Van Der Waals Energy Research Articles

The Interaction of Monosubstituted Benzenes with the Stationary Liquid in Gas Liquid Chromatography

In gas liquid chromatography (GLC), the relative retention values log gamma was mainly expressed by van der Waals energy (the sum of the dispersion E(dis) and repulsive E(rep) energies) to the interactions between monosubstituted benzene derivatives and the nonpolar stationary liquid as squalane. The single exception was that of anilines, and it was corrected by the electrostatic energy (E(ES)) due to C-H/pi hydrogen bond. When the stationary liquid changed from the nonpolar to polar, log gamma was estimated by the inductive interaction energy (included in E(ES)) in addition to the sum of E(dis) and E(rep). In the benzene solution, the relative equilibrium values log K/K(o) introduced from the interactions between phenol and substituted benzene derivatives were estimated by E(ES). The E(ES) of COCH(3), CO(2)C(2)H(5) groups is especially originated in the excited dipole moments micro(e). The relative frequency values log nu/nu(o) derived from O-H or O-D stretching vibration of phenol or methanol-D gave the correlation to E(ES) as well as log K/K(o). That of anilines-methanol-D however had been out of a linear relation to E(ES). The cause is concluded that the aniline-methanol-D is making the proton transfer structure from the discussion about the proton affinity (PA) of the base.

Stability of the I-motif Structure Is Related to the Interactions between Phosphodiester Backbones

The i-motif DNA tetrameric structure is formed of two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. The four phosphodiester backbones forming the structure define two narrow and wide grooves. The short interphosphate distances across the narrow groove induce a strong repulsion which should destabilize the tetramer. To investigate this point, molecular dynamics simulations were run on the [d(C2)]4 and [d(C4)]4 tetramers in 3′E and 5′E topologies, for which the interaction of the phosphodiester backbones through the narrow groove is different. The analysis of the simulations, using the Molecular Mechanics Generalized Born Solvation Area and Molecular Mechanics Poisson-Boltzmann Solvation Area approaches, shows that it is the van der Waals energy contribution which displays the largest relative difference between the two topologies. The comparison of the solvent-accessible area of each topology reveals that the sugar-sugar interactions account for the greater stability of the 3′E topology. This stresses the importance of the sugar-sugar contacts across the narrow groove which, enforcing the optimal backbone twisting, are essential to the base stacking and the i-motif stability. Tighter interactions between the sugars are observed in the case of N-type sugar puckers.

N-1-alkylitaconamic acids- co-styrene copolymers. Surface characterization

A serie of six N-1-alkylitaconamic acids- co-styrene copolymers with alkyl groups varying in side chain length from 3 to 12 was used in this study. The surface behaviour of the copolymers has been studied as function of the side chain length. Contact angle data for two of these copolymer surfaces were obtained in water and several liquids. From this information the surface energy was determined. Differences in the wettability of N-1-alkylitaconamic acid- co-styrene are found. The results are discussed in terms of hydrophobic and polar effect of the copolymers. Results on spread monolayers characteristics of these copolymers on water surfaces are also reported. Surface pressure–area (π– A) isotherms on a pure water subphase exhibit a transition region depending on the length of the alkyl side chain of the itaconamic acid moiety. It was also analyzed the phase transition in the monolayer at the air/water interface by brewster angle microscopy (BAM). Molecular mechanics approach was used to obtain predictions about the local interaction energies between segments. It was possible to conclude that the local interaction energies of propyl and decyl derivatives are quite similar while the hexyl derivative has higher interaction energy. The analysis of the coulombic energies together with the dispersion van der Waals energies (VDW) would be indicative, in first approximation, that carbonyl groups are more exposed in the case of propyl than in the other copolymers studied.

Solvent activities of ordinary and associated binary polymer solutions: group-contribution method

A specified group-contribution method is proposed to estimate vapor–liquid equilibria (VLE) of ordinary and associated binary polymer solutions. van der Waals (vdW) energy parameters for dispersion and polar forces for ordinary systems without hydrogen bonding (h-b; Case I) are determined. In addition, the h-b energy parameters for associated systems are employed. Two cases are, respectively, taken into account for associated systems: solvent activities by the h-b interactions are nearly independent of the temperature (Case II); and solvent activities by the h-b interactions strongly depend on the system temperature (Case III). The temperature-dependent h-b parameter is also considered. Our proposed model shows good agreements with experimental data in solvent activity estimations for ordinary and associated binary polymer solution.

Discrete structure of van der Waals domains in globular proteins.

Most globular proteins are divisible by domains, distinct substructures of the globule. The notion of hierarchy of the domains was introduced earlier via van der Waals energy profiles that allow one to subdivide the proteins into domains (subdomains). The question remains open as to what is the possible structural connection of the energy profiles. The recent discovery of the loop-n-lock elements in the globular proteins suggests such a structural connection. A direct comparison of the segmentation by van der Waals energy criteria with the maps of the locked loops of nearly standard size reveals a striking correlation: domains in general appear to consist of one to several such loops. In addition, it was demonstrated that a variety of subdivisions of the same protein into domains is just a regrouping of the loop-n-lock elements.

A study of different approaches to the electrostatic interaction in force field methods for organic crystalsElectronic supplementary information (ESI) available: The full results for Tables 2 and 4. See http://www.rsc.org/suppdata/cp/b3/b306396h/

We investigated five different methods for evaluating the electrostatic interaction between atoms in force field calculations on organic solids. Atomic charges and multipoles were obtained by fitting them to the molecular electrostatic potential, calculated in vacuum with an ab initio quantum mechanical method. Multipole moments were derived using three schemes, differing in the order in which the monopoles, dipoles and quadrupoles were fitted. For comparison, Gasteiger charges were also calculated. Using these electrostatic models, the lattice parameters and the molecular geometry of 48 organic crystals were optimised with the DREIDING force field. During the optimisation, the atomic multipoles were rotated with their local environment to account for molecular flexibility. For comparative reasons, rigid-body optimisations were performed on a subset of structures. The results were analysed in terms of structural parameters of the lattice and the molecules, and, for the ten polymorphic systems present in the test set, in terms of relative stability. On average, the multipole methods were not superior to the point charge methods for the full optimisation. For rigid molecules, however, the multipole models gave a substantial improvement in lattice parameters. No evidence was found that parameters for van der Waals energies need to be refitted for a specific electrostatic model. Energy differences between polymorphs were less than 5 kcal mol−1 in eight out of ten cases, independent of the electrostatic model used. The results show that our use of distributed multipoles to describe the intra-molecular as well as inter-molecular electrostatic interactions does lead to an improvement in accuracy for rigid molecules, but not for flexible molecules. The investigation shows that accurate descriptions of the intra-molecular as well as the inter-molecular energies are crucial for the successful optimisation of crystal structures of organic solids.

Influence of cation–π interactions in different folding types of membrane proteins

Cation–π interactions play an important role to the stability of protein structures. In this work, we analyze the influence of cation–π interactions in three-dimensional structures of membrane proteins. We found that transmembrane strand (TMS) proteins have more number of cation–π interactions than transmembrane helical (TMH) proteins. In TMH proteins, both the positively charged residues Lys and Arg equally experience favorable cation–π interactions whereas in TMS proteins, Arg is more likely than Lys to be in such interactions. There is no relationship between number of cation–π interactions and number of residues in TMH proteins whereas a good correlation was observed in TMS proteins. The average cation–π interaction energy for TMH proteins is −16 kcal/mol and that for TMS proteins is −27 kcal/mol. The pair-wise cation–π interaction energy between aromatic and positively charged residues showed that Lys–Trp energy is stronger in TMS proteins than TMH proteins; Arg–Phe, Arg–Tyr and Lys–Phe have higher energy in TMH proteins than TMS proteins. The decomposition of energies into electrostatic and van der Waals revealed that the contribution from electrostatic energy is twice as that from van der Waals energy in both TMH and TMS proteins. The results obtained in the present study would be helpful to understand the contribution of cation–π interactions to the stability of membrane proteins.

QSPR models based on molecular mechanics and quantum chemical calculations. 1. Construction of Boltzmann-averaged descriptors for alkanes, alcohols, diols, ethers and cyclic compounds.

Values for nine descriptors for QSPR (quantitative structure-property relationships) modeling of physical properties of 96 alkanes, alcohols, ethers, diols, triols and cyclic alkanes and alcohols in conjunction with the program Codessa are presented. The descriptors are Boltzmann-averaged by selection of the most relevant conformers out of a set of possible molecular conformers generated by a systematic scheme presented in this paper. Six of these descriptors are calculated with molecular mechanics and three with quantum chemical methods. Especially interesting descriptors are the relative van der Waals energies and the molecular polarizabilities, which correlate very well with boiling points. Five more simple descriptors that only depend on the molecular constitutional formula are also discussed briefly.

Energetic and entropic contributions to the interactions between like-charged groups in cationic peptides: A molecular dynamics simulation study.

The interaction between like-charged amino acid residues has been proposed to stabilize the folded state of peptides and proteins, and to modulate the substrate binding and the action mechanism of enzymes. We have used an alanine- and lysine-based peptide as a model system to study the interaction between like charges, and we have performed a 16-nsec molecular dynamics simulation in solution. The calculated potential of mean force for the approach of the lysine's Nzeta atoms showed a minimum at a distance of 0.7 nm, in agreement with the separation probabilities obtained from analysis of protein crystal structures. The analysis of the individual energy components showed that the solvent polarization pays for the approach of the like charges and that the van der Waals energies do not contribute significantly. The entropic contributions have been divided in conformational and desolvation terms. Both terms favor the formation of the charge pair. A 10-fold increase in counterion concentration was observed-with respect to its bulk concentration-next to the peptide charges, which helps to stabilize the peptide charges at a close distance.

Calculated Hydration Free Energies of Small Organic Molecules Using a Nonlinear Dielectric Continuum Model

Prediction of solvation free energies is an important subject in fundamental natural science but also important to the pharmaceutical and food industry. A popular modeling approach is to treat the solution by an implicit solvent model. The solute molecule is rigid with a fixed effective charge distribution localized at the atomic nuclei positions. The hydration free energy is described by the van der Waals energy, the solute cavity formation energy in the water phase, and the change in electrostatic solute−solvent interaction energy. The dielectric continuum is generally assumed to be a simple medium, that is, linear, homogeneous, and isotropic. However, this approximation is quite severe and will give too hydrophilic solvation free energies. We show here that the simple medium approximation must be relaxed and nonlinearity must be taken into consideration. In strong electric fields, the solvent polarization becomes saturated and the dielectric no longer responds linearly in the applied field. This effect is well-described by the modified Langevin−Debye model. This nonlinear solvation model is used to study the hydration of 181 small organic molecules. Atomic charges and radii of the solute molecule are described by a standard classical force field. We apply the optimized potentials for liquid simulation all atom (OPLS-AA) force field, which is parametrized to reproduce both structural and thermodynamical data. This leads to a mean unsigned error of 0.6 kcal/mol, which is a 25% improvement compared to a simple medium approach. The nonlinear solvation model is further improved by introducing a few charge-scaling parameters for some functional groups that show a systematic deviation from their experimental data. This yields a mean unsigned error of 0.4 kcal/mol, which is only twice the experimental uncertainty. Hence, we conclude that nonlinear dielectric effects are indeed important to incorporate in implicit solvent models, even for neutral polar molecules.

Dialkyl Effect on Enantioselectivity: π-Stacking as a Structural Feature in P,N Complexes of Palladium(II)

A phosphino,oxazoline P,N-bidentate ligand, 4, containing 3,5-di-tert-butylphenyl groups has been prepared. In the Heck arylation of dihydrofuran, 4 is shown to afford higher ee's than either 2 or 3, the unsubstituted and m-dimethylphenyl analogues, respectively. Several Pd(0) complexes of 4 are reported. The exchange dynamics of Pd(4)(dba) are shown to involve an interconversion of diastereomers via an intramolecular process. The X-ray structure for PdCl2(4), 8, was determined by X-ray diffraction methods. Comparison of data with PdCl2(2), 9, and PdCl2(3), 10, suggests that differing amounts of π−π stacking influence the structures of these relatively simple Pd complexes, with 9 and 10 revealing the strongest π−π interactions. An estimation of the van der Waals energies involved in the interaction supports a ca. 4 kcal/mol stabilization via π−π stacking.

Excess van der Waals interaction energy of a multiwalled carbon nanotube with an extruded core and the induced core oscillation

It has been observed that the van der Waals interaction can cause an extruded core of a multiwalled carbon nanotube (MWNT) to retract into the outer shells. In a previous report [Q. Zheng and Q. Jiang, Phys. Rev. Lett. $88,$ 045503 (2002)], the authors pointed out that the restoring force resulted from the excess van der Waals interaction energy due to the core extrusion would drive the core to oscillate with respect to its fully retracted position because of the small intershell sliding resistance force and they predicted that the oscillation frequency could be in the gigahertz range. The present article gives detailed theoretical calculations of the excess van der Waals energy due to the extrusion and the corresponding restoring force. The authors have further derived an explicit expression of the oscillation frequency in terms of the physical and geometrical parameters of the MWNT, with the interatomic locking effect taken into account, and they have shown that the oscillation frequency can be significantly higher than one gigahertz.

Water activities of florinated solid polymer electrolyte/water systems using group-contribution method

A new group-contribution model based on the modified double-lattice theory is developed and applied to describe vapor-liquid equilibria of solid polymer electrolyte/water systems. The proposed model includes the combinatorial energy contribution that is responsible for the revised Flory–Huggins entropy of mixing, the van der Waals energy contribution from dispersion, polar force and the specific energy contribution. Quantitative description according to the proposed model is in good agreement with experimentally observed water activities of polymer electrolyte fuel cell systems.

Molecular Dynamics Free-Energy Simulations of the Binding Contribution to the Fidelity of T7 DNA Polymerase

The relative stability of Watson−Crick and mismatched dNTP·template base pairs in the active site of T7 DNA polymerase (pol T7) was examined using linear-response (LRA) molecular dynamics simulations. The LRA method approximates the relative binding free energies by evaluating average electrostatic and van der Waals energies. The results of these computer simulations and the previous simulations of the human DNA polymerase β (pol β) ternary complex (Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B, 2002, 106, 5739) carried out at the same theoretical level were compared. It was found that pol T7 provides a larger binding contribution to the replication fidelity than pol β by discriminating more effectively against mismatches that are most probable to occur in the neutral anti−anti configurations. The selectivity of the pol T7 in the binding step is largely determined by the template−dNTP interactions. These interactions are strengthened by the preorganized protein active site and the contribution...

Fluorescence properties of tryptophan residues in the monomeric d-chain of Glossoscolex paulistus hemoglobin: an interpretation based on a comparative molecular model

The primary structure of the 142 residue Glossoscolex paulistus d-chain hemoglobin has been determined from Edman degradation data of 11 endo-Glu-C peptides and 11 endo-Lys-C peptides, plus the results of Edman degradation of the intact globin. Tryptophan occupies positions 15, 33 and 129. Homology modeling allowed us to assign the positions of these Trp residues relative to the heme and its environment. The reference coordinates of the indole rings (average coordinates of the C ε2 and C δ2 atoms) for W15 and W129 were 16.8 and 18.5 Å, respectively, from the geometric center of the heme, and W33 was located in close proximity to the heme group at a distance which was approximately half of that for W15 and W129. It was possible to identify three rotamers of W33 on the basis of electrostatic and Van der Waals energy criteria. The calculated distances from the center of the heme were 8.3, 8.4 and 9.1 Å for Rot1, Rot2 and Rot3, respectively. Radiationless energy transfer from the excited indole to the heme was calculated on the basis of Förster theory. For W33, the distance was more important than the orientation factor, κ 2, due to its proximity to the heme. However, based on κ 2, Rot2 (κ 2=0.945) was more favorable for the energy transfer than Rot1 (κ 2=0.433) or Rot3 (κ 2=0.125). In contrast, despite its greater distance from the heme, the κ 2 of W129 (2.903) established it as a candidate to be more efficiently quenched by the heme than W15 (κ 2=0.191). Although the Förster approach is powerful for the evaluation of the relative efficiency of quenching, it can only explain pico- and sub-nanosecond lifetimes. With the average lifetime, 〈τ〉=3 ns, measured for the apomonomer as the reference, the lifetimes calculated for each emitter were: W33-1 (1 ps), W33-2 (2 ps), W33-3 (18 ps), W129 (100 ps), and W15 (600 ps). Experimentally, there are four components for oxymonomers at pH 7: two long ones of 4.6 and 2.1 ns, which contribute approximately 90% of the total fluorescence, one of 300 ps (4%), and the last one of 33 ps (7.4%). It is clear that the equilibrium structure resulting from homology modeling explains the sub-nanosecond fluorescence lifetimes, while the nanosecond range lifetimes require more information about the protein in solution, since there is a significant contribution of lifetimes that resemble the apo molecule.

Van der Waals interaction between an atom and a metallic nanowire

The nonretarded linear-response potential of a metallic cylindrical nanowire in the vicinity at which an atom, assimilated to a fluctuating dipole, is placed is determined using (i) a complete orthogonal basis set over which the potential inside the solid is expanded and (ii) the boundary conditions at the solid surface. Exact analytical expressions of the reflection factors are obtained. The dipole-dipole van der Waals energy is then derived by use of the propagator method. This energy is numerically calculated for an argon atom in the vicinity of an aluminum wire. At short distance a repulsive potential, calculated by summing terms in ${r}^{\ensuremath{-}12}$ over the solid lattice, is added to the previous one. The collision at thermal energies of Ar atoms with the Al wire is then studied. The potential well makes a rainbow effect appear at angles easily accessible experimentally.

Improving an EVM QSPR model for glass transition temperature prediction using optimal design

An energy, volume and mass (EVM) model, involving four physico-chemical descriptor variables, i.e. van der Waals energy, internal energy, volume, and mass, to successfully predict the glass transition temperatures ( T g) of aliphatic acrylate and methacrylate polymers, has been previously described. The EVM model is as good, or better, as the previous models in terms of accuracy of calculated T g values of polymers. However, the classical EVM approach is still limited by the validity of the experimental data that were used to derive the regressor coefficients of the quantitative structure–properties relationship (QSPR). In fact, one major problem is the large variation in the experimental T g values that were reported in the literature. Deciding which values to use for modelling the relationship and the evaluation set of polymers is a problem to tackle with. For these reasons, an a priori design approach to the selection of a database of acrylate and methacrylate polymers for the evaluation of the EVM model has been adopted. In particular, the selection of the molecules to be considered was performed by two computed-assisted procedures based on the exchange algorithm for obtaining D-optimal design and the uniform method for finding experimental designs characterized by a stable structure. Based on the a priori design criteria, the selection of the optimal and uniform designs was “carried out”, in particular according to G-optimality.

Assessing short-range membrane–colloid interactions using surface energetics

The contribution of acid–base (AB) (polar) interactions to the total interaction energy between membranes and colloids was investigated. The surface energetics of several membranes and colloids were evaluated using the Lifshitz–van der Waals acid-base approach. This provides the van der Waals (LW) and polar interaction energies between various surfaces from measurements of contact angles of different probe liquids on these surfaces. In addition, the surface potentials of the membranes and colloids were determined using electrokinetic measurements, yielding the electrostatic (EL) interaction between these surfaces. The three interaction energy components (LW, EL, and AB) were combined according to the extended Derjaguin–Landau–Verwey–Overbeek (extended DLVO or XDLVO) approach to evaluate membrane–colloid interaction energies. Predictions of interaction energy based on the XDLVO approach were compared to the corresponding predictions from the classical DLVO theory. For all the membrane–colloid combinations studied, the DLVO potentials were quite similar. However, inclusion of AB interactions resulted in a substantially different (qualitative and quantitative) prediction of short-range (separation distances <5 nm) interaction energies for several of the membrane–colloid combinations investigated. Finally, all of the membranes studied were found to have substantially low surface energies compared to the colloids and the interaction energy between the membranes and colloids was primarily dictated by the surface energies of the colloids. Fouling experiments for a membrane and three colloids supported the fouling trends predicted by the XDLVO approach.

Calculation of pull-in voltagesfor carbon-nanotube-based nanoelectromechanical switches

We study the pull-in voltage characteristics ofseveral nanotube electromechanical switches, such as double-wall carbon nanotubes suspended over a graphitic groundelectrode. We propose parametrized continuum models for threecoupled energy domains: the elastostatic energy domain, theelectrostatic energy domain and the van der Waals energy domain.We compare the accuracy of the continuum models with atomistic simulations. Numerical simulations based on continuum modelsclosely match the experimental data reported for carbon-nanotube-based nanotweezers. An analytical expression, based on a lumped model, is derived to compute the pull-in voltage ofcantilever and fixed-fixed switches. We investigate thesignificance of van der Waals interactions in the design ofnanoelectromechanical switches.

Molecular Modeling Study Of Chiral Drug Crystals: Lattice Energy Calculations

The lattice energies of a number of chiral drugs with known crystal structures were calculated using Dreiding II force field. The lattice energies, including van der Waals, Coulombic, and hydrogen-bonding energies, of homochiral and racemic crystals of some ephedrine derivatives and of several other chiral drugs, are compared. The calculated energies are correlated with experimental data to probe the underlying intermolecular forces responsible for the formation of racemic species, racemic conglomerates, or racemic compounds, termed chiral discrimination. Comparison of the calculated energies among ephedrine derivatives reveals that a greater Coulombic energy corresponds to a higher melting temperature, while a greater van der Waals energy corresponds to a larger enthalpy of fusion. For seven pairs of homochiral and racemic compounds, correlation of the differences between the two forms in the calculated energies and experimental enthalpy of fusion suggests that the van der Waals interactions play a key role in the chiral discrimination in the crystalline state. For salts of the chiral drugs, the counter ions diminish chiral discrimination by increasing the Coulombic interactions. This result may explain why salt forms favor the formation of racemic conglomerates, thereby facilitating the resolution of racemates.