van der Waals interaction Research Papers (original) (raw)

2025, Bulletin of the American Physical Society

Submitted for the TSF09 Meeting of The American Physical Society Characterization of functionalized carbon nanotubes and their composites Z.P. LUO, Texas A&M University, L. CARSON, L. ADAMS, N. SOBOYEJO, A. OKI, E.G.C. REGISFORD, Prairie View A&M University — Carbon nanotubes (CNTs) have received considerable attention due to their extraordinary properties of strength, toughness, as well as thermal and electrical conductivities. They are ideal fillers for polymer nanocomposites to enhance the composite physical and mechanical properties. In order to overcome the problem of tangling caused by intrinsic van der Waals forces during the composite fabrication, chemical functionalization process has been introduced. In this work, we characterized the chemical coating on the functionalized CNTs and their composites using analytical electron microscopy. It was observed that the CNT surfaces were coated with reactants from the chemical reactions. In the CNT/epoxy nanocomposites, such a coati...

2025, Journal of the Physical Society of Japan

We have derived and implemented a stress tensor formulation for the van der Waals density functional (vdW-DF) with spin-polarization-dependent gradient correction (GC) recently proposed by the authors [J. Phys. Soc. Jpn. 82, 093701 (2013)] and applied it to nonmagnetic and magnetic molecular crystals under ambient condition. We found that the cell parameters of the molecular crystals obtained with vdW-DF show an overall improvement compared with those obtained using local density and generalized gradient approximations. In particular, the original vdW-DF with GC gives the equilibrium structural parameters of solid oxygen in the α-phase, which are in good agreement with the experiment.

2025, Journal of the Physical Society of Japan

We propose a practical approach to spin-polarized systems within the van der Waals density functional (vdW-DF). The method was applied to a gas phase oxygen molecule and a parallel (H-type) pair of oxygen molecules. It was found that vdW-DF improves the equilibrium distance and binding energy. In particular, one type of vdW-DF can describe such systems reasonably well. The van der Waals interaction has been confirmed to have an energy comparable to the magnetic one, while emerging at a distance rather longer than the latter.

2025, Journal of Inclusion Phenomena and Macrocyclic Chemistry

Intercalates of vanadyl phosphate with aliphatic nitriles (acetonitrile, propionitrile, butyronitrile, valeronitrile and hexanenitrile) were prepared and characterized by X-ray powder diffraction, thermogravimetric analysis, IR and Raman spectroscopies. The basal spacings of all the intercalates prepared are practically identical. The nitrile intercalates (except acetonitrile) contain one nitrile molecule per formula unit. The nitrile molecules are anchored to the host layers by an N-V donor-acceptor bond and their aliphatic chains are parallel to the host layers. The acetonitrile intercalate contains two guest molecules per formula unit. Only half of them can be bonded to the vanadium atom, the second half is probably anchored by van der Waals interaction. The intercalates prepared are moisture-sensitive and the guest molecules are easily replaced by water molecules.

2025, Bulletin of the American Physical Society

and Engineering -Benzene dimers provide the prototypical system for weak pi-pi interactions that determine the bonding for various organic materials and carbon nanostructures. Several previous studies using coupled-cluster, symmetry adapted perturbation theory, and quantum Monte Carlo methods have determined the binding energies of various configurations of the benzene dimer. In this work we investigate the accuracy of different trial wave functions for variational and diffusion Monte Carlo calculations for a set of candidate ground state dimer geometries. We compare Slater, Slater Jastrow, Slater Jastrow Backflow, and Multi-determinant wave functions. The inclusion of backflow improves our VMC and DMC total energies more than orbital optimization, larger basis sets, and increasing the number of determinants in the trial wave function. Using Slater Jastrow Backflow wave functions, we calculate the binding energies of the benzene dimers. 1 Funded by the DOE petascale initiative and a NSF GRF.

2025, Bulletin of the American Physical Society

2025, Journal of Chemical Physics

Analytical empirical potential energy surfaces describing the van der Waals interaction between rare-gas atoms and cyclopropane are presented. The functional form is based on pairwise Lennard-Jones-type potentials which have been widely used to describe rare-gas-benzene complexes, also studied in this work in order to check our theoretical method and for comparison. The parameters have been chosen in order to accurately fit the high resolution microwave spectra recently reported by Xu and Ja ¨ger ͓J. Chem. Phys. 106, 7968 ͑1997͔͒. The observed splitting in the microwave spectra of Ne-cyclopropane, associated with rotational tunneling, is well reproduced. Moreover, such tunneling is also important for complexes of Ar and Kr in excited van der Waals states. These phenomena involve a high delocalization of the wave functions and, therefore, intermolecular spectroscopy techniques would provide a good check of the potential energy surface over a broad region of the configuration space.

2025

The Finite Element Analysis in the field of Nanotechnology is continually contributing to the areas ranging from electronics, micro computing, material science, quantum science, engineering, biotechnology, medicine, aerospace, and environment and in computational nanotechnology. The finite element method (FEM) is widely used for solving problems of traditional fields of engineering and Nano research where experimental analysis is unaffordable. This numerical technique can provide accurate solution to complex engineering problems. Over decades this method has become the noted research area for the mathematicians. The popularity of FEM is due to the advent of computer FEA software such as NASTRAN, ANSYS, ABAQUS, Matlab, OPEN Foam, Simscale and the like. With the development of nanoscience, the researchers found difficulties in spending funds for nano related projects. The FEA has evolved as the affordable methodology and offers solutions to all complicated systems of research.

2025, ACS Applied Materials & Interfaces

The geometries and electronic characteristics of the graphene monoxide (GMO) bilayer are predicted via density functional theory (DFT) calculations. All the possible sequences of the GMO bilayer show the typical interlayer bonding characteristics of two dimensional bilayer systems with a weak van der Waals interaction. The band gap energies of the GMO bilayers are predicted to be adequate for electronic device application, indicating slightly smaller energy gaps (0.418 ̶ 0.448 eV) compared to the energy gap of the monolayer (0.536 eV). Above all, in light of the band gap engineering, the band gap of the GMO bilayer responds to the external electric field sensitively. As a result, a semiconductor-metal transition occurs at a small critical electric field (E C =0.22 ̶ 0.30 V/Å). It is therefore confirmed that the GMO bilayer is a strong candidate for nanoelectronics.

2025, Nature structural biology

Potential smoothing, a deterministic analog of stochastic simulated annealing, is a powerful paradigm for the solution of conformational search problems that require extensive sampling, and should be a useful tool in computational approaches to structure prediction and refinement. A novel potential smoothing and search (PSS) algorithm has been developed and applied to predict the packing of transmembrane helices. The highlight of this method is the efficient manner in which it circumvents the combinatorial explosion associated with the large number of minima on multidimensional potential energy surfaces in order to converge to the global energy minimum. Here we show how our potential smoothing and search method succeeds in finding the global minimum energy structure for the glycophorin A (GpA) transmembrane helix dimer by optimizing interhelical van der Waals interactions over rigid and semi-rigid helices. Structures obtained from our ab initio predictions are in close agreement wit...

2025, Journal of the American Chemical Society

Thermodynamic measurements of the solvation of salts and electrolytes are relatively straightforward, but it is not possible to separate total solvation free energies into distinct cation and anion contributions without reference to an additional extrathermodynamic assumption. The present work attempts to resolve this difficulty using molecular dynamics simulations with the AMOEBA polarizable force field and perturbation techniques to directly compute absolute solvation free energies for potassium, sodium, and chloride ions in liquid water and formamide. Corresponding calculations are also performed with two widely used nonpolarizable force fields. The simulations with the polarizable force field accurately reproduce in vacuo quantum mechanical results, experimental ion-cluster solvation enthalpies, and experimental solvation free energies for whole salts, while the other force fields do not. The results indicate that calculations with a polarizable force field can capture the thermodynamics of ion solvation and that the solvation free energies of the individual ions differ by several kilocalories from commonly cited values.

2025, Proceedings of the National Academy of Sciences of the United States of America

It is shown that the van der Waals interaction can lead at low temperatures to a condensed state of excitons with properties in qualitative agreement with the observations of exciton droplets. Our calculation gives a binding energy of the correct sign and magnitude for the exciton condensate. In a dielectric medium, the strong enhancement of the exciton polarizability leads to a giant van der Waals interaction, and this interaction appears to make possible a condensed exciton phase.

2025, Proceedings of the National Academy of Sciences

It is shown that the van der Waals interaction can lead at low temperatures to a condensed state of excitons with properties in qualitative agreement with the observations of exciton droplets. Our calculation gives a binding energy of the correct sign and magnitude for the exciton condensate. In a diclectric medium, the strong enhancement of the exciton polarizability leads to a giant van der Waals interaction, and this interaction appears to make possible a condensed exciton phase.

2025

The ground state of the van der Waals-type lanthanide dimer Yb 2 has been studied by means of relativistic energy-consistent ab initio pseudopotentials using three dierent core de®nitions. Electron correlation was treated by coupled-cluster theory, whereby core-valence correlation eects have been accounted for either explicitly by correlating the energetically highest coreorbitals or implicitly by means of an eective corepolarization potential. Results for the ®rst and second atomic ionization potentials, the atomic dipole polarizability, and the spectroscopic constants of the molecular ground state are reported. Low-lying excited states have been investigated with spin-orbit con®guration interaction calculations. It is also demonstrated for the whole lanthanide series that correlation eects due to the atomic-like, possibly open 4f -shell in lanthanides can be modeled eectively by adding a core-polarization potential to pseudopotentials attributing the 4f -shell to the core.

2025

Characteristic properties as well as possible differences in bonding of small group 12 clusters Mn (M = Zn, Cd, Hg; n = 2, . . . , 6) have been investigated by quantum chemical ab initio methods, i.e., relativistic large-core pseudopotentials, core-polarization potentials and coupled-cluster correlation treatments. A comparison of cohesive energies and spectroscopic properties like ionization potentials, electron affinities, and vibrational frequencies reveals a close similarity between the clusters of Cd and Hg. For Zn clusters we observed an exceptional increase in stability between Zn3 and Zn4. In order to get a more qualitative picture of the covalent contributions to bonding we have calculated the electron localization function (ELF). The ELF analysis is in accordance with the calculated spectroscopic properties and shows predominant van der Waals interactions with weak covalent contributions for all the cluster sizes considered.

2025, European Physical Journal B

In anisotropic or layered superconductors thermal fluctuations as well as impurities induce a van der Waals (vdW) attraction between flux lines, as has recently been shown by Blatter and Geshkenbein in the thermal case [Phys. Rev. Lett. 77, 4958 (1996)] and by Mukherji and Nattermann in the disorder dominated case [Phys. Rev. Lett. 79, 139 (1997)]. This attraction together with the entropic or disorder induced repulsion has interesting consequences for the low field phase diagram. We present two derivations of the vdW attraction, one of which is based on an intuitive picture, the other one following from a systematic expansion of the free energy of two interacting flux lines. Both the thermal and the disorder dominated case are considered. In the thermal case in the absence of disorder, we use scaling arguments as well as a functional renormalization of the vortex-vortex interaction energy to calculate the effective Gibbs free energy on the scale of the mean flux line distance. We discuss the resulting low field phase diagram and make quantitative predictions for pure BiSCCO (Bi 2 Sr 2 CaCu 2 O 8 ). In the case with impurities, the Gibbs free energy is calculated on the basis of scaling arguments, allowing for a semi-quantitative discussion of the low-field, low-temperature phase diagram in the presence of impurities.

2025

Ultralong-Range Interactions and Blockade of Excitation in a Cold Rydberg Gas to appear in Atomic Physics XIX (Proceedings of ICAP 2004) and in Braz. J. Phys. (2004) • K. Singer, J. Stanojevic, M. Weidemüller, and R. Côté Long range interaction potentials for the ns-ns, np-np and nd-nd asymptotes for rubidium Rydberg atom pairs J. Phys. B in press ( ) * We estimate a factor of 2 as the systematic error for the determination of the density and number of atoms.

2025

A new inverse approach is proposed in this paper, which combines elements of nonlocal theory and molecular mechanics, based on the experimental results available in the nanoindentation literature. The effect of the inlayer van der Waals atomistic interactions for carbon nanotubes with multiple walls (MWCNT) is included by means of the Brenner-Tersoff potential and experimental results. The neighboring walls of MWCNT are coupled through van der Waals interactions, and the shell buckling would initiate in the outermost shell, when nanotubes are short. The nanoindentation technique is simulated for the axially compressed of individual nanotubes, in order to evaluate the load-unloaded-displacement, the curve critical buckling and the appropriate values for local Lamé constants.

2025, Molecular Physics

We report the development of a transferable force field for the accurate modelling of perfluoroethers. The potential model takes the general form in which separate bond bending and torsional terms describe the intramolecular interactions, with the addition of van der Waals and electrostatic terms to describe the non-bonded interactions. Ab initio quantum mechanical calculations were carried out to obtain the partial charges and intramolecular torsional and bending potentials. The van der Waals interactions are described by Lennard-Jones potentials, the parameters of which are optimized to reproduce the available experimental vapour-liquid equilibrium data. An extension of the Gibbs-Duhem method was used to speed up the optimization.

2025, New Journal of Physics

Optical detection of Rydberg states using electromagnetically induced transparency (EIT) enables continuous measurement of electric fields in a confined geometry. In this paper, we demonstrate the formation of rf-dressed EIT resonances in a thermal Rb vapour and show that such states exhibit enhanced sensitivity to dc electric fields compared to their bare counterparts. Fitting the corresponding EIT profile enables precise measurements of the dc field independent of laser frequency fluctuations. Our results indicate that space charges within the enclosed cell reduce electric field inhomogeneities within the interaction region.

2025, Computational Materials Science

In this work, we report about the electronic and elastic properties of crystalline poly(3,4-ethylenedioxythiophene), known as PEDOT, in an undiluted state, studied in the framework of semilocal DFT, using the PBE and PBEsol exchange-correlation functional and PAW pseudopotentials. Contrary to previous molecular dynamics simulations, our calculations revealed that the most stable state structure of pristine PEDOT is monoclinic. We calculated the 13 independent elastic constants and the elastic compliance which enables us to establish other elastic properties of pristine PEDOT; the Pugh's ratio and the Vicker's hardness computed with PBE and PBEsol are in good agreement with each other. Finally, we compute the directional elastic modulii and found remarkable differences between different DFT functionals.

2025, Physical Review B

The method for quantifying the amount of each carbon nanotube specie, as defined by its diameter and chiral angle, as well as the semiconducting-to-metallic ratio in any type of carbon nanotube sample is discussed. Single-wall carbon nanotubes grown by the cobalt-molybdenum catalyst based ͑CoMoCAT͒ process are characterized. The semiconducting-to-metallic ratio is found to be 11:1. A single semiconducting specie, named the ͑6,5͒ nanotube represents 2 / 5 of the sample, while the most abundant metallic nanotube is the ͑7,4͒, which exhibits a diameter similar to the ͑6,5͒.

2025, Bulletin of the American Physical Society

Carbon nanotubes (CNTs) hold great promise for applications in biomedicine and biotechnology, in particular, as biosensors. For such applications, it is essential to understand the interaction of CNTs and water and/or other biomolecules in the aqueous environment. In this regard, the short-ranged van der Waals interaction together with the Coulomb interaction arising from atomic partial charges and dielectrically induced charges on the CNT play an important role. We have developed an accurate, yet computationally efficient, empirical method to model the electrostatics of finite-length single-walled armchair CNTs. Atomic partial charges are fitted to electrostatic potentials computed at a B3LYP/6-31G* level of density functional theory. The dielectric properties are calculated self-consistently from a third-nearest-neighbor tight-binding Hamiltonian, and are found to be in good agreement with density functional theory results. We demonstrate our description for water transport through a finite-length CNT channel. The atomic partial charges on the edges are found to greatly contribute to the total interaction energy and may influence water entering the CNT, while the polarizability of the CNT significantly lowers the electrostatic energy in the tube center.

2025, The Journal of Steroid Biochemistry and Molecular Biology

We achieved exhaustive alanine scanning mutational analysis of the amino acid residues lining the ligand binding pocket of the Vitamin D receptor to investigate the mechanism of the ligand recognition by the receptor. This is the first exhaustive analysis in the nuclear receptor superfamily. Our results demonstrated the role and importance of all the residues lining the ligand binding pocket. In addition, this analysis was found to indicate ligand-specific ligand-protein interactions, which have key importance in determining the transactivation potency of the individual ligands. Thus, the analysis using 1␤-methyl-1␣,25-dihydroxyvitamin D 3 revealed the specific van der Waals interactions of 1␤-methyl group with the receptor.

2025

In this presentation we shortly describe our methods for predicting monomer, Widom and Frenkel borders in fluids. We have previously done this using ethylene, but here we use CO2 as a model compound. Our starting point is that motion is the most essential property of matter – from subatomic particles, atoms, molecules to terrestrial and celestial bodies. Therefore, here we consider the changes in molecular motion from the ideal gas state (i.e. maximum mobility of molecules) to the solid state at 0 K (i.e. complete absence of molecular motion). In this process, the modes of molecular motion change, from translation to various forms of rotation; different rotating supramolecular particles are formed – molecular pairs, bimolecules, and oligomolecules – and different phases and phase transitions occur at the monomer, Widom and Frenkel borders, which are at Vr=2, Vr = 1 and Vr = 0.5, respectively. Here Vr is reduced volume, i.e. Vr = V/Vc and Vc is critical volume.

2025, Journal of Computer-Aided Molecular Design

We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

2025, Journal of Computer-Aided Molecular Design

2025, Bulletin of the American Physical Society

We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) study of the binding energy and dispersion curve of the water dimer. One the aim of the present work is to investigate how the bonding of two water molecules, as a prototype of the hydrogen-bonded complexes, could be described by a JAGP wave function, an implementation of the resonating valence bond idea.Using a pseudopotential for the inert core of the Oxygen, with a full optimization of the variational parameters, we obtain at the VMC level a binding energy of -4.5(0.1) Kcal/mol, while LRDMC gives -4.9(0.1)Kcal/mol (exp. 5 Kcal/Mol). The calculated dispersion curve reproduces both at the VMC and LRDMC level the miminum position and the right curvature.The quality of the WF gives us the possibility to dissect the binding energy in different contributions by appropriately switching off determinantal and Jastrow terms in the JAGP: we estimate the dynamical contribution to the binding energy of the order of 1.4(0.2) Kcal/Mol whereas the covalent one about 1.0(0.2) Kcal/Mol. JAGP reveales thus a promising WF for describing systems where dispersive and covalent forces play an important role

2025

2025, Analytica Chimica Acta

2025, Journal of Proteome Research

The study and prediction of kinase function (kinomics) is of major importance for proteome research due to the widespread distribution of kinases. However, the prediction of protein function based on the similarity between a functionally annotated 3D template and a query structure may fail, for instance, if a similar protein structure cannot be identified. Alternatively, function can be assigned using 3D-structural empirical parameters. In previous studies, we introduced parameters based on electrostatic entropy (Proteins 2004, 56, 715) and molecular vibration entropy (Bioinformatics 2003, 19, 2079) but ignored other important factors such as van der Waals (vdw) interactions. In the work described here, we define 3D-vdw entropies (°θ k ) and use them for the first time to derive a classifier for protein kinases. The model classifies correctly 88.0% of proteins in training and more than 85.0% of proteins in validation studies. Principal components analysis of heterogeneous proteins demonstrated that °θk codify information that is different to that described by other bulk or folding parameters. In additional validation experiments, the model recognized 129 out of 142 kinases (90.8%) and 592 out of 677 non-kinases (87.4%) not used above. This study provides a basis for further consideration of °θk as parameters for the empirical search for structure-function relationships.

2025, Tetrahedron: Asymmetry

The terpenoid chiral selectors dehydroabietic acid, 12,14-dinitrodehydroabietic acid and friedelin have been covalently linked to silica gel yielding three chiral stationary phases CSP 1, CSP 2 and CSP 3, respectively. The enantiodiscriminating capability of each one of these phases was evaluated by HPLC with four families of chiral aromatic compounds composed of alcohols, amines, phenylalanine and tryptophan amino acid derivatives and b-lactams. The CSP 3 phase, containing a selector with a large friedelane backbone is particularly suitable for resolving free alcohols and their derivatives bearing fluorine substituents, while CSP 2 with a dehydroabietic architecture is the only phase that efficiently discriminates 1,1 0 -binaphthol atropisomers. CSP 3 also gives efficient resolution of the free amines. All three phases resolve well the racemates of N-trifluoracetyl and N-3,5-dinitrobenzoyl phenylalanine amino acid ester derivatives. Good enantioseparation of b-lactams and N-benzoyl tryptophan amino acid derivatives was achieved on CSP 1. In order to understand the structural factors that govern the chiral molecular recognition ability of these phases, molecular dynamics simulations were carried out in the gas phase with binary diastereomeric complexes formed by the selectors of CSP 1 and CSP 2 and several amino acid derivatives. Decomposition of molecular mechanics energies shows that van der Waals interactions dominate the formation of the diastereomeric transient complexes while the electrostatic binding interactions are primarily responsible for the enantioselective binding of the (R)-and (S)-analytes. Analysis of the hydrogen bonds shows that electrostatic interactions are mainly associated with the formation of N-HÁ Á ÁO@C enantioselective hydrogen bonds between the amide binding sites from the selectors and the carbonyl groups of the analytes. The role of mobile phase polarity, a mixture of n-hexane and propan-2-ol in different ratios, was also evaluated through molecular dynamics simulations in explicit solvent.

2025, Tetrahedron: Asymmetry

2025, The Journal of Chemical Physics

The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution.

2025

Charge-dipole interactions are very common interactions among atoms and molecules, especially materials that can emit light or contain free charges. The second-order charge-dipole interactions, proportional to 1 R 4 , are stronger than the second-order dipole-dipole interactions or van der Waals interactions, proportional to 1 R 6 , at longer distances. In reality, there is more than one atom or charge; therefore, we focus on few-body charge-dipole interactions, such as charge-dipole-dipole interactions. Laser cooling and trapping allow us to study such interactions with much higher precision. In this article, charge-dipole interactions will be investigated in cold gases. To increase the interaction strength, we excite the cold atoms to highly excited states, Rydberg states. Here, we treat one Rydberg atom as a dipole; the excited electron and the ion core are the two poles of an electric dipole. Specifically, we study charge-atom interactions in cold Rydberg gases. The laser-cooled lower level atoms were excited to highly excited states, and we scanned a microwave to look at the line shape of a particular transition between two Rydberg states. It has been shown that adding a charge can enhance atom-atom interactions under certain circumstances.

2025, Science

A known host-guest assembly, organized only by means of relatively weak dispersive forces, exhibits hitherto unappreciated thermal stability. The hexagonal close-packed arrangement of calix[4]arene contains lattice voids that can occlude small, highly volatile molecules. This host-guest system can be exploited to retain a range of freons, as well as methane, not only well above their normal boiling points, but also at relatively high temperatures and low pressures. The usually overlooked van der Waals interactions in organic crystals can indeed be used in a highly stable supramolecular system for gas storage.

2025, Protoplasma

A variety of lipid molecules are involved in the structure of hiol()gical memhranes. The study •of the forces hetween lipid molecules is important for an understanding of the properties of these membranes. The results of a series of studies on pure model lipid systems were reported. These studies were on lipids at a'que()us interfaces {examined by surface pressure [1]. surface potential [2]. and surface polar1zation [3] techniques} and on paraffinic colloidal electrolytes in aqueous solutions and micelles -(examined by NMR [4 J and Raman spectl'oso()PY [5]). Thoorclicrulca1culaiiollis on the electl'()static and van der Waals interactions of lipids in membrane-liike structures were also discussed [6]. These various lines of evidence suggest that phospholipid zwitterions are somewhat polarized normal to the membrane by applied electric fields of the magnitude of action potentials. The van cler vVaals interaction of the chains is also important ihut does not appear to ohey the interaction law proposed by Sal e m [71. Evidence of phase ,changes in lipid films was also presented in support of some of the schematic memhrane changes discussed hy K a van a u . The importance of water as an essential component of memhrane structures was illustrated hy reference to spectroscopic data on chain-water interactions at the surface of micelles and in sub-micellar solutions of soap-like molecules. These data very strongly support the general view of water-chain interactions discussed by N em e thy and S c her a g a [9] and show that water is ,stabilized by the interaction. The paraffin chain is free to rotate internally. contrary to the view of A ra now and Wi He n [10] that the water chain 'interaotlion Ileads to a hindering of the chain rotation. References [1] van Dee n e n, 1.

2025, International Journal of Biological Macromolecules

In this report, the effect of topiramate (TPM), an anticonvulsant sulfamate drug, on the structure of human carbonic anhydrase II (hCA II) was investigated by spectroscopic techniques. The intrinsic fluorescence experiments indicated that TPM binding causes enhancement of enzyme fluorescence via decreasing the internal quenching and energy transfer efficiency, the result supported by molecular dynamics simulation. Thermodynamic analysis of the binding process suggested that hydrogen bonding and van der Waals interactions are the major forces in the interaction of TPM with hCA II. The far-UV circular dichroism (CD) results showed that TPM caused increment in ␣-helical and ˇ-sheet content of hCA II whereas, near-UV CD experiments in the presence of the drug showed induction of some compactness in the enzyme tertiary structure. The number of accessible tryptophans and protein surface hydrophobicity index of the enzyme were reduced in the presence of TPM which confirms the enzyme structural compactness upon drug binding. In addition, the enzyme thermal stability was increased in the presence of the drug. It seems that the induction of compactness in the enzyme structure upon drug binding may be responsible for increment of its conformational stability.

2025, Theoretical Chemistry Accounts

The protein MDM2 forms a complex with the tumor suppressing protein p53 and targets it for proteolysis in order to down-regulate p53 in normal cells. Inhibition of this interaction is of therapeutic importance. Molecular dynamics simulations of the association between p53 and MDM2 have revealed mutual modulation of the two surfaces. Analysis of the simulations of the two species approaching each other in solution shows how long range electrostatics steers these two proteins together. The net electrostatics is controlled largely by a few cationic residues that surround the MDM2 binding site. There is an overall separation in electrostatics of MDM2 and p53 that are mutually complementary and drive association. Upon close approach, there is significant energetic strain as the charges are occluded from water (desolvated). However, the complexation is driven by packing interactions that lead to highly favorable van der Waals interactions. Although the complementarity of the electrostatics of the two surfaces is essential for the two partners to form a complex, steric collisions of Y100 and short ranged van der Waals interactions of F19, W23, L26 of p53 determine the final steps of native complex formation. The electrostatics seem to be evolutionarily conserved, including variations in both partners.

2025, The Journal of Chemical Physics

We introduce a method for accurate quantum chemical calculations based on a simple variational wave function, defined by a single geminal that couples all the electrons into singlet pairs, combined with a real space correlation factor. The method uses a constrained variational optimization, based on an expansion of the geminal in terms of molecular orbitals. It is shown that the most relevant nondynamical correlations are correctly reproduced once an appropriate number n of molecular orbitals is considered. The value of n is determined by requiring that, in the atomization limit, the atoms are described by Hartree–Fock Slater determinants with Jastrow correlations. The energetics, as well as other physical and chemical properties, are then given by an efficient variational approach based on standard quantum Monte Carlo techniques. We test this method on a set of homonuclear (Be2, B2, C2, N2, O2, and F2) and heteronuclear (LiF and CN) dimers for which strong nondynamical correlations...

2025, Nano Letters

Reactivity control of graphene is an important issue because chemical functionalization can modulate graphene's unique mechanical, optical, and electronic properties. Using systematic optical studies, we demonstrate that van der Waals interaction is the dominant factor for the chemical reactivity of graphene on two-dimensional (2D) heterostructures. A significant enhancement in the chemical stability of graphene is achieved by replacing the common SiO 2 substrate with 2D crystals such as an additional graphene layer, WS 2 , MoS 2 , or h-BN. Our theoretical and experimental results show that its origin is a strong van der Waals interaction between the graphene layer and the 2D substrate. This results in a high resistive force on graphene toward geometric lattice deformation. We also demonstrate that the chemical reactivity of graphene can be controlled by the relative lattice orientation with respect to the substrates and thus can be used for a wide range of applications including hydrogen storage.

2025, Physical Review E

We investigate a magnetic fluid composed of magnetite nanoparticles surfacted with dodecanoic acid molecules and stably dispersed in a hydrocarbon solvent. A comparison between Monte Carlo simulation and different experimental techniques allows us to validate our methodology and investigate the behavior of the surfactant molecules. Our analysis, based on the Langmuir model, suggests that the surfactant grafting number on isolate nanoparticles increases with the nanoparticle concentration, while the grafting on agglomerated nanoparticles presents a more complicated behavior. Our results suggests that, if properly coated and at a certain concentration range, colloids can become stable even in the presence of agglomerates. The role of the Hamaker constant, which controls the van der Waals interaction intensity, was also investigated. We have found that the ratio between grafting and Hamaker constant governs the level of nanoparticle agglomeration.

2025, RSC Advances

At the interface between monolayer coated solid substrate and fluid, the effect of interfacial mismatch on Kapitza length due to the monolayer particles has been extensively analyzed through a series of non-equilibrium molecular dynamics... more

2025

Nanomechanics of single-_aU C, BN and BC$_35 and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {_it ab-initio} electronic structure methods.

2025, Bulletin of the American Physical Society

Submitted for the MAR06 Meeting of The American Physical Society Elastic properties of SiC nanoscopic wires MAXIM MAKEEV,

2025, Bulletin of the American Physical Society

with ultrastrong coupling could demonstrate nonlinear optical effects such as photon blockade. The system-bath couplings in these systems play an essential role in observing these effects. In this work, we use a dressed-state master equation approach to study the quantum coherence of an optomechanical system. In this approach, the system-bath couplings are decomposed in terms of the eigenbasis of the optomechanical system, where the mechanical state is displaced by finite photon occupation. Compared with the standard master equation often seen in the literature, our master equation includes photon-number-dependent terms that induce dephasing. We calculate cavity dephasing, second-order photon correlation, and two-cavity entanglement using the dressed-state master equation. At high temperature, our master equation predicts faster decay of the quantum coherence than with the standard master equation. The second-order photon correlation derived with our master equation shows less antibunching than that with the standard master equation.

2024, Acta Biochimica Polonica

Imidazoacridinones (IAs) are a new group of highly active antitumor compounds. The intercalation of the IA molecule into DNA is the preliminary step in the mode of action of these compounds. There are no experimental data about the structure of an intercalation complex formed by imidazoacridinones. Therefore the design of new potentially better compounds of this group should employ the molecular modelling techniques. The results of molecular dynamics simulations performed for four IA analogues are presented. Each of the compounds was studied in two systems: i) in water, and ii) in the intercalation complex with dodecamer duplex d(GCGCGCGCGCGC)2. Significant differences in the conformation of the side chain in the two environments were observed for all studied IAs. These changes were induced by electrostatic as well as van der Waals interactions between the intercalator and DNA. Moreover, the results showed that the geometry of the intercalation complex depends on: i) the chemical co...

2024, Physical Review E

We present a theoretical model which describes the polarization modulated and layer undulated structure of the B7 phase and gives the phase transition from the synclinic ferroelectric B2 phase to the B7 phase as observed experimentally. The system is driven into the modulated phase due to the coupling between the polarization splay and the tilt of the molecules with respect to the smectic layer normal. The modulation wavelength and the width of the wall between two domains of opposite chirality are estimated.

2024, Physical Review B

Single-walled carbon nanotubes can function as nanoscale reaction chambers for growing smaller nanotubes within the host tube from encapsulated fullerenes by annealing. The diameter of the host outer tube restricts the diameter of the inner tube due to van der Waals interactions but not its chirality: it is possible that inner tubes with different chiralities start to grow in different places at the same time. A straight junction occurs at the connection of these two tubes which we refer to as bamboo defects. We show that localized states appear in the calculated density of states associated with these bamboo defects, some of them close to the Fermi level, and present a detailed theoretical study of ballistic transport through double-walled tubes where the inner shell contains bamboo defects. We find that the presence of bamboo defects should be possible to detect through electronic-transport measurements and the number of bamboo defects per unit length can be extracted from the structure of the resonances appearing in the transmission coefficient.

2024, Journal of the Mechanics and Physics of Solids

This paper investigates the transverse and torsional wave in single-and double-walled carbon nanotubes (SWCNTs and DWCNTs), focusing on the effect of carbon nanotube microstructure on wave dispersion. The SWCNTs and DWCNTs are modeled as nonlocal single and double elastic cylindrical shells. Molecular dynamics (MD) simulations indicate that the wave dispersion predicted by the nonlocal elastic cylindrical shell theory shows good agreement with that of the MD simulations in a wide frequency range up to the terahertz region. The nonlocal elastic shell theory provides a better prediction of the dispersion relationships than the classical shell theory when the wavenumber is large enough for the carbon nanotube microstructure to have a significant influence on the wave dispersion. The nonlocal shell models are required when the wavelengths are approximately less than 2.36 Â 10 À9 and 0.95 Â 10 À9 m for transverse wave in armchair (15,15) SWCNT and torsional wave in armchair (10,10) SWCNT, respectively. Moreover, an MD-based estimation of the scale coefficient e 0 for the nonlocal elastic cylindrical shell model is suggested. Due to the small-scale effects of SWCNTs and the interlayer van der Waals interaction of DWCNTs, the phase difference of the transverse wave in the inner and outer tube can be observed in MD simulations in wave propagation at high frequency. However, the van der Waals interaction has little effect on the phase difference of transverse wave.