Wave spectra assimilation in typhoon wave modeling for the East China Sea

The East China Sea is a hot area for typhoon waves to occur. A wave spectra assimilation model has been developed to predict the typhoon wave more accurately and operationally. This is the first time where wave data from Taiwan have been used to predict typhoon wave along the mainland China coast. The two-dimensional spectra observed in Taiwan northeast coast modify the wave field output by SWAN model through the technology of optimal interpolation (OI) scheme. The wind field correction is not involved as it contributes less than a quarter of the correction achieved by assimilation of waves. The initialization issue for assimilation is discussed. A linear evolution law for noise in the wave field is derived from the SWAN governing equations. A two-dimensional digital low-pass filter is used to obtain the initialized wave fields. The data assimilation model is optimized during the typhoon Sinlaku. During typhoons Krosa and Morakot, data assimilation significantly improves the low frequency wave energy and wave propagation direction in Taiwan coast. For the far-field region, the assimilation model shows an expected ability of improving typhoon wave forecast as well, as data assimilation enhances the low frequency wave energy. The proportion of positive assimilation indexes is over 81% for all the periods of comparison. The paper also finds that the impact of data assimilation on the far-field region depends on the state of the typhoon developing and the swell propagation direction.

Vibration-rotation spectra of CH3F

Rotational structure has been resolved and analyzed in the 1049-cm−1 parallel fundamental and the 1182 cm−1 perpendicular fundamental bands in the infrared spectrum of the CH3F molecule. Combination bands at 2223 cm−1 and around 2650 cm−1 have also been studied. The effective resolving power of the spectrometer was 0.25 cm−1 for all these bands. The two long-wavelength fundamentals have been analyzed in much greater detail than in previous work, and a complete analysis of the perpendicular band has been made, including the J-structure in the P and R branches of the sub-bands. Rotational constants of CH3F determined in this work and elsewhere are summarized in Table XIII of the text. Some anomalous intensity perturbations in the rotation lines of the 1182-cm−1 fundamental have been observed, and are discussed.

The two-dimensional anharmonic oscillator III: the CCC bending mode of C3O2

Newly observed data on the rotational constants of carbon suboxide in excited vibrational states of the low-wavenumber bending vibration ν7 have been successfully interpreted in terms of the two-dimensional anharmonic oscillator wavefunctions associated with this vibration. By combining these results with published infrared and Raman spectra the vibrational assignment has been extended and a refined bending potential for ν7 has been derived: this has a minimum at a bending angle of about 24° at the central C atom, with an energy maximum at the linear configuration some 23 cm−1 above the minimum. From similar data on the combination and hot bands of ν7 with ν4 (1587 cm−1) and ν2 (786 cm−1) the effective ν7 bending potential has also been determined in the one-quantum excited states of ν4 and ν2. The effective ν7 potential shows significant changes from the ground vibrational state; the central hump in the ν7 potential surface is increased to about 50 cm−1 in the v4 = 1 state, and decreased to about 1 cm−1 in the v2 = 1 state. In the light of these results vibrational assignments are suggested for most of the observed bands in the infrared and Raman spectra of C3O2.

Excited vibrational state microwave spectra, structure, and force-field of trifluorosilane

The J = 2−1 microwave spectrum of six isotopic species of HSiF3 has been observed and assigned in excited states of five of the six fundamental vibrations. The assignment is based on relative intensities, double resonance experiments, and trial anharmonic force constant calculations. Analysis of the spectra leads to experimental values for five of the constants, all three l-doubling constants qt, one Fermi resonance constant φ233, and one zeta constant. The harmonic force field has been refined to all the available data on vibration wavenumbers, centrifugal distortion constants, and zeta constants. The cubic anharmonic force field has been refined to the data on and qt constants, using two models: a valence force model with two cubic force constants for SiH and SiF stretching, and a more sophisticated model. With the help of these calculations, the following equilibrium structure has been determined: re(SiH) = 1.4468(±5) Å, re(SiF) = 1.5624(±1) Å, HSiF = 110.64(±3)°,

Vibrational overtone spectra of monofluoroacetylene: a preliminary report

High-resolution infrared and near-infrared spectra have been observed for more than 80 overtone bands of the HCCF molecule, including two CH stretching overtones in the visible region. Many of these have been analysed, and many more are in the course of analysis and will be reported later. All fundamentals have now been rotationally analysed and the equilibrium rotational constant determined. These data provide a testing ground for anharmonic force-field analyses, and they are discussed briefly in this connection.

Vibration-rotation spectra of nitrous acid, HONO

High-resolution Fourier-transform infrared spectra have been recorded and analyzed for the nu4, nu5, and nu6 fundamental bands of trans-HONO, and for the nu4 fundamental of cis-HONO. The spectral resolution was better than 0.01/cm, and the rotational structure has been analyzed to give improved ground-state and excited-state rotational constants, with a standard deviation of the fit to the observed line positions of around 0.0006/cm. Two Coriolis interactions have been analyzed between the nu5 and nu6 bands of trans-HONO.

The power of NMR: in two and three dimensions

Two dimensional NMR experiments use a sequence of two or more pulses with a variable time delay to generate spectra. COSY spectra clarify where the protons are in a molecule. Two and three dimensional NMR are used to solve protein structures.

Ferric and ferrous iron in nitroso-myoglobin: computer simulations of stable and metastable states and their infrared spectra

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O-2, which only bind to ferrous (Fe-II) iron, NO binds to both ferrous and ferric (Fe-II) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ob initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta'-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe-II-NO, which ex- hibits only two minima (the eta(2) coordination mode for Fe-II is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe-III than for Fe-II. We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Binding of pentagalloyl glucose to two globular proteins occurs via multiple surface sites

The interaction between pentagalloyl glucose (PGG) and two globular proteins, bovine serum albumin (BSA) and ribulose-1,5-bisphosphate carboxylase oxygenase (rubisco), was investigated by isothermal titration calorimetry (ITC). ITC data fit to a binding model consisting of two sets of multiple binding sites, which reveal similarities in the mode of binding of PGG to BSA and rubisco. In both cases, the interaction is characterized by a high number of binding sites, which suggests that binding occurs by a surface adsorption mechanism that leads to coating of the protein surface, which promotes aggregation and precipitation of the PGG-protein complex. This model was confirmed by turbidimetry analysis of the PGG-BSA interaction. Analysis of tryptophan fluorescence quenching during the interaction of PGG with BSA suggests that binding of PGG leads to some conformational changes that are energetically closer to the unfolded state of the BSA structure, because small red shifts in the resulting emission spectra were observed.

A new interpretation of the bonding properties and UV–vis spectra of [M3(CO)12] clusters (M = Ru, Os): a TD-DFT study

DFT and TD-DFT calculations (ADF program) were performed in order to analyze the electronic structure of the [M-3(CO)(12)] clusters (M = Ru, Os) and interpret their electronic spectra. The highest occupied molecular orbitals are M-M bonding (sigma) involving different M-M bonds, both for Ru and Os. They participate in low-energy excitation processes and their depopulation should weaken M-M bonds in general. While the LUMO is M-NI and M-CO anti-bonding (sigma*), the next, higher-lying empty orbitals have a main contribution from CO (pi*) and either a small (Ru) or an almost negligible one (Os) from the metal atoms. The main difference between the two clusters comes from the different nature of these low-energy unoccupied orbitals that have a larger metal contribution in the case of ruthenium. The photochemical reactivity of the two clusters is reexamined and compared to earlier interpretations.

Unusually high differential attenuation at C band: Results from a two-year analysis of the French Trappes polarimetric radar data

The differential phase (ΦDP) measured by polarimetric radars is recognized to be a very good indicator of the path integrated by rain. Moreover, if a linear relationship is assumed between the specific differential phase (KDP) and the specific attenuation (AH) and specific differential attenuation (ADP), then attenuation can easily be corrected. The coefficients of proportionality, γH and γDP, are, however, known to be dependent in rain upon drop temperature, drop shapes, drop size distribution, and the presence of large drops causing Mie scattering. In this paper, the authors extensively apply a physically based method, often referred to as the “Smyth and Illingworth constraint,” which uses the constraint that the value of the differential reflectivity ZDR on the far side of the storm should be low to retrieve the γDP coefficient. More than 30 convective episodes observed by the French operational C-band polarimetric Trappes radar during two summers (2005 and 2006) are used to document the variability of γDP with respect to the intrinsic three-dimensional characteristics of the attenuating cells. The Smyth and Illingworth constraint could be applied to only 20% of all attenuated rays of the 2-yr dataset so it cannot be considered the unique solution for attenuation correction in an operational setting but is useful for characterizing the properties of the strongly attenuating cells. The range of variation of γDP is shown to be extremely large, with minimal, maximal, and mean values being, respectively, equal to 0.01, 0.11, and 0.025 dB °−1. Coefficient γDP appears to be almost linearly correlated with the horizontal reflectivity (ZH), differential reflectivity (ZDR), and specific differential phase (KDP) and correlation coefficient (ρHV) of the attenuating cells. The temperature effect is negligible with respect to that of the microphysical properties of the attenuating cells. Unusually large values of γDP, above 0.06 dB °−1, often referred to as “hot spots,” are reported for 15%—a nonnegligible figure—of the rays presenting a significant total differential phase shift (ΔϕDP > 30°). The corresponding strongly attenuating cells are shown to have extremely high ZDR (above 4 dB) and ZH (above 55 dBZ), very low ρHV (below 0.94), and high KDP (above 4° km−1). Analysis of 4 yr of observed raindrop spectra does not reproduce such low values of ρHV, suggesting that (wet) ice is likely to be present in the precipitation medium and responsible for the attenuation and high phase shifts. Furthermore, if melting ice is responsible for the high phase shifts, this suggests that KDP may not be uniquely related to rainfall rate but can result from the presence of wet ice. This hypothesis is supported by the analysis of the vertical profiles of horizontal reflectivity and the values of conventional probability of hail indexes.

Dimetallic complexes of macrocycles with two rigid dibenzofuran units as receptors for detection of anionic substrates

The hexaazamacrocycles [28](DBF)2N6 {cyclo[bis(4,6-dimethyldibenzo[b,d]furaniminoethyleneiminoethylene]} and [32](DBF)2N6 {cyclo[bis(4,6-dimethyldibenzo[b,d]furaniminopropyleneiminopropylene]} form stable dinuclear copper(II) complexes suitable to behave as receptors for several anionic substrates. These two receptors were used to study the binding interactions with several substrates, such as imidazole (Him) and some carboxylates [benzoate (bz−), oxalate (ox2−), malonate (mal2−), phthalate (ph2−), isophthalate (iph2−), and terephthalate (tph2−)] by spectrophotometric titrations and EPR spectroscopy in MeOH (or H2O):DMSO (1:1 v/v) solution. The largest association constant was found for ox2− with Cu2[32](DBF)2N64+, whereas for the aromatic dicarboxylate anions the binding constants follow the trend ph2− > iph2− > tph2−, i.e. decrease with the increase of the distance of the two binding sites of the substrate. On the other hand, the large blue shift of 68 nm observed by addition of Him to Cu2[32](DBF)2N64+ points out for the formation of the bridged CuimCu cascade complex, indicating this receptor as a potential sensor for the detection and determination of imidazole in solution. The X-band EPR spectra of the Cu2[28](DBF)2N64+ and Cu2[32](DBF)2N6]4+ complexes and the cascade complexes with the substrates, performed in H2O:DMSO (1:1 v/v) at 5 to 15 K, showed that the CuCu distance is slightly larger than the one found in crystal state and that this distance increases when the substrate is accommodated between the two copper centres. The crystal structure of [Cu2[28](DBF)2N6(ph)2]·CH3OH was determined by X-ray diffraction and revealed the two copper centres bridged by two ph2− anions at a Cu···Cu distance of 5.419(1) Å. Each copper centre is surrounded by three carboxylate oxygen atoms from two phthalate anions and three contiguous nitrogen atoms of the macrocycle in a pseudo octahedral coordination environment.

Configurational preferences of two 1,2-diamine adducts of bis(1-(2-thienyl)-4,4,4-trifluoro-1,3-butanedionato)cobalt(II)

The preparation, the IR and ligand field spectra and the structures of the mixed-ligand addition compounds [(N,N-dimethyl-1,2-diaminoethane)bis(1-(2-thienyl)-4,4,4-trifluoro-1,3-butanedionato)cobalt(II)], [Co(thtf)2me2en], and [(N,N,N′,N′-tetramethyl-1,2-diaminoethane)bis(1-(2-thienyl)-4,4,4-trifluoro-1,3-butanedionato)cobalt(II)], [Co(thtf)2me4en], are reported. The structures were determined by single crystal X-ray diffraction analysis (monoclinic, space group P21/c, Z=4 with a=10.708(6), b=19.531(6), c=13.352(6) Å, β=111.64(10)°, R1=0.0642 and wR2=0.1719 for [Co(thtf)2(me2en)] and a=12.033(6), b=15.565(6), c=15.339(6) Å, β=92.57(6)°, R1=0.0612 and wR2=0.1504 for [Co(thtf)2me4en]). The structures are distorted octahedral and the shortest cobalt–cobalt separation distances are 5.388(2) Å in [Co(thtf)2me2en] and 8.675(3) Å in [Co(thtf)2me4en]. In both compounds the diamine molecules attain the gauche conformation. The U(Z,Z) conformation of the β-dione leads to a semi-chair conformation of the β-dionato chelate rings. The relative orientation of the groups attached to the β-dionato moiety depends on the extent of stereoelectronic effects the N-substitution of the diamine entails. In [Co(thtf)2me2en] the intraligand distance separating the trifluoromethyl carbon atoms is 5.281(18) Å while in [Co(thtf)2me2en] it increases to 8.338(9) Å. The cobalt–cobalt separation distance, the orientation of the chelate rings and the extent of N-substitution seem to affect hydrogen bonding. While in [Co(thtf)2me2en] inter- and intraligand hydrogen bonding is implicated, it is totally absent in [Co(thtf)2me4en].

Two macrocyclic pentaaza compounds containing pyridine evaluated as novel chelating agents in copper(II) and nickel(II) overload

Two pentaaza macrocycles containing pyridine in the backbone, namely 3,6,9,12,18-pentaazabicyclo[12.3.1] octadeca-1(18),14,16-triene ([15]pyN(5)), and 3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19),15,17-triene ([16]pyN(5)), were synthesized in good yields. The acid-base behaviour of these compounds was studied by potentiometry at 298.2 K in aqueous solution and ionic strength 0.10 M in KNO3. The protonation sequence of [15]pyN(5) was investigated by H-1 NMR titration that also allowed the determination of protonation constants in D2O. Binding studies of the two ligands with Ca2+, Ni2+, Cu2+, Zn2+, Cd2+, and Pb2+ metal ions were performed under the same experimental conditions. The results showed that all the complexes formed with the 15-membered ligand, particularly those of Cu2+ and especially Ni2+, are thermodynamically more stable than with the larger macrocycle. Cyclic voltammetric data showed that the copper(II) complexes of the two macrocycles exhibited analogous behaviour, with a single quasi-reversible one-electron transfer reduction process assigned to the Cu(II)/Cu(I) couple. The UV-visible-near IR spectroscopic and magnetic moment data of the nickel(II) complexes in solution indicated a tetragonal distorted coordination geometry for the metal centre. X-band EPR spectra of the copper(II) complexes are consistent with distorted square pyramidal geometries. The crystal structure of [Cu([15]pyN(5))](2+) determined by X-ray diffraction showed the copper(II) centre coordinated to all five macrocyclic nitrogen donors in a distorted square pyramidal environment.