Intermolecular Van Der Waals Interactions Research Articles

Selective adsorption and electronic interaction ofF16CuPcon epitaxial graphene

We investigate the electronic coupling between copper hexadecafluoro-phthalocyanine $({\text{F}}_{16}\text{CuPc})$ and epitaxial graphene (EG) on 6H-SiC(0001) using a combined approach of low-temperature scanning tunneling spectroscopy and electronic structure calculations. The molecules are preferentially adsorbed on monolayer EG than bilayer EG. Competing molecule-surface and intermolecular van der Waals interactions result in two well-ordered incommensurate phases. We show that the amount of charge transfer from EG to ${\text{F}}_{16}\text{CuPc}$ can be tuned by applied voltage or the thickness of graphene layers. A characteristic feature at $\ensuremath{\sim}0.4\text{ }\text{eV}$ above the Dirac point is identified in bilayer EG, which indicates its electronic structure is modified via introducing extra unoccupied states upon adsorption.

Interfacial Forces between a Silica Particle and Phosphatidylcholine Monolayers at the Air−Water Interface

Interfacial forces between a silica or borosilicate particle in water and phospholipids at the air-water interface were studied using the Monolayer Particle Interaction Apparatus. This instrument allowed the forces to be measured as the colloidal probe approached the monolayer from the liquid phase. The proper working principle of this setup was demonstrated by measuring the forces between a particle and a mica plate in 0.1 mM NaCl. The effect of the alkyl chain length on the adhesion between the particle and the monolayer was investigated using four different 1,2-dialkyl-sn-glycero-3-phosphocholines (DMPC, DPPC, DSPC, and DBPC), which had 14, 16, 18, and 22 carbon atoms per alkyl chain, respectively. The adhesion force increased with the square of the particle radius. The lipids in the liquid-expanded (LE) phase showed an attraction to the particle, explained by an electrostatic attraction and/or the formation of a three-phase contact line that lead to a capillary force. All monolayers showed an adhesion in their retract force curve, which decreased with an increased chain length and surface pressure. Interfacial stiffness was generally seen to increase with the phospholipid chain length and to decrease with surface pressure, explained by an increase in the intermolecular van der Waals interaction and a decrease in the interfacial tension, respectively. The adhesion between the particle and monolayer was concluded to be controlled by the contact area between the particle and monolayer, and therefore the monolayer stiffness and the electrostatic interactions.

Influence of Intermolecular Interactions on the Structure of Copper Phthalocyanine Layers on Passivated Semiconductor Surfaces

The surface structures of copper phthalocyanine (CuPc) thin films deposited on sulphur-passivated and plane perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA)-covered InAs(100) surfaces have been studied by low energy electron diffraction (LEED) and van der Waals (vdW) intermolecular interaction energy calculations. The annealing to <TEX>$300^{\circ}C$</TEX> and <TEX>$450^{\circ}C$</TEX> of <TEX>$(NH_4)_2S_x$</TEX>-treated InAs(100) substrates produces a (<TEX>$1{\times}1$</TEX>) and (<TEX>$2{\times}1$</TEX>) S-passivated surface respectively. The CuPc deposition onto the PTCDA-covered InAs(100) surface leads to a ring-like diffraction pattern, indicating that the 2D ordered overlayer exists and the structure is dominantly determined by the intermolecular interactions rather than substrate-molecule interactions. However, no ordered LEED patterns were observed for the CuPc on S-passivated InAs(100) surface. The intermolecular interaction energy calculations have been carried out to rationalise this structural difference. In the case of CuPc unit cells on PTCDA layer, the planar layered CuPc structure is more stable than the <TEX>$\alpha$</TEX>-herringbone structure, consistent with the experimental LEED results. For CuPc unit cells on a S-(<TEX>$1{\times}1$</TEX>) layer, however, the <TEX>$\alpha$</TEX>-herringbone structure is more stable than the planar layered structure, consistent with the absence of diffraction pattern. The results show that the lattice structure during the initial stages of thin film growth is influenced strongly by the intermolecular interactions at the interface.

Helical Nanostructures of an Optically Active Metal‐Free Porphyrin with Four Optically Active Binaphthyl Moieties: Effect of Metal–Ligand Coordination on the Morphology

AbstractAn optically active metal‐free porphyrin (1) with four chiral binaphthyl units attached at the meso‐phenyl substituents through crown ether moieties has been designed, synthesized, and characterized. Its self‐assembly behavior in the absence and presence of K+ was comparatively investigated by electronic absorption and circular dichroism (CD) spectra, transmission electron microscopy (TEM), scanning electron microscopy (SEM), atom force microscopy (AFM), and energy‐dispersive X‐ray (EDX) spectroscopy. In the absence of K+, metal‐free porphyrin self‐assembles into nanoparticles depending mainly on the van der Waals interaction among neighboring metal‐free molecules. In the presence of K+, additionally formed metal–ligand K–Ocrown coordination bonds between K+ and crown units of (R)‐ and (S)‐1 molecules, together with chiral discrimination of chiral side chains and intermolecular van der Waals interactions, induce a right‐handed and left‐handed helical arrangement in a stack of (R)‐ and (S)‐1 molecules, respectively, with an ordered “head‐to‐tail” internal molecular arrangement. This then further hierarchically self‐assembles into highly ordered fibrous nanostructures with a helicity opposite to that of the original porphyrin stack. This clearly reveals the effect of the metal–ligand coordination bonding interaction on the morphology and handedness of self‐assembled nanostructures.

Intermolecular Interactions in a 44 kDa Interferon−Receptor Complex Detected by Asymmetric Reverse-Protonation and Two-Dimensional NOESY

Type I interferons (IFNs) make up a family of homologous helical cytokines initiating strong antiviral and antiproliferative activity. All type I IFNs bind to a common cell surface receptor consisting of two subunits, IFNAR1 and IFNAR2, associating upon binding of interferon. We studied intermolecular interactions between IFNAR2-EC and IFNalpha2 using asymmetric reverse-protonation of the different complex components and two-dimensional homonuclear NOESY. This new approach revealed with an excellent signal-to-noise ratio 24 new intermolecular NOEs between the two molecules despite the low concentration of the complex (0.25 mM) and its high molecular mass (44 kDa). Sequential and side chain assignment of IFNAR2-EC and IFNalpha2 in their binary complex helped assign the intermolecular NOEs to the corresponding protons. A docking model of the IFNAR2-EC-IFNalpha2 complex was calculated on the basis of the intermolecular interactions found in this study as well as four double mutant cycle constraints, previously observed NOEs between a single pair of residues and the NMR mapping of the binding sites on IFNAR2-EC and IFNalpha2. Our docking model doubles the buried surface area of the previous model and significantly increases the number of intermolecular hydrogen bonds, salt bridges, and van der Waals interactions. Furthermore, our model reveals the participation of several new regions in the binding site such as the N-terminus and A helix of IFNalpha2 and the C domain of IFNAR2-EC. As a result of these additions, the orientation of IFNAR2-EC relative to IFNalpha2 has changed by 30 degrees in comparison with a previously calculated model that was based on NMR mapping of the binding sites and double mutant cycle constraints. In addition, the new model strongly supports the recently proposed allosteric changes in IFNalpha2 upon binding of IFNAR1-EC to the binary IFNalpha2-IFNAR2-EC complex.

Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20

Peptide T20, which targets the HIV protein gp41, represents the first approved member of the class of HIV drugs known as membrane fusion inhibitors. However, mechanisms which lead to resistance through clinical use of T20 are not well-understood because the structure of the bound complex remains undetermined. In this report, an atomic-level model of a T20-gp41 complex embedded in an explicit DOPC membrane was constructed, and molecular dynamics simulations, followed by binding energy analysis (MM-GBSA method), were performed to delineate structural and energetic features that contribute to drug resistance. Per-residue binding footprints for T20 with wild-type gp41 reveal strong intermolecular van der Waals, Coulombic, and H-bond interactions in striking agreement with clinically observed resistance patterns. In addition, seven deleterious gp41 point mutations (L33Q, L33S, G36V, I37K, V38E, Q40H, and Q40K) were simulated, and all correctly exhibited decreases in the level of binding, including the fact that L33Q and Q40K are most detrimental. Six of the seven simulations yield good quantitative agreement (r(2) = 0.72; N = 6) with available experimental fold resistance data. Results from energy decomposition, heat map analysis, and differential (mutant minus wild-type) footprinting indicate the following. (1) Mutations disrupt intermolecular H-bonding and reduce the level of favorable contact with gp41 at M19. (2) Charged mutations (I37K, Q40K, and V38E) lead to significant Coulombic changes that weaken favorable van der Waals interactions. (3) Q40K is more detrimental than I37K because of interaction differences with a polar/charged patch on T20 in the initial (wild-type) state. (4) Resistance for L33S versus L33Q likely involves side chain packing differences in the final (mutated) state. A valuable finding of the work involves identification of favorable interactions among the C-terminal end of T20 (WNWF motif), residues on gp41 (including the fusion peptide), and headgroups in the adjacent membrane. The results suggest a complete T20 binding site would contribute to a stable complex, which could help to explain why prior studies, which employed truncated gp41 constructs, reported that C-terminal T20 residues may not interact with gp41. A hypothesis resulting from this study is that peptides could be designed to increase the level of favorable contact with both the membrane and gp41 which would lead to enhanced activity.

Solid-state assembly of oxyfunctionalized calix[4]arene derivatives

The solid-state assembly of four calix[4]arene derivatives bearing one or two rings oxyfunctionalized with epoxy and hydroxyl functional groups has been structurally studied by X-ray crystallography. In three cases the presence of OH groups pointing towards the exterior of the molecule allows the formation of intermolecular OH⋯epoxy H-bonds, which give rise to columnar structures, with zigzag or parallel oriented molecules, or helical arrangement of quadruplex elements. In one instance, in the absence of intermolecular H-bonds, columnar stacks of molecules are obtained mainly through intermolecular van der Waals interactions.

(E)-3-[(3-(Trifluoromethyl)phenylimino)methyl] benzene-1,2-diol: X-ray and DFT calculated structures

The crystal structure of (E)-3-[(3-(Trifluoromethyl)phenylimino)- methyl]benzene-1,2-diol was determined using X-ray diffraction and the molecular structure was investigated with density functional theory (DFT). The X-ray study showed that the title compound has a strong intramolecular O-H...N hydrogen bond and 3-dimensional crystal networks are primarily determined by O-H...O intermolecular hydrogen bonds and weak van der Waals interactions. The strong O-H...N bond is evidence of the preference for the phenol-imine tautomeric form in the solid state. Optimized molecular geometry was calculated with DFT at the B3LYP/6-31G(d,p) level. The results from both experiment and theoretical calculations for the title compound are compared with each other in this study.

Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

The emergence of the extremely aggressive influenza recently has highlighted the urgent need for new effective treatments. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer including PA, PB1 and PB2 has crucial roles in viral RNA replication and transcription. The highly conserved PB1 binding site on PA can be considered as a novel potential drug target site. The interaction between PB1 binding site and PA is crucial to many functions of the virus. In this study, to understand the detailed interaction profile and to characterize the binding hot spots in the interactions of the PA-PB1 complex, an 8 ns molecular dynamics simulation of the subunit PA-PB1 combined with MM-PBSA (molecular mechanics Poisson-Boltzmann surface area), MM-GBSA (molecular mechanics generalized Born surface area) computations and virtual alanine scanning were performed. The results from the free energy decomposition indicate that the intermolecular van der Waals interaction and the nonpolar solvation term provide the driving force for binding process. Through the pair interaction analysis and virtual alanine scanning, we identified the binding hot spots of PA and the basic binding motif of PB1. This information can provide some insights for the structure-based RNA-dependent RNA polymerase inhibitors design. The identified binding motif can be used as the starting point for the rational design of small molecules or peptide mimics. This study will also lead to new opportunities toward the development of new generation therapeutic agents exhibiting specificity and low resistance to influenza virus.

Design of supramolecular β-sheet forming β-turns containing aromatic rings and non-coded α-aminoisobutyric acid and the formation of flat fibrillar structures through self-assembly

Single crystal X-ray diffraction studies show that the three designed tripeptides Boc-Leu-Aib-m-NA-NO2 (I), Boc-Phe-Aib-m-NA-NO2 (II) and Boc-Pro-Aib-m-ABA-OMe (III) (Aib, α-aminoisobutyric acid; m-NA, m-nitroaniline; m-ABA, m-aminobenzoic acid; Boc, t-butyloxycarbonyl) containing aromatic rings in the backbones adopt β-turn structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of β-sheets. Solvent-dependent NMR titration and CD studies show that the β-turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic and transmission electron microscopic images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through β-sheet mediated self-assembly of the preorganised β-turn building blocks.

Reversible Photoswitching of Azobenzene-Based Monolayers Physisorbed on a Mica Surface

The formation of compact and large-scale self-assembled monolayers (SAMs) adsorbed on a mica surface has been achieved by insertion of alkyl chains on azobenzene derivatives, leading to strong intermolecular van der Waals interactions and hydrogen bonding. The reversible photoswitching of monolayers was investigated by monitoring the variation of the thickness of the SAMs during the cis-trans isomerization of the azobenzene cores with an atomic force microscope (AFM). The absence of covalent bonds between molecules and substrate induces a molecular diffusion which leads to the complete isomerization of the molecules constituting the SAMs.

Formation of fibrillar structures through self-assembly of designed peptide turns

Three tripeptides Boc-Phe-Aib-Val-OMe (1), Boc-Leu-Aib-p-NA-NO2 (2) and Boc-Pro-Aib-m-NA-NO2 (3) (Aib: alpha-aminoisobutyric acid; p- and m-NA: para- and meta-nitroaniline) have been designed by incorporating aromatic rings to study the self-assembly and fibril formation. Single crystal X-ray diffraction studies show that all the peptides adopt turn-like structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of beta-sheets. Solvent dependent NMR titration and CD studies show that the turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic (FE-SEM) images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through beta-sheet mediated self-assembly of the preorganized turn building blocks.

Effect of Electrostatic Interactions on Metallophthalocyanine Single Molecular Arrays with &lt;I&gt;n&lt;/I&gt;-Octadecyl Mercaptan Templates

By changing central metal ions or by tuning the length of substituted alkyl chains, metallophthalocyanines or their derivatives exhibit various assembling behaviors when co-adsorbed with n-octadecyl mercaptan on highly oriented pyrolytic graphite surfaces. Repeated scanning tunneling microscopy experiments demonstrate that planar or short alkyl chain substituted MPcs could form single molecular arrays while phase separation occurred when non-planar or longer alkyl chain substituted MPcs were co-adsorbed with C18SH templates. The experimental results combined with the density functional theory calculations reveal that intermolecular electrostatic and van der Waals interactions play essential roles in the formation of single molecular arrays.

Adsorption of phenolic compounds on some hybrid xerogels

The ability of some hybrid xerogels (HyXs) to adsorb phenolic compounds from aqueous media was studied. It was shown that by incorporating n-alkylormosils (30–50%, v/v) into the composition of the HyXs the ability to adsorb phenolic compounds was improved. Aging of the HyXs was also shown to have an effect on the adsorptive capacity. Sol–gels dried at room temperature had higher adsorptive capacity compared with the analogous gels aged at 4 °C. All HyXs with an ormosil content between 0 and 80% exhibited a base reaction with the phenolic substances. It was also shown that hydrogen bonding appeared to have a negligible effect on the adsorption of the selected phenolic substances for the HyXs studied. It is proposed that adsorption occurs as a result of non-ionic but strong intermolecular Van der Waals interactions and as a consequence is geometry and weight dependant. Considering the molecular weights of the selected phenolic compounds for this study, it is proposed that phenolic substances with a p K a < 7 and MW > 180 will be adsorbed by the HyXs selected. In addition, the non-ionic-based adsorption of the phenolic compounds did not follow the Langmuir monolayer adsorption model.

γ-Cyclodextrin Forms a Highly Compressible Complex with 1-Adamantanecarboxylic Acid

We report temperature-dependent ultrasonic velocimetric and densimetric data on changes in volume, expansibility, and adiabatic compressibility associated with the binding of 1-adamantanecarboxylic acid (AD) to gamma-cyclodextrin (gamma-CD). We compare these results with our previous data on the binding of AD to beta-cyclodextrin (beta-CD) [Taulier, N.; Chalikian, T.V.J. Phys. Chem. B 2006, 110, 12222-12224]. The comparison reveals that, in contrast to the tight AD-beta-CD complex with little void space left inside the cavity, AD forms a loose complex with gamma-CD with approximately 30 A3 of void space between the guest molecule and the inner walls of the cavity. The presence of the void renders the AD-gamma-CD complex highly compressible; the intrinsic coefficient of compressibility of the AD-gamma-CD complex is 37x10(-6) bar(-1) at 18 degrees C and decreases to 23x10(-6) bar(-1) at 55 degrees C. Such large compressibility is suggestive of only weak contacts between the interacting AD and gamma-CD atomic groups in the cavity. Our results are consistent with the notion that the AD-gamma-CD complex is predominantly stabilized by the hydrophobic effect with only modest contribution from intermolecular van der Waals interactions. This notion is in contrast to the AD-beta-CD complex which is stabilized by strong host-guest van der Waals interactions in addition to the hydrophobic effect.

Electrostatic Adhesion of Nanosized Particles: The Cohesive Role of Water

Adhesion between chemically dissimilar solids is not often observed for fundamental reasons, especially the large solid−solid interfacial tensions involved that, in turn, derive from the fundamental characteristics of van der Waals and other intermolecular interactions. However, this difficulty can be overcome in many cases by mixing particulate solids within aqueous media and drying the resulting dispersion. In this work, transmission electron microscopy (TEM) and scanning probe microscopy (SPM) were used to obtain evidence for strong adhesion between the following pairs of organic and inorganic nanoparticles: Stober silica and poly(styrene-co-butyl acrylate-co-acrylic acid) (SA) latex, calcium montmorillonite and the same latex, and titanium dioxide and another SA latex. Adhesion was observed even though the particles in each pair are highly dissimilar and thus are expected to have a high interfacial tension. Bulk or aggregate particle nanohybrids were obtained by drying mixed aqueous dispersions at dif...

Dimethyl Sulfide on Cu{111}: Molecular Self-Assembly and Submolecular Resolution Imaging

The literature contains many studies of thiol-based, self-assembled monolayers (RSH); however, thioethers (RSR) have barely begun to be explored, despite having the potential advantages of being more resistant to oxidation and allowing for the control of self-assembly parallel to the surface. This paper describes a low-temperature scanning tunneling microscopy investigation of dimethyl sulfide on Cu{111}. Previous work on the adsorption of dibutyl sulfide on Cu{111} revealed that intermolecular van der Waals interactions directed the parallel ordering of dibutyl sulfide molecules in linear rows. Upon annealing to 120 K, small dibutyl sulfide domains reordered into very large, ordered domains free of defects. The current study reveals the effect of the shorter alkyl chain length of dimethyl sulfide on both the rate of diffusion and the packing structure of the molecule. At a medium surface coverage and at 78 K, it was found that dimethyl sulfide is mobile and forms large, ordered islands without the 120 K annealing that was required for dibutyl sulfide to arrange. Also, the molecular packing structure evolves from quadrupole-quadrupole interactions and results in a perpendicular arrangement of neighboring molecules instead of the parallel arrangement observed for dibutyl sulfide. We show high-resolution images of the dimethyl sulfide islands in which submolecular features are revealed. These high-resolution data allow us to propose a structural model for the adsorption site of each dimethyl sulfide molecule within the ordered structures. These results demonstrate that the length of the alkyl side chain is an important factor in determining how thioethers self-assemble on metal surfaces.

Modeling the Alzheimer A β17-42 Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities

We investigate A β 17-42 protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the A β protofibril as a longitudinal stack of U-shaped molecules, creating an in-parallel β-sheet and loop spine. Here we study the molecular architecture of the fibril formed by spine-spine association. We model in-register intermolecular β-sheet– β-sheet associations and study the consequences of Alzheimer's mutations (E22G, E22Q, E22K, and M35A) on the organization. We assess the structural stability and association force of A β oligomers with different sheet-sheet interfaces. Double-layered oligomers associating through the C-terminal–C-terminal interface are energetically more favorable than those with the N-terminal–N-terminal interface, although both interfaces exhibit high structural stability. The C-terminal–C-terminal interface is essentially stabilized by hydrophobic and van der Waals (shape complementarity via M35-M35 contacts) intermolecular interactions, whereas the N-terminal–N-terminal interface is stabilized by hydrophobic and electrostatic interactions. Hence, shape complementarity, or the “steric zipper” motif plays an important role in amyloid formation. On the other hand, the intramolecular A β β-strand-loop- β-strand U-shaped motif creates a hydrophobic cavity with a diameter of 6–7 Å, allowing water molecules and ions to conduct through. The hydrated hydrophobic cavities may allow optimization of the sheet association and constitute a typical feature of fibrils, in addition to the tight sheet-sheet association. Thus, we propose that A β fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging.

The Immunoglobulin Heavy Chain Constant Region Affects Kinetic and Thermodynamic Parameters of Antibody Variable Region Interactions with Antigen

A central dogma in immunology is that antibody specificity is a function of the variable (V) region. However serological analysis of IgG(1), IgG(2a), and IgG(2b) switch variants of murine monoclonal antibody (mAb) 3E5 IgG(3) with identical V domains revealed apparent specificity differences for Cryptococcus neoformans glucuronoxylomannan (GXM). Kinetic and thermodynamic binding properties of mAbs 3E5 to a 12-mer peptide mimetic of GXM revealed differences in the affinity of these mAbs for a monovalent ligand, a result that implied that the constant (C) region affects the secondary structure of the antigen binding site, thus accounting for variations in specificity. Structural models of mAbs 3E5 suggested that isotype-related differences in binding resulted from amino acid sequence polymorphisms in the C region. This study implies that isotype switching is another mechanism for generating diversity in antigen binding and that isotype restriction of certain antibody responses may reflect structural constraints imposed by C region on V region binding. Furthermore, isotype affected the polyreactivity of V region identical antibodies, implying a role for C region in determining self-reactivity.

An examination of polymorphic stability and molecular conformational flexibility as a function of crystal size associated with the nucleation and growth of benzophenone

The polymorphic behaviour of the aromatic ketone, benzophenone, which is a conformationally flexible molecule and forms crystal structures dominated by van der Waals intermolecular interactions, is examined. Crystallization of this material from the undercooled molten state yields the two known polymorphic forms, i.e. the stable alpha-form and the metastable beta-form. The relative, energetic stabilities are examined using both crystal lattice and molecular conformational modelling techniques. Examination of nano-sized faceted molecular clusters of these forms, with cluster sizes ranging from 3 to 100 molecules, reveals that at very small cluster size (< 5 molecules) the relative energetic stability of clusters representative for the two forms become very similar, indicating that for high melting undercooling (i.e. small critical cluster size for nucleation) crystallization of the metastable beta-phase becomes more likely. Detailed analysis of the variation in molecular conformations within the simulated molecular clusters reveals more disordered three-dimensional structures at small compared to larger cluster sizes. The conformational disorder was found to be higher for the metastable beta-form. This observation, together with the lower stability of clusters for this form is indicative of the difficulty in achieving crystallization of the metastable beta-form from the melt, which requires a considerable undercooling.