Modified Urey Bradley Force Field Research Articles

Theoretical investigation of iron isotope fractionation between Fe(H 2O) 63+ and Fe(H 2O) 62+: Implications for iron stable isotope geochemistry

The magnitude of equilibrium iron isotope fractionation between Fe(H 2O) 6 3+ and Fe(H 2O) 6 2+ is calculated using density functional theory (DFT) and compared to prior theoretical and experimental results. DFT is a quantum chemical approach that permits a priori estimation of all vibrational modes and frequencies of these complexes and the effects of isotopic substitution. This information is used to calculate reduced partition function ratios of the complexes (10 3 · ln(β)), and hence, the equilibrium isotope fractionation factor (10 3 · ln(α)). Solvent effects are considered using the polarization continuum model (PCM). DFT calculations predict fractionations of several per mil in 56Fe/ 54Fe favoring partitioning of heavy isotopes in the ferric complex. Quantitatively, 10 3 · ln(α) predicted at 22°C, ∼ 3 ‰, agrees with experimental determinations but is roughly half the size predicted by prior theoretical results using the Modified Urey-Bradley Force Field (MUBFF) model. Similar comparisons are seen at other temperatures. MUBFF makes a number of simplifying assumptions about molecular geometry and requires as input IR spectroscopic data. The difference between DFT and MUBFF results is primarily due to the difference between the DFT-predicted frequency for the ν 4 mode (O-Fe-O deformation) of Fe(H 2O) 6 3+ and spectroscopic determinations of this frequency used as input for MUBFF models (185–190 cm −1 vs. 304 cm −1, respectively). Hence, DFT-PCM estimates of 10 3 · ln(β) for this complex are ∼ 20% smaller than MUBFF estimates. The DFT derived values can be used to refine predictions of equilibrium fractionation between ferric minerals and dissolved ferric iron, important for the interpretation of Fe isotope variations in ancient sediments. Our findings increase confidence in experimental determinations of the Fe(H 2O) 6 3+ − Fe(H 2O) 6 2+ fractionation factor and demonstrate the utility of DFT for applications in “heavy” stable isotope geochemistry.

Vibrational spectra and normal coordinate analysis of a weak ligand complex, Co( p-DMABA) 2Cl 2 · 2H 2O

The complex Co( p-DMABA) 2Cl 2 · 2H 2O ( p-dimethylaminobenzaldehyde, p-DMABA) was prepared from the solid-state reaction of a weak ligand p-DMABA and CoCl 2 · 6H 2O at lower heating temperature (60°C). It is very difficult to obtain the title complex using solution reaction method, less than isolating single crystals. In order to determine the crystal structure of the title compound, we have to rely on the X-ray powder diffraction data. That is, the crystal structure can be solved directly from powder data, which crucial step is to constitute the structure model. Indirect spectroscopic methods, such as infrared and Raman spectroscopes, and further vibrational assignments made with the aid of normal coordinate calculations by using a modified Urey–Bradley force field, were analyzed to proposed molecular structure. One hundred and fifty-seven internal coordinates were established and 129 theoretical vibrational frequencies were calculated. An appropriate set of internal coordinates and force constants in the course of calculation were introduced, so that the calculated vibration frequencies are good agreement with the observed values. The average difference and the maximum deviation between theoretic and experimental frequencies are 2.44 and 8.0 cm −1, respectively. Thus the normal coordinate analysis is a powerful tool to the molecular structure. Other structural and spectral properties are also discussed in this paper. The purpose of the present paper is to obtain a good structural model. This model was used as starting model for crystal structure determination from powder X-ray diffraction (XRD) data.

NH–S hydrogen bonding in zinc enzyme model complex with S 2N 2 binding set studied by normal coordinate analysis of vibrational spectra

In order to provide theoretical evidence for the existence and effect of NH–S hydrogen bonding in the zinc enzyme model complex [Zn(S-2-C 6H 4NHCOC 6H 5) 2(1-MeIm) 2] (1-MeIm=1-methylimidazole) in addition to the spectroscopic and crystallographic investigations, normal coordinate analysis (NCA) was carried out using a modified Urey–Bradley force field. The vibrational frequencies of the complex with and without the NH–S hydrogen bonding as well as the corresponding internal coordinates were obtained. The good agreement found between the calculated and observed frequencies in the presence of the NH–S hydrogen bond, supports the reliability of the analysis. The stretching force constant of the NH–S hydrogen bond obtained from the calculation is 0.18 mdyne per Å. The calculation shows that the N–H bond is weakened by formation of the NH–S hydrogen bond. The results are indicative of the existence of the NH–S hydrogen bond in the complex.

Structure and vibrational properties of tetragonal scheelite NaBi(MoO4)2

The structure of the tetragonal NaBi(MoO4)2 crystal was determined. The space group is I4=S42 with cell dimensions a=5.267, c=11.565 A and Z=2. The molybdenum atoms occupy two different sites of 4 symmetry. The Na+ and Bi3+ cations are situated on two positions with different occupancy factors and are short-range ordered. The IR and Raman polarized spectra are discussed on the basis of the factor group analysis and phonon calculations. The modified Urey–Bradley force field and potential energy distribution were applied for three molecular models of local disorder. Polarization properties are explained and related to the crystal structure. © 1997 John Wiley & Sons, Ltd.

Vibrational spectra and normal coordinate analysis for cis-diamminetetrachloroplatinum

Abstract The normal coordinate analysis of cis -diamminetetrachloroplatinum has been carried out by using a modified Urey—Bradley force field. According to the molecular structure, 45 internal coordinates were established and 33 theoretical vibrational frequencies were calculated. Due to considering the interaction between non-neighbouring stretching vibrations and between bending vibrations and introducing an appropriate set of internal coordinates in the course of calculation, the calculated frequencies agree well with the observed values, with an average difference 3.61 cm −1 between them. The rationality and the reliability of the results are discussed and the questionable empirical assignment of ν(PtCl) in the literature is corrected.

Raman spectra and normal vibrations of dipeptides. II. Glycyl-L-proline.

AbstractRaman and ir spectra of the glycyl‐L‐proline (GP) dipeptide were recorded. A normal‐coordinate treatment was performed on the basis of the experimental spectra, using a modified Urey‐Bradley force field (MUBFF). Cyclic redundancies were eliminated, and those due to the ring methylene groups, particularly distorted in regard to the tetrahedral conformation, were treated. An assignment of the experimental frequencies is proposed on the basis of the normal treatment.

Vibrational spectra and normal coordinate analysis of diamminemercury(II) chloride with 14N/ 15N and H/D isotopic substitution

The IR and Raman spectra of solid diamminemercury(II) chloride with 14N/ 15N and H/D isotopic substitution have been measured. The spectra have been interpreted assuming D 3d symmetry for the [Hg(NH 3) 2] 2+ cations which have a linear framework structure. The skeletal metal-ligand modes ν as(HgN) and ° as(NH gN) in the IR spectra were confirmed by the observed isotopic shifts. A normal coordinate analysis for the three isotopic compounds has been carried out, based on a modified valence force field and on a modified Urey—Bradley force field.

Phosphine–borane derivatives. 10. Vibrational spectra of the dimethylphosphine adducts of boron trihalides

The infrared (200–4000 cm−1) and Raman (0–3100 cm−1) spectra of (CH3)2PHBX3, (CH3)2PDBX3, and (CD3)2PHBX3, where X = Cl, Br, I, have been recorded in solid state and in solutions at room temperature. The fundamentals have been assigned on the basis of Cs molecular symmetry. A modified Urey–Bradley force field model has been used in calculating the frequencies and potential energy distributions as well as the force constants. The (P—B) force constant was found to be consistent with the structural change upon adduct formation.

Vibrational spectroscopic investigations of s nse 8-n molecules

The fundamental vibrations of 13 cyclic S nSe 8-n (n = 7—2) molecules have been calculated using a modified Urey—Bradley force field with 9–14 independent force constants whose values have been adapted from those of Se 8 and S 8. Calculated wavenumbers are compared to those obtained by Raman spectroscopy for sulfur—selenium phases prepared by recrystallizing quenched molten mixtures of the elements as previously described. Agreement between the observed spectra and calculated wavenumbers is closest by assuming the existence of selenium—selenium bonds and the absence of isolated selenium atoms in S nSe 8-n molecules. It is assumed that sulfur—selenium phases are mixed crystals with the following components in varying concentrations: 1,2-S 6Se 2, 1,2,3-S 5Se 3, 1,2,3,4-S 4Se 4, 1,2,5,6-S 4Se 4, 1,2,3-S 3Se 5 and 1,2-S 2Se 6. The presence of S 8 and Se 8 in some of the phases is indicated by the Raman spectra.

Molecular structure of bis(acetylacetonato)beryllium in the gas phase as determined from electron diffraction data

The molecular structure of bis(acetylacetonato)beryllium has been determined by gas electron diffraction. The experimental data were found to be consistent with the D 2d model in which the oxygen atoms are arranged tetrahedrally around the central beryllium atom (∠OBeO = 106.0 ± 1.0°). The structural parameters are as follows: r g(Be-O) = 1.615 ± 0.006 Å, r g (C-O) = 1.270 ± 0.004 Å, r g (C-C ring) = 1.397 ± 0.004 Å, r g (C-C meth) = 1.499 ± 0.005 Å. The mean amplitudes of vibration were calculated from the normal-vibration treatment using the modified Urey—Bradley force field

Inference of vibrational anharmonicity in hot SF6: An electron diffraction study

In an investigation of gaseous SF6 at temperatures ranging from 298 to almost 1000 K, the observed thermal expansion of the mean bond length as a function of the mean-square amplitude of vibration was found to be much too large to be accounted for by the commonly invoked model of Morse anharmonicity. Experimental results can be reproduced quantitatively, however, with the aid of existing potential constants fed into an anharmonic, modified Urey–Bradley force field proposed previously.

Resonance Raman spectra of octaethylporphyrinato-Ni(II) and m e s o-deuterated and 15N substituted derivatives. II. A normal coordinate analysis

Normal coordinate calculations are carried out for all the in-plane modes of octaethylporphyrinato-Ni (II) and its meso-deuterated and 15N substituted derivatives. With 37 constants of a modified Urey–Bradley force field and a structural model with D4h symmetry, 59 resonance Raman lines (A1g+B1g +A2g+B2g) and 38 infrared bands (Eu) of these three molecules are assigned. The vibrational modes of the Raman active species are represented in terms of the Cartesian atomic displacement vectors. Based on the present results, some important resonance Raman lines of hemoproteins are interpreted. The so-called ’’oxidation state maker’’ (Band IV) is due to an in-phase breathing-like mode of four pyrrole rings although being somewhat deformed by the large contribution of the Cα–N symmetric stretching term. The spin state sensitive Raman lines, namely, Band I and III, are associated mainly with methine bridge (Cα–Cm) stretching modes. Two prominent anomalously-polarized Raman lines of hemoproteins around 1580 and 1300 cm−1 are primarily due to the Cα–Cm stretching and Cm–H bending modes, respectively.

Two-photon excitation spectra of naphthalene- h8 and - d8: Vibronic coupling involving the ground state

Two-photon excitation spectra of the lowest 1B 2u state of naphthalene- h 8 and - d 8 at 4.2 K were observed and many vibronic bands coupled with u vibrations were analyzed by polarization measurements for single crystals. The b 2u vibration of 1535 cm −1 (- h 8) was found to be the most prominent perturbing vibration in the excited state and it should correspond to the ground state vibration ν 21 (b2u) of 1361 cm −1 (- h 8) whose mode is CC stretching of the bond alternating type. It was shown that this is the key vibration for the two-photon spectra of naphthalene as well as of benzene and is most effective in the vibronic coupling between the ground state and the lowest 1L b( 1B 2u) state.The vibronic coupling involving the ground state gives a physical meaning of the modified Urey—Bradley force field proposed by Scherer.

Schwingungsspektren und kraftkonstanten von tetraschwefeltetraimid, (SNH) 4 und (SND) 4

Infrared and Raman spectra of the cyclic tetrasulfur tetraimide, (SNH) 4, and its deuteriated derivative, (SND) 4, are reported for the region 50–4000 cm −1. 39 of the 46 fundamental frequencies of both molecules have been observed and assigned in accordance with the molecular symmetry C 4 v . Intermolecular hydrogen bonds in solid tetrasulfur tetraimide influence the NH stretching frequencies only. Using a modified Urey—Bradley force field with 15 independent force constants good agreement between observed and calculated frequencies was obtained. Urey—Bradley as well as valence force constants are reported and discussed.

Effect of Environmental Cations on Force Constants, Vibrational Mean Amplitudes and Bond Order of Metaloxygen Bonds in Some Octahedral Oxyanions

Abstract The general valenoe force field (GVFF), modified orbital valence force field (MOVFF), and modified Urey-Bradley force field (MUBFF) have been employed to calculate the force constants of octahedral Te6+o6, and Ti4+o6 anions in the presence of different environmental cations. The mean amplitudes and generalized mean square amplitudes of vibrations for these anions at temperatures; O°K,298. 16°K, and 500°K have also been calculated. Further, the metaloxygen bond order was estimated with the help of general valence stretching force constants. The effects of environmental cations on the force constants, mean amplitudes and π-bonding of metal-oxygen bonds have been critically discussed. The effect of atomic masses of anions on the ooriolis coupling constants of ‘fiu species has also been outlined.

Infrared spectra of methanesulfonamide and its C- and N-deuterated compounds

The i.r. spectra of methanesulfonamide and its C- and N-deuterated compounds in the crystalline state have been recorded. Vibrational assignments have been made on the basis of the i.r. dichroism and the isotope effects. Normal coordinate analyses for CH 3SO 2NH 2, CH 3SO 2ND 2, CD 3SO 2NH 2 and CD 3SO 2ND 2 have been carried out by using the C s , molecular model and a modified Urey—Bradley force field. The potential energy distribution indicates that the shift of the SN stretching frequency on the N-deuteration is attributed to the vibrational coupling between the SN stretching and the ND 2 bending vibration.

Vibrational spectra of methanesulfonyl chloride and methanesulfonyl chloride- d3

The i.r. and Raman spectra of methanesulfonyl chloride and methanesulfonyl chloride- d 3 have been recorded in the liquid state, and consistent assignments of the fundamental frequencies of the two isotopic compounds have been given. The normal coordinate calculation based on a modified Urey—Bradley force field has been carried out to give the satisfactory fit between the observed and calculated frequencies.

Normal coordinate treatment of XeO2F2

A normal coordinate treatment (NCT) using a modified Urey–Bradley force field (MUBFF) was made for XeO2F2. New analyses were also performed on XeOF4 and XeO3F2. Force constants obtained were compared with force constants from other xenon compounds containing fluorine and/or oxygen atoms. In general, as oxygen atoms are added to XeF2 the bond distance of the Xe–F decreases while the KXeF force constant increases, and the Xe–O bond distances increase while the KXeO force constant decreases.

Normal coordinate analysis of s-tetrazine in modified Urey—Bradley force field

A normal coordinate treatment of s-tetrazine-d 0 and s-tetrazine-d 2 has been performed using a modified Urey—Bradley force field. Three possible assignments by Sigworth and Pace have been tested and the best assignment in the modified Urey—Bradley force field agreed with their results using a modified valence force field.

Vibrational assignment and force constants of S 8O[1

A complete vibrational assignment and normal coordinate treatment were made for S 8O using a modified Urey—Bradley force field with 12 force constants. The valence force constants obtained from the UB values are compared with those of S 8.