Minimum Interaction Energy Research Articles

ChemInform Abstract: Synthesis and 1H NMR Spectra of Some 1-Aryl-2,5-pyrrolidinediones.

Three 1-aryl-2,5 pyrrolidinediones, two of which are novel, were prepared by reaction of the requisite primary aromatic amines with succinic anhydride, followed by treatment with acetic anhydride. The 1H nmr spectra for the derivatives in which aryl is 1-naphthyl and 1-anthracenyl exhibit 32-line multiplets for the four aliphatic hydrogens, indicating that all four are in different environments. Examination of molecular models demonstrates that the pyrrolidinedione and aryl ring systems cannot be coplanar and that rotation about the nitrogen-aryl bond is restricted. Molecular mechanics calculations reveal that a dihedral angle of 50–65° for the two ring systems results in the minimum steric interaction energy.

Evaluation of Some Synthetic Oligolignols as Adhesives: A Molecular Docking Study

We have investigated alternative adhesives based on some oligomers that have structural units similar to lignins. The favorable interactions for a set of synthetic oligolignols were determined through a computational docking scheme, considering their conformational changes to adapt themselves on the surface of a three-dimensional model of cellulose I-β, to describe and elucidate the interactions that drove their adhesion ability based on the minimum interaction energy calculated for each of the oligolignols conformations. The selected oligolignols included nine dimers, five trimers and one tetramer all of these were built from two lignin precursors, coniferol and sinapol, bonded in four different linkages: β–O4′, β′–β′, β–5′ and γ–β′. Our results showed that trimers were the most favorable oligolignols to dock over the cellulose model, considering their individual docking energy. We hope that this work contributes to the field of wood adhesives design and helps in understanding the interaction between the cellulose and structural components of lignin.

Interfacial thermodynamics of confined water near molecularly rough surfaces.

We study the effects of nanoscopic roughness on the interfacial free energy of water confined between solid surfaces. SPC/E water is simulated in confinement between two infinite planar surfaces that differ in their physical topology: one is smooth and the other one is physically rough on a sub-nanometre length scale. The two thermodynamic ensembles considered, with constant pressure either normal or parallel to the walls, correspond to different experimental conditions. We find that molecular-scale surface roughness significantly increases the solid-liquid interfacial free energy compared to the smooth surface. For our surfaces with a water-wall interaction energy minimum of -1.2 kcal mol(-1), we observe a transition from a hydrophilic surface to a hydrophobic surface at a roughness amplitude of about 3 angstroms and a wavelength of 11.6 angstroms, with the interfacial free energy changing sign from negative to positive. In agreement with previous studies of water near hydrophobic surfaces, we find an increase in the isothermal compressibility of water with increasing surface roughness. Interestingly, average measures of the water density and hydrogen-bond number do not contain distinct signatures of increased hydrophobicity. In contrast, a local analysis indicates transient dewetting of water in the valleys of the rough surface, together with a significant loss of hydrogen bonds, and a change in the dipole orientation toward the surface. These microscopic changes in the density, hydrogen bonding, and water orientation contribute to the large increase in the interfacial free energy, and the change from a hydrophilic to a hydrophobic character of the surface.

2D and 3D‐QSPR Models for the Fluorophilicity of Organic Compounds in Consideration of Chirality

AbstractFluorous biphase system (FBS) exhibits significant prospect in synthesis and catalysis fields. With the development of FBS, the design and prediction on the fluorophilicity of compounds show major importance. QSPR models are established by using three‐dimensional structural descriptors derived from VolSurf program and two‐dimensional topological descriptors derived from Tsar program. Good results are received and the training set model has satisfactory predictive capability for the test set. MLR method is applicative for Tsar descriptors and the equation shows that more number of F atoms in the compound will result in higher fluorophilicity. PLS analysis is suitable for VolSurf descriptors. Analysis on VolSurf descriptors demonstrates that large hydrophilic regions at medium energy level are beneficial to the fluorophilicity. The capacity factor is negative correlation with the fluorophilicity, so do the best local interaction energy minimum and its distance. High hydrophobic descriptor values and large hydrogen bond acceptor regions at medium energy levels are favorable elements. High anionic regions, low POL value and high MW are advantageous to the fluorophilicity. 3D‐VolSurf descriptors (R2=0.976, Q2=0.966) are more satisfying and suitable to build the QSPR model for the fluorophilicity than other descriptors. In addition, chirality has different extent influence on the calculated result for the different chiral molecules or with the different modeling methods. Using single configuration to compute for chiral molecules will be hopeful to bring about more accurate and credible result.

FRODOCK: a new approach for fast rotational protein–protein docking

Prediction of protein-protein complexes from the coordinates of their unbound components usually starts by generating many potential predictions from a rigid-body 6D search followed by a second stage that aims to refine such predictions. Here, we present and evaluate a new method to effectively address the complexity and sampling requirements of the initial exhaustive search. In this approach we combine the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations to accelerate the search. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. The interaction-energy minima are identified by a novel, fast and exhaustive rotational docking search combined with a simple translational scanning. Results obtained on standard protein-protein benchmarks demonstrate its general applicability and robustness. The accuracy is comparable to that of existing state-of-the-art initial exhaustive rigid-body docking tools, but achieving superior efficiency. Moreover, a parallel version of the method performs the docking search in just a few minutes, opening new application opportunities in the current 'omics' world. http://sbg.cib.csic.es/Software/FRODOCK/

Ground state potential energy surfaces and bound states of M–He dimers (M=Cu,Ag,Au): A theoretical investigation

We present an ab initio investigation on the ground state interaction potentials [potential energy surface (PES)] between helium and the group 11 metal atoms: copper, silver, and gold. To the best of our knowledge, there are no previous theoretical PESs proposed for Cu-He and Au-He, and a single one for Ag-He [Z. J. Jakubek and M. Takami, Chem. Phys. Lett. 265, 653 (1997)], computed about 10 years ago at MP2 level and significantly improved by our study. To reach a high degree of accuracy in the determination of the three M-He potentials (M=Cu,Ag,Au), we performed extensive series of test computations to establish the appropriate basis set, the theoretical method, and the computational scheme for these systems. For each M-He dimer we computed the PES at the CCSD(T) level of theory, starting from the reference unrestricted Hartree-Fock wave function. We described the inner shells with relativistic small core pseudopotentials, and we adopted high quality basis sets for the valence electrons. We also performed CCSDT computations in a limited set of M-He internuclear distances, adopting a medium-sized basis set, such as to define for each dimer a CCSD(T) to CCSDT correction term and to improve further the quality of the CCSD(T) interaction potentials. The Cu-He complex has minimum interaction energy (E(min)) of -28.4 microhartree at the internuclear distance of 4.59 A (R(min)), and the short-range repulsive wall starts at 4.04 A (R(E=0)). Quite interestingly, the PES of Ag-He is more attractive (E(min)=-33.8 microhartree) but presents nearly the same R(min) and R(E=0) values, 4.60 and 4.04 A, respectively. The interaction potential for Au-He is markedly deeper and shifted at shorter distances as compared to the lighter complexes, with E(min)=-69.6 microhartree, R(min)=4.09 A and R(E=0)=3.60 A. As a first insight in the structure of M-He(n) aggregates, we determined the rovibrational structure of the three M-He dimers. The Cu-He and Ag-He potentials support just few rotational excitations, while the Au-He PES admits also a bound vibrational excitation.

Preferred orientation of albumin adsorption on a hydrophilic surface from molecular simulation

In general, non-specific protein adsorption follows a two-step procedure, i.e. first adsorption onto a surface in native form, and a subsequent conformational change on the surface. In order to predict the subsequent conformational change, it is important to determine the preferred orientation of an adsorbed protein in the first step of the adsorption. In this work, a method based on finding the global minimum of the interaction potential energy of an adsorbed protein has been developed to delineate the preferred orientations for the adsorption of human serum albumin (HSA) on a model surface with a hydrophilic self-assembled monolayer (SAM). For computational efficiency, solvation effects were greatly simplified by only including the dampening of electrostatic effects while neglecting contributions due to the competition of water molecules for the functional groups on the surface. A contour map obtained by systematic rotation of a molecule in conjunction with perpendicular motion to the surface gives the minimum interaction energy of the adsorbed molecule at various adsorption orientations. Simulation results show that for an –OH terminated SAM surface, a “back-on” orientation of HSA is the preferred orientation. The projection area of this adsorption orientation corresponds with the “triangular-side-on” adsorption of a heart shaped HSA molecule. The method proposed herein is able to provide results which are consistent with those predicted by Monte Carlo (MC) simulations with a substantially less computing cost. The high computing efficiency of the current method makes it possible to be implemented as a design tool for the control of protein adsorption on surfaces; however, before this can be fully realized, these methods must be further developed to enable interaction free energy to be calculated in place of potential energy, along with a more realistic representation of solvation effects.

Anomalously Increased Lifetimes of Biological Complexes at Zero Force Due to the Protein−Water Interface

A number of biological bonds show dramatically increased lifetimes at zero-force conditions, compared to lifetimes when even a small tensile force is applied to the ligand. The discrepancy is so great that it cannot be explained by the traditional receptor-ligand binding models. This generic phenomenon is rationalized here by considering the interaction of water with the receptor-ligand complex. It is argued that the water-protein interaction creates an energy barrier that prevents the ligand unbinding in the absence of the force. The properties of the interaction are such that even application of a relatively low force results in a dramatic drop of the bond lifetime due to the alteration of the water-receptor and water-ligand interaction network. The phenomenon is described by the presence of a second shallow interaction energy minimum for the bound ligand followed by a wide receptor-ligand dissociation barrier. The general analysis is applied quantitatively to the actin-myosin system, which demonstrates the gigantic drop of the bond lifetime at small forces and catch behavior (an increase in the lifetime) at moderate forces. The base hypothesis proposed to explain the small-force abnormal drop in the bond lifetime suggests that the majority of biological bonds may exhibit this phenomenon irrespectively whether they behave as slip or catch-slip bonds.

The Structure of Molten Lithium Carbonate Calculated by DFT and MD Simulations

The structures having the minimum interaction energy of the Li2CO3 monomer, dimer, trimer and tetramer were derived using the density functional theory (DFT). These structures were optimized. The structures of the monomer and the dimer agreed with the ab initio molecular orbital calculation results at a Hartree - Fock level. The structures of the trimer and the tetramer model were C3h and C2 symmetry, respectively. Then we carried out the harmonic frequency analysis of these geometries. The tetramer model showed the best agreement among these results with the Raman spectrum of the liquid state. On the other hand, we calculated the total structure factor S(Q) of the trimer and tetramer geometries considered from the DFT calculation to examine the local structure of molten Li2CO3. The calculation result corresponding to the tetramer model reproduced satisfactorily the position and the height of the S(Q) peaks.

Physical Nature of Ethidium and Proflavine Interactions with Nucleic Acid Bases in the Intercalation Plane

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Electrostatic Potential of Charged Macroparticles in Plasma under Conditions of Thermal Equilibrium

An exact analytical solution of the Poisson-Boltzmann equation (PBE) is found in the case of spherical, axial, or plane geometry, which describes the potential distribution around a charged macroparticle (wire or plane) in plasma under conditions of thermal equilibrium with an arbitrary relationship between the charge densities of macroparticles and plasma. The solution is obtained as a logarithm of the power series in several different forms. A recurrent relation is found for coefficients of the power series. The exact solution of the PBE for the case of plane geometry is already known; its identity to that found in this study is shown in a particular case. In the case of not too high charges of macroparticles, the exact solution is approximated by the solution of linearized PBE; for a solitary particle, this solution corresponds to the DLVO and Debye-Huckel approximations. For high charges, the exact solution deviates from an approximate one (very appreciably too) only in the vicinity of the macroparticle. An approximate solution is used to renormalize the macroparticle charge and to construct a simple model of electrostatic interaction of like-charged particles, which demonstrates the possibility of their attraction. The equilibrium distance of attracting particles (the position of minimum of interaction energy) agrees well with the position of maximum of the experimentally obtained pair correlation function for dust particles in thermal plasma.

Me-PTCDI thin film deposition on InSb(1 1 1)A

The evolution of N, N′-dimethylperylene-3,4,9,10-dicarboxyimide (Me-PTCDI) thin films formed by vapour deposition on InSb(1 1 1)A substrates has been studied by X-ray photoelectron spectroscopy (XPS), high-resolution electron energy loss spectroscopy (HREELS) and low energy electron diffraction (LEED). XPS studies of the Me-PTCDI covered surface indicate that no significant interaction occurs at sub-monolayer coverage when compared to multilayer Me-PTCDI films. HREELS studies suggest only a weak interaction as evidenced by very small changes in the frequencies of several molecular vibrational modes. LEED patterns show the Me-PTCDI overlayer adopts a structure commensurate with the underlying InSb(1 1 1)A substrate surface and that can be rationalised by van der Waals intermolecular energy calculations for the Me-PTCDI unit cell. The results are consistent with a weak interaction at the Me-PTCDI/InSb interface, the formation of the commensurate structure being sufficient to overcome the small energetic penalty associated with deviation from the calculated intermolecular interaction energy minimum.

A Refined Force Field for Molecular Simulation of Imidazolium-Based Ionic Liquids

An all-atom force field for a class of the room temperature ionic liquids of the 1-alkyl-3-methylimidazolium cation family was developed. The model is based on the AMBER force field with modifications on several parameters. The refinements include three aspects. (1) The force coefficients of the bond and angle parameters were adjusted to fit the vibrational frequency data, from both experiment and ab initio calculations. (2) The parameters for two types of torsions, which are absent in the original AMBER, were obtained by fitting the torsion energy profiles depending on dihedral angles. (3) The results of the minimum interaction energies and geometries for several ion pairs, calculated from ab initio and the force field, respectively, are compared. Then, the van der Waals (VDW) diameter of a type of hydrogen atom (H5) is adjusted. To validate the force field, we performed molecular dynamics (MD) simulations for five RTILs. The predicted densities are in better agreement than those reported from other simu...

Parametrization of 2-Bromo-2-Chloro-1,1,1-Trifluoroethane (Halothane) and Hexafluoroethane for Nonbonded Interactions

Ab initio and empirical methods were combined to optimize the partial atomic charges and Lennard-Jones parameters for two halogenated compounds, halothane (CF3CHClBr, a potent volatile anesthetic) and hexafluoroethane (CF3CF3, a nonanesthetic). Charge optimization was achieved using empirical calculations by systematically adjusting the charge assignments to fit minimum interaction energies and geometries between a TIP3 water molecule and the halogenated compounds to the corresponding values from the ab initio calculations, which were carried out at the HF/6-311+G(2d,p) and HF/6-31G(d) levels for halothane and hexafluoroethane, respectively. To optimize the Lennard-Jones parameters, the initial estimates were obtained from scaling the values from the ab initio minimum interaction energies and geometries between neon and the halogenated compounds calculated at the MP3/6-311++G(3d,3p) level. The Lennard-Jones parameters were further refined by fitting the empirical interaction energies to the corresponding ...

Aggregation of protein-coated colloidal particles: Interaction energy, cluster morphology, and aggregation kinetics

The salt-induced aggregation of polystyrene particles, partially coated with monomeric bovine serum albumin molecules, has been studied. For this purpose, the cluster fractal dimension df and the van Dongen–Ernst homogeneity parameter λ have been measured by means of static and dynamic light scattering techniques. The theoretical analysis indicates that aggregation takes places at an interaction energy minimum predicted by a modified Derjaguin–Landau–Verwey–Overbeeck (DLVO) theory when additional osmotic and elastic terms are considered. It could be shown that the depth of the energy minimum is directly related to df and λ. Moreover, the particle–particle distance within the cluster could also be assessed and compared with the interparticle distance at which the DLVO-predicted minimum appears.

SCC‐DFTB‐D study of intercalating carcinogens: Benzo(a)pyrene and its metabolites complexed with the G–C base pair

AbstractThe interaction of benzo(a)pyrene (BP) and its metabolites with the G–C base pair has been studied using the self‐consistent‐charge, density functional tight‐binding(SCC‐DFTB‐D) method, augmented by the empirical London dispersion energy term. Structures of the complexes corresponding to a minimum interaction energy obtained using a constrained rigid body search were fully optimized. It is found that the benzylic ring of BP and its anti‐conformers is located below the NH2 group of guanine while the syn‐conformers exhibit a different binding pattern. The BP triol carbocation (BPTC) in the anti‐conformation is stabilized by an additional hydrogen bond between the hydrogen atom of the OH group of BPTC and the N3 atom of guanine of the G–C base pair. The benzylic ring of BPTC directed toward the minor groove side whereas the pyrenyl ring stacks below the cytosine covering the hydrogen bond region. Guanine bends toward the benzylic ring, making an angle of ∼11–15° with the pyrene ring. The calculated equilibrium structures are in good agreement with the available experimental and other theoretical results. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 95: 44–59, 2003

Estimation of surface free energy of pyrites by contact angle measurements

The surface properties of coal-pyrite play a major role in determining its separation from coal in processes such as flotation. The solution pH is an important parameter in determining the surface properties of both coal and coal-pyrite such as surface free energy and zeta-potential. In the present investigation, the effect of pH on the surface free energy of pyrites from different sources was studied. The surface free energy of solids is made up of two components, i.e. the dispersive surface free energy and the acid-base interaction energy. Various methods have been used by previous researchers to evaluate these two components for different solids. In the present study, a new approach was developed and used to study the surface free energy of pyrite surfaces. Results indicate that the dispersion surface free energy of various pyrites is independent of pH while the acid-base interaction energy is strongly dependent on the pH. The acid-base interaction energy is different for each pyrite sample and also the change with pH varies with the type of pyrite. Coal-pyrite was found to be more hydrophobic than ore-pyrite which may be attributed to the presence of carbon in coal-pyrites. The acid-base interaction energy varied little with pH for coal pyrites than ore-pyrite. Comparison of acid-base interaction energy with zeta-potential measurements shows a good correlation between the minimum in acid-base interaction energy and the pH pzc.

The effects of PC‐PMMA block copolymer on the compatibility and interfacial properties of PC/SAN blends

AbstractBlock copolymers of polycarbonate (PC) and polymethylmethacrylate (PMMA), PCb‐PMMA, were examined as compatibilizers for blends of PC with styrene‐co‐acrylonitrile (SAN) copolymer. PC‐b‐PMMA was added to blends of PC with SAN containing various amounts of AN. The average diameter of the dispersed particles was measured with an image analyzer, and the interfacial properties of the blends were analyzed with an imbedded fiber retraction (IFR) test and an asymmetric double cantilever beam fracture test. The average particle size and interfacial tension of the PC/SAN blends reached a minimum value when the SAN copolymer contained about 24 wt% AN. A maximum in the adhesion energy was also observed at the same AN content. Interfacial tension and particle size were further reduced by adding PC‐b‐PMMA to the PC/SAN blends. Fracture toughness of the blends was also improved by enhancing the interfacial adhesion by the addition of PC‐b‐PMMA. The addition of PC‐b‐PMMA copolymer was more effective at improving the interfacial properties of PC/SAN blends than was varying the AN content of the SAN copolymers. The interfacial properties of the PC/SAN blends were optimized by adding a block copolymer and using an SAN copolymer that had minimum interaction energy with PC.

Influence of the Secondary Interaction Energy Minimum on the Early Stages of Colloidal Aggregation

The pair interaction energy of charged colloidal particles in electrolyte solutions can exhibit a large barrier as well as a pronounced secondary minimum. We discuss the effect of a secondary energy minimum on aggregation kinetics by modeling irreversible dimer formation as a two-step process in which charged colloidal particles in electrolyte solutions first aggregate reversibly into the secondary minimum before they can cross the energy barrier. In the classical regime of slow aggregation, the secondary minimum is seen to have a pronounced effect if either the ionic strength of the solution is high (e.g., 0.1 M for particles of 150-nm radius) or particles are large (≥350-nm radius for an ionic strength of 0.01 M). Under these conditions, our calculations predict a transient period of fast aggregation into the secondary minimum followed by slow primary aggregation. The aggregation in this second regime is found to take place at a lower rate than what would be expected in the absence of the secondary minimum or from an earlier linearized model for secondary aggregation. The crossover time between the two regimes strongly depends on the particle size but not on the particle concentration, which however determines the degree of aggregation reached within the fast regime. We also conclude that a previously observed severe discrepancy between measured and predicted aggregation rate constants for submicron particles is not due to the neglect of secondary aggregation in the theoretical treatment.

Combinedab initio/empirical approach for optimization of Lennard-Jones parameters

Obtaining accurate Lennard–Jones (L-J) parameters is a vital part of the optimization of empirical force fields due to their significant contribution to condensed-phase properties. We present a novel approach to optimize L-J parameters via the use of ab initio data on interactions between rare gas atoms and model compounds combined with the reproduction of experimental pure solvent properties. Relative values of ab initio minimum interaction energies and geometries between helium or neon and model compounds were used to optimize the relative magnitude of the L-J parameters. Absolute values of the L-J parameters were determined by reproducing experimental heats of vaporization and molecular volumes for pure solvents. Application of the approach was performed on methane, ethane, and propane. Free energies of aqueous solvation and butane pure solvent and aqueous solvation calculations were used to test the developed L-J parameters. The new alkane parameters are similar or improved as compared with current empirical force field parameters with respect to experimental pure solvent properties and free energies of aqueous solvation. Also included is a description of the internal portion of the force field. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 334–348, 1998