Urey-Bradley Potential Research Articles

Influence of the spectroscopic potential energy function spasiba on molecular dynamics of proteins: comparison with the amber potential

The spasiba potential energy function developed for proteins on the basis of vibrational frequencies of peptides is compared to the amber force field by studying the molecular conformational flexibility of the alanine α-decapeptide and Ecballium elaterium trypsin inhibitor II (EETI-II), a 28-residues peptide. Two molecular dynamics (MD) simulations of 500 ps duration using a distance-dependent dielectric function were carried out for the decapeptide with two different bond angle potential representations: the classical harmonic bond angle potential and the combination of this potential and the 1–3 geminal Urey-Bradley potential. We also performed two 200 ps simulations of EETI-II with a sigmoidal distance-dependent function and examined the effects of the V 1–4tg energetics component, which deals with the 1–4 vicinal interactions taking effect on the dynamics in some side-chains. In comparing the MD results, the two potentials that better reproduce the observed vibrational frequencies act differently on the flexibility of proteins. On the one hand, the Urey-Bradley potential increases the mobilities of backbone atoms; on the other hand, the V 1–4tg potential generally constraints the side-chains to explore fewer conformations. Together, these results are in agreement with a better fit of the X-ray temperature factors, but do not give a new dynamical picture of proteins on a time scale less than 1 ns, because localized rather than collective conformational changes are generated.

Comparison of the IR and Raman vibrational frequencies and intensities of alkanes using the AMBER and SPASIBA force fields. Application to ethane, and gauche- and trans-n-butane

The SPASIBA and AMBER force fields were used to study the IR and Raman frequencies and intensities of ethane and trans- and gauche-n-butane. The intensity parameters came from ab initio molecular orbital calculations. A total of nine basis sets at the Hartree—Fock level of theory was picked out: STO-3G, 3-–21 G, 6–21 G, 6–31 G, 3–21 G *, 6–31 G *, 6–21 G **, D95 and D95 **. Some of the calculations were repeated with electron correlation, included through Møller—Plesset perturbation to second-order (MP2). A better fit of the experimental IR and Raman spectra of n-butane is obtained with the present force field than with the AMBER force field. The discrepancies come mainly from the difference in the vibrational frequencies and then in the form of the normal modes of vibration. Although ab initio methods bear high degrees of uncertainty, the calculated intensities using SPASIBA are closer to the experimental ones. The Urey—Bradley potential, which is commonly omitted from molecular mechanics force fields, seems to be required for improving the goodnes-of-fit of the Raman intensities.

Harmonic and molecular dynamics of n-octane. Comparison between the AMBER and SPASIBA force fields

Molecular and harmonic dynamics calculations were performed for n-octane using the AMBER and SPASIBA potential energy functions. The main difference between the two potentials is the addition of a set of Urey—Bradley—Shimanouchi interaction terms to the commonly harmonic bond angle potential, otherwise the non-bonded interactions and the torsional energies are calculated identically with the same set of parameters. Various models with different combinations of interacting terms were studied and compared with the AMBER results. In agreement with the general belief that low frequency modes dominate in the harmonic approximation, the atomic fluctuations are independent of the form of the bond angle potential. In contrast, the 320 ps molecular dynamics simulations exhibit different degrees of fluctuation and show that the SPASIBA potential samples more of the conformational space than the AMBER potential. While the AMBER simulation indicates harmonic behavior, the SPASIBA runs exhibit many interconversions between trans and gauche conformers. It is shown that the harmonic Urey—Bradley potential is mainly responsible for the alteraction of the dynamical properties of alkanes on a time scale of one nanosecond, but the other geminal (1–3) potentials and vicinal (1–4) terms also affect the r.m.s. fluctuations. This result is contrary to the common belief that approximate reproduction of the high frequency modes is sufficient for spanning the potential energy surface.

Vibrational spectra of imidazoline-2-thione and imidazoline-2-one

Raman and infrared spectra of imidazoline-2-thione (IMZT) and imidazoline-2-one (IMZO) have been recorded. Normal coordinate analyses have been performed for all the fundamental vibrations of IMZT, IMZT-d 2 and IMZO employing a Urey—Bradley potential function supplemented with valence type force constants for the out of plane modes. The results of the vibrational analyses are discussed in relation to the assignments in related molecules. The vibrational assignments for IMZT and IMZO have been compared with those in structurally similar molecules and the need to obtain more reliable band assignments for some of the molecules considered is emphasised.

Vibrational assignments of six-membered heterocyclic compounds: Normal vibrations of 6-amino uracil and 6-amino 2-thio uracil

Infrared spectra of 6-amino uracil (6AU), 6-amino-2-thio uracil (6A2TU) and their N-deuterated derivatives have been measured over the range 4000-200 cm −1. The fundamental frequencies of these molecules have been assigned on the basis of normal coordinate calculations carried out using a Urey—Bradley potential function supplemented with valence type constants for the out-of-plane modes of the planar skeleton. The results of the vibrational analysis are discussed and correlated with the assignments available for other related molecules.

Molecular vibrations of pyridine-2-thione and pyrimidine-2-thione

Molecular vibrational analyses of two biochemically important molecules, namely pyridine-2-thione and pyrimidine-2-thione, have been made for all the fundamentals employing the Urey—Bradley potential function supplemented with valence force function for the out-of-plane vibrations. The spectra of N-deuterated molecules have also been utilized. The results of the vibrational analyses are discussed in relation to the assignments in structurally related molecules to note the consistency in the assignments.

Force-field model for the stretching anharmonicities of sulfur hexafluoride

A geometrical intramolecular force-field model for the SF/sub 6/ molecule is used to compute spectroscopic parameters. The model includes a general valence harmonic potential whose constants were determined from spectroscopic analysis, plus explicit anharmonicities in the form of (a) a Morse potential in each stretching S-F bond and (b) a Urey-Bradley interaction between each nearest-neighbor nonbonded pair of F atoms. Problems with the Urey-Bradley potential are recognized and treated. Three of the five Morse and Urey-Bradley parameters are constrained to impose consistency with properties of the stretching bond. The other two parameters are varied to find the best agreement with 10 observed anharmonicities involving the stretching modes, nu/sub 1/, nu/sub 2/, and nu/sub 3/. The fits are good, and the best parameters are used to predict unobserved stretching anharmonicities. Attempts to model the bending motions are less successful. 90 references, 8 figures, 9 tables.

Lattice Dynamics of M2XY6 Hexabromometallates: Cs2UBr6

A seven parameter model based on a modified Urey-Bradley potential with long range Coulomb terms is used to describe the lattice dynamics of M2XY6 compounds. Optical data are used to evaluate the force constants for the case of Cs2UBr6. The model is to be used as a starting point for a comprehensive calculation of the vibronic structure of Cs2UBr6.

Far-Infrared and Raman Spectra of Hexachloro Salts of Tetravalent Neptunium

The far-infrared and Raman spectra have been analyzed for the following compounds: dicesium neptunium hexachloride Cs2NpCl6, ditetramethyl ammonium neptunium hexachloride [(CH3)4N]2NpCl6, and ditetraethyl ammonium neptunium hexachloride [(C2H5)4N]2NpCl6. Infrared studies on polycrystalline samples were carried out at room temperature and 98°K. Single-crystal Raman spectra were recorded at room temperature. Far-infrared absorption peaks were found as follows: Cs2NpCl6−265, 117, and 58 cm−1; [(CH3)4N]2NpCl6−259, 116, and 65 cm−1; and [(C2H5)4N]2NpCl6−259, 117, and 59 cm−1. Observed Raman spectra were found as follows: Cs2NpCl6−310 and 128 cm−1; [(C2H5)4N]2NpCl6−301 and 123 cm−1. An interpretation of the observed spectra was made. The interaction force constants necessary to describe the observed spectrum are the Np–Cl stretch, K; the Cl–Np–Cl bend, H; the nonbonded Cl–Cl stretch, F; the interaction, k, between two Np–Cl stretches on opposite sides of the Np atom; and an angle-angle interaction, h, between angles at right angles to each other which share a common bond. The spectrum of the complex NpCl6−2 in each salt can be described by a given set of octahedral force constants, calculated using the Wilson FG matrix technique and a Urey-Bradley potential. The Cs2NpCl6 spectra are described by force constants K=1.31 mdyn/Å, H=0.053 mdyn/Å, F=0.061 mdyn/Å, k=0.40 mdynÅ, and h=0.015 mdyn/Å. The [(CH3)4N]2NpCl6 and [(C2H5)4N]2NpCl6 salts can be described by the force constants K=1.271 mdyn/Å, H=0.053 mdyn/Å, F=0.05 mdyn/Å, k=0.38 mdyn/Å, and h=0.015 mdyn/Å. The spectrum calculated using these parameters agrees to within 1% of the observed spectrum.

Rotational Isomerism in Fluoroacetyl Halides

Infrared and Raman spectra have been recorded for fluoroacetyl fluoride, chloride, and bromide. The data show that each compound exists as an equilibrium mixture of two isomers in the vapor and liquid states. Normal coordinate analysis calculations based on a Urey–Bradley potential function indicate that the two preferred conformations are a trans and a staggered conformation which is close to the cis. In all three compounds the trans isomer is found to be the more stable in both liquid and vapor phases, with its stability being relatively diminished in the vapor state. Approximate, but nearly complete vibrational frequency assignments are made for each isomer. The vapor phase enthalpy difference ΔH° = (H°trans − H°staggered) was measured as − 2.05 ± 0.25 kcal/mole for fluoroacetyl bromide.

Vibrational Assignments and Potential Constants for cis- and trans-1,2-Difluoroethylenes and Their Deuterated Modifications

Infrared and Raman spectra and a complete assignment of vibrational fundamentals are presented for cis- and trans-1,2-difluoroethylenes and their deuterated modifications. For cis-CFHCFH the fundamentals are: (a1) 3122, 1716, 1263, 1015, 237; (a2) 839, 495; (b1) 3136, 1374, 1130, 769; and (b2) 756 cm−1. For trans-CFHCFH the fundamentals are: (ag) 3111, 1694, 1286, 1123, 548; (au) 875, 329; (bg) 788; and (bu) 3114, 1274, 1159, 341 cm−1. The near degeneracy in ν7 and ν12 of the trans isomer is shown from low-temperature crystal and matrix studies and zero-order normal coordinate calculations. Analysis of the rotational structure in the region of the overlapped bands proves that these fundamentals are strongly perturbed by Coriolis coupling. From the vibrational fundamentals and a previous measurement of ΔH°650, the cis isomer is shown to have 1086 cal/mole less electronic energy than the trans isomer. For the in-plane vibrations refined Urey–Bradley potential constants are presented. These constants are obtained from an overlay calculation involving the full set of six molecules. For the out-of-plane vibrations, refined general valence constants, obtained for the separate isomers, are presented.

Rotational Isomerism in Chloroacetyl Halides

Infrared and Raman spectra are reported for the acid fluoride, chloride, and bromide derivatives of chloroacetic acid. Data from vapor, liquid, and solid spectra are given. The results show that these acid halides exist in the vapor and liquid states as a mixture of two isomers, only one of which remains in the solid state. The more stable isomer was found to have the trans conformation. Calculations of the normal vibrations using a Urey–Bradley potential function serve to indicate that the other isomer has a staggered conformation with an azimuthal angle close to 180°. The measured enthalpy differences (H°trans − H°staggered) between the isomers in the vapor state were − 0.76 ± 0.2 kcal/mole, − 0.97 ± 0.2 kcal/mole, and − 1.86 ± 0.27 kcal/mole for the acid fluoride, chloride, and bromide, respectively.

The absorption spectrum of potassium hexafluoronickelate(IV): Infrared and Raman spectra

The infrared and Raman spectra of solid K 2NiF 6 was studied. All the active frequencies ν 1, ν 2, ν 3, ν 4, and ν 5 belonging to the isolated ion point group ( O h ) were ascertained. Several lattice modes were also found in the Raman spectrum. Force constant calculations were carried out for both the general quadratic potential function and the Urey-Bradley potential and the results are compared with those for a similar tetravalent hexafluoro complex K 2PtF 6.

Influence of Nonbonded Interactions on Molecular Geometry and Energy: Calculations for Hydrocarbons Based on Urey—Bradley Field

A modified Urey—Bradley potential energy function comprised of quadratic terms for bond stretches, bond-angle bends, and torsional displacements together with analytical expressions for pairwise nonbonded interactions was chosen to represent the force field for hydrocarbon molecules. Quadratic constants were taken from the spectroscopic U–B analyses of Schachtschneider and Snyder [Spectrochim. Acta 19, 117 (1963)], while the nonbonded functions adopted were those proposed by Bartell [J. Chem. Phys. 32, 827 (1960)]. Reference bond angles for the quadratic terms were taken to be 109.5° or 120° for tetrahedral or trigonal coordination, respectively. Reference single-bond lengths and the torsional constant were adjusted to fit the experimental data for CH4 and C2H6. Double bonds and ring bonds in cyclopropyl compounds were considered to be rigid. The above selections served to establish a universal model force field for hydrocarbons with no remaining adjustable parameters. The potential energy functions for a variety of saturated hydrocarbons and several olefins and cyclopropyl derivatives were minimized with respect to independent structure parameters (i.e., bond stretches, bends, and internal rotations). Even though all C–H (and C–C) bonds were input to be identical to those in CH4 (and C2H6) except for nonbonded environment, the bond lengths and angles corresponding to the minimum potential energy exhibited an appreciable variation from molecule to molecule, as did also the strain energies of geometric and rotational isomers. Calculated trends in structures, isomerization energies, and barriers to rotation agreed quite well with experimentally observed trends, provided that experimental isomerization energies were corrected to 0°K and zero-point energies were taken into account. Some novel features of the results and applications of the model for predicting deformations in strained systems are discussed. The present study differs from previous work in the area of ``molecular mechanics'' in the use of a more general force field, in allowing the strained molecules to relax in all degrees of freedom (except for unsaturated groups and cyclopropyl rings), in the selection of molecular systems, and in a detailed comparison with experiment.

Vibrational Spectra of Vanadium Pentafluoride

The infrared spectrum of VF5 vapor has been studied from 140 to 4000 cm−1. The Raman spectrum has been obtained for the vapor and for the liquid at various temperatures. The spectra indicate a D3h symmetry for the molecule. Fundamental vibrational frequencies observed are: a1′, 719 and 608; a2″, 784 and 331; e′, 810, 282, and (∼200); e″, 350; all in cm−1. Approximate bond-stretching force constants for a modified Urey—Bradley potential function are: Kr=5.51 Mdyn/Å, Kd(axial)=3.94 Mdyn/Å. The Raman spectra show that monomeric molecules are in low concentration in the room-temperature liquid but constitute the main component in the liquid at temperatures above 100°C.

Spectres de vibration et fréquences fondamentales de composés amminés du platine

The infrared spectra of K 2[PtCl 4], [Pt(NH 3) 4]Cl 2, Pt(NH 3) 2Cl 2, [Pt(NH 3) 4] [PtCl 4] and [Pt(NH 3) 4 Cl 2]Cl 2 have been measured between 60 and 3500 cm −1. Assignment of the absorption and Raman bands is reported. The fundamental frequencies of [Pt(NH 3) 4] are calculated assuming a modified Urey-Bradley potential

Normal coordinate analysis of CF 3CH 3, C 2H 6, and C 2F 6

A normal coordinate analysis based on a Urey-Bradley potential has been made of 1,1,1-trifluoroethane. As a check on the transferability of the force constants determined, the vibrational frequencies of ethane and hexafluoroethane were calculated from essentially these constants.

Normal Coordinates of the Planar Vibrations of Pyridine and Its Deuteroisomers with a Modified Urey—Bradley Force Field

A Urey—Bradley potential function has been fitted to the observed vibrational frequencies of pyridine, pyridine-2,6-d2, pyridine-3,5-d2, pyridine-4-d1, and pyridine-d5. As in the case of benzene, it was necessary to include an additional non-Urey—Bradley force constant ρ to describe the aromatic character of the molecule. Our results suggest several minor changes in the vibrational assignment of some of these molecules.

Raman and Infrared Intensities in the Vibrational Spectra of Hydrocarbons. I. Skeletal Vibrations of Straight Zigzag Chains

The vibrational frequencies and normal coordinates of finite, straight, zigzag chains are calculated from an Urey-Bradley potential, the boundary effects being taken into account by a perturbation method. The dominant perturbation terms fall off with 1/N2 (N = number of C atoms) and are found to be negligible for N>5. The intensities of infrared and Raman bands are calculated without using the simplifications implied in ``bond moment'' and ``bond polarizability'' theories. All the vibrations are found inactive as fundamentals in infrared absorption. The Raman active vibrations produce branches of lines with relative intensities approximately 1, 1/9, 1/25..., 1/N2 and with line spacing rapidly decreasing with increasing N. The strong Raman line observed near 890 cm-1 cannot be assigned to a vibration of the carbon skeleton. One low-frequency vibration (v∼1150/N cm-1) perpendicular to the molecular plane should be Raman active. Its low intensity (it has not been observed so far) indicates cylindrical symmetry of the polarizability about the molecular axis.