Interaction Potential Of Molecules Research Articles

Density functional theory and molecular dynamics simulation of water molecules confined between parallel graphene oxide surfaces using new interaction potentials

In this study, the interaction potential of water molecule with a graphene oxide (GO) plate containing OH and O groups has been calculated using the M06-2X/6-31g(d,p) level of theory at different orientations and intermolecular distances and fitted to the Born-Huggins-Meyer (BHM) model. There are good agreements between the calculated and the OPLS-AA and Dreiding models, especially for the GO(O)-H2O interactions. To examine the new computed models, we have used the closer potentials to the OPLS-AA and Dreiding models in the molecular dynamics (MD) simulations. We have calculated several properties using the different obtained interaction potentials including average number of hydrogen bonds per water molecule (〈HB〉) between confined water molecules and between water and GO-surfaces, radial distribution function (RDF), self-diffusion coefficient, and angle distribution function of the confined water molecules between the GO plates. Our results showed good agreements between the OPLS-AA and Dreiding models and some calculated potentials. However, some calculated models showed completely different behavior which discussed in details. According to the results, we concluded that the OH-2 and O1-OH2 models show totally better agreement with the famous force fields than the other calculated potentials. This work provides a simple method for the development of new force fields specifically for these types of systems which are in good agreement with the well-known force fields.

SIMULATION OF OSCILLATIONS OF WATER MOLECULES USING THE MODEL OF A TWO-FREQUENCY PENDULUM IN THE JAHN-TELLER POTENTIAL

The interaction potential for water molecules is considered, which corresponds to the presence of bends in hydrogen bonds in it. To explain the nature of this phenomenon, the theory of the Jahn-Teller effect (JTE) is applied. A model of the Jahn–Teller potential (JTP) was constructed, which has a minimum at a certain angle Θ. To simulate oscillations of water molecules in JTP using a pendulum, a correction of the angular potential U1 in the potential of directed forces (PDF) of intermolecular interaction is proposed using a wavelet type additive ΔU1 = c cos(mΘ)/exp(sΘ2). The parameters for the wavelet are selected based on the magnitude of the bending of hydrogen bonds in water (m=s=8, c=0…0.1). Modeling of rotational oscillations of molecules in JTP was carried out using the model of a two-frequency pendulum, which takes into account the ratio of the moments of inertia of the molecule (pendulum) along the axes k=3 and the PDF index n=8 in JTP Un =U1n. New types of pendulum oscillations in the JTP are determined in comparison with the original PDF (c=0) and their features. It is established that several types of oscillations are observed for this potential. These are new: sector, rotation of the pendulum in the potential trough – disordered or ordered, as well as types for PDF: two-frequency independent oscillations (IO) along the axes and ellipse-like oscillations (ELO) at one frequency. Oscillations in the JTP chute are observed for the main range of initial velocities inside an elliptical ring compressed along the Y axis, and only for the ELO, in an elliptical region elongated along the Y axis, as in the PDF. The methodology for calculating and analyzing the oscillation parameters of a two-frequency pendulum has been improved. The boundaries of oscillation types are determined for given parameters of the potential and a number of initial data. The difference between the patterns of oscillations is established for cases when the initial displacement of the pendulum is greater or less than the position of the minimum of the JTP. It is shown that the velocities at the boundary of the transition from the rotation of the pendulum in the potential trough to the IO correlate with the magnitude of the JTP maximum on the axis of the pendulum. The presence of stable transverse vibrations in the JTP for the case of protons of water molecules can apparently be considered as a new degree of freedom for vibrations of water molecules, which can lead to an explanation of the large contribution of rotational vibration modes to its heat capacity.

Analysis of temperature effect in the CO2 absorption using a deep eutectic solvent: An in silico approach

The excess level of carbon dioxide in the atmosphere has contributed a lot to global warming, occasioning several damages to the planet. Therefore, it is urgent to find ways to capture this gas. Then, the present work analyzed the temperature effect in CO2 absorption through deep eutectic solvents (DESs) based on urea and choline chloride using an in silico approach. The Molecular Dynamics (MD) simulations indicated that the increased temperature reduced the interaction potential of carbon dioxide molecules with the DESs components, indicating that the absorption process is more favorable at 303 K. On the other hand, the Noncovalent Interactions (NCI) simulations suggest that the increased temperature reduced the strong attractions and increased repulsive interactions between the carbon dioxide molecules with the solvent analyzed. Therefore, both in silico approaches suggest that the carbon dioxide absorption is more indicated at 303 K.

Molecular van der Waals Fluids in Cavity Quantum Electrodynamics.

Intermolecular van der Waals interactions are central to chemical and physical phenomena ranging from biomolecule binding to soft-matter phase transitions. In this work, we demonstrate that strong light-matter coupling can be used to control the thermodynamic properties of many-molecule systems. Our analyses reveal orientation dependent single molecule energies and interaction energies for van der Waals molecules. For example, we find intermolecular interactions that depend on the distance between the molecules R as R-3 and R0. Moreover, we employ ab initio cavity quantum electrodynamics calculations to develop machine-learning-based interaction potentials for molecules inside optical cavities. By simulating systems ranging from 12 H2 to 144 H2 molecules, we observe varying degrees of orientational order because of cavity-modified interactions, and we explain how quantum nuclear effects, light-matter coupling strengths, number of cavity modes, molecular anisotropies, and system size all impact the extent of orientational order.

HIF1 inhibition of the biflavonoids against pancreas cancer: drug-likeness, bioavailability, ADMET, PASS, molecular docking, molecular dynamics, and MM/GBSA calculations

Pancreatic cancer is an aggressive disease with a high death rate and is difficult to treat. This disease, in the most cases, is asymptomatic until it progresses to an advanced stage. Therefore, the search for bioactive molecules is urgent to combat pancreatic cancer. Then, this work analyzed the interaction potential of agathisflavone and amentoflavone molecules against the HIF1 target using the ADMET, molecular docking, and molecular dynamics simulations. More recent drug-likeness filters that combine physicochemical and physiological parameters have shown that high polar surface area (TPSA > 75 Å2) drives biflavonoids out of the toxic drug space of Pfizer dataset. Regarding the pharmacokinetic descriptors, it was possible to notice that Amentoflavone showed a better order of passive cell permeability (Papp = 8 × 10−6 cm/s) and better metabolic stability, biotransformed by aromatic hydroxylation reactions by the CYP3A4 isoenzyme on the human liver, that favor its hepatic clearance. The molecular docking and molecular dynamics simulations indicated the high interaction potential and stability between the ligands analyzed (highlighted the amentoflavone molecule), respectively. The MM/GBSA calculations showed that the amentoflavone ligand registered the highest ΔG binding value of −32.6957 kcal/mol with the HIF1 target. Then, this molecule may be used as a potential inhibitor of pancreatic cancer. In this perspective, the present work represents an initial step in the virtual bioprospecting a pharmacological tool for treating of pancreatic cancer. Communicated by Ramaswamy H. Sarma

Multipole-moment effects in ion-molecule reactions at low temperatures: part II - charge-quadrupole-interaction-induced suppression of the He+ + N2 reaction at collision energies below kB·10 K.

We report on an experimental and theoretical investigation of the He+ + N2 reaction at collision energies in the range between 0 and kB·10 K. The reaction is studied within the orbit of a highly excited Rydberg electron after merging a beam of He Rydberg atoms (He(n), n is the principal quantum number), with a supersonic beam of ground-state N2 molecules using a surface-electrode Rydberg–Stark decelerator and deflector. The collision energy Ecoll is varied by changing the velocity of the He(n) atoms for a fixed velocity of the N2 beam and the relative yields of the ionic reaction products N+ and N2+ are monitored in a time-of-flight mass spectrometer. We observe a reduction of the total reaction-product yield of ∼30% as Ecoll is reduced from ≈kB·10 K to zero. An adiabatic capture model is used to calculate the rotational-state-dependent interaction potentials experienced by the N2 molecules in the electric field of the He+ ion and the corresponding collision-energy-dependent capture rate coefficients. The total collision-energy-dependent capture rate coefficient is then determined by summing over the contributions of the N2 rotational states populated at the 7.0 K rotational temperature of the supersonic beam. The measured and calculated rate coefficients are in good agreement, which enables us to attribute the observed reduction of the reaction rate at low collision energies to the negative quadrupole moment, Qzz, of the N2 molecules. The effect of the sign of the quadrupole moment is illustrated by calculations of the rotational-state-dependent capture rate coefficients for ion–molecule reactions involving N2 (negative Qzz value) and H2 (positive Qzz value) for |J, M〉 rotational states with J ≤ 5 (M is the quantum number associated with the projection of the rotational angular momentum vector J⃑ on the collision axis). With decreasing value of |M|, J⃑ gradually aligns perpendicularly to the collision axis, leading to increasingly repulsive (attractive) interaction potentials for diatomic molecules with positive (negative) Qzz values and to reaction rate coefficients that decrease (increase) with decreasing collision energies.

The Role of pH and Ionic Strength in the Attraction-Repulsion Balance of Fibrinogen Interactions.

Fibrinogen (Fg) self-assembly is sensitive to the physicochemical properties of an environment like pH and ionic strength. These parameters tune the direction and strength of noncovalent physical driving forces determining protein intermolecular interactions. The attraction-repulsion balance in intermolecular interactions of the multidomain protein Fg at pH values 3.5, 7.4, and 9.5 and varying ionic strengths of the water medium has been analyzed by the complex diffusive approach, proposed by us previously. The concentration dependence of protein collective diffusion was analyzed within the phenomenological approach, based on the frictional formalism of nonequilibrium thermodynamics proposed by H. Vink. The analysis of protein diffusion data has shown the fundamental difference in the physical nature and direction of interaction forces between protein molecules at different conditions. The paired interaction potential of protein molecules was characterized in terms of second virial coefficients and Hamaker constants within the Deryaguin-Landau-Verwey-Overbeek theory and the "porous" colloid particle model. Our results indicated the maximum Hamaker constant and dominance of the van der Waals attraction between Fg molecules at pH 7.4. The increase in pH up to 9.5 results in the zero values of the second virial coefficient and Hamaker constant, corresponding to the full reciprocal compensation for electrostatic repulsion and van der Waals attraction. In the acidic medium (pH 3.5), the strong electrostatic repulsion substantially exceeds the van der Waals attraction. A high ionic strength is characterized by a significant decrease of all intermolecular interactions, which is expressed in almost zero values of virial coefficients and the Hamaker constant. Thus, it is experimentally shown that the physiological conditions of the Fg environment (pH 7.4 and slight ionic strength) provide a high probability for peak physical attraction between fibrinogen molecules, which is used in nature to facilitate blood clotting.

Structural insights on the interaction potential of natural leads against major protein targets of SARS-CoV-2: Molecular modelling, docking and dynamic simulation studies

Though significant efforts are in progress for developing drugs and vaccines against COVID-19, limited therapeutic agents are available currently. Thus, it is essential to undertake COVID-19 research and to identify therapeutic interventions in which computational modeling and virtual screening of lead molecules provide significant insights. The present study aimed to predict the interaction potential of natural lead molecules against prospective protein targets of SARS-CoV-2 by molecular modeling, docking, and dynamic simulation. Based on the literature survey and database search, fourteen molecular targets were selected and the three targets which lack the native structures were computationally modeled. The drug-likeliness and pharmacokinetic features of ninety-two natural molecules were predicted. Four lead molecules with ideal drug-likeliness and pharmacokinetic properties were selected and docked against fourteen targets, and their binding energies were compared with the binding energy of the interaction between Chloroquine and Hydroxychloroquine to their usual targets. The stabilities of selected docked complexes were confirmed by MD simulation and energy calculations. Four natural molecules demonstrated profound binding to most of the prioritized targets, especially, Hyoscyamine and Tamaridone to spike glycoprotein and Rotiorinol-C and Scutifoliamide-A to replicase polyprotein-1ab main protease of SARS-CoV-2 showed better binding energy, conformational and dynamic stabilities compared to the binding energy of Chloroquine and its usual target glutathione-S-transferase. The aforementioned lead molecules can be used to develop novel therapeutic agents towards the protein targets of SARS-CoV-2, and the study provides significant insight for structure-based drug development against COVID-19.

Molecular dynamics simulation of water-based nanofluids viscosity

The shear viscosity coefficients of water and water-based nanofluids with copper particles are calculated by the molecular dynamics method. Copper nanoparticles with a diameter of 2, 4 and 10 nm were used in the simulation. The volume fraction of nanoparticles was varied from 1 to 5%. The interaction of water molecules with each other was modeled using the Lennard–Jones potential. The Rudyak–Krasnolutskii and Rudyak–Krasnolutskii–Ivanov potentials were used as nanoparticle–molecule and nanoparticles interaction potentials, respectively. The viscosity coefficient was calculated using the fluctuation–dissipation theorem by the Green–Kubo formula. It is shown that the viscosity of the nanofluid significantly exceeds the viscosity of the coarse-grained suspension and increases with a decrease in the nanoparticles size at their fixed volume fraction. The correlation functions determining the viscosity coefficient of the nanofluid were analyzed in detail. The radial distribution functions of pure water and nanofluids are also presented in the paper. It is shown that the liquid near the nanoparticle is structured much more strongly than in the bulk. This greater ordering of the nanofluid is one of the main factors determining the increase in nanofluids viscosity.

The Interaction Potential of Molecules in Multicomponent Gaseous Media

To determine the transport factors in multicomponent gaseous media, the authors used an approach based on the molecular-kinetic theory of gases. A mathematical model of the interaction potential of molecules in multicomponent media is proposed. This model takes into account elastic and geometric parameters of molecules as well as an algorithm for determining the parameters in it.

Effects of Fermi resonance of ν1 and 2ν2 on the Raman scattering of fundamental mode ν2 from liquid carbon disulfide

Raman scattering from liquid carbon disulfide has been studied for different concentrations in benzene. Modes ν1 (656cm−1) and 2ν2 (796cm−1) are allowed bands of carbon disulfide, while ν2 (396cm−1) is forbidden by the selection rules. However, a weak band has been observed along with the strong allowed totally symmetrical stretching mode ν1. The observation is ascribed to the effects of the vibrational anharmonicity of free molecule and intermolecular interaction potential. The ν1 and 2ν2 Fermi resonance can be influenced by the external conditions. The effects of the ν1 and 2ν2 Fermi resonance on the Raman frequency and relative intensity are discussed and the Raman scattering cross section of ν2 is studied for different concentration of carbon disulfide in benzene. The second-order perturbation quantum theory is introduced to explain the results that the Raman scattering of ν2 is influenced by 2ν2 and its Fermi resonance with ν1.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Description of heat transfer through a cylindrical liquid–vapor interface surface

Linear and nonlinear relations, which make it possible to determine the rate of heat flux in the mode of film boiling on a cylindrical heating surface, have been obtained by transforming the system of moment conservation equations derived from the Boltzmann kinetic equation based on the four-term approximation in the form of a two-sided Maxwellian. For this problem and the interaction potential of Maxwell molecules, the Boltzmann kinetic equation is solved by the moment method in elaboration of the approach of L. Lees and C.-Y. Liu to the description of thermal conductivity through a gas-filled cylindrical gap between two impermeable interfaces. The obtained analytical expressions for the heat flux can be used at any values of the Knudsen number determined from the cylindrical heater radius.

A novel theoretical approach to the temperature–viscosity relation for fluidic fuels

Viscosity is a first and foremost function both for theory and application. By approximating the interaction potential of molecule in fluidic fuel as constant and proposing a new method to calculate the momentum transfer by means of the radius of averaged volume per molecule, an equation of viscosity versus temperature was derived, which were found in good agreement with a lot of data from gaseous to liquid fuels by the curve fit. The equation also predicted that the viscosity initially decreased with temperature and then slowly increased in the high temperature region. When using it as correlation equation for the dependence of viscosity on temperature, it was able to cover more fluids from gaseous to liquid fuels.

Experimentally proven liquid-liquid critical point of dilute glycerol-water solution at 150 K.

The experimental and theoretical studies of supercooled liquid water strongly suggest that the two liquid waters and their liquid-liquid critical point (LLCP) exist at low temperature. However, the decisive experimental evidence of the LLCP has not been obtained because of the rapid crystallization of liquid water in the "no-man's land." Here, we observed experimentally the pressure-induced polyamorphic transition in the dilute glycerol-water solution which relates to the water polyamorphism. We examined the effect of the glycerol concentration on the liquid-liquid transition, and found its LLCP around 0.12-0.15 mole fraction, 0.03-0.05 GPa, and ~150 K. A 150 K was above, or around, the recently recognized glass transition temperatures of amorphous ices, and the crystallization did not occur, indicating that the direct observation of LLCP is feasible. The low-temperature LLCP has implication to the argument of the relation between the interaction potential of water molecule and the polyamorphic phase diagram.

Molecular theory of proper ferroelectricity in bent-core liquid crystals

Antiferro- and ferro-electric ordering has been discovered in orthogonal smectic phases composed of nonchiral bent-core molecules. These systems are the only proper fluid ferroelectrics confirmed experimentally so far. We consider a molecular theory of proper ferroelectric ordering in isotropic, nematic and smectic A phases and conclude that the delicate balance between the tendencies for local parallel and antiparallel ordering of molecular electric and steric dipoles is strongly shifted in restricted geometries. This is a reason why dipolar ordering is more likely to occur within a smectic layer. We derive model interaction potentials for polar bent-core molecules and present the results of the mean-field theory of ferroelectric ordering in the orthogonal smectic phase taking into account also the molecular biaxiality. Order parameter profiles have been calculated numerically and phase diagrams are presented which enable one to analyze the relative importance of dipole-dipole interaction and intermolecular attraction modulated by polar bent-core molecular shape.

Quantum Mechanics of In Situ Synthesis of Metal Nanoparticles within Anionic Microgels

We discuss the quantum mechanics of many-body systems, that is, hybrid microgel consisting of negatively charged anionic microgels possessing thick sheath of water molecules solvating protruding anionic moieties and nanoparticle captivated within the microgel. Thermodynamic feasibility of synthesis of particular nanoparticle within the microgel is dependent upon the magnitude of interaction between nanoparticle, water molecules, and microgel relative to sum of magnitude of self-interaction between counterions and interaction between counterions and microgel. Nanoparticles synthesized with in the microgels have thick electronic cloud that oscillates under the influence of net interaction potential of charged anionic moieties and solvent water molecules which constitutes the chemical environment of hybrid microgel. Hamiltonian describing energy of oscillating electronic cloud of wrapped around nanoparticle is mathematically derived to be equal to product of integral electron density and product of its position vector overall space and net force acting on the oscillating electronic cloud of nanoparticle is mathematically defined as; ℱ∫ρn{n}n^ dn.

Elastic and inelastic collisions of2Σmolecules in a magnetic field

We calculate the cross sections for elastic scattering and Zeeman relaxation in binary collisions of molecules in the ro-vibrational ground state of a $^2\Sigma$ electronic state and the Zeeman state with the electron spin projection $M_S=1/2$ on the magnetic field axis. This is the lowest-energy state of $^2\Sigma$ molecules confined in a magnetic trap. The results are averaged over calculations with multiple molecule - molecule interaction potentials, which yields the expectation intervals for the cross sections and the elastic-to-inelastic cross section ratios. We find that the elastic-to-inelastic cross section ratios under conditions corresponding to trapped molecular ensembles at $T \sim 10^{-3}$ K exceed 100 for the majority of $^2\Sigma$ molecules. The range of $^2\Sigma$ molecules expected to be collisionally unstable in magnetic traps at $T < 10^{-3}$ K is limited to molecules with the spin-rotation interaction constant $\gamma_{\rm SR} > 0.5$ cm$^{-1}$ and the rotational constant $B_e < 4$ cm$^{-1}$.

Virial theorem and the two molecule interaction potential

A method for determining the parameters of the two-molecule interaction potential is shown by the example of the Mie potential or the four-parameter Lennard-Jones potential (GLJ). The application of the virial theorem with respect to the Mie potential allows one to determine exponents at the intermolecular distance. The application of the theory of pair collisions for determination of the intermolecular repulsion potential is shown by the example of a number of substances. The statistic characteristic of gases that allows one to formulate the intermolecular attraction potential is found.

Application of perturbation theory to a mixture of hydrogen atoms and molecules with the Morse intermolecular interaction potential

The thermodynamic parameters of the two-component mixture of hydrogen atoms and molecules are calculated on the basis of perturbation theory with the use of the basic system of hard spheres. To eliminate the nonadditivity of hard sphere diameters and to obtain the best agreement of the calculated thermodynamic parameters with the Monte Carlo data, different schemes of subdivision of the interaction potential of hydrogen atoms and molecules into the basic and perturbing components are investigated.