Strength Of Intermolecular Interactions Research Articles

Molecular self-assembly in substituted alanine derivatives: XRD, Hirshfeld surfaces and DFT studies

The molecular assemblage in the crystal structures of three modified chiral amino acids, two of which are isomeric d- and l-pairs boc-l-benzothienylalanine (BLA), boc-d-benzothienylalanine (BDA) and the other boc-d-naphthylalanine (NDA) differing from this pair very slightly in the chemical modification introduced, is accurately described. The aggregation of amino acid molecules is similar in all the crystals and may be described as a twisted double helical ladder in which two complementary long helical chains formed through O—H⋯O hydrogen bonds are interconnected through the characteristic head-to-tail N—H⋯O hydrogen bonds. Thus the molecular aggregation enabled through classical hydrogen bonds may be regarded as a mimic of the characteristic double helical structure of DNA. Also, precise structural information involving these amino acid molecules with lower symmetry exhibiting higher trigonal symmetry in their self-assembly is expected to throw light on the nature and strength of intermolecular interactions and their role in self-assembly of molecular aggregates, which are crucial in developing new or at least supplement existing crystal engineering strategies. Single crystal X-ray analysis and their electronic structures were calculated at the DFT level with a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed using CRYSTAL09 with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N-N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C-H···N, C-H···O and N-H···N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Computational Analysis of the Single Molecule AFM Force Spectroscopy Data

AFM force spectroscopy is a widely applied to various molecular systems providing an important information on the strength of intramolecular and intermolecular interactions. However, a structural characterization of the systems is limited by the lack of theoretical approaches capable of direct comparison with experiment. Steered Molecular Dynamic (SMD) simulation is widely used for modeling of the AFM pulling experiments, but it is typically performed at pulling rates 5 nm/ns which are 107 times higher than those for typical experimental conditions. Here we describe the computational approach utilizing Monte Carlo Pulling (MPC) simulation enabling us to model AFM pulling experiments at conditions corresponding to experimental ones. Tested by the comparison with experimental data for titin I-band(PDB ID: 1TIT), the approach was applied to modeling of the AFM force spectroscopy experiments on probing of interaction of misfolded peptides CGNNQQNY and Aβ14-23 within dimers. The structures of the CGNNQQNY dimers were obtained from the Replica Exchanged MD simulations. The results for antiparallel out-of-register β sheet of CGNNQQNY produce the force ∼100 pN which is in line with the experimental data. At the same time, pulling of antiparallel in-register β sheet provides much higher rupture force, suggesting that CGNNQQNY monomers adopt the out-of-register arrangement in the dimer. Similar analysis applied to Aβ14-23 peptide demonstrated that the out-of-register antiparallel β-sheet arrangement of monomers is realized for this peptide as well. The elevated rupture forces for Aβ14-23 compared to CGNNQQNY dimers is explained by elevated contribution of hydrophobic, salt bridge and aromatic interactions in Aβ peptide.

Densities and Viscosities for Binary and Ternary Mixtures of 2-Methylbutan-2-ol (1) + Trichloroethylene (2) + Acetonitrile (3) at 298.15 K and at Ambient Pressure (81.5 kPa)

Densities (ρ) and viscosities (η) of ternary mixtures of 2-methylbutan-2-ol (1) + trichloroethylene (2) + acetonitrile (3) and the related binary mixtures of {2-methylbutan-2-ol (1) + trichloroethylene (2)}, {2-methylbutan-2-ol (1) + acetonitrile (3)}, and {trichloroethylene (2) + acetonitrile (3)} have been measured over the whole composition range at 298.15 K and at ambient pressure (81.5 kPa). Excess molar volumes $$ V_{\text{m}}^{\text{E}} $$ , viscosity deviations Δη, and excess Gibbs energies of activation ΔG *E were derived from the experimental data. The binary and ternary data of $$ V_{\text{m}}^{\text{E}} $$ , Δη, and ΔG *E for the binary and ternary mixtures were correlated as functions of the mole fraction by using the Redlich–Kister and the Cibulka equations. Kinematic viscosities of the binary mixtures were correlated by means of several semi-empirical equations to determine the fitting parameters and the SDs. The experimental results are analyzed to discuss the nature and strength of intermolecular interactions in these mixtures.

Theoretical study of cyclometalated Ru(II) dyes: Implications on the open-circuit voltage of dye-sensitized solar cells

A density functional theory (DFT) study was performed to elucidate why variations in the 2-phenylpyrimidinato (L) ligand of cyclometalated Ru(H3tcterpy)L(NCS) dye affect the open-circuit photovoltage (Voc) of a dye-sensitized solar cell (DSSC) using an iodine/iodide redox couple, where tcterpy represents 4,4′,4″-tricarboxy-2,2′:6′,2″-terpyridine. Neutral dye molecules interact with I2 via the N atom of the L ligand and the S atom of the NCS ligand. Among the nine tested dyes, the intermolecular interaction strengths between the dye and I2 correspond to the reduced Voc of DSSC. Additionally, I− interacts with oxidized dye via the L ligand and via the NCS ligand, and a second I− bonds to the first I−. The interaction strengths of I− with oxidized dyes strongly correlate with the enhanced Voc. The computational results suggest that the L ligand structure influences the regeneration of oxidized dye and recombination. Consequently, the L ligand structure changes Voc.

The quantum nature of the OH stretching mode in ice and water probed by neutron scattering experiments

The OH stretching vibrational spectrum of water was measured in a wide range of temperatures across the triple point, 269 K <T < 296 K, using Inelastic Neutron Scattering (INS). The hydrogen projected density of states and the proton mean kinetic energy, <EK>OH, were determined for the first time within the framework of a harmonic description of the proton dynamics. We found that in the liquid the value of <EK>OH is nearly constant as a function of T, indicating that quantum effects on the OH stretching frequency are weakly dependent on temperature. In the case of ice, ab initio electronic structure calculations, using non-local van der Waals functionals, provided <EK>OH values in agreement with INS experiments. We also found that the ratio of the stretching (<EK>OH) to the total (<EK>exp) kinetic energy, obtained from the present measurements, increases in going from ice, where hydrogen bonding is the strongest, to the liquid at ambient conditions and then to the vapour phase, where hydrogen bonding is the weakest. The same ratio was also derived from the combination of previous deep inelastic neutron scattering data, which does not rely upon the harmonic approximation, and the present measurements. We found that the ratio of stretching to the total kinetic energy shows a minimum in the metastable liquid phase. This finding suggests that the strength of intermolecular interactions increases in the supercooled phase, with respect to that in ice, contrary to the accepted view that supercooled water exhibits weaker hydrogen bonding than ice.

Materials produced from plant biomass: part III: degradation kinetics and hydrogen bonding in lignin

In this study Klason lignins from Eucalyptus grandis (LEUG) and Pinus taeda (LPIT) were characterized using Fourier transform infrared (FTIR) spectroscopy and thermogravimetry (TGA). The degradation kinetic parameters were determined by TGA using the Kissinger method. Thermogravimetric results showed that LPIT had higher thermal stability and also higher activation energy than LEUG. FTIR results showed that the average strength of intermolecular interactions and enthalpy of hydrogen bond formation among the phenolic groups are higher for LPIT than for LEUG. The results demonstrated that differences between thermal stability and degradation mechanisms might be associated with differences in hydrogen bonding in lignin.

Mechanisms of the Charge Transfer in IrQ(ppy)2–5Cl Dual-Emitter Compound

The synthesis of IrQ(ppy)2-5Cl has the advantage of a dual phosphorescence (green and red) which comes from the two ligands, phenylpyridine and quinoline. Their spectroscopic properties evidences the absorption range between 350 nm to 700 nm which is composed from the singlet and triplet states, as a result of hybridizations between Ir and the two ligands, the first one being at 625 nm. The first low energy state comes from the quinoline ligand and is responsible for the red phosphorescence at 660 nm, as results from the Density Functional Theory (DFT) analysis. The hybridization between Ir 5d orbitals and pi ligand orbitals shows strong metallic character with phenylpyridine orbitals (66% and 43%) and weak metallic character with quinoline ligand (16.8%). This fact suggests weak phosphorescence intensity in the emission spectra. Population analysis of each metallic orbital shows a small charge delocalization on the quinoline ligand for the first molecular orbital and a strong delocalization on the phenylpyridine ligands. Solvation effects induce a tuning process for the phosphorescence by changing of the matrix of the organometallic compounds which can be adjusted by the strength of intermolecular dipole-dipole interactions, using a doped guest-host molecular organic thin film system.

Excess Molar Volumes and Viscosities for the Binary Mixtures of n-Octane, n-Decane, n-Dodecane, and n-Tetradecane with Octan-2-ol at 298.15 K

Experimental values of densities (ρ) and viscosities (η) in the binary mixtures of n-octane, n-decane, n-dodecane, and n-tetradecane with octan-2-ol are presented over the whole range of mixture composition at T=298.15 K. From these data, excess molar volume (VmE), deviations in viscosity (Δη), and excess Gibbs free energy of activation ΔG∗E have been calculated. These results were fitted to Redlich-Kister polynomial equations to estimate the binary coefficients and standard errors. Jouyban-Acree model is used to correlate the experimental values of density and viscosity at T=298.15 K. The values of VmE have been analyzed using Prigogine-Flory-Patterson (PFP) theory. The results of the viscosity composition are discussed in the light of various viscosity equations suggested by Grunberg-Nissan, Tamara and Kurata, Hind et al., Katti and Chaudhri, Heric, Heric and Brewer, and McAllister multibody model. The values of Δlnη have also been analyzed using Bloomfield and Dewan model. The experiments on the constituted binaries are analyzed to discuss the nature and strength of intermolecular interactions in these mixtures.

Excess molar volumes, viscosity deviations and excess thermal expansion coefficients for binary and ternary mixtures consist of diethylketone + 2-butanol + ethylchloroacetate at (298.15, 308.15 and 318.15) K

Densities and viscosities for ternary mixtures of diethylketone+2-butanol+ethylchloroacetate, and related binary mixtures have been reported as a function of mole fraction at temperatures (298.15K, 308.15K and 318.15K) for binary and 298.15K for ternary mixtures. Excess molar volumes VmE, viscosity deviations Δη, and excess thermal expansion coefficients αE, were calculated from the experimental data. Redlich–Kister and Cibulka equations were used to correlation of calculated data for binary and ternary mixtures, respectively. The experimental results of VmE are positive for the mixtures of (diethylketone+2-butanol) and (2-butanol+ethylchloroacetate) and negative for (diethylketone+ethylchloroacetate) over the whole composition range. The values of Δη are negative for three binary mixtures. The results were analyzed to discuss the nature and strength of intermolecular interactions in these mixtures.

Intermolecular interactions of polyimides containing benzimidazole and benzoxazole moieties

Thermal analysis and infrared spectroscopic studies were performed to investigate the strength of intermolecular interactions of the polyimides derived from 5,4′-diamino-2-phenyl benzimidazole (DAPBI) and 5,4′-diamino-2-phenyl benzoxazole (DAPBO). Polyimide films were prepared based on biphenyltetracarboxylic dianhydride (BPDA) isomers, difference of glass transition temperatures (ΔTg) between DAPBI and DAPBO type polyimides decreased consistently as the steric impedance increased, implying that polyimides containing benzimidazole group had higher degree of intermolecular interactions. Infrared spectra of polyimide films displayed that the imide carbonyl (CO) stretching band for DAPBI derived polyimides shifted to lower frequency compared to the DAPBO counterpart. In the IR spectra of the copolyimides based on DAPBI and DAPBO, significant red shift was observed for CO stretching band and Tg increased as a function of DAPBI content. This suggests the presence of strong intermolecular interactions due to the hydrogen bonding for the DAPBI based polyimides.

Study of molecular interactions in binary mixtures of formamide with 2-methoxyethanol and 2-ethoxyethanol at varying temperatures

The thermophysical properties of binary mixtures of formamide with 2-methoxyethanol and 2-ethoxyethanol have been investigated in this article. Densities, refractive index, ultrasonic velocity and viscosity for the two binary mixtures viz. formamide with 2-methoxyethanol and 2-ethoxyethanol have been measured over the entire composition range at 293, 303 and 313 K and at atmospheric pressure. The excess molar volume, the molar refraction deviation, excess Gibb's free energy of activation for viscous flow, excess isentropic compressibility, deviation in viscosity, excess free volume and excess molar enthalpy have been computed using experimental data. These excess parameters have been correlated with Redlich–Kister polynomial equation. The results have been interpreted on the basis of strength of intermolecular interaction occurring in these mixtures. Densities, refractive index and ultrasonic velocity were correlated with second-order polynomial equation. The molar volume and excess partial molar volume at infinite dilution have also been calculated for both the mixtures.

Volumetric and ultrasonic study of mixtures of 2-phenylethanol with 1-butanol, 2-butanol, and 2-methyl-1-butanol at T = (298.15–323.15) K and atmospheric pressure: Measurement and prediction

Densities and speeds of sound for three binary mixtures 2-phenylethanol with 1-butanol, 2-butanol and 2-methyl-1-butanol were measured over the entire range of composition and at six temperatures from 298.15K to 323.15K at 5K interval and atmospheric pressure using a vibrating tube densimeter. Besides, the densities for pure compounds in the above-mentioned temperature range were measured. The experimental densities were used to calculate the excess molar volumes, VmE, isentropic compressibility change, ΔκS, the excess thermal expansion coefficients, αpE and the excess partial molar volumes at infinite dilution, V¯iE,∞. The results have been used to discuss the nature and strength of intermolecular interactions in these mixtures. The values of excess volumes and molar isentropic compressibilites over the entire composition range were negative. The calculated excess and deviations quantities are correlated with the third-order Redlich–Kister equation. Finally the predictive power of a statistically-based equation of state for volumetric properties of the studied mixtures of alcohols has been examined.

A Study of Intrinsically Disordered Proteins from Nuclear Pore Complex

Nuclear pore complex (NPC) is giant molecular assembly that acts as a highly selective gate. Its central channel is composed of FG repeat-containing nucleoporins (FG nups), which are natively disordered proteins that facilitate the passage of receptor-cargo complexes through the NPC. However, their mechanism to facilitate selective transport is still unknown. We carried out molecular dynamics simulations of single and multiple FG nups to unveil their dynamics and structures. As an important aspect of our studies of intrinsically disordered proteins (IDPs), we made extensive comparisons between two popular water models, TIP3P and TIP4P-Ew, in combination with Amber ff99sb force field to simulate different IDPs. We found that TIP4P-Ew combined with ff99sb gives better reproduction of experimental observations for FG nups. The reason is because of better solvation of water model to charged side chain of amino acid residues. However, we also identified a caveat of current force field by studying the mutated form of FG nups. We found that the shape of IDPs is much closer to a rod-like shape regardless of whether they are extended or collapsed, which could be a signature of IDPs. Then, we explored the interaction of multiple FG nups to show that the arrangement of the FG nups can be different depending on the inter-chain distances. We identified the influence from the types of FG nups and inter-molecular spacing. FG nups showed a strong dependence of inter-molecular interaction strength on molecular spacing. However, inter-molecular interaction for one type is weaker compared to that of another type. While most of the FG nups of the two types are mainly disordered despite inter- and intra- molecular interactions, we observed noticeable beta-sheet formation at certain inter-molecular spacings, indicating a significant role between inter-molecular interaction and secondary structure formation.

The interplay between hydrogen bonding and π-π stacking interactions in the crystal packing of N1-thyminyl derivatives, and implications for the photo-chemical [2π + 2π]-cycloaddition of thyminyl compounds

The solid-state photo-chemical dimerisation of thyminyl derivatives occurs when two thyminyl units are aligned in such a way that the olefinic moieties are separated by a distance of less than 4.2 Å. When irradiated with >270 nm UV, the thyminyl olefinic groups undergo [2π + 2π]-cycloaddition to form a dimeric cyclobutane derivative. However, the design and execution of [2π + 2π]-cycloaddition reactions can be challenging due to the requirement to produce molecular crystals with the necessary olefinic alignment. In this investigation, the crystallographic and solid-state photo-chemical reactions of six N1-thyminyl derivatives are studied. Only one derivative, thyminyl propanamide (), was found to undergo [2π + 2π]-cycloaddition in the crystalline state. As such, quantum chemical methods were employed to study the photo-chemical transition states of the derivatives, as well as the strengths of typical intermolecular interactions that were observed in their crystal structures (such as π-π stacking between the thyminyl rings, Watson and Crick style hydrogen bonding and hydrogen bonding between functional groups of N1 substituents). These results were used to rationalise the solid-state photo-reactivity of more complex bis-thyminyl monomers.

Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4′-bipy and methyl benzoates

Two manganese complexes containing 4,4′-bipyridine and methyl benzoate as ligands have been prepared and crystallized by solvent evaporation method in DMF. The single crystal X-ray crystallographic analyses reveal that the complexes crystallize in monoclinic system. Crystal of 1 [Mn2(4,4′-bipy)2 (o-MBA)4]n has space group of P21/c with unit cell parameters of a=17.508(Å), b=11.6229(Å), c=27.983(Å), β=128.123°, V=4.4797nm3, empirical formula: C52H44Mn2N4O8, Mr=962.79, Z=4, Dc=1.428g/cm3, μ=0.625mm−1, and F(000)=1992. The crystal of 2 [Mn (4,4′-bipy)(m-MBA)2]n belongs to space group C2/c with a=16.079(Å), b=11.652(Å), c=24.887(Å), β=92.02°, V=4.660nm3, empirical formula: C26H22MnN2O4, Mr=481.40, Z=8, Dc=1.372g/cm3, μ=1.179mm−1, F(000)=1992. The weak interactions in structures are observed from the X-ray crystallographic data. These include the CH⋯O hydrogen bonds, π–π stacking and CH⋯π interactions found in 1. The different strength of intermolecular interaction in the structures is reflected on their different thermal stability of the two complexes measured by thermal gravimetric analysis and the 2D-IR correlation spectroscopy. The study of weak interactions is meaningful to provide supporting data for potential application in molecular biology.

Thermal resistance at a liquid–solid interface dependent on the ratio of thermal oscillation frequencies

Non-equilibrium molecular dynamics simulations of atomic-scale thermal resistance at a solid–liquid interface are theoretically investigated with a simple modal analysis of a one-dimensional lattice system. In the modal analysis, the solid–liquid intermolecular interaction strength between is taken into account as the stiffness constant between the solid and liquid molecular masses, and plays a key role in understanding the interfacial thermal resistance. The results show that the interfacial thermal resistance is proportional to the 4th power of the ratio of the thermal oscillation frequencies for the solid and liquid molecules, which provides a better physical description for the interfacial thermal resistance.

Topological Electron Density Analysis and Electrostatic Properties of Aspirin: An Experimental and Theoretical Study

The topological and the electrostatic properties of the aspirin drug molecule were determined from high-resolution X-ray diffraction data at 90 K, and the corresponding results are compared with the theoretical calculations. The electron density at the bond critical point of all chemical bonds including the intermolecular interactions of aspirin has been quantitatively described using Bader’s quantum theory of “Atoms in Molecules”. The electrostatic potential of the molecule emphasizes the preferable binding sites of the drug and the interaction features of the molecule, which are crucial for drug–receptor recognition. The topological analysis of hydrogen bonds reveals the strength of intermolecular interactions.

Interpreting the widespread nonlinear force spectra of intermolecular bonds

Single molecule force spectroscopy probes the strength, lifetime, and energetic details of intermolecular interactions in a simple experiment. A growing number of these studies have reported distinctly nonlinear trends in rupture force with loading rate that are typically explained in conventional models by invoking complex escape pathways. Recent analyses suggested that these trends should be expected even for simple barriers based on the basic assumptions of bond rupture dynamics and thus may represent the norm rather than the exception. Here we explore how these nonlinear trends reflect the two fundamental regimes of bond rupture: (i) a near-equilibrium regime, produced either by bond reforming in the case of a single bond or by asynchronized rupture of multiple individual bonds, and (ii) a kinetic regime produced by fast, non-equilibrium bond rupture. We analyze both single- and multi-bonded cases, describe the full evolution of the system as it transitions between near- and far-from-equilibrium loading regimes, and show that both interpretations produce essentially identical force spectra. Data from 10 different molecular systems show that this model provides a comprehensive description of force spectra for a diverse suite of bonds over experimentally relevant loading rates, removes the inconsistencies of previous interpretations of transition state distances, and gives ready access to both kinetic and thermodynamic information about the interaction. These results imply that single-molecule binding free energies for a vast number of bonds have already been measured.

Controlled Crystallization, Structure, and Molecular Properties of Iodoacetylamphotericin B

A new crystallization method of N-iodoacetylamphotericin B derivative is reported. The crystallization process in the presence of different quantities of amphotericin B additives was extensively studied and its mechanism was proposed. It also resulted in good quality single crystals suitable for X-ray structure determination (100 K). The structural information obtained allowed for periodic and dimer single point computational studies at the B3LYP/6-31G** level of theory. These confirmed the proposed controlled crystallization mechanism and the stabilization of crystals formed by the iodoacetyl derivative and parent amphotericin B. The calculation results indicate the strength of different intermolecular interactions and reveal the great contribution of the solvent molecules to the crystal lattice formation, with the total energy gain of about 335 kJ·mol–1, which almost doubles the cohesive energy value. Hirshfeld surface analysis shows the more efficient crystal packing of N-iodoacetylamphotericin versus ...