for several extensions and applications of QED–DMFT. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Modified Slater potential and its application to the ground‐states and excited‐states of atomic systems
Authors: Harbola Manoj K. , Sen K. D.
Published: October 2002

The exact Slater potential (Slater, J. C. Phys Rev 1951, 81, 385) is calculated by treating the Fermi hole as a static charge distribution. However, the Fermi hole is a dynamic quantity and changes as an electron moves through an inhomogeneous electron gas. In this article, we follow the ideas of Harbola and Sahni (Phys Rev Lett 1989, 62, 489) to modify the Slater potential by adding to it a term that accounts for the dynamic nature of the Fermi hole in an approximate manner. The results obtained from this potential are shown to be highly accurate over a wide range of atomic systems. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Dissipative dynamics in many‐atom systems: A density matrix treatment
Authors: Micha David A. , Thorndyke Brian
Published: October 2002

The dynamics of a many‐atom system are described in terms of the density operator solution of the Liouville–von Neumann equation, for either isolated or dissipative (open) conditions. The treatment introduces a partial Wigner transform of the density operator of the isolated system or of a primary region of interest, respectively, classifying degrees of freedom as quantal or quasi‐classical. A secondary region (the medium) is treated as a stochastic environment leading to a dissipative dynamics of the primary region. Dissipative phenomena are described in terms of dissipative potentials and rate operators. The quantum and quasi‐classical degrees of freedom can be identified with the electronic and nuclear variables of a many‐atom system to provide a description of electronic rearrangement and excitations during dissipative phenomena. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Geometric picture for coupled electron–nuclear dynamics
Authors: Chernyak Vladimir , Mukamel Shaul
Published: October 2002

Equations of coupled electron–nuclear dynamics (CEND) that describe molecular dynamics within a fully classical approach have been derived. Utilization of the language of fiber bundles and connections (gauge fields) allows one to represent the resulting classical Hamilton equations in an invariant (coordinate‐covariant) form. Applications of the CEND equations to calculations of off‐resonant nonlinear molecular polarizabilities are outlined. The CEND equations are shown to resemble the END equations derived earlier once the Thouless representation of single Slater determinants is adopted. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Aluminum (III) interactions with the side chains of aromatic aminoacids
Authors: Mercero Jose M. , Matxain Jon M. , Lopez Xabier , Fowler Joseph E. , Ugalde Jesus M.
Published: October 2002

Aluminum (III) and magnesium (II) interactions with the aromatic containing aminoacid side chains are studied using the B3LYP approximate density functional. Bader and the natural bonding orbital (NBO) analyses have been performed on the optimized structures in order to shed light on the effect of the metal on the aromatic rings. We began by studying the interactions between the metal cations and benzene. Then a methyl was added to represent more accurately the phenylalanine functional group. We have also studied, in a similar way, the functional groups of the tyrosine and tryptophan aminoacids. The strongest bond is 447 kcal/mol, which occurs between the Al(III) and the indole. For magnesium, the strongest bond is 151 kcal/mol for the methyl–indole complex. As in the complexes of previous sections, the addition of the methyl leads to stronger binding complex, and this effect is significantly larger for aluminum than for magnesium. The NBO and Bader analyses revealed that the aromaticity of the carbon rings remains after interaction with magnesium. However, when the ring interacts with aluminum, aromaticity is lost, even though certain delocalization is kept. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Unified analytical treatment of one‐electron multicenter integrals of central and noncentral potentials over Slater orbitals
Authors: Guseinov I. I.
Published: October 2002

Using new complete orthonormal sets of exponential‐type orbitals introduced by the author (I. I. Guseinov, Int J Quantum Chem, submitted), the different analytical expressions are derived for the expansion of one‐ and two‐center electron charge density over Slater‐type orbitals (STOs) in terms of STOs about a new center. The expansion coefficients in these formulas are expressed through the overlap integrals with the same screening parameters. The one‐center expansion formulas in terms of STOs are also obtained for arbitrary central and noncentral potentials (CPs and NCPs). Using the expansion formulas obtained for the electron charge density and potentials, the general formulas are established for the multicenter molecular integrals of CPs and NCPs. In the formulas for the multicenter molecular integrals of CPs and NCPs, all the expansion coefficients and the overlap integrals are expressed through the binomial coefficients. The final results are especially useful for the calculation of these quantities for large quantum numbers. Using the derived expressions in terms of binomial coefficients, one‐electron molecular integrals over STOs can be evaluated efficiently and accurately from the series expansion formulas. The relationships obtained are valid for the arbitrary location, quantum numbers, and screening constants of atomic orbitals. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Interplay of intra‐ and intermolecular H‐bonds for the addition of a water molecule to the neutral and N‐protonated forms of noradrenaline
Authors: Alagona Giuliano , Ghio Caterina
Published: October 2002

The conformational flexibility of noradrenaline in its N‐protonated and neutral forms was considered at the Hartree–Fock (HF)/6‐31G* level, taking into account the orientation of the two hydroxy groups located on the catechol ring and the interconversion pathways between their stable arrangements. The difference in stability among the various forms of N‐protonated noradrenaline was maintained including either more diffuse functions on the heteroatoms or Møller–Plesset second order (MP2) correlation corrections. The embedding in aqueous solution, in the polarizable continuum model framework, of the conformers kept rigid at their in vacuo geometries favored the T conformers with respect to the G ones at the HF level (for neutral noradrenaline at the MP2 level as well). The addition of a single water molecule to noradrenaline (either N‐protonated or not) caused the intramolecular H‐bond within the side chain to weaken until formation of one or two intermolecular H‐bonds with water. This fact, coupled to the intramolecular H‐bond strain relaxation, further stabilized the G1 and T conformers. Continuum solvation of the hydrated clusters of neutral noradrenaline favored significantly the Twater adducts at the HF level, but only slightly at the MP2 level, because of their large energy gap in vacuo with respect to G1water, even enhanced by MP2 geometry optimizations. The dependence of the potential energy profile for the NH2 group rotation on the catechol ring and side chain OH group orientation was examined in noradrenaline and compared to the trend shown by dopamine. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Comparison of two‐electron densities reconstructed from one‐electron density matrices
Authors: Herbert John M. , Harriman John E.
Published: October 2002

We consider approximate reconstruction of spinless and spin‐resolved two‐electron charge densities, intracule densities, and extracule densities utilizing only the one‐electron reduced density matrix. Using large basis set, configuration interaction density matrices for the ground state of Be, we compare the two‐electron densities obtained using several proposed reconstruction functionals (“natural orbital functionals”) for the two‐electron density and density matrix. We also analyze the intracule and extracule densities obtained from these reconstructions. Several of the proposed natural orbital functionals are found to produce unphysical negative values for the pair density when two parallel‐spin electrons approach one another. Ancillary results from this study include new, simplified formulas for the intracule and extracule densities, and a mathematical justification for an approximate relation between atomic intracule and extracule densities that has previously been reported on the basis of extensive Hartree–Fock calculations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Local kinetic energy and local temperature in the density‐functional theory of electronic structure
Authors: Ayers Paul W. , Parr Robert G. , Nagy Agnes
Published: October 2002

Various thermodynamic elements of the density functional theory of electronic structure are reviewed and clarified. Detailed argumentation is given for the particular “del dot del” definition of the local kinetic energy density and local temperature. The temperature measures the “nighness” of an electron pair, thus playing a key role in quantitative (exchange and kinetic energy functionals) and qualitative (electron localization functions) tools based on the electron pair density. Two different derivations are given of the Gaussian model for the phase‐space distribution function, from which one obtains an approximation to the entropy of the charge distribution. The full thermodynamic description is briefly discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Trends in hyperfine coupling constants and electron‐spin g factors for X\documentclass{article}\pagestyle{empty}\begin{document}$^{2}\Sigma^{+}_{(g,u)}$\end{document} diatomics with 1,3, and 5 valence  electrons
Authors: Bruna Pablo J. , Grein Friedrich
Published: October 2002

A comparison of electron spin resonance (ESR) parameters calculated for X2Σ(g,u)+ diatomic radicals is presented, including Li2+, LiK+ with one valence electron (VE); Li2−, LiK−, LiBe, LiCa, LiB+, LiGa+, Be2+, and BeCa+ with 3 VEs; and B2+, BGa+ with 5 VEs. The Aiso and Adip constants are studied using 6‐311+G(2df) basis sets and several methods (UHF, CISD, MP2, B3LYP, PW91PW91). For the s‐rich radicals with 1 and 3 VEs, it is found that Aiso≫Adip≈0, whereas for those of pσ‐type (such as LiB+/LiGa+ with 3 VEs, and all present 5 VE radicals), the values of Aiso and Adip are generally similar. The electron‐spin g factors are calculated using perturbation expansions up to second order, a Hamiltonian based on Breit–Pauli theory, and correlated (MRCI) wave functions. All radicals have negative values of Δg∥ and Δg⊥. The sum‐over‐states expansions for Δg⊥ are dominated by the coupling with just one or two 2Π excited states. The Δg⊥'s of the first‐row radicals Li2+, Li2−, Be2+, LiBe, LiB+, and B2+ are about −60, −5, −120, −215, −3290, and −1300 ppm, respectively, while for the mixed first/third‐row counterparts LiK+, LiK−, BeCa+, LiCa, LiGa+, and BGa+ they are about −1200, −2480, −1000, −7840, −93700, and −800 ppm, respectively. These results show the strong influence heavier atoms with larger spin‐orbit constants have on g⊥ shifts. The smaller Δg⊥ of BGa+ (when compared with B2+) is caused by the 3σ→1π and 3σ→2π excited states contributing positively and negatively, respectively, to this shift. Such positive contribution is at variance with the rule stating that an excitation of type σ→π (SOMO→virtual MO) should contribute negatively. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Cumulant‐based approximations to reduced density matrices
Authors: Harris Frank E.
Published: October 2002

The use of cumulant expansions for the approximation of reduced density matrices (RDMs) is reviewed. It is pointed out that the oft‐cited theorems of Nakatsuji and Rosina are insufficient to guarantee either N‐representability or that an N‐representable RDM has a unique antecedent wave function. Approximations involved in Mazziotti's recently proposed “formal solution for reconstruction” are identified. The behavior of his scheme, and of an older one in which all cumulants beyond the second are neglected, are illustrated by detailed examination of a model problem. The limited experience provided by this example casts doubt as to the probable effectiveness of Mazziotti's reconstruction scheme. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Nuclear electromagnetic shieldings via charge and current density functions
Authors: Lazzeretti Paolo
Published: October 2002

The general concept of time‐dependent charge and current densities for the electrons in a molecule responding to electromagnetic fields is considered. It is shown that nuclear electric and electromagnetic shieldings, related to absorption intensity in infrared and vibrational circular dichroism spectroscopies, can be expressed in terms of density functions in real space. Plots of charge and current densities obtained by the theoretical methods developed in the present study are expected to provide a physical basis on the absorption process and simple tools for the interpretation of vibrational spectroscopy parameters. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002
Electron ionization mass spectral fragmentation of deoxynivalenol and related tricothecenes
Authors: Rodrigues‐Fo Edson , Mirocha C. J. , Xie Weiping , Krick Thomas P. , Martinelli J. A.
Published: October 2002

Careful analysis of the electron impact (EI) mass spectral data obtained for the trimethylsilyl (TMS) ethers of known trichothecene mycotoxins of the deoxynivalenol group permitted the construction of a database useful for the identification of these mycotoxins directly from a gas chromatography/mass spectrometry (GC/MS) run. Structures of the ions at m/z 103, 117, 147 and 191 were elucidated by high‐resolution mass spectrometry (HRMS) and a fragmentation scheme was suggested. The relative abundances of these ions in the mass spectra of the trichothecenes allowed a fast structural diagnosis during analysis of biological matrices. A new mycotoxin of this group, 3‐acetylnivalenol, was tentatively identified by using MS data interpretation only. Copyright © 2002 John Wiley & Sons, Ltd.