Net Interaction Energy Research Articles

Orientation, positional, additivity, and oligomerization-state effects of interhelical ion pairs in α-helical coiled-coils

The role of interhelical g-e′ ion pairs in the dimerization specificity and stability of α-helical coiled-coils is highly controversial. Synthetic 35-residue coiled-coils based on the heptad repeat Q gV aG bA cL dQ eK f were used to investigate the effect of orientation of interhelical ion pairs between lysine and glutamic acid residues on coiled-coil stability. Stability was estimated from urea denaturation at 20°C, monitoring unfolding with circular-dichroism spectroscopy. Double mutant cycles were employed to estimate the net interaction energy, ΔΔ G u int, for the two orientations of the ion pair; E e-K g and K e-E g. ΔΔ G u int was found to be about 1.4-fold higher for the E e-K g orientation in a coiled-coil containing an N-terminal disulfide bridge. The ΔΔ G u int value was similar whether obtained from the middle heptad or averaged over all five heptads of the coiled-coil, suggesting that ion pairs contribute additively to coiled-coil stability. The effect of uncompensated charges was also illustrated by single substitutions of Gln with either Lys or Glu, resulting in Lys-Gln or Glu-Gln g-e′ pairs. These substitutions were found to be twice as destabilizing at position g as at position e, and Lys was about twice as destabilizing as Glu at both positions e and g. In the absence of an interhelical disulfide bridge, Glu and Lys substitutions in the middle heptad were equally destabilizing at positions e and g (Lys continued to be more destabilizing than Glu) and the ΔΔ G u intvalue for Lys-Glu ion pairs was not orientation dependent. These and previous results suggest the non-covalently-linked synthetic coiled-coils behave as molten globules, whereas a disulfide-bridge may “lock in” the structural differences between positions of the heptad repeat. Interhelical Lys-Glu ion pairs in either orientation promoted the formation of trimeric coiled-coils (in the absence of a disulfide bridge) while Gln-Gln g-e′ interactions led to dimer formation. The results support a role for g-e′ ionic attractions in controlling coiled-coil specificity, stability and oligomerization state, possibly through effects on the side-chain packing at the subunit interface.

Recognition and interaction of small rings with the ricin A-chain binding site.

Ricin A-chain is an N-glucosidase that attacks ribosomal RNA at a highly conserved adenine residue. Our recent crystallographic studies show that not only adenine and formycin, but also pterin-based rings can bind in the active site of ricin. For a better understanding of the means by which ricin recognizes adenine rings, the geometries and interaction energies were calculated for a number of complexes between ricin and tautomeric modifications of formycin, adenine, pterin, and guanine. These were studied by molecular mechanics, semi-empirical quantum mechanics, and ab initio quantum mechanical methods. The calculations indicate that the formycin ring binds better than adenine and pterin better than formycin, a result that is consistent with the crystallographic data. A tautomer of pterin that is not in the low energy form in either the gas phase or in aqueous solution has the best interaction with the enzyme. The net interaction energy, defined as the interaction energy calculated in vacuo between the receptor and an inhibitor minus the solvation energy of the inhibitor, provides a good prediction of the ability of the inhibitor to bind to the receptor. The results from experimental and molecular modeling work suggest that the ricin binding site is not flexible and may only recognize a limited range of adenine-like rings.

Stability of water-in-oil-in-water type globules

A method for producing a single water-in-oil-in-water (W/O/W) type globule is used to study its stability microscopically, by bringing the internal water droplets in contact with each other and with the external interface between water and oil. Each experiment lasted 24 h unless there was rupture within a shorter period, and the parameters that were studied are pH, ionic strength and the concentration of Span 80 surfactant. Under all experimental conditions that produced limited stability, the internal water droplets did not coalesce among themselves, and when the globule broke it was because the internal water droplets coalesced with the external phase. In the absence of surfactant the globule was found intrinsically unstable at all pHs and salinities. Experimental results are explained through a model for the interaction energy, van der Waals and Coulombic, between a single internal water droplet and the external aqueous phase as well as between two internal water droplets. A key parameter in the model is the ‘effective thickness’ of the adsorbed layer of surfactant, which determines whether the net interaction energy is attractive or repulsive.

The influence of pH on the high gradient magnetic separation of < 10 μm particles of hematite and quartz

This paper presents the influence of surface interaction on wet high gradient magnetic separation (WHGMS) for hematite and quartz particles (<10 μm), by controlling the pH value of the slurry flow. This influence is discussed by computing the net interaction energies for the particle-particle and particle-matrix element systems at various pH values. Such an approach leads to an improvement in the efficiency of separating the mineral ultrafines by WHGMS.

Miscible Polymer Blends: Local interaction energy theories and simulations

AbstractPolymer blends of two components, in general, are not miscible. However, according to Karasz‐MacKnight theory, intramolecular repulsion may outweigh intermolecular repulsion and cause two polymers to have a net interaction. Using a simple short chain molecular model incorporating both interand intramolecular interactions, estimates of net interaction energies for a series of polymeric imides, benzimidazoles and related high‐performance polymers can be calculated and used to predict miscibility in excellent agreement with experimental results, thus providing a useful confirmation of theory and a focus for the direction of further experimental work.

Scaling relations in hyperfine shifts of impurity atoms in rare gas crystals

The hf interaction of impurity atoms in rare gas crystals is investiga The ratio of the orbital moments of the impurity atom and the rare gas atom serveas a measure of each constituent’s contribution to the net interaction energy. (AIP)

Quantitative structure-activity relationships (QSAR) and molecular modelling in cancer research

The methods of quantitative structure-activity relationships and molecular modelling that have developed during the last 25 years are nowadays widely applied to describe the relationships between chemical structures of molecules and their biological activities in a quantitative manner. In cancer research also, many attempts have been made to understand structure-activity relationships and to design new antitumor drugs on a more rational basis. Owing to the enormous number of publications, only a few, typical examples are reviewed in this editorial. Much emphasis is given to a discussion of the limitations and the inherent problems of all the different approaches. As a result of the progress in our knowledge derived from experimental methods, the computational methods improve in their predictive ability, thus leading to more reliable results. However, the quantitative description of structure-activity relationships, as well as the modelling of drug-receptor interactions, are still (and will remain for the near future) very difficult. The transport and the distribution of a drug in a biological system is a function of its lipophilicity and its degree of dissociation or ionization at the pH value of the aqueous phases of the system. The interaction of the drug with its binding site at the receptor is determined by the lipophilicity pattern, the charge distribution, the electron density, and the polarizability pattern at the surface of the molecule. Of course, the three-dimensional structure of the molecule is of utmost importance for its fit to the binding site; however, in the case of a more or less flexible molecule, the bound conformation need not be identical to the minimum energy conformation; a less favored conformation may bind to the receptor, when the net interaction energy is large enough to compensate for the energy differences, provided the energy barriers between these conformations are not too large. Not only the ligand, but also the binding site can change its conformation, thus, a flexible fit between both partners occurs. Additional complications arise from different binding modes of chemically closely related molecules, from the insertion of water molecules at the binding site, and from entropy effects. Nature, as well as science, is not trivial. How can we then expect simple answers to complex questions?

The solid-state electronic structure and the nature of the chemical bond of the ternary Zintl-phase Li8MgSi6. A tight-binding analysis

Abstract The electronic strcuture of the ternary Zintl-phase Li 8 MgSi 6 has been investigated in the computational framework of a semi-empirical crystal orbital (CO) formalism based on the tight-binding approximation. Li 8 MgSi 6 crystallizes in the space group P2 1 /m-C 2h 2 with a = 12.701 A, b = 4.347 A, c = 10.507 A and β = 107.58°. A self-consistent-field (SCF) Hartree-Fock (HF) INDO CO procedure has been employed for the numerical approach. In order to reduce the computational expenditure of the CO calculations we have adopted a one-dimensional (ID) model simulating the real solid. To allow for a clear theoretical analysis the ID system is divided into simpler subfragments (MgSi 2- , Li 3 MgSi + , Li 5 Si 5 − ); the solid-state electronic structures of these moieties can be rationalized in a straightforward way. The band structure properties, density of states distributions, net charges and atomic orbital populations of Li 8 MgSi 6 are interpreted. A forbidden band gap of 0.62 eV is calculated by the semi-empirical tight-binding scheme, a value that is in excellent agreement to the measured band gap of the semiconducting compound which amounts to = 0.7 eV. The nature of chemical bond in the Li 8 MgSi 6 phase is analyzed by fragmenting the net diatomic interaction energies between SiSi, SiLi and MgSi pairs into covalent resonance elements as well as exchange and classical electrostatic (Coulomb) contributions. Partial coordination numbers (PCN) are defined for the various atomic species of the ternary phase that are labels of strongly stabilizing interactions (bonds) in the low-dimensional units. The calculated charge distributions show a striking 1:1 correspondence between the present CO results and the expectations derived on the basis of classical (Zintl-Klemm) electron-counting rules thus corroborating the utility of extended Zintl-Klemm conceptions in solids with atoms beyond the first two rows.

The band structure of bis-(1,2-benzoquinonedioximato)-nickel(II)-a crystal orbital approach based on the INDO approximation

The band structure of bis-(1,2-benzoquinonedioximato)nickel(II), Ni(bqd)2, is investigated by means of crystal orbital calculations based on a semiempirical INDO model. The nature of the metal-metal interaction in the stack as well as the intercell coupling between the 3d centre and the ligand atoms is analysed in detail. There is no evidence for an attractive Ni-Ni interaction; stabilising contributions in the intercell potential are predicted for the coupling between the positivated Ni centres and ligand atoms with a surplus of charge. The net interaction energy is decomposed into increments of physical significance. A large number of ligand bands is predicted on top of the Ni 3d bands; strong metal-ligand mixing in the latter band set leads to significantly reduced 3d amplitudes in most of the transition metal bands (3dz2, 3dxz, 3dyz). The partially oxidised Ni(bqd)2 polymers belong to the class of organic metals, the charge transport is due to ligand functions of lone-pair and pi character.

Clay-Polymer Interactions: Summary and Perspectives

AbstractThe adsorption of uncharged polymers by clays is largely “entropy-driven.” Polymer conformation changes from a random coil in solution to an extended form at the surface in which adsorbed polymer segments or trains alternate with loops and tails extending away from the surface. Although the net interaction energy, ε, per segment-surface contact is small (~1 kT unit), the total energy of adsorption is large because the fraction of train segments, p, is commonly between 0.3 and 0.5. The adsorption isotherms are typically of the high-affinity type, and there is an apparent lack of desorption on dilution. Positively charged polymers (polycations) are adsorbed largely through electrostatic interactions between the cationic groups of the polymer and the negatively charged sites at the clay surface. Here ε ≫ 1 kT unit and p &gt; 0.7, leading to an almost complete collapse of the polymer chain onto the surface. Indeed, beyond a given level of adsorption charge reversal can occur in that the clay-polycation system effectively behaves as an anion exchanger. Little adsorption occurs with negatively charged polymers (polyanions) due to initial charge repulsion between the polymer and the clay surface. Acid pH, a high ionic strength, and the presence of polyvalent cations in the system enhance and promote polyanion adsorption. Uncharged polymers and polycations can enter the interlayer space of expanding 2:1 type layer silicates but polyanions generally fail to intercalate.The interactions of clays with biopolymers, such as proteins, nucleic acids, and polysaccharides, can be rationalized in similar terms. When intercalation occurs, the interlayer biopolymer is further stabilized against microbial (enzymatic) degradation giving rise to practical applications of clay-polymer complexes as flocculants and soil conditioners. Polyanions are effective as flocculants because of their large “grappling distance,” whereas uncharged polymers are better suited as soil conditioners because they can spread over adjacent clay/soil particle surfaces like a coat of paint.

The ammonia—sulfur trioxide interaction. An ab initio study

Ab initio calculations are reported on the formation of the donor—acceptor adduct of SO 3 with NH 3. This adduct is the zwitterionic form of sulfamic acid. For a partially optimized structure ( R NS = 2.55 Å, φ(OSO) = 117°), a net interaction energy of −17.8 kcal/mol is found, showing SO 3 to be an unusually strong Lewis acid.

Elastic interactions between disclination loops and inclusion particles

An analysis is made of the interaction between inclusion particles and disclination loops. Two aspects of this interaction have been taken into consideration, namely, the effects of volumetric mismatch and modulus mismatch. It can be shown that there is no resultant interaction energy between a particle and a twist disclination loop due to volumetric misfit. On the other hand, the interaction between wedge disclination loops and impurity particles with volumetric misfit results in net interaction energy. Closed−form solutions are obtained for the total interaction force as a function of the separation distance between the defects. As to the effects of modulus mismatch, the long−range interactions between second−phase particles and twist disclination loops have been examined. Inclusion particles with shear moduli higher than those of the matrices tend to repel the disclinations. The forces on the disclination line segments are determined by evaluating the Peach−Koehler forces on the dislocation models of disclination loops.

The elastic interaction between a screw dislocation and a spherical inclusion

Using an extension of a classical technique due to Kelvin, the general solution for the interaction between a spherical inclusion in an infinite medium and any self-equilibrated source of stress outside the inclusion is derived in the form of infinite series involving spherical surface harmonics. This solution is then applied to the special case of the interaction between a screw dislocation and a spherical inclusion. The main features of the interaction are illustrated by examining the Peach-Koehler force per unit length on the dislocation. Expressions for the net force and interaction energy are also found, and it is seen that truncation of these various expansions leads to expressions which agree with existing long-range interaction expressions. The long-range prediction of the net force and energy is seen to be in good agreement with the exact results when the dislocation is sufficiently far from the inclusion. Finally a comparison is made between the spherical inclusion-screw dislocation interaction problem and its two dimensional analogue involving a cylindrical inclusion, and it is shown that there is not good agreement between the distribution of force on the dislocation for these two problems.

The structure of water and the thermodynamic properties of aqueous solutions.

The model proposed in the preceding paper for the theoretical derivation of the thermodynamic parameters of liquid water is extended to a treatment of the structure and the thermodynamic behavior of aqueous solutions of hydrocarbons. It is shown that the net intermolecular interaction energies of the solute with non-hydrogen-bonded water molecules differ from the interaction energies with the water molecules participating in the formation of hydrogen-bonded clusters. The differences are reflected in a change of the coordination number of the hydrogen-bonded water molecules near the solute. As a result, the amount of hydrogen bonding of the water in the immediate neighborhood of the solute is increased over its average value in pure water. The hydrogen-bonded clusters extend around part of the solute molecule, resulting in the formation of an incomplete cage. Equations are derived, expressing the mole fractions of molecular species of water having various numbers of hydrogen bonds within the first layer next to the solute. The partition function derived earlier for liquid water is modified in order to describe the water in this first layer. It is used to compute the contribution of the structural changes of water in this layer to the total free energy of solution. The contribution of the solute to the free energy is estimated in terms of changes in molecular configuration and van der Waals interactions when the solute is transferred from a nonpolar environment into water. The number of water molecules in the first layer surrounding the hydrocarbon, and the magnitude of the various intermolecular interaction energies, are introduced as variable parameters; their values used in the computations are shown to be of physically reasonable magnitude. The standard free energies, enthalpies, and entropies of solution are calculated for the normal saturated aliphatic hydrocarbons containing 1 to 8 carbon atoms, and for benzene and several of its homologs within the temperature range from 0° to 70°C. Observed values available for the same quantities in the literature are summarized and analyzed. The calculated thermodynamic parameters are shown to be in good agreement with the limited number of experimental data. The model also explains the unusually high heat capacity of the solutions discussed; the values calculated are in fair agreement with the available experimental data. The use of the term ``increased ice-likeness'' for the characterization of the changes occurring in the formation of aqueous solutions of nonpolar substances is shown to be justified on the basis of the model. The volume changes of solution are derived semiquantitatively, and an estimate of the volume change is given. Possible extensions of the method to other classes of nonpolar solutes are indicated.

The effect of adsorption on the van der waals interaction of spherical colloidal particles

A general formula has been derived for the interaction of spherical particles surrounded by any number of concentric shells of adsorbed material. The net interaction energy seems to be invariably negative (attraction) regardless of the magnitude of the van der Waals' constants of the materials comprising the particle, medium, and adsorbed substances. This result is demonstrated for one and for two adsorbed layers (i.e., a single layer of oriented amphipathic molecules), although it was not found feasible to develop a general proof. The interaction energy of solvated particles may be reduced by factors of the order of 5 to 50 compared to that of unsolvated particles. However, if current estimates of the magnitude of the van der Waals' constants are correct, flocculation can be inhibited by solvation alone only for small particles (<ca. 500 A. radius) and quite thick layers (> ca. 20 A.). Stabilization is most effective when the van der Waals' constant for the adsorbed material is either greater or less than the van der Waals' constants for both particle and medium.

Interlayer Forces in Bentonite

AbstractAn attempt is being made to analyze the forces between unit layers of a bentonite particle and between the flat surfaces of two particles from colloid chemical data and theory. The electric double-layer interaction, the van der Waals attraction, and the hydration energies are considered.From experimental observations the general qualitative shape of the net potential curve of interaction may be derived.In a quantitative discussion, first the long-range interaction is considered by applying the theory of Verwey and Overbeek in which the net interaction curve is found as the sum of the double-layer repulsion and van der Waals attraction. The fact that the layers do not spontaneously dissociate in solution despite the high charge density of the surfaces points to a considerable specific adsorption potential of the counter ions (the exchangeable ions) to the surface (≈0.2 ev). The consequences for ion exchange are briefly discussed.Next, two possibilities for the status and position of the counter ions are considered: the cations are either unhydrated and located in or close to the holes in the tetrahedral sheet in six coordination with the oxygen six rings or they are partly or completely hydrated and with their hydration shell adsorbed on top of the oxygen sheet.Then the short-range interaction of the unit layers is considered. In the case of bentonite there is the fortuitous situation that the net short-range potential curve for the layer interaction can be found experimentally from adsorption isotherms and x-ray diffraction. This net interaction energy is the sum of three contributing energies: the van der Waals attraction, the electrostatic interaction, and the hydration energies. Therefore, on computing the first two for either model mentioned above, the hydration term can be evaluated and its order of magnitude may decide between the two possibilities since ion hydration energy would be expected to be much higher than surface hydration energy.For the model of unhydrated ions the van der Waals attraction is relatively small and partly compensated by the rather small electrostatic repulsion (repulsion of two finite layers of dipoles). Thus the net repulsion energy measured is practically the hydration energy in this case. This hydration energy figure is of the right order of magnitude if interpreted as hydrogen bonding of a Hendricks water layer to the oxygen surface.For the model of the at least partly hydrated cations the van der Waals attraction is small, the same as in the first model, but the electrostatic interaction is now an appreciable attraction since the cations take up a midway position between the negative bentonite layers for at least the mono- and dilayer adsorption complex. This makes the computed hydration energy higher; this is readily explained by the availability of the higher ion hydration energy as compared with the surface hydration energy.Thus the analysis shows both pictures to be acceptable within the limits with which the adsorption isotherms and therefore the net potential curve can be evaluated. More elaborate adsorption data at very low relative humidities would be required to obtain a better estimate of the energies involved in the removal of the last layer of water where the major portion of the ion hydration energy would enter the picture if ion hydration would indeed take place and be the primary cause of interlayer swelling of bentonite.There is a correlation of bentonite hydration energy with the hydration energy of the counter ions present, but this correlation does not constitute positive evidence of ion hydration. A secondary effect of the ions on the formation of ideal Hendricks’ layers (and thus on their bonding energy to the clay surface), which also depends on ion size, is possible.Other experimental and theoretical approaches to the problem are briefly mentioned and finally the differences between swelling and nonswelling clays are dealt with.