Relation between dielectric behavior and structure in some solid polypeptides

An attempt to interpret the prominent dielectric relaxations of poly(γ-benzyl L-glutamate) and poly(γ-methyl L-glutamate) in terms of their structures was made by applying the barrier theory of Hoffman. Potential energy maps for the rotation of the polar side group, which are required in this application, were calculated by taking account of molecular environment of the polar side group. The dichroic ratios from infrared measurements were satisfactorily calculated, based on the maps. This provides evidence that the maps are reliable. In applying the barrier theory, it was modified by the assumption that the conformations of the side groups are distributed according to the Boltzmann law. On the basis of the maps, the magnitude of the dielectric absorption and the mean relaxation time were calculated in terms of the modified barrier theory; these were in fairly good agreement with the experimental data.     

Location of protons in N-H···N hydrogen-bonded systems: a theoretical study on intramolecular pyridine-dihydropyridine and pyridine-pyridinium pairs

Two-dimensional potential energy surfaces (PESs) were calculated for the degenerate intramolecular proton transfer (PT) in two N-H···N hydrogen-bonded systems, (Z)-2-(2-pyridylmethylidene)-1,2-dihydropyridine (1) and monoprotonated di(2-pyridyl) ether (2), at the MP2/cc-pVDZ level of theory. The calculated PES had two minima in both cases. The energy barrier in 1 was higher than the zero-point energy (ZPE) level, while that in 2 was close to the ZPE. Vibrational wavefunctions were obtained by solving time-independent Schr?dinger equations with the calculated PESs. The maximum points of the probability density were shifted from the energy minima towards the region where the covalent N-H bond was elongated and the N···N distance shortened. The effects of a polar solvent on the PES were investigated with the continuum or cluster models in such a way that the solute-solvent electrostatic interactions could be taken into account under non-equilibrated conditions. A solvated contact ion-pair was modelled by a cluster consisting of one cation 2, one chloride ion and 26 molecules of acetonitrile. The calculation with this model suggested that the bridging proton is localised in the deeper well due to the significant asymmetry of the PES and the high potential barrier.     

Conformational energy analysis of substituted diphenylethanes: Part VI. Calculations of the solvent dependence of the conformational equilibria in stilbene dihalogenides. Intramolecular interactions in the PCILO fr

As part of a theoretical analysis of the conformational equilibria of stilbene dihalogenides, the free energy at 300 K of each stable conformational isomer of these molecules has been estimated for a solvent of dielectric constant 3.5. Classical empirical potential functions were used. Interaction with the solvent was considered only in terms of a continuous dielectric medium interacting with the local dipoles and quadrupoles of the molecule. Simulation of the experimental conditions (i.e. appropriate values for the dielectric constant of the solvent) yielded better agreement with the available experimental data, which were mainly dipole moments and optical rotation values. The quadrupole energy term has a very small influence on the calculated conformational populations and can be neglected when dibenzyl derivatives are considered. The mechanism of the intramolecular interactions is discussed within the PCILO framework.     

Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins

We report a detailed analysis of the potential energy surface of N-acetyl-l-tryptophan-N-methylamide, (NATMA) both in the gas phase and in solution. The minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. The full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. The calculated energy maps correspond to the intrinsic conformational propensities of the individual NATMA molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. For this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. In native proteins, tryptophan conformations have strong preferences for the beta sheet, right-handed helix, tight turn, and bridge structures. The conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.     

Ab initio Study on Ionization Energies of 3-Amino-1-propanol

Fourteen conformers of 3-amino-1-propanol as the minima on the potential energy surface are examined at the MP2/6-311++G** level. Their relative energies calculated at B3LYP, MP3 and MP4 levels of theory indicated that two most stable conformers display the in-tramolecular OH…N hydrogen bonds. The vertical ionization energies of these conformers calculated with ab initio electron propagator theory in the P3/aug-cc-pVTZ approximation are in agreement with experimental data from photoelectron spectroscopy. Natural bond orbital analyses were used to explain the differences of IEs of the highest occupied molec-ular ortibal of conformers. Combined with statistical mechanics principles, conformational distributions at various temperatures are obtained and the temperature dependence of pho-toelectron spectra is interpreted.     

Theoretical studies of the N2O van der Waals dimer: ab initio potential energy surface, intermolecular vibrations and rotational transition frequencies

Theoretical studies of the potential energy surface and bound states were performed for the N(2)O dimer. A four-dimensional intermolecular potential energy surface (PES) was constructed at the CCSD(T) level with aug-cc-pVTZ basis set supplemented with bond functions. Three co-planar local minima were found on this surface. They correspond to a nonpolar isomer with slipped-antiparallel planar structure and two equivalent polar isomers with slipped-parallel planar structures. The nonpolar isomer is energetically more stable than the polar ones by 162 cm(-1). To assign the fundamental vibrational frequencies for both isomers, more than 150 vibrational bound states were calculated based on this PES. The orientation of the nodal surface of the wave functions plays an important role in the assignment of disrotation and conrotation vibrational modes. The calculated vibrational frequencies are in good agreement with the available experimental data. We have also found a quantum tunneling effect between the two equivalent polar structures in the higher vibrational excited states. Rotational transition frequencies of the polar structure were also calculated. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters.     

Ab initio vibrational transition dipole moments and intensities of formaldehyde

Vibrational transition dipole moments and absorption band intensities for the ground state of formaldehyde, including the deuterated isotopic forms, are calculated. The analysis is based on ab initio SCF and CI potential energy and dipole moment surfaces. The formalism derives from second-order perturbation theory and involves the expansion of the dipole moment in terms of normal coordinates, as well as the incorporation of point group symmetry in the selection of the dipole moment components for the allowed transitions. Dipole moment expansion coefficients for the three molecule-fixed Cartesian coordinates of formaldehyde are calculated for internal and normal coordinate representations. Transition dipole moments and absorption band intensities of the fundamental, first overtone, combination, and second overtone transitions are reported. The calculated intensities and dipole moment derivatives are compared to experiment and discussed in the context of molecular orbital and bond polarization theory.     

Relative stability,potential barrier and intensity parameters of the trans and cis isomers of fluoroacetyl fluoride: An ab initio study

Ab initio calculations have been performed to determine molecular geometries, relative stabilities and the potential barrier of the fluoroacetyl fluoride molecule. The calculations indicate the existence of two stable conformations, trans and cis, in agreement with experimental studies. The potential barrier presents a maximum around 80° and an energy difference of ⋍ 17.5 kJ mol⁻¹ with respect to the most stable conformer (trans). These calculations also confirm that this conformer is more polar than the cis form, with the total dipole moment oriented along the carbonylic bond. The intensity parameters of the trans and cis isomers in terms of their atomic polar tensors have been analysed using the “charge-charge flux-overlap” model. The calculations predict similar atomic polar tensors for both forms, suggesting practically equivalent electronic structures in the ground state.     

Molecular theory of dielectric relaxation in nematic dimers

This paper reports a theory for the dielectric relaxation of dimeric mesogenic molecules in a nematic liquid crystal phase. Liquid crystal dimers consist of two mesogenic groups linked by a flexible chain. Recent experimental studies [D. A. Dunmur, G. R. Luckhurst, M. R. de la Fuente, S. Diez, and M. A. Perez Jubindo, J. Chem. Phys. 115, 8681 (2001)] of the dielectric properties of polar liquid crystal dimers have found unexpected results for both the static (low frequency) and variable frequency dielectric response of these materials. The theory developed in this paper provides a quantitative model with which to understand the observed experimental results. The mean-square dipole moments of alpha,omega-bis[(4-cyanobiphenyl-4'-yl]alkanes in a nematic phase have been calculated using both the rotational isomeric state model and a full torsional potential for the carbon-carbon bonds of the flexible chain. The orienting effect of the nematic phase is taken into account by a parametrized potential of mean torque acting on the mesogenic groups and the segments in the flexible chain. Results of calculations using the full torsional potential are in excellent agreement with experimental results for comparable systems. The probability density p(eq)(beta(A),beta(B)) for the orientation of the mesogenic groups (A,B) along the nematic director is also calculated. The resultant potential of mean torque is a surface characterized by four deep energy wells or sites equivalent to alignment of the terminal groups A and B approximately parallel and antiparallel to the director; of course, the reversal of the director leads to equivalent sites. This potential energy surface provides the basis for a kinetic model of dielectric relaxation in nematic dimers. Solution of the Fokker-Planck equation corresponding to this four-site model gives the time dependence of the site populations, and hence the time-correlation functions for the total dipole moment along the director. In this model the end-over-end rotation of the molecule, corresponding to simultaneous reversal of both mesogenic groups, is excluded because the activation energy is too large. Results are presented for a number of cases, in which a dipole is located on one or both of the mesogenic groups, and additionally where the groups differ in size. For the latter, under particular conditions, the correlation function exhibits a biexponential decay, which corresponds to two low frequency absorptions in the dielectric spectrum. This is exactly what has been observed for nonsymmetric nematic dimers having different groups terminating a flexible chain. Experimental results over a range of temperature for the nonsymmetric dimer alpha-[(4-cyanobiphenyl)-4'-yloxy]-omega-(4-decylanilinebenzylidene-4'-oxy)nonane can be fitted precisely to the theory, which provides new insight into the orientational and conformational dynamics of molecules in ordered liquid crystalline phases.     

Empirical methods for computing molecular partition coefficients: II. Inclusion of conformational flexibility within fragment–based approaches

A novel algorithm for computing the water/1-octanol partition coefficient, log P , of conformationally flexible molecules, has been investigated using calculations upon a number of uncharged, linear dipeptides. In this method (which appears to be the first to consider explicitly the effects of the population of accessible conformational minima in both phases), the partition coefficient for each dipeptide was calculated from the overall energy change associated with moving the relevant gas-phase conformational distribution into water and into 1-octanol. These energies were computed using solvation contributions based upon the solvent accessible molecular surface area and two sets of empirical parameters. In these initial studies, gas-phase conformational minima were generated using systematic search methods. While the standard error in the computed log P values was disappointing, reasonable agreement was observed between calculated and experimental log P values for the set of model dipeptides, especially when specific hydration interactions involving polar fragments were correctly included in the empirical solvation term. These results indicate that the physical basis of many correction factors employed in the ClogP algorithm for computing log P probably arise from neglect of the redistribution of conformer populations as flexible molecules partition between water and 1-octanol.     

Relationship between structure and dielectric behavior of stereoregular poly(methyl methacrylate) in the glassy state

In order to elucidate the relationship between dielectric behavior and structure in solid polymers, we studied the dielectric relaxation of stereoregular poly(methyl methacrylate) (PMMA) in the glassy state. Assuming that the extremes of molecular structure are attained in the crystal and in solution, the most probable conformation of the main chain in the glassy state is estimated for isotactic and syndiotactic PMMA in terms of conformational analysis, the unperturbed mean-square end-to-end distance in solution, and the NMR second moment in the glassy state. Under the assumption that the molecular structure varies in a limited range near the most probable conformation and that the α-methyl group rotates freely, the energy barrier for the rotation of the side group is calculated. With the calculated energy barrier, the dielectric relaxation due to the side group is interpreted fairly satisfactorily by the barrier theory of Hoffman and Lauritzen, although the width of the relaxation curve is not. The experimental result that the loss peak of syndiotactic PMMA is located at higher temperature than that of isotactic PMMA is interpreted qualitatively in terms of different conformations for the syndiotactic and isotactic chains.     

Nonlinear dielectric effect (NDE) and molecular orbital study of the conformational equilibrium in 1,4-dimethoxybenzene in benzene solution

The conformational equilibrium in 1,4-dimethoxybenzene (1,4-DMB) in benzene solutions has been studied. On the basis of experimental values of the nonlinear dielectric effect (NDE) parameter, electric permittivity and density, determined in this work, and applying the general statistical theory of NDE, the contributions of the syn-anti and syn-syn conformers and the electric dipole moment of the polar syn-syn conformer were calculated. The molecular orbital method (PM3) has also been applied for calculation of the dipole moments and energies of particular conformers. The results of the NDE study and PM3 calculations are consistent and they reveal the existence of two conformers (syn-anti and syn-syn) of comparable energy values, but different values of dipole moments, and the predominance of the polar form (syn-syn) of the mole fraction in benzene. Moreover, the energies of intermolecular interactions have been determined from the concentration dependence of linear and nonlinear polarisability.     

Density functional theory study of the Jahn-Teller effect and spin-orbit coupling for copper and gold trimers

The Born-Oppenheimer potential energy hypersurfaces of copper and gold trimers were calculated using density functional theory with an analytic potential. The calculated Jahn-Teller distortion energies, pseudorotation barriers, dissociation, and isomerization energies for the two trimers are discussed. Global minima from the surfaces were optimized using the density functional theory method as well as the coupled cluster-singles-doubles-with-triples energies technique. The agreement of the optimized structures with the analytic potential was very good. The Mulliken population analysis compared favorably with the experimental electron spin resonance results. Spin-orbit coupling was subsequently included and the effect was significant for gold, but negligible for copper. The spin-orbit effect suppressed the Jahn-Teller distortion of the gold trimer, and the potential surface with the spin-orbit effect included was also obtained. The spin-orbit splitting for the D(3h) geometry of the gold trimer was in excellent agreement with the most recent infrared spectroscopic results.     

DFT and MD studies on the influence of the orientation of ester linkage groups in banana-shaped mesogens

The influence of the direction of ester linkage groups on the structural and electronic properties of five-ring banana-shaped molecules with a central 1,3-phenylene unit has been investigated including hexyloxy and dodecyloxy terminal chains. DFT studies on the B3LYP/6-31G(d) level were performed on the conformational behaviour of the ten isomers in a systematic way. The one- and two-fold potential energy scans show that the flexibility of the wings significantly depends on the orientation of the carboxyl linkage groups. Moreover, the different directions of the carboxyl groups between the aromatic rings cause remarkable changes on the dipole moment and its components of the molecules. These findings are supported by investigations on the global charge pattern of the molecules calculated from electrostatic potential group charges. The bending angle alpha obtained from a simple model for the five-ring bent-core molecules is a characteristic structural parameter which can be correlated with experimental findings. Calculations on the bent-core molecules in an external electric dipole field related to the direction of their polar axis show remarkable effects with respect to the flexibility and polarity of the isomers. First molecular dynamics simulations on the banana-shaped molecules were carried out within the AMBER 7 package. The trajectories of relevant structural parameters support the findings of the DFT studies. The results concerning the structure and polarity revealed from the DFT and MD calculations of the ten isomers can be correlated with data from dielectric measurements and mesophase properties.     

A theoretical study of the electronic structure of nitroethylene

The electronic ground state of nitroethylene in its planar and perpendicular conformations is studied by ab initio SCF calculations using Gaussian-lobe basis functions. The internal-rotation barrier of the nitro group has been calculated to be 6.02 kcal/mole. The dipole moment, the electric field gradient at the nitrogen and the diamagnetic contribution to the nuclear shielding for the protons have been calculated from the molecular wavefunction. Calculated and reported experimental values are in satisfactory agreement with each other. In terms of the population analysis, the electronic charge distribution has also been studied.     

Torsion angle preference and energetics of small-molecule ligands bound to proteins

Small organic molecules can assume conformations in the protein-bound state that are significantly different from those in solution. We have analyzed the conformations of 21 common torsion motifs of small molecules extracted from crystal structures of protein-ligand complexes and compared them with their torsion potentials calculated by an ab initio DFT method. We find a good correlation between the potential energy of the torsion motifs and their conformational distribution in the protein-bound state: The most probable conformations of the torsion motifs agree well with the calculated global energy minima, and the lowest torsion-energy state becomes increasingly dominant as the torsion barrier height increases. The torsion motifs can be divided into 3 groups based on torsion barrier heights: high (>4 kcal/mol), medium (2-4 kcal/mol), and low (<2 kcal/mol). The calculated torsion energy profiles are predictive for the most preferred bound conformation for the high and medium barrier groups, the latter group common in druglike molecules. In the high-barrier group of druglike ligands, >95% of conformational torsions occur in the energy region <4 kcal/mol. The conformations of the torsion motifs in the protein-bound state can be modeled by a Boltzmann distribution with a temperature factor much higher than room temperature. This high-temperature factor, derived by fitting the theoretical model to the experimentally observed conformation occurrence of torsions, can be interpreted as the perturbation that proteins inflict on the conformation of the bound ligand. Using this model, it is calculated that the average strain energy of a torsion motif in ligands bound to proteins is approximately 0.6 kcal/mol, a result which can be related to the lower binding efficiency of larger ligands with more rotatable bonds. The above results indicate that torsion potentials play an important role in dictating ligand conformations in both the free and the bound states.     

Density Functional Studies of the C?F Bond Activation of CF3 Radical by Bare Co+

The C? F bond activation mechanism of CF₃ radical by bare Co⁺ has been studied by density functional theory. Three local minima and two first‐order saddle points were located for the potential energy surface (PES) of [Co, C, F₃]⁺. The activation barrier involving C? F bond activation was calculated to be only 14.73 kJ/mol, while the largest barrier of 149.29 kJ/mol on the FES involves Co? C bond rupture. The bonding mechanism between Co⁺, C and F atoms were discussed based on Mulliken population. The relevant bond dissociation energy and thermochemistry data were calculated with the limited experimental values, and the results are in good agreement with the experimental findings.     

Conformational equilibria in halocyclohexanones,an NMR and solvation study

The conformational equilibrium in 2-chloro cyclohexanone is measured in thirteen solvents from the 220 MHz¹H NMR spectrum using the C₂-H couplings and chemical shifts and the cis and trans 4-t-butyl-2-chlorocyclohexanones as reference compounds. ΔG_ea varies from 1.04 $\text{kcal}\text{mole}$ in n-pentane to ?0.58 $\text{kcal}\text{mole}$ in DMSO. The large concentration dependence of the NMR parameters in non-polar solvents noted previously is confirmed.Generalised reaction-field theory is used to calculate this solvent dependence, using a refined model of the geometry and dipole moments of the conformers.The cyclohexanone ring is considerably flatter than that of cyclohexane and this has an appreciable effect on the resultant dipole moments. Use of this geometry and CO and C-Cl bond moments which reproduce the observed dipole moments of the t-butyl compounds together with the generalised reaction field theory gives calculated solvation energies in good agreement with the observed data and hence allows the prediction of the vapour state energy difference.The model is applied to a variety of halo-ketones and gives both a reasonable explanation of the observed solvent dependencies and also the vapour state energy differences.The vapour state conformer energies are compared with the corresponding values for the halocyclohexanes and illustrate the large polar and steric effects due to the introduction of the CO group.     

Potential energy surface, van der Waals motions, and vibronic transitions in phenol-argon complex

The structure and intermolecular vibrational energy levels of the phenol-Ar complex are calculated from its potential energy surface. This surface is constructed from a large set of the interaction energy values computed using second-order Moller-Plesset perturbation theory with the augmented correlation consistent polarized valence double-zeta basis set. The global minimum in the potential energy surface corresponds to a cluster structure with Ar located over the geometric center of the phenol ring at a distance of 3.510 A and shifted by 0.1355 A towards oxygen. The calculated dissociation energy of 371 cm(-1) is in accordance with the experiment. Additional local minima higher in energy are with Ar placed in the phenol plane. However, they are too shallow to form the bound states corresponding to planar isomers. The deformation of the potential energy surface shape, created by the interaction of Ar with the phenolic oxygen, is responsible for a pronounced intermode mixing. As a result, a set of hybrid stretching-bending states appears which cannot be described in terms of the standard models. The intermode coupling is reflected in the vibronic structure of the S1-S0 electronic transition. The intensities of the vibronic bands are calculated from the electronic transition dipole moment surfaces determined using the ab initio single-excitation configuration interaction method. They allow us to correct and complete the assignment of the spectra observed in phenol-Ar, as well as in the analogous complexes of phenol with Kr and Xe.     

Local Structures and Chemical Properties of Deprotonated Arginine

The potential energy surface of gaseous deprotonated arginine has been systematically in- vestigated by first principles calculations. At the B3LYP/6-31G(d) level, apart from the identification of several stable local structures, a new global minimum is located which is about 6.56 kJ/mol more stable than what has been reported. The deprotonated arginine molecule has two distinct forms with the deprotonation at the carboxylate group (COO^-). These two forms are bridged by a very high energy barrier and possess very different IR spectral profiles. Our calculated proton dissociation energy and gas-phase acidity of argi-nine molecule are found to be in good agreement with the corresponding experimental results. The predicted geometries, dipole moments, rotational constants, vertical ionization energies and IR spectra of low energy conformers will be useful for future experimental measurements.