First principles electronic structure investigation of order of singlet and triplet states of oxyhemoglobin and analysis of possible influence of muon trapping

Interest in the possibility of magnetic character for oxyhemoglobin (OxyHb) has been recently stimulated by the observations of muon spin-lattice relaxation effects studied (Nagamine et al., Proc Jpn Acad Ser B Phys Biol Sci 83:120–126, 2007) with the muon-spin rotation (μSR) technique. In view of this, we have carried out first-principles electronic structure investigations involving Hartree–Fock theory combined with many body perturbation effects for the singlet and triplet states of OxyHb. Our results indicate that using two recent x-ray structural data (Paoli et al., J Mol Biol 256:775, 1996; Park et al., J Mol Biol 360:690, 2006) for OxyHb, for only Hartree–Fock theory without many-body effects included, the singlet state lies above the triplet state by energies of about 0.08 and 0.13 a.u. for the two structures in Paoli et al. (J Mol Biol 256:775, 1996) and Park et al. (J Mol Biol 360:690, 2006). Incorporation of many-body effects by the perturbation method reverses the order, with the triplet state located 0.18 and 0.14 a.u. above the singlet state for the structures in Paoli et al. (J Mol Biol 256:775, 1996) and Park et al. (J Mol Biol 360:690, 2006). Physical reasons for these relative orderings of the singlet and triplet states will be discussed. It is clear that OxyHb by itself would be in a singlet state at room temperature or below, since from our calculation, the triplet state lies about KT above the singlet state with T having the value of 44,098 K and 56,449 K for the two structural data in Paoli et al. (J Mol Biol 256:775, 1996) and Park et al. (J Mol Biol 360:690, 2006). As regards the muon spin-lattice relaxation effects obtained by recent μSR measurements (by Nagamine et al., Proc Jpn Acad Ser B Phys Biol Sci 83:120–126, 2007) at room temperature, the sensitive dependence of the singlet-triplet separation on many-body effects in our investigation suggests that it is possible that the singlet-triplet separation could be reversed or reduced significantly when a muon is trapped near an oxygen atom of the oxygen molecule, allowing the triplet to be occupied at room temperature and lead to significant muon spin-lattice relaxation.     

Measurement of angular dependence of M X-ray production cross-sections in Re,Bi and U at 5.96 keV

The M X-ray production differential cross sections in Re, Bi and U elements have been measured at the 5.96 keV incident photon energy in an angular range 135°–155°. The measurements were performed using a ⁵⁵Fe source and a Si(Li) detector. The present results contradict the predictions of Cooper and Zare [Atomic Collision Processes, Gordon and Breach, New York (1969)] and experimental results of Kumar et al. [J. Phys. B: At. Mol. Opt. 34, 613 (2001)]. that, after photoionization of inner shells, the vacancy state has equal population of magnetic substates and the subsequent X-ray emission is isotropic, but confirm the predictions of the calculations of Flügge et al. [Phys. Rev. Lett. 29, 7 (1972)] and experimental results of Sharma and Allawadhi [J. Phys. B: At. Mol. Opt. 32, 2343 (1999)] and Ertugrul [Nucl. Instrum. Meth. B 119, 345 (1996)]. Total M X-ray production cross sections from the decay at the 5.96 keV photon energies are found to be in good agreement with the calculated theoretical results using the theoretical values of M shell photoionization cross section.     

Relation between proteins tertiary structure, tryptophan fluorescence lifetimes and tryptophan S(o)→(1)L(b) and S(o)→(1)L(a) transitions. Studies on α1-acid glycoprotein and β-lactoglobulin

We measured fluorescence lifetimes and fluorescence spectra (excitation and emission) of tryptophan residues of α₁-acid glycoprotein (three Trp residues) and β-lactoglobulin (two Trp residues) in absence and presence of 450 μM progesterone. Progesterone binds only to α₁-acid glycoprotein. In absence of progesterone, each of the two proteins displays three fluorescence lifetimes. Addition of progesterone induces a partial inhibition of the S _o → ¹ L _a transition without affecting fluorescence lifetimes. The same experiments performed in presence of denatured proteins in 6 M guanidine show that addition of progesterone inhibits partially the S _o → ¹ L _a transition and its peak is 15 nm shifted to the red compared to that obtained for native proteins. However, the S _o → ¹ L _b transition position peak is not affected by protein denaturation. Thus, the tertiary structure of the protein plays an important role by modulating the tryptophan electronic transitions. Fluorescence emission decay recorded in absence and presence of progesterone yields three fluorescence lifetimes whether proteins are denatured or not. Thus, protein tertiary structure is not responsible for the presence of three fluorescence lifetimes. These characterize tryptophan substructures reached at the excited states and which population (pre-exponential values) depend on the tryptophan residues interaction with their microenvironment(s) and thus on the global conformation of the protein.     

Perturbation of Conformational Dynamics of ASCUT-1 from Ascaris lumbricoides by Temperature and Sodium Dodecyl Sulfate

ASCUT-1 is a protein found in cuticlin, the insoluble residue of the cuticles of the nematode Ascaris lumbricoides. It contains the CUT-1-like domain which is shared by members of a novel family of components of extracellular matrices. The monomeric form of ASCUT-1 contains a single tryptophan residue. An understanding of the structure-function relationship of the protein under different chemical-physical conditions is of fundamental importance for an understanding of its structure and function in cuticles. In this paper we report the effect of the temperature and sodium dodecyl sulfate on the structural stability of this protein. The structure of the protein was studied in the temperature range 25–85°C in the absence and in the presence of sodium dodecyl sulfate by frequency-domain measurements of the intrinsic fluorescence intensity and anisotropy decays. The time-resolved fluorescence data in the absence of SDS indicated that the tryptophanyl emission decays were well described by a bimodal lifetime distribution, and that the temperature increases resulted in the sharpening and in the shortening of the tryptophanyl lifetime distribution. In the presence of SDS an unimodal fluorescence lifetime distribution as well as a marked decrease in the anisotropy decay values were observed.     

Interplay between elastic fields due to gravity and a partial dislocation for a hard-sphere crystal coherently grown under gravity: driving force for defect disappearance

We previously observed that an intrinsic staking fault shrunk through a glide of a Shockley partial dislocation terminating its lower end in a hard-sphere crystal under gravity coherently grown in ?001? by Monte Carlo simulations [Mori et al., Molec. Phys. 105, 1377 (2007)]; it was an answer to a one-decade long standing question why the stacking disorder in colloidal crystals reduced under gravity [Zhu et al., Nature 387, 883 (1997)]. Here, we present an elastic energy calculation; in addition to the self-energy of the partial dislocation [Mori et al., Prog. Theor. Phys. Suppl. 178, 33 (2009)] we calculate the cross-coupling term between elastic field due to gravity and that due to a Shockley partial dislocation. The cross-term is an increasing function of the linear dimension R over which the elastic field expands, showing that a driving force arises for the partial dislocation moving toward the upper boundary of a grain.     

On the experimental verification of the Landau-Pomeranchuk-Migdal effect

A theoretical explanation is given for the “unexpected” behavior recently observed in the radiation spectrum of ultrarelativistic electrons in a thin layer of matter in an experimental investigation of the Landau-Pomeranchuk-Migdal effect at SLAC [S. R. Klein et al., Preprint SLAC-6378, Stanford (1993); P. L. Anthony et al., Phys. Rev. Lett. 75, 1949 (1995)]. Pis’ma Zh. éksp. Teor. Fiz. 63, No. 11, 837–840 (10 June 1996)     

Effective atomic numbers of some H-, C-, N- and O-based composite materials derived from differential incoherent scattering cross-sections

In this work, we have made an effort to determine whether the effective atomic numbers of H-, C-, N- and O-based composite materials would indeed remain a constant over the energy grid of 280–1200 keV wherein incoherent scattering dominates their interaction with photons. For this purpose, the differential incoherent scattering cross-sections of Be, C, Mg, Al, Ca and Ti were measured for three scattering angles 60°, 80° and 100° at 279.1, 661.6 and 1115.5 keV using which an expression for the effective atomic number was derived. The differential incoherent scattering cross-sections of the composite materials of interest measured at these three angles in the same set-up and substituted in this expression would yield their effective atomic number at the three energies. Results obtained in this manner for bakelite, nylon, epoxy, teflon, perspex and some sugars, fatty acids as well as amino acids agreed to within 2% of some of the other available values. It was also observed that for each of these samples, Z _eff was almost a constant at the three energies which unambiguously justified the conclusions drawn by other authors earlier [Manjunathaguru and Umesh, J. Phys. B: At. Mol. Opt. Phys. 39, 3969 (2006); Manohara et al,Nucl. Instrum. Methods B266, 3906 (2008); Manohara et al Phys. Med. Biol. 53, M377 (2008)] based on total interaction cross-sections in the energy grid of interest.     

Steady State Fluorescence Studies of Wild Type Recombinant Cinnamoyl CoA Reductase (Ll-CCRH1) and its Active Site Mutants

Fluorescence quenching and time resolved fluorescence studies of wild type recombinant cinnamoyl CoA reductase (Ll-CCRH1), a multitryptophan protein from Leucaena leucocephala and 10 different active site mutants were carried out to investigate tryptophan environment. The enzyme showed highest affinity for feruloyl CoA (K _a ?=?3.72?×?10⁵ M^?1) over other CoA esters and cinnamaldehydes, as determined by fluorescence spectroscopy. Quenching of the fluorescence by acrylamide for wild type and active site mutants was collisional with almost 100 % of the tryptophan fluorescence accessible under native condition and remained same after denaturation of protein with 6 M GdnHCl. In wild type Ll-CCRH1, the extent of quenching achieved with iodide (f _a?=?1.0) was significantly higher than cesium ions (f _a?=?0.33) suggesting more density of positive charge around surface of trp conformers under native conditions. Denaturation of wild type protein with 6 M GdnHCl led to significant increase in the quenching with cesium (f _a?=?0.54), whereas quenching with iodide ion was decreased (f _a?=?0.78), indicating reorientation of charge density around trp from positive to negative and heterogeneity in trp environment. The Stern-Volmer plots for wild type and mutants Ll-CCRH1 under native and denatured conditions, with cesium ion yielded biphasic quenching profiles. The extent of quenching for cesium and iodide ions under native and denatured conditions observed in active site mutants was significantly different from wild type Ll-CCRH1 under the same conditions. Thus, single substitution type mutations of active site residues showed heterogeneity in tryptophan microenvironment and differential degree of conformation of protein under native or denatured conditions.     

From effective BCS action to vortex dynamics

The topological term in the effective action for the electrically neutral BCS system is discussed. It is applied for the calculation of the transverse force acting on a vortex in the limit of a smooth vortex core and vanishing interlevel distance in the vortex core. The controversy between the topological terms in the articles by I. J. R. Aitchison et al., Phys. Rev. B 51, 6531 (1995) and A. van Otterlo et al., cond-mat/9703124 is resolved. Pis’ma Zh. éksp. Teor. Fiz. 65, No. 8, 641–646 (25 April 1997) Published in English in the original Russian journal. Edited by Steve Torstveit.     

A Nanosecond Time-Resolved Fluorescence Study of Recombinant Human Myelin Basic Protein

Myelin basic protein (MBP) is a major component of myelin and plays a central role in the maintenance of its compact multilayered structure. Tryptophan fluorescence is sensitive to environmental factors such as polarity and rotational mobility and often reflects conformational changes in proteins. This work describes a detailed examination of the time-resolved emission properties of the single tryptophan of recombinant human myelin basic protein. Fluorescence decay curves were collected at two separate excitation wavelengths and at different wavelengths across the emission spectrum. The fitting parameters obtained with the aid of global analysis were combined with steady-state emission spectra collected from the same samples and are presented as decay-associated spectra (DAS) and time-resolved emission spectra (TRES). The effects of temperature and binding to anionic membranes on the decay of emission of MBP were investigated. The changes in fitted parameters and the appearance of DAS and TRES as a function of experimental conditions are interpreted in terms of variation in the local environment of the single tryptophan in MBP. The implications of the changes in local environment resulting from experimental treatments are discussed in the context of the overall conformation of MBP and are compared to structural and photophysical properties of MBP obtained from the central nervous system tissue of several species [P. Cavatorta, S. Giovanelli, A. Bobba, P. Riccio, and E. Quagliariello, Acta Neurol. (Napoli) 13, 162–169, (1991; P. Cavatorta, S. Giovanelli, A. Bobba, P. Riccio, A. G. Szabo, and E. Quagliarello, Biophys. J. 66, 1174–1179, 1994; P. Cavatorta, L. Masotti, A. G. Szabo, D. Juretic, P. Riccio, and E. Quagliariello, Cell Biophys. 13, 201–215, 1988].     

Poissonian Obstacles with Gaussian Walls Discriminate Between Classical and Quantum Lifshits Tailing in Magnetic Fields

We investigate the leading low-energy falloff of the integrated density of states of a charged quantum particle in the Euclidean plane subject to a perpendicular constant magnetic field and repulsive impurities randomly distributed according to Poisson's law. This so-called magnetic Lifshits tail was determined by K. Broderix et al. [J. Stat. Phys. 80:1 (1995)] for algebraically decaying and by L. Erds [Probab. Theory Relat. Fields 112:321 (1998)] for compactly supported single-impurity potentials. While the result in the first case coincides with the corresponding classical one, the Lifshits tail in Erds' case exhibits a genuine quantum behavior. Building on both works, we determine magnetic Lifshits tails for a wide class of positive impurity potentials with a leading long-distance decay in between these limiting cases. Gaussian decay may be shown to discriminate between classical and quantum behavior. The Lifshits tail caused by Gaussian decay reveals power-law falloff with an exponent not yet completely determined.     

Origin of Fluorescence Lifetimes in Human Serum Albumin. Studies on Native and Denatured Protein

Human serum albumin consists of a single polypeptide of 585 amino acid residues with 1 Trp residue. In the present work, we measured fluorescence lifetimes of the protein in both native and denatured states. The results indicate that Trp emission occurs with three lifetimes in both states. Lifetimes values and contribution to the global emission decay differ between the two states. Data are interpreted as the results of an emission occurring from three substructures of the tryptophan formed in the excited state. Two of these substructures are already present for the tryptophan free in solution. The third lifetime is the result of the interaction between the tryptophan residue and surrounding microenvironment. The populations of these substructures characterized by the pre-exponential parameters of the fluorescence lifetimes are dependent on the fluorophore microenvironment and on the global protein structure.     

The determination of the lifetime of hot electrons in metals by time-resolved two-photon photoemission: the role of transport effects, virtual states, and transient excitons

Experience has shown that theoretically determined lifetimes of bulk states of hot electrons in real metals agree quantitatively with the experimental ones, if theory fully takes into account the crystal structure and many-body effects of the investigated metal, i.e., if the Dyson equation is solved at the ab initio level and the effective electron–electron interaction is determined beyond the plasmon-pole approximation. Therefore the hitherto invoked transport effect [Knoesel et al.: Phys. Rev. B 57, 12812 (1998)] does not seem to exist. In this paper we show that likewise neither virtual states [Hertel: et al. Phys. Rev. Lett. 76, 535 (1996)] nor damped band-gap states [Ogawa: et al.: Phys. Rev. B 55, 10869 (1997)] exist, but that the hitherto unexplained d-band catastrophe in Cu [Cu(111), Cu(110)] can be naturally resolved by the concept of the transient exciton. This is a new quasiparticle in metals, which owes its existence to the dynamical character of dielectric screening at the microscopic level. This means that excitons, though they do not exist under stationary conditions, can be observed under ultrafast experimental conditions. Received: 30 March 2000 / Accepted: 2 September 2000 / Published online: 12 October 2000     

An accurate,global, ab initio potential energy surface for the H+ 3 molecule

A new global, ground-state, Born-Oppenheimer surface is presented for the H⁺ ₃ system. The energy switching approach has been used to combine different functional forms for three different regimes: a spectroscopic expansion at low energy, a Sorbie-Murrell function at high energy and known long-range terms combined with accurate diatomic potentials at large separations. At low energies we have used the ultra high accuracy ab initio data of Cencek et al. (1998, J. chem. Phys., 108, 2831). At intermediate energy we have calculated 134 new ab initio energies using a high accuracy, explicitly correlated procedure. The ab initio data of Schinke et al. (1980, J. chem. Phys., 72, 3909) has been used to constrain the high energy region. Two fits are presented which differ somewhat in their behaviour at energies over 45 000 cm^?1 above the H⁺ ₃ minimum. Below this energy, the fits reproduce each set of ab initio data close to their intrinsic accuracy. The ground state surface should provide a suitable starting point for renewed studies of the near-threshold photodissociation spectrum originally reported by Carrington et al. (1982, Molec. Phys., 45, 753).     

Efficient nonlinear-optical frequency conversion in periodic media in the presence of diffraction of the pump and harmonic fields

It has been predicted by Shelton and Shen [Phys. Rev. A 5, 1867 (1972)] and observed by Kajikawa et al. [Jpn. J. Appl. Phys. Lett. 31, L679 (1992)] and Yamada et al. [Appl. Phys. B 60, 485 (1995)] that the efficiency of nonlinear-optical frequency conversion increases significantly in a nonlinear periodic medium and, accordingly, the intensity of the generated harmonic increases as the fourth power of the sample thickness, as opposed to the square law observed in homogeneous media. In this paper it is shown that the same enhancement of the efficiency of nonlinear-optical frequency conversion in a nonlinear periodic medium can be achieved using an ordinary pump wave in the form of a plane wave when both the pump wave and the harmonics are diffracted by the periodic structure of the nonlinear medium. The phenomenon is analyzed quantitatively in the example of second-harmonic generation. Pis’ma Zh. éksp. Teor. Fiz. 70, No. 12, 793–799 (25 December 1999)     

Steady-State and Time-Resolved Fluorescence Polarization Behavior of Acenaphthene

Steady-state and time-resolved fluorescence polarization studies have been carried out on acenaphthene (ACE) in low-temperature glass solutions and at room temperature. In the low-temperature glass the fluorescence polarization values vary considerably with both emission and excitation wavelength. There is a time dependence (on the nanosecond time scale) of the fluorescence anisotropy, r(t), at 77 K, which has a strong dependence upon the excitation and emission wavelengths. Under these conditions, the time-dependent decay of the anisotropy is not attributable to chromophoric motion. The observations are consistent with emission from two closely lying and interconverting excited states. Rate constants for the photophysical processes involved have been determined by fitting the data using a model proposed by Fleming et. al. The results are discussed with particular reference to the care required in using dynamic fluorescence polarization measurements to determine energy transfer rates in systems containing this chromophore.     

Fluorescence of jet-cooled naphthalene: Emission spectra, lifetimes and quantum yields

Fluorescence spectra of naphthalene, C₁₀H₈, were obtained in the laboratory under conditions which provide an appropriate simulation of the cometary conditions: super-cooled gas phase molecules in a collision-free environment. Five spectra were recorded, the excitation energies ranging from 1422 to 5293 cm⁻¹ above the first electronic state S₁ at 32 020 cm⁻¹. A comparison with previous jet-cooled naphthalene fluorescence spectra obtained by Beck et al. [1] and Hermine [2] shows that the former results are not consistent with the present ones. Spectra obtained by Beck et al. show weaker intensities at greater wavelengths compared to those obtained by Hermine and ourselves. We also measured the fluorescence lifetimes by recording the fluorescence decay as a function of time after the excitation of the molecules by monochromatic lasers and deduced the fluorescence quantum yields. A synthetic emission spectrum under solar irradiation is obtained for astrophysical implications.     

The problems with M

M² is now widely used to characterize the quality of laser radiation. In the paraxial approach the inequality M²1 holds, if M² is defined by the second moments. Nevertheless, in some publications M²<1 is presented, either theoretically or experimentally (Wang et al., Optik 1995;100(1):8; Lu et al., Optik 1995;100(2):91; Wang et al., Optics and Laser Technology 1999;31:151). In particular, it is stated that for a superposition of axially shifted Gaussian spherical beams, M² can become smaller than one (Wang et al., Optics and Laser Technology 1999;31:151). These problems with M² are briefly summarized.     

Scalar and axial-vector mesons

Almost thirty years ago, Penny G. Estabrooks asked “Where and what are the scalar mesons?” (P. Estabrooks, Phys. Rev. D 19, 2678 (1979)). The first part of her question can now be confidently responded (E. van Beveren et al., Z. Phys. C 30, 615 (1986)). However, with respect to the “What” many puzzles remain unanswered. Scalar and axial-vector mesons form part of a large family of mesons. Consequently, though it is useful to pay them some extra attention, there is no point in discussing them as isolated phenomena. The particularity of structures in the scattering of --basically-- pions and kaons with zero angular momentum is the absence of the centrifugal barrier, which allows us to “see” strong interactions at short distances. Experimentally observed differences and similarities between scalar and axial-vector mesons on the one hand, and other mesons on the other hand, are very instructive for further studies. Nowadays, there exists an abundance of theoretical approaches towards the mesonic spectrum, ranging from confinement models of all kinds, i.e., glueballs, and quark-antiquark, multiquark and hybrid configurations, to models in which only mesonic degrees of freedom are taken into account. Nature seems to come out somewhere in the middle, neither preferring pure bound states, nor effective meson-meson physics with only coupling constants and possibly form factors. As a matter of fact, apart from a few exceptions, like pions and kaons, Nature does not allow us to study mesonic bound states of any kind, which is equivalent to saying that such states do not really exist. Hence, instead of extrapolating from pions and kaons to the remainder of the meson family, it is more democratic to consider pions and kaons mesonic resonances that happen to come out below the lowest threshold for strong decay. Nevertheless, confinement is an important ingredient for understanding the many regularities observed in mesonic spectra. Therefore, excluding quark degrees of freedom is also not the most obvious way of describing mesons in general, and scalars and axial-vectors in particular.     

Polarization correlation in the two-photon decay of atomic hydrogen: nonlocality versus entanglement

From the work by Perrie et al. [Phys. Rev. Lett. 54, 1790 (1985)], photon pairs from the 2s _1/2 → 1s _1/2 (two-photon) decay of atomic hydrogen are known to be quantum mechanically correlated. In these experiments, the polarization states of the photons emitted in back-to-back geometry were shown to violate the Bell inequality as a qualitative sign of nonlocality and entanglement. In the present contribution, we analyze how these nonlocal quantum correlations, as given by the violation of the Bell inequality, differ from the concurrence as a true entanglement measure. Results are shown for both quantifiers in dependence of the decay geometry and the initial polarization of the atoms for the 2s _1/2 → 1s _1/2 and 3d _5/2 → 1s _1/2 two-photon decay of atomic hydrogen. These results display the difference between nonlocality and entanglement and, hence, may stimulate further experiments on nonlocal quantum correlations in atomic systems.