Dipole Interaction Model Research Articles

Microscopic and Macroscopic Polarization in C60 Fullerene Clusters as Calculated by an Electrostatic Interaction Model

The dipole−dipole polarizability, α, and the second hyperpolarizability, γ, as well as the corresponding linear and third-order susceptibilities, χ(1) and χ(3), have been calculated for C60 fullerene clusters by a point−dipole interaction (PDI) model. The size dependences of a linear chain, a monolayer film, and a face-centered cubic crystal cluster have been investigated. It is found that the effects of the surrounding molecules on the molecular α and γ are large, in particular for the chain and the film because of the anisotropic surroundings, and that large clusters are required to obtain converged results. A localized PDI model gives the opportunity to divide α and γ into fragment contributions, and it is found that α and γ of molecules in the middle of the chain converge slower than the properties for the end molecules with respect to the length of the chain. Similar results are found for the monolayer film. Finally, χ(1) and χ(3) have been calculated by using a modified local-field theory including ...

Computation and Analysis of Protein Circular Dichroism Spectra

Publisher Summary This chapter presents computation and analysis of protein circular dichroism (CD) spectra. The origins of electronic CD in proteins, theoretical methods for computing protein CD, and empirical analysis of CD for estimating structural composition of proteins are described. The phenomenon of CD involves the absorption of light and it can be considered as a special type of absorption spectroscopy. The CD spectra of proteins are generally divided into three wavelength ranges, based on the energy of the electronic transitions that dominate in the given range. The basic approach used to compute the CD of complex systems, such as proteins and nucleic acids, is the divide and conquer approach. In addition to the isotropic atomic polarizabilities, the anisotropic polarizability of the first electrically allowed peptide transition was included in the dipole interaction model for protein CD calculations. Polarizability anisotropy data for simple amides were used for obtaining polarizability parameters. It is found that the CD spectrum of the typical β sheet has a negative band near 215-nm and a positive band near 198 nm.

Non-covalent and coordination interactions in Cu(II) systems with uridine, uridine 5′-monophosphate and triamine or tetramine as biogenic amine analogues in aqueous solutions

Reactions of metallation and non-covalent interactions have been studied in ternary systems of Cu(II) ions with uridine, uridine 5′-monophosphate and diamines or triamines. It has been found that in metal-free systems the reaction centres of the nucleoside with the polyamine are the donor nitrogen atoms N(3) and protonated –NH x groups of the amines. In comparison to systems with adenosine or cytidine, the pH range of complex formation is shifted towards higher values. It is a consequence of significantly higher basicity of uridine and in agreement with the ion–ion, ion–dipole interaction model assumed. Formation of molecular complexes of uridine 5′-monophosphate with polyamines at a low pH is the result of activity of the phosphate group which plays the role of a negatively charged reaction site. Non-covalent interactions interfere in processes of bioligand metallation. Centres of weak interactions are simultaneously binding sites of metal ions. In protonated Cu(Urd)(PA)H x complexes, coordination has been found to involve the N(3) atom from the nucleoside and two donor nitrogen atoms from the polyamine (PA). In the heteroligand species Cu(Urd)(PA), despite deprotonation of all amine groups, one of these groups is located outside the inner coordination sphere. In complexes with uridine-5′-monophosphate, the phosphate group is active in metallation. Moreover, in certain coordination compounds this group is engaged in non-covalent interactions with PA molecules, despite binding Cu ions, as has been shown on the basis of equilibrium and spectral studies.

A discrete solvent reaction field model for calculating molecular linear response properties in solution

A discrete solvent reaction field model for calculating frequency-dependent molecular linear response properties of molecules in solution is presented. The model combines a time-dependent density functional theory (QM) description of the solute molecule with a classical (MM) description of the discrete solvent molecules. The classical solvent molecules are represented using distributed atomic charges and polarizabilities. All the atomic parameters have been chosen so as to describe molecular gas phase properties of the solvent molecule, i.e., the atomic charges reproduce the molecular dipole moment and the atomic polarizabilities reproduce the molecular polarizability tensor using a modified dipole interaction model. The QM/MM interactions are introduced into the Kohn–Sham equations and all interactions are solved self-consistently, thereby allowing for the solute to be polarized by the solvent. Furthermore, the inclusion of polarizabilities in the MM part allows for the solvent molecules to be polarized by the solute and by interactions with other solvent molecules. Initial applications of the model to calculate the vertical electronic excitation energies and frequency-dependent molecular polarizability of a water molecule in a cluster of 127 classical water molecules are presented. The effect of using different exchange correlation (xc)-potentials is investigated and the results are compared with results from wave function methods combined with a similar solvent model both at the correlated and uncorrelated level of theory. It is shown that accurate results in agreement with correlated wave function results can be obtained using xc-potentials with the correct asymptotic behavior.

Saturation of the Third-Order Polarizability of Carbon Nanotubes Characterized by a Dipole Interaction Model

An atomic dipole interaction model has been used for calculating the second hyperpolarizability of carbon nanotubes on a length scale up to 75 nm. It is demonstrated that an atomistic representation of mesoscale systems such as nanotubes can be used to obtain a cubic response property up to a size of the system where the property scales linearly with increasing size. In particular, it demonstrates that atomistic models are useful also for designing nonlinear molecular materials, where local modifications may give large macroscopic contributions. The saturation length has been calculated for carbon nanotubes. It is found that carbon nanotubes are comparable to conjugated polymers with respect to the magnitude of the second hyperpolarizability and are therefore very promising candidates for future nonlinear optical materials.

Dipole interaction model predicted pi-pi* circular dichroism of cyclo(L-Pro)3 using structures created by semi-empirical, ab initio, and molecular mechanics methods.

Cyclo(l-Pro)3 (CP3) is a synthetic peptide created to model cis and torsionally strained peptide bonds that also exhibits a strong distinctive UV circular dichroic (CD) spectrum. Circular dichroic spectra were computed for the amide pi-pi* transition using the dipole interaction model for various conformations of the peptide. Conformations of CP3 were created initially from crystal data, and followed by energy minimizations via molecular mechanics using the cvff force field; the effects of additional geometric optimizations by semi-empirical and ab initio quantum mechanics were investigated. The CD spectra for each conformation were calculated using a variety of different parameters, and each result was compared with the published experimental spectrum [Deber, C.M., Scatturin, A., Vaidya, V.M. & Blout, E.R. (1970) Small cyclic proline peptides: UV absorption and CD. In: Peptides: Chemistry and Biochemistry, Proceedings of the First American Peptide Symposium (Weinstein, B., ed.), Marcel Dekker, New York pp. 163-173]. Herein, two distinct conformations, a C3 symmetric and an asymmetric form, gave CD predictions that separately did not resemble the experimental spectrum. Energy differences were predicted at various theoretical levels, including MP2 and density functional theory. When the predicted CD spectra for each conformation were multiplied by Boltzmann weighting factors created using heats of formation determined by the AM1 optimizations, the weighted composite CD spectrum created did resemble experiment for the pi-pi* transition indicating that both conformations may exist simultaneously in solution.

A Dipole Interaction Model for the Molecular Second Hyperpolarizability

A dipole interaction model (IM) for calculating the molecular second hyperpolarizability, γ, of aliphatic and aromatic molecules has been investigated. The model has been parametrized from quantum chemical calculations of γ at the self-consistent field (SCF) level of theory for 72 molecules. The model consists of three parameters for each element p: an atomic polarizability, an atomic second hyperpolarizability, and an atomic parameter, Φp, describing the width of the atomic charge distribution. The Φp parameters are used for modeling the damping of the interatomic interactions. Parameters for elements H, C, N, O, F, and Cl were determined, and typical differences between the molecular γ derived from quantum chemical calculations and from the IM are below 30% and on average around 10%. As a preliminary test, the dipole interaction model was applied to the following molecular systems not included in the training set: the urea molecule, linear chains of urea molecules, and C60. For these molecules deviations of the IM result for the molecular γ from the corresponding SCF value were at most around 30% for the individual components, which in all cases is a better performance than obtained with semiempirical methods.

Medium perturbations on the molecular polarizability calculated within a localized dipole interaction model

We have studied the medium effects on the frequency-dependent polarizability of water by separating the total polarizability of water clusters into polarizabilities of the individual water molecules. A classical frequency-dependent dipole–dipole interaction model based on classical electrostatics and an Unsöld dispersion formula has been used. It is shown that the model reproduces the polarizabilities of small water clusters calculated with time-dependent density functional theory. A comparison between supermolecular calculations and the localized interaction model illustrate the problems arising from using supermolecular calculations to predict the medium perturbations on the solute polarizability. It is also noted that the solute polarizability is more dependent on the local geometry of the cluster than on the size of the cluster.

Amide I vibrational modes in glycine dipeptide analog: Ab initio calculation studies

Coupling between two local amide I vibrational motions of peptides has been quantitatively estimated by assuming that the two peptides interact with each other via dipole–dipole interaction, the so-called transition dipole coupling (TDC) model. The TDC theory has been applied to describing amide I IR and Raman band envelopes and further used to interpret the two-dimensional IR pump–probe and photon echo spectra of polypeptides recently. In order to quantitatively test the validity of the TDC model or in general dipole–dipole interaction model for a dipeptide, we carry out systematic investigations, by using both the ab initio calculation methods and extended TDC theory, on the potential energy surface, vibrational frequencies of symmetric and antisymmetric amide I vibrational normal modes, transition dipole and transition polarizability, IR and Raman intensities of the two modes, IR-Raman noncoincidence phenomena in the full Ramachandran space for a model dipeptide, glycine dipeptide analog. It is found that the spectroscopic properties of dipeptide can be quantitatively well described by the TDC model, but the quantities related to the potential energy surface such as absolute magnitudes of vibrational frequencies and frequency splitting between the two normal modes cannot be accounted for by using the TDC model. A further investigation of dimeric system with two formamide molecules is presented and the applicability of the TDC model to through space vibrational interaction as a function of intermolecular distance between the two peptides is examined.

Polarizability of molecular clusters as calculated by a dipole interaction model

We have developed and investigated a dipole interaction model for calculating the polarizability of molecular clusters. The model has been parametrized from the frequency-dependent molecular polarizability as obtained from quantum chemical calculations for a series of 184 aliphatic, aromatic, and heterocyclic compounds. A damping of the interatomic interaction at short distances is introduced in such a way as to retain a traceless interaction tensor and a good description of the damping over a wide range of interatomic distances. By adopting atomic polarizabilities in addition to atom-type parameters describing the damping and the frequency dependence, respectively, the model is found to reproduce the molecular frequency-dependent polarizability tensor calculated with ab initio methods. A study of the polarizability of four dimers has been carried out: the hydrogen fluoride, methane, benzene, and urea dimers. We find in general good agreement between the model and the quantum chemical results over a wide range of intermolecular distances. To demonstrate the power of the model, the polarizability has been calculated for a linear chain of urea molecules with up to 300 molecules and one- and two-dimensional clusters of C60 with up to 25 molecules. Substantial intermolecular contributions are found for the polarizability anisotropy, whereas the effects are small for the mean polarizability. For the mean polarizability of C60, we find good agreement between the model and experiments both in the case of an isolated molecule and in a comparison of a planar cluster of 25 C60 molecules with experimental results on thin films.

Frequency-Dependent Polarizability of Boron Nitride Nanotubes: A Theoretical Study

In the present work, we have calculated the static and frequency-dependent polarizability tensors for a series of single-walled boron nitride nanotubes and compared them with corresponding results for carbon nanotubes. The calculations have been performed by employing a dipole−dipole interaction model based on classical electrostatics and an Unsold dispersion formula. In comparison, we have carried out ab intio calculations at the SCF level of the static polarizability of the smaller nanotubes with the STO-3G basis set. For the frequency-dependent polarizability of C60, we found excellent agreement among the most accurate SCF calculations in the literature, the interaction model, and experimental results. In particular, the frequency dependence is modeled accurately indicating that the interaction model is a useful tool for studying the frequency dependence of materials. For the nanotubes, we observe the same trends in the interaction model and in the SCF STO-3G results when the number of atoms is increas...

Simulation théorique du spectre d'absorption UV du carbazole et de quelques molécules analogues: Theoretical simulation of UV absorption spectrum of carbazole and some homocyclic analogues

The UV absorption spectra structures of carbazole, fluorene and dibenzofurane are studied using the atom monopole–dipole interaction (AMDI) model and atomic dipolar polarisabilities and effective charge given by Fraga. The absorption spectra corresponding to these molecules and their self-associations are presented. The original obtained results are discussed and compared to previous works.

Etude des transitions électroniques de l’azulène et de quelques-uns de ses dérivés et de leurs auto-associations par le modèle d’interaction monopôle–dipôle atomique (AMDI)

The corresponding hydrogen, carbon and nitrogen atomic dipolar polarisabilities and effective charges given by Fraga are used for the determination of theoretical UV absorption spectra of azulene, 1,3-diaza-azulene and 2-phenyl-1,3-diaza-azulene and their self-associations. These spectra are obtained for the first time using the atom monopole–dipole interaction model and compared to those given experimentally by other authors.

Electron Spin−Lattice Relaxation Measurement of the 3Fe-4S (S-3) Cluster in Succinate:Ubiquinone Reductase from Paracoccus Denitrificans. A Detailed Analysis Based on a Dipole−Dipole Interaction Model

The electron spin−lattice relaxation for the 3Fe-4S (S-3) center in succinate:ubiquinone reductase has been examined using both inversion recovery and “picket-fence” pulse sequences at a temperature range of 4−8 K. The latter pulse sequence is used to eliminate the interference of spectral diffusion in frozen solids. An abnormally fast relaxation was observed for the S-3 center. We attribute this rapid relaxation to a magnetic dipolar interaction between the S-3 center and a nearby paramagnetic b-heme (cytochrome b). A model has been developed to treat the interaction between two paramagnetic redox centers in a rigid lattice at a fixed distance apart but with random orientations in a magnetic field. Both the contribution to the spin−lattice relaxation rate from the dipolar interaction (k1θ), which is anisotropic, and the intrinsic electron spin relaxation, which is scalar (k1scalar), have been deduced. We find that the contribution of exchange interaction to the anisotropic part of the relaxation rate (k1θ) is very small. Accordingly, we conclude that k1scalar is dominated by the intrinsic electron spin−lattice relaxation. From k1θ, a lower limit (r > 10 Å) has been deduced for the distance between the S-3 center and the b-heme.

Molecular dynamics simulation of the homogeneous nucleation of UF6 molecules: Configurations and infrared spectra of the excited hot clusters

The temperature, potential energy, and configurations of the clusters produced in the homogeneous nucleation of UF6 molecules from the supercooled (supersaturated) vapor phase were determined by classical molecular dynamics (MD) simulations. We observed two phenomena which demonstrate that the nucleation process occurs in the state far from thermal equilibrium. First, the excited hot clusters, the temperature of which is much higher than that of the monomer, were produced and continued to exist during the nucleation process. Second, the relationship between the potential energy and temperature of the clusters depends on the monomer temperature, that is, the potential energy at a temperature decreases with the increase in monomer temperature. In the simulations, various types of cluster configurations were observed: prolate, oblate, spherelike, and confeitolike. The confeitolike cluster is composed of one core and a few horns, and it was found predominantly in the hotter clusters. The infrared spectra of the UF6 clusters were calculated using a dipole–dipole and dipole-induced dipole interaction model and compared with those measured in a supercooled state by Tanimura et al. [J. Chem. Phys. 107, 7096 (1997)]. As a result, we found that the spectra measured in the supercooled state can be attributed to the excited hot clusters, the configuration of which are confeitolike.

Helix bundles and coiled coils in alpha-spectrin and tropomyosin: a theoretical CD study.

The dipole interaction model is used to investigate the effects of interactions between helices and supertwisting of helices by determining whether the predicted UV absorption and CD spectra for the three-helix bundle and coiled coil are significantly different from spectra for the single straight alpha-helix. Crystallographic data by Yan et al. for alpha-spectrin are used to construct a three-helix bundle of poly(L-alanine) modeling the protein. Backbone torsion angles represented by Fourier series are used to generate supertwisted helices and coiled coil models of poly(L-alanine) that have pitch, radius, and residue repeat similar to experimental crystallographic data on tropomyosin. Calculated CD spectra are compared with available experimental data. Theoretical spectra for the three-helix bundle and the supertwisted structures are quite similar to predictions for the straight alpha-helix of the same length with similar torsion angles, suggesting that CD is primarily dependent on the average backbone conformation and would not be a sensitive tool for distinguishing between single straight helices and closely packed or twisted alpha-helices.

Globular Protein Ultraviolet Circular Dichroic Spectra. Calculation from Crystal Structures via the Dipole Interaction Model J. Am. Chem. Soc. 1998, 120, 10938−10946

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionGlobular Protein Ultraviolet Circular Dichroic Spectra. Calculation from Crystal Structures via the Dipole Interaction Model J. Am. Chem. Soc.1998, 120, 10938−10946Kimberly A. Bode and Jon ApplequistCite this: J. Am. Chem. Soc. 1998, 120, 51, 13545Publication Date (Web):December 11, 1998Publication History Published online11 December 1998Published inissue 1 December 1998https://doi.org/10.1021/ja9855343Copyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views207Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (20 KB) Get e-Alerts Get e-Alerts

Globular Protein Ultraviolet Circular Dichroic Spectra. Calculation from Crystal Structures via the Dipole Interaction Model

The dipole interaction model is used to calculate ultraviolet circular dichroic spectra of 16 globular proteins with various amounts of helix, sheet, and disordered regions. Structures for the calculations are based on crystal coordinates taken from the Brookhaven Protein Data Bank. Calculations for “reassembled fragment” models of the proteins reproduce the main features of observed solution CD spectra in the region of the amide π−π* transition near 200 nm. The predicted spectra for helix and sheet regions show considerable variation in magnitudes and wavelengths of the CD peaks, and a still wider variation is predicted for the disordered regions. A comparison of reassembled-molecule spectra with weighted averages of the spectra of the component fragments shows that deviations from additivity of the component spectra are generally small. The implications of these findings for attempts to resolve observed CD spectra in terms of a small number of components are discussed.

Molecular and Atomic Polarizabilities: Thole's Model Revisited

Thole's modified dipole interaction model for constructing molecular polarizabilities from effective, isotropic atomic polarizabilities is reviewed and extended. We report effective atomic polarizabilities for H, C, N, O, S, and the halogen atoms, independent of their chemical environment. They are obtained by fitting the model both to experimental and calculated molecular polarizabilities, the latter to enable one to model ab initio polarizabilities for various basis sets.

Helix bundles and coiled coils in α-spectrin and tropomyosin: A theoretical CD study

The dipole interaction model is used to investigate the effects of interactions between helices and supertwisting of helices by determining whether the predicted UV absorption and CD spectra for the three-helix bundle and coiled coil are significantly different from spectra for the single straight α-helix. Crystallographic data by Yan et al. for α-spectrin are used to construct a three-helix bundle of poly(L-alanine) modeling the protein. Backbone torsion angles represented by Fourier series are used to generate supertwisted helices and coiled coil models of poly(L-alanine) that have pitch, radius, and residue repeat similar to experimental crystallographic data on tropomyosin. Calculated CD spectra are compared with available experimental data. Theoretical spectra for the three-helix bundle and the supertwisted structures are quite similar to predictions for the straight α-helix of the same length with similar torsion angles, suggesting that CD is primarily dependent on the average backbone conformation and would not be a sensitive tool for distinguishing between single straight helices and closely packed or twisted α-helices. © 1997 John Wiley & Sons, Inc. Biopoly 42: 855–860, 1997