Attraction Energy Research Articles

Coulomb and CH-πinteractions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities.

(6–4) Photolyases ((6–4)PLs) are flavoenzymes that repair the carcinogenic UV-induced DNA damage, pyrimidine(6–4)pyrimidone photoproducts ((6–4)PPs), in a light-dependent manner. Although the reaction mechanism of DNA photorepair by (6–4)PLs has been intensively investigated, the molecular mechanism of the lesion recognition remains obscure. We show that a well-conserved arginine residue in Xenopus laevis (6–4)PL (Xl64) participates in DNA binding, through Coulomb and CH–π interactions. Fragment molecular orbital calculations estimated attractive interaction energies of –80–100 kcal mol–1 for the Coulomb interaction and –6 kcal mol–1 for the CH–π interaction, and the loss of either of them significantly reduced the affinity for (6–4)PP-containing oligonucleotides, as well as the quantum yield of DNA photorepair. From experimental and theoretical observations, we formulated a DNA binding model of (6–4)PLs. Based on the binding model, we mutated this Arg in Xl64 to His, which is well conserved among the animal cryptochromes (CRYs), and found that the CRY-type mutant exhibited reduced affinity for the (6–4)PP-containing oligonucleotides, implying the possible molecular origin of the functional diversity of the photolyase/cryptochrome superfamily.

On the Unusual Synclinal Conformations of Hexafluorobutadiene and Structurally Similar Molecules.

An explanation is presented for the unusual conformations of some molecules that contain the C═C-C═C core, namely, butadienes, biphenyls, and styrenes. Small substituents often induce a synclinal conformation, which brings the substituents into close proximity, and sometimes, there is no anticlinal minimum at all. This would not be predicted from steric repulsion arguments nor would it be expected that atoms that are nonbonded in a Lewis structure would approach closer than the sum of their van der Waals radii. Atomic energies calculated according to the quantum theory of atoms in molecules (QTAIM) do not show a consistent pattern for these structurally similar molecules, nor are intersubstituent bond paths consistently found, nor favorable diatomic interaction energies calculated using the interacting quantum atoms (IQA) scheme. Instead, the synclinal conformations are found to be driven by the attraction energy of the electron distribution of the carbon atoms and the nuclei of the molecule.

Mutual interplay between pnicogen–π and tetrel bond in PF3⊥X–Pyr…SiH3CN complexes: NMR, SAPT, AIM, NBO, and MEP analysis

The mutual interplay between pnicogen–π and tetrel bond in the formation of PF3⊥X–Pyr…SiH3CN ternary complexes has been investigated via a computational chemistry at MP2/aug-cc-pVDZ level of theory. We proved by computational NMR data the effect of electron-withdrawing and electron-donating substituents on 1tJ(N-Si) across 15N...35Si tetrel bonds was investigated at M06-2X/aug-cc-pVDZ levels of theory in PF3⊥CN–Pyr…SiH3CN complex. The nature of the interactions has been studied by means of symmetry-adapted perturbation theory (SAPT) and molecular electrostatic potentials (MEP). The electrostatic interaction played a major role in the change of tetrel bond interaction strength in the X–Pyr…SiH3CN binary systems, whereas the change of pnicogen–π strength in the PF3⊥X–Pyr complexes was caused jointly by the dispersion interactions. Energy decomposition indicates that the percentage of the electrostatic term in the tetrel bond system constitutes in the total attractive binding energies, while the percentage of the dispersion term in the pnicogen bonding constitutes in the attractive binding energies. In addition, atoms in molecules (AIM) and natural bond orbital (NBO) analyses were also performed to unveil the mechanism of these interactions in the title complexes.

Attractive interaction between interstitial solutes and screw dislocations in bcc iron from first principles

Plasticity in steels depends largely on how dislocations interact with solute atoms. We consider here typical interstitial solutes (B, C, N, O) in body-centered cubic (bcc) Fe and show using ab initio calculations that, systematically, when a row of interstitial solutes is in the vicinity of a 1/2〈111〉 screw dislocation, the dislocation adopts a hard core, forming regular prisms of Fe atoms centered on the solute atoms. This low-energy configuration, previously known only for C atoms, induces attractive dislocation-solute interaction energies ranging from −1.3 to −0.2 eV, depending on the nature of the solutes and their separation distance along the dislocation line. This attractive reconstruction is explained by the larger Voronoi volume of the prismatic sites in the dislocation core compared to bulk octahedral sites. Moreover, an analysis of the local density of states gives a first insight into the chemical contribution responsible for the solute dependence of the interaction energy.

Iron Oxide Colloid Mobility as Affected by Solid Matrix Wetting Properties

Core Ideas Decreasing quartz sand wettability leads to attractive hydrophobic interactions with colloids. In flow columns, transport of Fe oxide colloids is not affected by sand matrix wettability. The short‐range hydrophobic attraction is probably counteracted by colloid surface roughness. The influence of porous media wettability on the mobility of colloids is mostly unknown. In the present work, organic‐matter‐coated goethite (OMCG) colloids were percolated through three saturated soil materials differing in wettability: untreated quartz sand and two variants of hydrophobized sand. For each type of sand, three ionic strength levels were applied. Derjaguin–Landau–Verwey–Overbeek (DLVO) and Lewis acid–base extended DLVO (XDLVO) interaction energy profiles were calculated according to contact angles and zeta potentials. Flow column results elucidated that decreasing sand wettability had no relevant effect on OMCG colloid mobility. In contrast, colloid retention increased with ionic strength in each type of sand packing. Classic DLVO interactions could predict trends in colloid retention by the respective characteristics of energy barriers and secondary minima. The extension with Lewis acid–base interactions in the XDLVO approach led to the prediction of significant short‐range (∼2 nm) attractive interaction energies between colloids and hydrophobized sand, which were not reflected by colloid breakthrough behavior. This was probably due to substantial energy barriers calculated for larger distances (∼27 to ∼75 nm, depending on ionic strength) between the solid matrix and colloids. It is concluded that the distinct surface roughness of sand grains and colloids probably weakened the strength of the short‐range attractive interactions, because larger amounts of surface area were still outside the effective distance for the short‐range interactions predicted by XDLVO. Regarding colloidal mobility, we concluded for our saturated porous systems that near‐surface attractive XDLVO interaction energies between OMCG colloids and hyrophobized sand did not significantly affect colloid mobility.

Local Lewis Acidity of (TiO2)n (n = 7–10) Nanoparticles Characterized by DFT-Based Descriptors: Tools for Catalyst Design

Transition metal oxide nanoparticles are common materials in a multitude of applications including heterogeneous catalysis, solar energy harvesting, and energy storage. Understanding the particles’ interplay with their surroundings is key to their efficient usage and design. Herein two DFT-based descriptors are used to study local reactivity on (TiO2)n (n = 7–10) nanoparticles. The local electron attraction energy [E(r)] and the electrostatic potential [V(r)], evaluated on isodensity surfaces, are able to identify and rank Lewis acidic sites on the particles with high accuracy when compared to the interaction energies of the Lewis bases H2O, H2S, NH3, and CO. These interactions are characterized as mainly electrostatically controlled. Given the local character, low computational cost, and excellent performance of the ES(r) and VS(r) descriptors, they are anticipated to find widespread use in nanoparticle research and development.

A dark matter compact star in the framework of the pseudo‐complex general relativity

In the theory of pseudo‐complex general relativity (pc‐GR), the field equations have an extra term, associated with the nature of space‐time, of repulsive character, which may halt the gravitational attractive collapse of matter distributions in the evolution process of compact stars. This additional term arises from microscale phenomena due to vacuum fluctuations, which simulate the presence of dark energy in the Universe. In this paper, we explore the presence of this additional term and propose a toy model consisting of dark matter, represented by standard model Fermi gauge singlets having their origin in the Higgs portal model, held together by the presence of the gravitational interaction and superimposed on the repulsive background of dark energy forming a type of unconventional and nonluminous star, composed only of dark matter and dark energy, a rare compact object formed solely by exotic content. The combination of these two ingredients, namely gravitational attraction and dark energy repulsion, allows the hydrostatic equilibrium condition of the star to hold. Solving the corresponding field equations and the Tolman‐Oppenheimer‐Volkoff (TOV) equations, and assuming that the fluid components interact only gravitationally, we determine the hydrostatic equilibrium equations of the star. We then analyze the corresponding results obtained for the equation of state and for the mass–radius relations and then determine the maximum mass of the exotic star for different parameter configurations.

Instability Characteristics of Free-Standing Nanowires Based on the Strain Gradient Theory with the Consideration of Casimir Attraction and Surface Effects

AbstractSize-dependent dynamic instability of cylindrical nanowires incorporating the effects of Casimir attraction and surface energy is presented in this research work. To develop the attractive intermolecular force between the nanowire and its substrate, theproximity force approximation(PFA) for small separations, and the Dirichlet asymptotic approximation for large separations with a cylinder-plate geometry are employed. A nonlinear governing equation of motion for free-standing nanowires – based on the Gurtin-Murdoch model – and a strain gradient elasticity theory are derived. To overcome the complexity of the nonlinear problem in hand, a Garlerkin-based projection procedure for construction of a reduced-order model is implemented as a way of discretization of the governing differential equation. The effects of length-scale parameter, surface energy and vacuum fluctuations on the dynamic instability threshold and adhesion of nanowires are examined. It is demonstrated that in the absence of any actuation, a nanowire might behave unstably, due to the Casimir induction force.

Energy-decomposition analysis of ion-neutral complexes along reaction coordinates of unimolecular proton-transfer reaction in gas phase: Comparison between 2-butanol radical ion and protonated 2-ethoxypropane ion

An energy-decomposition analysis clarified the physical origins that change in gas-phase unimolecular proton-transfer reactions via ion-neutral complexes of the 2-butanol radical ion and protonated 2-ethoxypropane ion. In the bond cleavage and new bond-formation parts of the reaction coordinates, exchange and polarization energies provide a major source of the attraction. In the ion-neutral complex-formation part of the reaction coordinate, different major attractive sources, dispersion, and electrostatic energies were observed. The physical origins of weak interaction in the ion-neutral complexes were affected by the local charges and distances between the ion moieties and the neutral moieties.

Effects of solute concentration on the stacking fault energy in copper alloys at finite temperatures

Stacking-fault energy (SFE) is a critical parameter that influences plastic deformation of Cu alloys. Here, the SFEs of Cu solid solutions at various temperatures and solute concentrations were studied by using first-principles calculations. The interaction energies of 18 substitutional atoms and 5 interstitial atoms with stacking fault (SF) in Cu were obtained for the first time. The results show that the interactions can extend to the second layer with respect to the SF. Substitutional atoms Sn, Al, Zn, P, Si, Ge as well as interstitial atoms Be, C, N, O, H have large attraction energies with the SF; whereas, substitutional atoms Ti, Mn, Cr are repelled by the SF, and the rest of the atoms have small interaction energies. Then, the effects of uniform and Fermi-Dirac distribution of solute atoms on the SFE of Cu alloys were further investigated based on these interaction energies. It is found that the SFE of Cu can be drastically reduced by Sn, Al, Zn, P, Si, Ge, C, N and O atoms with relatively high concentration at low temperatures. Our research suggests that it is possible to obtain twins in bulk Cu by adding alloying elements at circumstances, since the SFEs can be significantly lowered.

First-principles study of noble gas atoms in bcc Fe

We investigate the energetics and clustering trend of noble gas atoms (He, Ne, and Ar) in bcc Fe, and their interactions with vacancy or H/He impurities using first-principles calculations. We determine the formation energy of single and double noble gas atoms inside Fe host lattice as well as the resulted volume changes. The Ne/Ar formation energy is two and three times that of He. The attraction between Ne/Ar and vacancy is stronger than He-vacancy, indicating higher dissolution energy of Ne/Ar. The interstitial Ne-Ne/Ar-Ar pairs have stronger attractions (−1.91 eV/−1.40 eV) than He-He (−0.37 eV), forming stable <110> configurations. Such strong attraction means that He/Ne/Ar tend to aggregate, which can be well explained by the lower electron density induced by interstitial noble gas atoms and its strong repulsion with Fe atoms. Moreover, H/He energetically prefers to occupy the tetrahedral sites nearby Ne/Ar atom. The attraction energies of He-Ne/He-Ar pairs (−1.01 eV/-0.85 eV) are much stronger than those of H-Ne/H-Ar (−0.22 eV/−0.10 eV) and their charge density differences are discussed. The distinct attraction strengths by various noble gas atoms provide a preliminary explanation for the difference in irradiation effects on Fe solid by He, Ne, Ar, and He+H/Ne+He. These findings improve our understanding about the behavior of noble gas atoms and gas bubble formation in iron under irradiation.

A one-dimensional model for water desalination by flow-through electrode capacitive deionization

Capacitive deionization (CDI) is a fast-emerging water desalination technology in which a small cell voltage of ~1V across porous carbon electrodes removes salt from feedwaters via electrosorption. In flow-through electrode (FTE) CDI cell architecture, feedwater is pumped through macropores or laser perforated channels in porous electrodes, enabling highly compact cells with parallel flow and electric field, as well as rapid salt removal. We here present a one-dimensional model describing water desalination by FTE CDI based on modified Donnan electric double layer theory, and employing simple cell boundary conditions derived via scaling arguments. We further provide a comparison of model results to data obtained from a custom-built FTE CDI cell. We show good model-to-equilibrium data fits with reasonable values for fitting parameters such as the Stern layer capacitance, micropore volume, and attraction energy. Further, the model well-describes dynamic effluent salt concentration and cell current obtained from the experimental cell. Thus, we demonstrate that from an engineering modeling perspective, an FTE CDI cell can be described with simpler one-dimensional models, unlike more typical flow-between electrodes architecture where 2D models are required.

The influence of interphase characteristics on the attraction of particles in aqueous and gaseous media

The dependence of the attraction energy of particles on the formation of thin layers on their surface with characteristics different from those of dispersion medium has been investigated. It is shown that at local reduction of the water density or formation of gaseous interlayer on the surface of hydrophobic particles, their attraction at small distances substantially increases. In contrast, the formation of a thin layer of water on the surface of hydrophilic particles in the air leads to weakening of their attraction. The most pronounced effect is obtained for the energy of interaction of hydrophobic disperse particle and bubble: the interaction value and sign changes depending on the specific ratio of parameters.

DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions.

Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduce DNA overcharging. In this paper, we focus on the effect of multivalent co-ions, specifically divalent co-ions such as SO[Formula: see text]. A computational experiment of DNA condensation using Monte Carlo simulation in grand canonical ensemble is carried out where the DNA system is in equilibrium with a bulk solution containing a mixture of salt of different valency of co-ions. Compared to systems with purely monovalent co-ions, the influence of divalent co-ions shows up in multiple aspects. Divalent co-ions lead to an increase of monovalent salt in the DNA condensate. Because monovalent salts mostly participate in linear screening of electrostatic interactions in the system, more monovalent salt molecules enter the condensate leads to screening out of short-range DNA-DNA like charge attraction and weaker DNA condensation free energy. The overcharging of DNA by multivalent counterions is also reduced in the presence of divalent co-ions. Strong repulsions between DNA and divalent co-ions and among divalent co-ions themselves lead to a depletion of negative ions near the DNA surface as compared to the case without divalent co-ions. At large distances, the DNA-DNA repulsive interaction is stronger in the presence of divalent co-ions, suggesting that divalent co-ions' role is not only that of simple stronger linear screening.

Interplay between non-covalent pnicogen bonds and halogen bonds interactions in ArH2N---PH2FO---BrF nanostructured complexes: a substituent effects investigation

The interplay between pnicogen bonds and halogen bonds in nanostructured 4-XPhNH2---PH2FO---BrF (X = H, Me, NH2, N(Me)2, OH, OMe, F, Cl, Br, CHO, CN and NO2) complexes have been investigated using M06-2X/aug-cc-pVDZ quantum chemical calculations. The attraction energy of P---N and O---Br in the nanostructured 4-XPhH2N---PH2FO and PH2FO---BrF dimer systems increased because of the introduction of a third molecule and hence a positive cooperativity is observed during formation of the pnicogen bond and halogen bond in trimer complexes. The effect of substituent exchange on cooperativity between pnicogen bonds and halogen bonds was studied and the results cleared that the cooperativity between pnicogen and halogen bonds increases with an increase in the electron donor capability of substituents. In addition, the obtained values for cooperativity, showed a good correlation with Hammett’s substituent constants. Both the pnicogen and halogen bonds distances in the trimer complexes are dependent on the power of the P---N and O---Br bonds respectively and are shortened compared to the corresponding dimer complex systems. The shortening of both the pnicogen and halogen bond distances in the trimer complexes increases as the electron withdrawing nature of the substituent increases. Natural bond orbital theory is used to investigate how charge redistribution during molecular interactions, leads to the positive cooperative effects. Good correlations between amounts of charge transfer and pnicogen/halogen bond distance variations are obtained. Finally, molecular electrostatic potential and electron density difference maps were used for to increase the depth of understanding. The positive interplay between pnicogen and halogen bonds within the studied complexes is consistent with the results of both the molecular electrostatic potential and electron density difference maps.

A density functional theory study of double proton transfer reactions in formamide, formamide-formic acid and formic acid dimers

We have performed a theoretical study on the double proton transfer (DPT) reactions for the formamide-formamide, formamide-formic acid and formic acid-formic acid dimeric complexes by using the ωB97XD/aug-cc-pVDZ level of density functional theory (DFT). The DFT calculated reaction energy barriers are calibrated by the high-level MP2 and CCSD(T) methods at the complete basis set limit. The reaction energy profiles along the intrinsic reaction coordinates have been analyzed using the symmetry adapted perturbation theory. The reaction mechanism is elucidated by examining the reaction force, the chemical potential and the reaction electronic flux. Our results show that the DPT reactions are essentially synchronous which can form an alternative reaction pathway to monomer tautomerization. The reactions proceed with significant intermolecular bond shortening and charge accumulation, yielding large increment in the exchange energy toward the formation of the reaction energy barrier. Once the transition state is reached, the energetic constraint is released by the attractive energies.

Electrophilicity of oxalic acid monomer is enhanced in the dimer by intermolecular proton transfer.

We have analyzed the effect of excess electron attachment on the network of hydrogen bonds in the oxalic acid dimer (OA)2. The most stable anionic structures may be viewed as complexes of a neutral hydrogenated moiety HOA˙ coordinated to an anionic deprotonated moiety (OA-H)-. HOA˙ acts as a double proton donor and (OA-H)- as a double proton acceptor. Thus the excess electron attachment drives intermolecular proton transfer. We have identified several cyclic hydrogen bonded structures of (OA)2-. Their stability has been analyzed in terms of the stability of the involved conformers, the energetic penalty for deformation of these conformers to the geometry of the dimer, and the two-body interaction energy between the deformed HOA˙ and (OA-H)-. There are at least seven isomers of (OA)2- with stabilization energies in the range of 1.26-1.39 eV. These energies are dominated by attractive two-body interaction energies. The anions are vertically bound electronically by 3.0-3.4 eV and adiabatically bound by at least 1.6 eV. The computational predictions are consistent with the anion photoelectron spectrum of (OA)2-. The spectrum consists of a broad feature, with an onset of 2.5 eV and spanning to 4.3 eV. The electron vertical detachment energy (VDE) is assigned to be 3.3 eV.

Molecular field origin for magnetic ordering of magnetic materials

In 1907, Weiss proposed that there is a molecular field to explain the magnetic ordering of magnetic materials. However, it has not been clarified where the molecular field comes from so far. In recent decades, the magnetic ordering of metals and alloys were explained by using the direct exchange interaction of between electrons on neighboring atoms, while magnetic ordering of oxides were explained by using the super exchange interaction and double exchange interaction models. The intrinsic relation between those exchange interactions has not been well explained. This resulted in the fact that there are many puzzles for magnetic ordering of the magnetic materials. For example, what role the Cr cations play in spinel ferrite CrFe2O4; why the calculated molecular magnetic moment (3.85B) for La0.85Sr0.15MnO3 by using double exchange interaction model is lower than its experimental value (4.20B); whether there is a relation between the average atom magnetic moment and their electrical resistivity for each of Fe, Co and Ni metals. These several puzzles have been explained recently by our group through using an O 2p itinerant electron model for magnetic oxides and a new itinerant electron model for magnetic metals. In this paper, a model for the molecular field origin is proposed. There are three states for the electrons rotating with high speed at the outer orbits of two adjacent ions of magnetic oxides or metals and alloys. 1) There is a probability with which form the electron pairs with opposite spin directions and a certain life time, named Weiss electron pairs (WEP); the static magnetic attraction energy between two electrons of WEP is the elementary origin of Weiss molecular field. 2) There is a probability with which two electrons with the same spin direction exchange mutually. 3) If there are two electrons at the outer orbit of an ion, then for its adjacent ion whose orbit has only one electron, the excess electron will itinerates between the ions. Furthermore, the energy equation of WEP, equilibrium distance, re0, and maximum distance, rem, between electrons of WEP are derived. The probability with which WEP forms in each of several perovskite manganites is investigated. For perovskite manganites La0.8Ca0.2MnO3, La0.75Ca0.25MnO3, La0.70Sr0.30MnO3, the crystal cell constants increase linearly with temperature when the temperature is much lower than the Curie temperature, TC, while they show a rapid increase nonlinearly near TC. We then calculate the difference in MnO bond length at TC between the linear and the nonlinear variation, △dobs. Obviously, when the distance between the two electrons of WEP, re, is larger than the rem, WEP and the magnetic ordering energy both disappear. Assuming △dobs=rem-re0, the probabilities with which WEP appears in La0.8Ca0.2MnO3, La0.75Ca.25MnO3, La0.70Sr0.30MnO3, are calculated to be 0.07%, 0.31% and 3.13%, respectively. These results indicate that the WEP model for the magnetic ordering energy is qualitatively reasonable.

Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study.

Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state". In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase separation observed in experiments of ELPs. Therefore, we utilize phenomenological coarse-grained (CG) MD simulations to probe how conjugating a block of generic-LCST polymer to another rigid unresponsive macromolecular block impacts the transition temperatures at concentrations and length scales larger than atomistic simulations. We find that when multiple LCST polymer chains are conjugated to a rigid unresponsive polymer block, the increased local crowding of the LCST polymers shifts the transition marked by onset of chain aggregation to smaller effective polymer-polymer attraction energies compared to the free LCST polymer chains. The driving force needed for aggregation is reduced in the conjugates compared to free LCST polymer due to reduction in the loss of polymer configurational entropy upon aggregation.

Quantifying Host–Guest Interaction Energies in Clathrates of Dianin’s Compound

The subtle intermolecular host–guest interaction energies have been quantified for 17 different clathrates of the Dianin’s compound. Energy framework analysis of the host structure reveals that, in addition to strong electrostatic forces due to H-bonding, the framework is stabilized by very strong dispersion interactions, resulting in a three-dimensional energy framework. Compared to the host framework, the host–guest interactions are rather weak, and the enclathration only perturbs the host energy framework. Larger guest molecules result in more attractive host–guest interactions, although the shape of the guest molecule is also found to be important. Easy rotation about the c-axis was found for the hexane guest molecule, while the rotation is hindered in the cases of CCl4, CCl3CN, and C(CH3)3CN. For the Dianin clathrates containing the C(CH3)3CN or the acetone guest species, attractive interaction energies between guest molecules in adjacent cavities suggest short-range ordering of the guest molecules. ...