Long-range Intermolecular Interactions Research Articles

7-Hexyloxy-3-[4’-(3-methylbutyloxy) phenyl]-4H-1-benzopyran-4-one: Study of Smectic behaviour and UV absorption profile

abstractThe intermolecular interaction energies between a pair of 7-Hexyloxy-3-[4’-(3-methylbutyloxy) phenyl]-4H-1-benzopyran-4-one (HMBPB) molecules have been estimated with respect to translational and orientational motions. The complete neglect differential overlap (CNDO/S) method has been employed to calculate the net atomic charge and atomic dipole moment components at each atomic center. The modified Rayleigh-Schrodinger perturbation theory along with multicentered-multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while a ‘6-exp’ potential function has been assumed for short-range interactions. The total interaction energy values obtained through these computations have been used to calculate the probability of each configuration at room temperature (300K), and isotropic-smectic transition temperature (412.6K). Molecular arrangements inside a bulk of materials and smectic behavior of the compound in terms of their relative order have been discussed. Translational and rotational rigidity of the molecule has been analyzed to understand the smectic behaviour. The UV absorption profile has been estimated using CNDO/S, and INDO/S methods.

Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.

Exciton dynamics in amide-I [Formula: see text] -helix protein chains with long-range intermolecular interactions.

The amide-I [Formula: see text] -helix protein is a long molecular chain made up of regularly spaced peptide groups interacting via C=O bonds. According to the current theory the energy released by hydrolyzed adenosine triphosphate is carried across the protein via vibration modes, caused by C=O bond stretchings which, in the presence of anharmonic molecular vibrations, can promote nonlinear localized excitations called excitons. In this work the effects of long-range interactions between amide-I molecules on the modulational instability of small-amplitude excitons, and on characteristic parameters of soliton wavetrain-type excitons, are investigated with emphasis on long-range interactions saturating at finite intermolecular interaction ranges. It is found that long-range interactions strongly affect the dispersion of vibration modes of the protein chain, causing a narrowing of the modulational-instability regions for small-amplitude excitons. Characteristic parameters of the exciton soliton wavetrain, including its velocity, tail and average width (i.e., the exciton width at half tail), are drastically enhanced with respect to their values when only the short-range interaction is considered. The results suggest a sizable increase of the energy carried by excitons along the protein chain above predictions based on short-range considerations.

Detection of long-range electrostatic interactions between charged molecules by means of fluorescence correlation spectroscopy.

In the present paper, an experimental feasibility study on the detection of long-range intermolecular interactions through three-dimensional molecular diffusion in solution is performed. This follows recent theoretical and numerical analyses reporting that long-range electrodynamic forces between biomolecules could be identified through deviations from Brownian diffusion. The suggested experimental technique was fluorescence correlation spectroscopy (FCS). By considering two oppositely charged molecular species in aqueous solution, namely, lysozymes and fluorescent dye molecules (Alexa488), the diffusion coefficient of the dyes has been measured for different values of the concentration of lysozyme, that is, for different average distances between the oppositely charged molecules. For our model, long-range interactions are of electrostatic origin, suggesting that their action radius can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular dynamics simulations provide a clear and unambiguous interpretation of the experimental results.

Probabilistic and thermodynamic approach on phase behavior of nematic liquid crystals: A comparative study

ABSTRACTThe systems chosen for the present investigation, p-n-alkylbenzoic acid (nBAC; n = 6, 7) exhibits nematic-isotropic transition. A comparative study based on quantum probabilistic and statistical thermodynamics has been carried out with respect to translational and orientational motions. The evaluation of net atomic charges and dipole moment at each atomic centre has been carried out through the complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory along with multicentered-multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while the ‘6-exp’ potential function has been assumed for short-range interactions. The total interaction energy values obtained through these computations have been used as input to calculate the probability of occurrence of a particular configuration using the Maxwell-Boltzmann formula. Further, thermodynamic parameters such as Helmholtz free energy, and entropy at room temperature (300 K), and nematic-isotropic transition temperatures have been computed. An attempt has been made to understand the structure-phase behaviour relationship at molecular level.

Collagen Membranes with Ribonuclease Inhibitors for Long-Term Stability of Electrochemical Aptamer-Based Sensors Employing RNA.

Electrochemical aptamer-based (E-AB) sensors offer advantageous analytical detection abilities due to their rapid response time (seconds to minutes), specificity to a target, and selectivity to function in complex media. Ribonucleic acid (RNA) aptamers employed in this class of sensor offer favorable binding characteristics resulting from the ability of RNA to form stable tertiary folds aided by long-range intermolecular interactions. As a result, RNA aptamers can fold into three-dimensional structures more complex than those of their DNA counterparts and consequently exhibit better binding ability to target analytes. Unfortunately, RNA aptamers are susceptible to degradation by nucleases, and for this reason, RNA-based sensors are scarce or require significant sample pretreatment before use in clinically relevant media. Here, we combine the usefulness of a collagen I hydrogel membrane with entrapped ribonuclease inhibitors (RI) to protect small molecule RNA E-AB sensors from endogenous nucleases in complex media. More specifically, the biocompatibility of the naturally polymerized hydrogel with encapsulated RI promotes the protection of an aminoglycoside-binding RNA E-AB sensor up to 6 h, enabling full sensor function in nuclease-rich environments (undiluted serum) without the need for prior sample preparation or oligonucleotide modification. The use of collagen as a biocompatible membrane represents a general approach to compatibly interface E-AB sensors with complex biological samples.

Direct observation of the conformational transitions of single pyridine molecules on a Ag(110) surface induced by long-range repulsive intermolecular interactions

The transition between two conformations of pyridine molecules adsorbed on a Ag(110) surface at 13 K was investigated by performing single-molecule manipulation at a very low coverage and the track-imaging of pyridines for various surface coverages using a variable low-temperature scanning tunneling microscope. A single tilted conformer was converted to an upright conformer when another coadsorbed tilted pyridine molecule approached to within ∼2 nm. The conversion probability depends on the molecular separation. The tilted conformers that are prevalent at a very low coverage were converted to upright conformers with an increasing surface coverage. The minimum molecular separation before this transition is induced was determined to be 2.2 nm using molecular track-imaging and statistical analysis of the pyridine separation as a function of the molecular coverage. The conformation transition was attributed to substrate-mediated long-range repulsive interactions between the pyridine molecules, which are produced by charge redistribution that occurs upon pyridine adsorption on the silver surface.

Pomegranate (Punica granatum): a natural source for the development of therapeutic compositions of food supplements with anticancer activities based on electron acceptor molecular characteristics

Background: Numerous in vitro and in vivo studies, in addition to clinical data, demonstrate that pomegranate juice can prevent or slow-down the progression of some types of cancers. Despite the well-documented effect of pomegranate ingredients on neoplastic changes, the molecular mechanism(s) underlying this phenomenon remains elusive.Methods: For the study of pomegranate ingredients the electron-ion interaction potential (EIIP) and the average quasi valence number (AQVN) were used. These molecular descriptors can be used to describe the long-range intermolecular interactions in biological systems and can identify substances with strong electron-acceptor properties. In this study, candidate human proteins interacting with pomegranate flavonoids have been analyzed by the informational spectrum method (ISM). This represents a virtual spectroscopy method for studying protein molecular interactions.Results: Our analysis indicates that the anti-cancer properties of pomegranate juice can be ascribed to the strong electron-acceptor properties of its chemical ingredients. This analysis also suggests that pomegranate flavonoids inhibit the “NF-kappaB” (NF-kB) pathway, which plays a critical role in the pathogenesis of cancer.Conclusion: The results offer a possible explanation for an important molecular mechanism underlying the anticancer activity of pomegranate ingredients, which could also serve as a basis for the development of new therapeutic compositions of food supplements with pomegranate-like anticancer properties.Key words: cancer, pomegranate, flavonoids, food supplement, informational spectrum method

A n-vector model for charge transport in molecular semiconductors.

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

Theoretical study of closo-decaborate novel nematogen: Thermodynamic behavior and phase stability

ABSTRACTThe present article deals with the thermodynamic behavior and phase stability of closo-decaborate nematogen viz. dinitrogen-10-(4-pentyl-1-thiacyclohexyl)-closo-decaborate (DPTD) at a molecular level. The atomic net charge and dipole moment at each atomic center have been evaluated using the complete neglect differential overlap (CNDO) method. The modified Rayleigh–Schrodinger perturbation method along with multicentered–multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while a ‘6-exp’ potential function has been assumed for the short-range interactions. The total interaction energy values obtained through these computations have been used to calculate the probability of each configuration at room temperature (300 K), nematic–isotropic transition temperature (435 K), and above transition temperature (500 K) using the Maxwell–Boltazman formula. Further, the entropy of each configuration has been computed during the different modes of interactions. The adopted framework provides valuable information on thermodynamic behavior, and phase stability of novel nematogen based on parameters, i.e., molecular and thermodynamic, introduced in this article.

Phase stability and ordering of nematogen at molecular level: A computer-aided modeling

ABSTRACTThe present article deals with the phase stability and ordering of nematogen, viz., 6-octyloxy-2-naphthylyl-4-octoxybenzoate (ONOB) at molecular level. A comparative picture has been given between molecular charge distribution, and phase stability based on AM1, PM3, CNDO, and MNDO methods. The modified Rayleigh–Schrodinger perturbation method along with multicentered-multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while a “6-exp” potential function has been assumed for the short-range interactions. The total interaction energy values obtained through these computations have been used to calculate the probability of each configuration at room temperature, nematic-isotropic transition temperature, and above transition temperature using the Maxwell–Boltzmann formula. Further, the entropy of each configuration has been computed during the different modes of interactions. An effort has been made to develop a computational model at molecular level based on configurational entropy, and translational rigidity parameters introduced in this article.

Describing excited states of [n]cycloparaphenylenes by hybrid and double-hybrid density functionals: from isolated to weakly interacting molecules

We theoretically study the excited-state properties of cycloparaphenylenes ([n]CPPs) for a deeper understanding of their photochemical properties with increasing size n, being $$n = 6-12$$ the number of repeat units forming the nanoring. We apply hybrid (e.g., PBE0 and PBE0-1/3), double-hybrid (e.g., PBE0-DH and PBE-QIDH) and range-separated (e.g., $$\omega$$ B97X) functionals within a Time-Dependent (Tamm–Dancoff) Density Functional Theory framework. For the [6]CPP case, we concomitantly address changes in the set of selected excited states when going from an isolated molecule to a pair of self-assembled molecules, employing for that a dimer of parallel-like or tubular-like molecules according to the solid-state supramolecular organization found in real samples. These nanorings challenge standard theoretical methods due to the compromise needed between medium-range intramolecular (in isolated molecules) and long-range intermolecular (for weakly interacting pairs of molecules in condensed phases) interactions.

Ordering and Nematic Phase Behavior of a Naphthyl Ester: A Computational Model Based on Semiempirical Approach

The present article deals with the ordering and nematic phase behavior of naphthyl-ester, viz., 4-octylphenyl-6-octyloxy-2-naphthoate based on semiempirical approach at a molecular level. The atomic net charge and dipole moment at each atomic centre has been evaluated using the complete neglect differential overlap method. The modified Rayleigh–Schrodinger perturbation method along with multicentered-multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while a “6-exp” potential function has been assumed for the short-range interactions. The total interaction energy values obtained through these computations have been used to calculate the probability of each configuration at room temperature, nematic-isotropic transition temperature, and above transition temperature using the Maxwell–Boltzmann formula. Further, the entropy of each configuration has been computed during the different modes of interactions. An effort has been made to develop a computational model at molecular level based on thermodynamic parameter introduced in this article.

Molecular hydrogen interacts more strongly when rotationally excited at low temperatures leading to faster reactions.

The role of internal molecular degrees of freedom, such as rotation, has scarcely been explored experimentally in low-energy collisions despite their significance to cold and ultracold chemistry. Particularly important to astrochemistry is the case of the most abundant molecule in interstellar space, hydrogen, for which two spin isomers have been detected, one of which exists in its rotational ground state whereas the other is rotationally excited. Here we demonstrate that quantization of molecular rotation plays a key role in cold reaction dynamics, where rotationally excited ortho-hydrogen reacts faster due to a stronger long-range attraction. We observe rotational state-dependent non-Arrhenius universal scaling laws in chemi-ionization reactions of para-H2 and ortho-H2 by He(2(3)P2), spanning three orders of magnitude in temperature. Different scaling laws serve as a sensitive gauge that enables us to directly determine the exact nature of the long-range intermolecular interactions. Our results show that the quantum state of the molecular rotor determines whether or not anisotropic long-range interactions dominate cold collisions.

Studying structural properties of rubidium and cesium liquid metals using an effective hard-core Yukawa potential

In this work, we investigate the applicability of a modification of the random phase approximation (RPA) theory with an effective hard-core Yukawa potential to the static structure factor for the rubidium and cesium liquid metals. Based upon the perturbation theory, we assume that the core contribution of the direct correlation function is related to the geometric effects via a linear form for a hard-sphere fluid, in which the molecular diameter is obtained at any temperature and, its tail contribution is related to the long-range intermolecular interactions of the system via a linear form. We use the long-range Yukawa potential in the modeling of liquid alkali metals (LAMs) with the decay parameter λ = 1.8 and a well depth potential that is state-dependent. The linear isotherm regularity (LIR) equation of state (EOS) is applied to obtain the long-range interactions. The results obtained show that the proposed approach for LAMs can predict the behavior of the structure factor, S(k), at a wide range of k values with a good accuracy, as compared to the experimental data, over the whole liquid states. The interaction model used is also successful in the presentation of the Ornstein–Zernike (OZ) behavior of S(k) at the low-k region including the S(0) values.

Signature of anomalous exciton localization in the optical response of self-assembled organic nanotubes.

We show that the disorder scaling of the low-temperature optical absorption linewidth of tubular molecular assemblies sharply contrasts with that known for one-dimensional aggregates. The difference can be explained by an anomalous localization of excitons, which arises from the combination of long-range intermolecular interactions and the tube's higher-dimensional geometry. As a result, the exciton density of states near the band bottom drops to zero, leading to a strong suppression of exciton localization. Our results explain the strong linear dichroism and weak exciton-exciton scattering in tubular J aggregates observed in experiments and suggest that for nanoscale wirelike applications a tubular shape is to be preferred over a truly one-dimensional chain.

Dipole-moment-driven cooperative supramolecular polymerization.

While the mechanism of self-assembly of π-conjugated molecules has been well studied to gain control over the structure and functionality of supramolecular polymers, the intermolecular interactions underpinning it are poorly understood. Here, we study the mechanism of self-assembly of perylene bisimide derivatives possessing dipolar carbonate groups as linkers. It was observed that the combination of carbonate linkers and cholesterol/dihydrocholesterol self-assembling moieties led to a cooperative mechanism of self-assembly. Atomistic molecular dynamics simulations of an assembly in explicit solvent strongly suggest that the dipole-dipole interaction between the carbonate groups imparts a macro-dipolar character to the assembly. This is confirmed experimentally through the observation of a significant polarization in the bulk phase for molecules following a cooperative mechanism. The cooperativity is attributed to the presence of dipole-dipole interaction in the assembly. Thus, anisotropic long-range intermolecular interactions such as dipole-dipole interaction can serve as a way to obtain cooperative self-assembly and aid in rationalizing and predicting the mechanisms in various synthetic supramolecular polymers.

Quantification of bulk solution limits for liquid and interfacial transport in nanoconfinements.

Liquid imbibition, the capillary-pressure-driven flow of a liquid into a gas, provides a mechanism for studying the effects of solid-liquid and solid-liquid-gas interfaces on nanoscale transport. Deviations from the classic Washburn equation for imbibition are generally observed for nanoscale imbibition, but the identification of the origin of these irregularities in terms of transport variables varies greatly among investigators. We present an experimental method and corresponding image and data analysis scheme that enable the determination of independent effective values of nanoscale capillary pressure, liquid viscosity, and interfacial gas partitioning coefficients, all critical transport variables, from imbibition within nanochannels. Experiments documented herein are performed within two-dimensional siliceous nanochannels of varying size and as small as 30 nm × 60 nm in cross section. The wetting fluid used is the organic solvent isopropanol and the nonwetting fluid is air, but investigations are not limited to these fluids. Optical data of dynamic flow are rare in geometries that are nanoscale in two dimensions due to the limited resolution of optical microscopy. We are able to capture tracer-free liquid imbibition with reflected differential interference contrast microscopy. Results with isopropanol show a significant departure from bulk transport values in the nanochannels: reduced capillary pressures, increased liquid viscosity, and nonconstant interfacial mass-transfer coefficients. The findings equate to the nucleation of structured, quasi-crystalline boundary layers consistently ∼10-25 nm in extent. This length is far thicker than the boundary layer range prescribed by long-range intermolecular force interactions. Slower but linear imbibition in some experimental cases suggests that structured boundary layers may inhibit viscous drag at confinement walls for critical nanochannel dimensions. Probing the effects of nanoconfinement on the definitions of capillary pressure, viscosity, and interfacial mass transfer is critical in determining and improving the functionality and fluid transport efficacy of geological, biological, and synthetic nanoporous media and materials.

Monte Carlo simulation study of the effect of chain tacticity on demixing of polyethylene/polypropylene blends

The molecular origin of the demixing behavior for 50: 50 (wt/wt) polyethylene/polypropylene (PE/PP) with different tacticity of PP at the melts (473 K) was investigated by Monte Carlo simulation of coarse-grained polymer model. Isotactic (iPP), atactic (aPP) and syndiotactic (sPP) polypropylenes were used for blending with PE. Coarse-graining polymer chains were represented by 50 beads, corresponding to C100H202 and C150H302 for PE and PP, respectively. The simulation was performed on a high coordination lattice incorporating short-range intramolecular interactions from the Rotational Isomeric State (RIS) model and long-range intermolecular interactions Lennard-Jones (LJ) potential function of ethane and propane units. Chain dimensions, the characteristic ratio (C n ) and self-diffusion coefficient (D) of PE in the blends are sensitive to the stereochemistry of PP chains. Compared with neat PE melts, PE dimension was relatively unchanged in PE/iPP and PE/aPP blends but slightly decreased in PE/sPP blends. PP dimension was increased in PE/iPP and PE/aPP mixture but decreased in PE/sPP blend in comparison with neat PP melts. In addition, diffusion of PE and PP chains in PE/PP mixture was decreased and increased, respectively, compared to the pure melts. Interchain pair correlation functions were used to detect the immiscibility of the blends. The tendency of demixing of PE/aPP and PE/iPP blends were weaker than that of PE/sPP blend.

Highlighting a Solid-Like Behavior in RTILs: Tri-octylmethylammonium Bis(trifluoromethanesulfonyl)imide TOMA-TFSI

Careful measurements of the dynamic response of the room -temperature ionic liquid (RTIL) trioctylmethylammonium bis(trifluoromethanesulfonyl)imide reveal that it exhibits actually a (low-frequency) solid-like response when solicited at the submillimeter scale with a low shear strain. The solid-like response is measured away from the glass transition (at around 100 °C above Tg), ruling out reminiscent transitional effects but suggesting that the dynamic properties of the RTIL are governed by long-range elastic intermolecular interactions.