Terms Of Interaction Energies Research Articles

Comparative ab initio study of the structures, energetics and spectra of X−⋅(H2O)n=1–4 [X=F, Cl, Br, I] clusters

X − ⋅(H 2 O) n=1–4 [X=F, Cl, Br, I] have been studied using high level ab initio calculations. This extensive work compares the structures of the different halide water clusters and has found that the predicted minimum energy geometries for different cluster are accompanied by several other structures close to these global minima. Hence the most highly populated structures can change depending on temperature due to the entropy effect. As the potential surfaces are flat, the wide-ranging zero point vibrational effects are important at 0 K, and not only a number of low-lying energy conformers but also large amplitude motions can be important in determining structures, energies, and spectra at finite temperatures. The binding energies, ionization potentials, charge-transfer-to-solvent (CTTS) energies, and the O–H stretching frequencies are reported, and compared with the experimental data available. A distinctive difference between F−⋅(H2O)n and X−⋅(H2O)n (X=Cl, Br, I) is noted, as the former tends to favor internal structures with negligible hydrogen bonding between water molecules, while the latter favors surface structures with significant hydrogen bonding between water molecules. These characteristics are well featured in their O–H spectra of the clusters. However, the spectra are forced to be very sensitive to the temperature, which explains some differences between different spectra. In case of F−⋅(H2O)n, a significant charge transfer is noted in the S0 ground state, which results in much less significant charge transfer in the S1 excited state compared with other hydrated halide clusters which show near full charge transfers in the S1 excited states. Finally, the nature of the stabilization interactions operative in these clusters has been explained in terms of many-body interaction energies.

Prediction of QCM gas sensor responses and calculation of electrostatic contribution to sensor responses using a computational chemistry method

When we construct an odor sensing system using a quartz crystal microbalance (QCM) odor sensor array, it is important to know the properties of sensing films coated on those electrodes and select the optimum combination of sensors in the array. However, they have not been characterized well enough to predict the sensor responses without any experiment. Then, we tried to predict sensor responses using a computational chemistry method. We have so far succeeded in predicting the responses using sensing films of typical liquid gas chromatography (GC) stationary phase materials to various kinds of gases and a few perfumes. In this study, we calculated the amount of sorbed gas molecules into the typical solid material of GC and the amount of sorbed perfumes into various sensing films, and it was found that this computational prediction method is useful in those cases. Next, we tried to evaluate the contribution of single interaction energy term to the sorption using this method although it cannot be revealed through the experiment. It was found from the results that the contribution of electrostatic interaction to the sorption can almost be evaluated and this calculation method is useful for knowing the properties of gases and sensing films.

A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing

Simulated annealing methods have been used with the effective fragment potential to locate the lowest energy structures for the water clusters (H2O)n with n=6, 8, 10, 12, 14, 16, 18, and 20. The most successful method uses a local minimization on each Monte Carlo step. The effective fragment potential method yielded interaction energies in excellent agreement with those calculated at the ab initio Hartree–Fock level and was quite successful at predicting the same energy ordering as the higher-level perturbation theory and coupled cluster methods. Analysis of the molecular interaction energies in terms of its electrostatic, polarization, and exchange-repulsion/charge-transfer components reveals that the electrostatic contribution is the dominant term in determining the energy ordering of the minima on the (H2O)n potential energy surfaces, but that differences in the polarization and repulsion components can be important in some cases.

3D Imaging and Simulation of the Polarisation Distribution in Molecular Crystals

The spatial polarisation distribution in inhomogeneously polar molecular crystals has been imaged by scanning pyroelectric tomography and simulated by a Markov process. The experimental technique combines scanning pyroelectric microscopy (SPEM) with layerwise thinning of crystals. The SPEM probes the local spontaneous polarisation by its temperature dependence (pyroelectric effect). A focused and intensity modulated laser beam scans the surface of a polar sample and induces temperature changes in a volume depending on the laser spot size and the thermal diffusion length λth. Since high lateral resolution of the SPEM is only available for small values of λth. depth information to a resolution of ∼ 10 μ is achieved by repeated scanning and stepwise thinning of crystals. A layer by layer technique can provide 3D imaging of the polar ordering with a lateral resolution of ∼ 20 μ at a probed layer thickness of ∼ 10 μ. Applied to perhydrotriphenylene (PHTP) co-crystallised with 1–(4-nitrophenyl)piperazine (NPP) two conical macro-domains of opposite and nearly constant polarisation were found. The SPEM results are in good agreement with a homogeneous Markov chain model driving dipolar molecules into a parallel state within channels of PHTP. The new tomographic view reveals that the opposing cones are partially overlapping at the tips. Lateral growth processes are assumed to be responsible for this. A theoretical section covers aspects of the convergency into the polar state and the length of polar chains discussed in terms of intermolecular interaction energies.

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase:ab initio and SIBFA molecular mechanics calculations

The interaction of Zn2+ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn2+ complex are first established via high-level ab initio calculations. Two low-energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas-phase affinity of glycine for Zn2+. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn2+-binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn2+–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all-electron 6-311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4-31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn2+. Thus, the supermolecule is treated as a three-body rather than a two-body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000

Translational and Rotational Diffusion of Probe Molecules in Polymer Films near Tg: Effect of Hydrogen Bonding

The effect of hydrogen bonding on the rotational and translational dynamics of two small molecule probes, lophine and S-lophine, in amorphous polymer films near the glass transition temperature, Tg, was studied using second harmonic generation (SHG) and fluorescence nonradiative energy transfer (NRET), respectively. The two probes are nearly identical in size and shape, with the only structural difference being related to an amine functional group in lophine replacing a sulfur atom in S-lophine. The two probes exhibited essentially identical rotational and translational dynamics in polystyrene, which has no polar units allowing for hydrogen-bonding interactions. However, in poly(isobutyl methacrylate), which can participate in hydrogen bonding with amine units, lophine average rotational reorientation times (〈τrot〉) were found to increase, and translational diffusion coefficients (D) were found to decrease by approximately an order of magnitude as compared to those of S-lophine. The magnitude of this effect is much greater than similar hydrogen-bonding effects reported for diffusion in polymer solutions. The hydrogen-bonding effects can be quantitatively taken into account using an interaction energy term with activation energy, Ea = 6 kJ/mol for translation and 9.5 kJ/mol for rotation. The differences in Ea for the two modes of motion are explained in terms of the differing ways in which D and 〈τrot〉 average over the broad distribution of relaxation times present in polymers near Tg. Implications associated with additive migration in polymers are discussed.

Non-empirical analysis of the nature of the inhibitor–active-site interactions in leucine aminopeptidase

Non-empirical analysis of the physical nature of the intermolecular interactions between several leucine aminopeptidase inhibitors and various constituents of the enzyme active site has been performed using a direct version of the hybrid variation–perturbation decomposition of SCF and MP2 interaction energies. The interaction energy terms obtained at different theory levels have been correlated with experimentally measured activities of the inhibitors, indicating that the more advanced the quantum-chemical method and, the larger the active-site model, the better is the correlation between calculated and measured binding energies. The electrostatic multipole term constitutes the dominant contribution in the total interaction energy, whereas Zn2+488 and Lys+262 enzyme residues play the crucial role in the binding of these inhibitors by leucine aminopeptidase.

Structure-activity relationships of RGD mimetics as fibrinogen-receptor antagonists.

The activities of a series of RGD mimetics, which contained a variety of cationic structures, for the inhibition of platelet aggregation and fibrinogen-receptor binding were measured. The stability of the coulombic ion-pairing complex of the model compounds with the acetate anion as a model for the receptor was calculated in terms of the ionic interaction energy. The results suggest that stability is one of the significant factors which govern the inhibitory potency of fibrinogen-receptor binding. The distance between cationic and anionic groups might also affect the potency. A compound which contained an amidinophenyl structure as the cationic moiety showed exceptionally high inhibitory activity, suggesting that some other factors, in addition to coulombic interaction and the distance, affect the potency.

Theoretical study of the methylic reactivity of substituted alkenes

A PM3/UHF study of the methylic reactivity of a series of about fifty alkenes was carried out. Several MP2/6-31G ∗∗ ab initio calculations were made for comparison. The semi-empirical method of calculation is proven to give good estimates of the reactivity under consideration. The computations brought to light the reactivity enhancement of alkenes when substituted on the same carbon of the double bond, whereas a lessening is observed when both carbons are substituted. An interpretation in terms of deformation (DBF) and interaction (INT) energies is made. Contrarily to phenyl, the vinyl group improves notably the reactivity of methylated and chlorinated mono or disubstituted alkenes. The prediction is made for the reactivity of more than fifteen compounds which were not studied experimentally.

Interactions between impurity atoms of 3d transition metals dissolved in iron

We present results of our Mössbauer spectroscopy study on the distribution of impurity atoms in iron based solid solutions of iron with Ti, V, Mn, Co and Ni as a solute. The results are analysed in the terms of interaction energies of impurity pairs in iron. The energies obtained for the Ti, V and Mn pairs are positive (repulsive interaction) whereas for Co and Ni pairs they are negative (attractive interaction). The data are compared with those resulting from the Miedema–Królas model for the energy. From the comparison it follows that our experimental values are in agreement with the model for Ti and V pairs but that they are in disagreement with the model predictions for Mn, Ni and Co pairs.

Representation of amino acid sequences in terms of interaction energy in protein globules

We suggest a new simple approach for comparing the primary structure of proteins and their spatial structure. It relies on the one-to-one correspondence between each residue of the polypeptide chain and the energy of van der Waals interactions between the regions of the native globule flanking this residue. The method obviates the sophisticated geometrical criteria for estimating similarity between spatial structures. Besides, it permits one to analyze structural units of different scale.

Conductometric study of Bu4NClO4 in propylene carbonate-acetonitrile and propylene carbonate-toluene mixtures at 25�C

Conductometric measurements of tetrabutylammonium perchlorate in propylene carbonate-acetonitrile and propylene carbonate-toluene mixtures at 25°C are reported. Limiting molar conductances, association constants and distance of closest approach of ions are calculated. The experimental data were analyzed by means of the Lee-Wheaton equation. The Gilkerson's solvent-solute interaction energy term was calculated from a plot of association constant logarithmvs. reciprocal dielectric constant.

Cooperative effects in water trimers. The performance of density functional approaches

The performance of B-LYP, B3-LYP, B3-P86 and B3-PW91 density functional to describe cooperative effects in water trimer was investigated. The geometries and vibrational frequencies of the monomer, the dimer and the trimer were obtained using a 6-31+G(d,p) basis set, while the final energies were calculated at the 6-311++G(3df,2p) level. Our results show that B3-LYP and B-LYP functionals seem to be a good alternative to ab initio calculations to account for cooperative or non-pairwise effects, either if these effects are measured in terms of additive interaction energies or in terms of the so-called cooperativity factors.

Symmetry-adapted perturbation theory for the calculation of Hartree-Fock interaction energies

A symmetry-adapted perturbation theory is formulated for the calculation of Hartree-Fock interaction energies of closed-shell dimers. The proposed scheme leads to a basis-set-independent interpretation of the Hartree-Fock interaction energy in terms of basic concepts of the theory of intermolecular forces: electrostatics, exchange and induction. Numerical results for different geometries of HE2, Ne2, He-C2H2, He-CO, Ar-HF, (HF)2 and (H2O)2 complexes show that in the region of the van der Waals minimum the proposed perturbation theory reproduces accurately the Hartree-Fock interaction energy. This fast convergence and relatively small computational cost of the proposed perturbation scheme suggest that this method is a practical alternative for the standard supermolecular approach.

Counterion binding of poly(allylamine) hydrochloride in aqueous alcohols

Abstract Counterion binding has been investigated for poly(allylamine) hydrochloride (PAlAmHCl) in aqueous alcohols (methanol, ethanol, and 2-propanol). The activity of Cl− was estimated as an apparent value by using an ion-specific electrode and compared with the theoretical prediction obtained from a counterion condensation theory. Marked deviations or overestimations of the counterion activity obtained by the theoretical method were observed for the higher-concentration regions of the respective alcohols. This has been attributed to a specific counterion binding which should be more favourable in a medium with a lower dielectric constant and of a lower solvation energy. Similar deviations were also observed for the molar conductivities of the polymer in the same solvent systems. These latter deviations could be remarkably reduced by introducing the extra interaction energy term, i.e., ΔEex, for the specific counterion binding that was used to correct the observed deviations for the counterion activities. By utilizing the ΔEex values as a measure of this specific counterion binding, the dependence on the alcohol species has been discussed in terms of the dielectric constant, preferential solvation and the Gutman-Mayer acceptor number.

A New Linear Solvation Energy Relationship for the Solubility of Liquids in Water

From a comparison between the linear solvation energy relationship (LSER) and the extended solubility parameter model, it has been found that the solute-solute interaction energy term is missing in the LSER equation. A new LSER equation with the supplementary interaction energy term has been proposed for the solvation process. It is shown that the new LSER equation yields the correct solute-solvent interaction terms for the solubilities of liquids in water.

Spectral Theory of Physical and Chemical Binding,

A spectral method which provides unified quantum mechanical descriptions of both physical and chemical binding phenomena is reported for constructing the adiabatic electronic potential energy surfaces of aggregates of atoms or other interacting fragments. The formal development, based on use of a direct product of complete sets of atomic spectral eigenstates and the pairwise-additive nature of the total Hamiltonian matrix in this basis, is seen to be exact when properly implemented and to provide a separation theorem for N-body interaction energies in terms of response matrices which can be calculated once and for all for atoms and other fragments of interest. Its perturbation theory expansion provides a generalization of familiar (Casimir−Polder) second-order pairwise-additive and (Axilrod−Teller) third-order nonadditive interaction energies, expressions which are recovered explicitly in the long-range-dipole expansion limit. A program of ab initio computational implementation of the formal development i...

Comparative Molecular Field Analysis of HIV‐1 Reverse Transcriptase Inhibitors in the Class of 1[(2‐Hydroxyethoxy)‐methyl]‐6‐(phenylthio)thymine

AbstractA Comparative Molecular Field Analysis of 40 HEPT (1‐[(2‐Hydroxyethoxy)‐methyl]‐6‐(phenylthio)thymine) analogues was performed. The 3D‐QSAR study correlates steric and electrostatic fields of the compounds with HIV‐1 RT inhibition, resulting in a model which has a high predictive ability. CoMFA results revealed that steric interaction explains a majority (70%) of the variance in the data. Using only steric interaction energy in the analyses provided a better predictive model. Inclusion of electrostatic descriptors in terms of coulomb interaction energies deteriorates the results. However, it was found in this study that variation of sp3 O charges had some influence on r and that the interaction energies using sp3 O probe with a charge of −0.3 led to the best predictive model.

The effect of nanopore shape on the structure and isotherms of adsorbed fluids

A Grand Canonical Monte Carlo simulation method is used to determine the adsorption isotherms, interaction energies, entropies, and density distribution of a Lennard-Jones fluid adsorbed in smooth-walled nanopores of varying size and shape. We specifically include very crowded pores, where packing effects are important. Differences in the isotherms of slit, cylindrical, and spherical nanopores of varying sizes can be explained in terms of the adsorbate-adsorbate interaction energy, the adsorbate-pore interaction energy, and the density profiles, which influence the balance between the former and the latter energy contributions. The expectation from low loading studies that the most energetically favorable adsorbate-pore interactions maximize adsorption is not borne out at intermediate and higher loadings. Instead, the relationships between adsorbed amounts and pore size and shape are found to be strong functions of the depth and steepness of the external potential, the extent to which adsorbate-adsorbate repulsion establishes short range fluid order, and the accessible pore volume. This study has implications for high pore density processes in nanoporous materials, such as zeolite catalysis, separations, and templating in zeolite synthesis.

Conformation and Dynamics of Membrane-Bound Digalactosyldiacylglycerol

The conformation and dynamics of a uniformly 13C-labeled glycolipid, digalactosyldiacylglycerol (DGDG), is studied in a membrane environment using NMR spectroscopy. Dipolar couplings and 13C chemical shift anisotropy offsets which appear in magnetically oriented phospholipid-based membrane fragments are used to derive a detailed description of the conformation and amplitudes of motion. 13C relaxation rates (T1, T2, and NOE) were then measured for 13C sites in DGDG anchored to isotropically tumbling phospholipid bilayers. Using a Lipari and Szabo type approach, a nonlinear least squares fit of relaxation rates to motional parameters yielded rates and amplitudes of internal motions for the first and terminal sugar of the glycolipid head group. Generalized order parameters extracted from relaxation data show good agreement with order parameters used to fit dipolar couplings. The combined model is analyzed in terms of potential energy maps generated using a version of AMBER modified to include a membrane interaction energy term. The experimental conformational preferences of the terminal α(1−6) linkage in DGDG agree quite well with predictions based on these calculations.