Order Interaction Energy Research Articles

Intermolecular interaction energies from fourth order many-body perturbation theory. Impact of individual electron correlation contributions.

The performance of Møller-Plesset perturbation theory methods for describing intermolecular interaction energies has been investigated with the focus on illuminating the impact of individual electron correlation energy contributions in fourth order. It is shown that a physically meaningful decomposition of the fourth order correlation energy can be obtained by grouping individual correlation energy terms that share the same diagrammatic loop structure. This decomposition of the fourth order singles (S), doubles (D), triples (T), and quadruples (Q) terms revealed that individual terms from each excitation class can have a huge impact on the energy that is much larger than the total fourth order correlation contribution. A partial summation of S, D, and Q terms has been derived that can reproduce the full fourth order interaction energies with a good accuracy and which does not include the computationally expensive triples energy term.

Theoretical study of the substituent effect on corrosion inhibition performance of benzimidazole and its derivatives

The substituent effects of electron-donating and -withdrawing on the efficiency of corrosion inhibition of benzimidazole and its derivatives have been studied by density functional theory DFT and Moller – Plesset perturbation theory MP2 calculations at aqueous medium. For this investigation, the corrosion inhibition efficiencies of the protonated and non-protonated spesies of benzimidazole and its derivatives were correlated with molecular electronic properties: high occupied molecular orbital (HOMO) and low unoccuppied molecular orbital (LUMO) energies, ionization potential, electron affinity, electronegativity and fraction number of electron transfer. The dipole moment and interaction energy represent the total surface coverage and the strength of the adsorption of inhibitors on the metal surface. Natural bond orbital NBO analysis in term of the second order interaction energies were used to study the contributions of the active sites of inhibitors toward corrosion inhibition performances. The ionization potential of the inhibitors has a strong influence on the efficiency of corrosion inhibitors. It was found that the MP2 method accurately predicted the ionization potential while the DFT failed to mimic the ionization potential of the experimental results. The linear correlation was shown between electronic properties and corrosion inhibition efficiency. Electron donating substituents increase the corrosion inhibition efficiency, whereas electron withdrawing substituents give the opposite effect. The NH2 substituent contributes highest, whereas NO2 provides the weakest contribution to the corrosion inhibition efficiency for both non-protonated and protonated species of inhibitors. The second order interaction energy indicated that heteroatom at imidazole position was the main center of electron donating and they received simultaneously significant amount of electron back donation from the metal

Моделирование водородных связей в молекулярных кристаллах тирозина

The problem of the study of hydrogen bonds in biomolecules and living systems is important. Among the drugs, doctors emphasize substances of natural origin involved in metabolic processes. Such compounds include amino acids, peptides, vitamins, enzymes, macro- and microelements, and other biologically active substances, many of which are capable of forming hydrogen bonds. Amino acids and their derivatives are drugs of metabolic pharmacotherapy, characterized by low toxicity and severity of side effects. They also have virtually no allergenic effect, which makes them promising for the creation of drugs or their modifications. The instability of the hydrogen bond can significantly affect the state of pharmaceutical drug containing, for example, amino acids, during their storage, transportation or technological processing. One of the methods for studying the nature and determining the strength of hydrogen bonds is quantum chemical simulation. The calculation of the interaction energy in the studied molecular associate and its decomposition have been carried out according to Morocuma’s method (HF/6-31G (PC GAMESS). The evaluation of such energy components as electrostatic, exchange repulsion, polarization, charge transfer, mixing is given. The main contribution to the interaction energy comes from the electrostatic component. All the studied models have the same distribution of the components of the interaction energy in order of magnitude. Significant difference in the interaction energy in two model systems was noted, that could be explained by different geometry of hydrogen bonds. The comparison of received data made it possible to conclude that there are three types of hydrogen bonds in the molecular tyrosine crystal, which differ from each other in energy and geometry.

Theoretical study on the binding selectivity of 18-membered azacrown ethers with alkaline earth metal species

The binding selectivity of 18-membered azacrown ethers (monoaza- N1, diaza- N2, triaza- N3, tetraaza- N4, pentaaza- N5, and hexaaza-18-crown-6 N6) with Ca2+, Sr2+, Ba2+ have been studied by density functional theory (DFT) calculations. The complex binding selectivity was analyzed in term of interaction energies, thermodynamic properties, second order interaction energies, and charge transfer effects. The geometrical study shows that Ca2+ and azacrown complexes acquire envelope like structure, leading to shorter bond lengths. As a result, these complex systems have the highest interaction energies. Theoretical study also showed that N6 complex with alkaline earth metal ion were shown to be more stable complex than those ligand with lower nitrogen number. The interaction energy order is N0 < N1 < N2 < N3 < N4 < N5 < N6. This trend shows that the presence of more nitrogen on the crown ether cavity increases the interaction energies by approx. 7.3 % in going from N0 to N6. It is clearly showed that the contribution of the number of nitrogen play a dominant role in the binding selectivity of these systems.

On the isomers of pyridine-4-carboxaldoxime and its nitrate salt, X-ray crystal structure and quantum chemical calculations

The reaction between nitric acid and pyridine-4-carboxaldoxime (P4A) afford the corresponding pyridinum nitrate salt (P4AN). Its X-ray structure is measured and compared with the related P4A salts. The DFT/B3LYP results showed that both the P4A and P4AN favored the Syn-I form which has the lowest energy among the other possible isomers. Transition state calculations predicted that the Syn-I form is the thermodynamically and kinetically most stable form. The X-ray solid state structure of the new nitrate salt (P4AN) indicated that the labile proton favored the N-atom of the pyridine ring. DFT studies showed that the same is true for its solution in polar solvents. In contrast, the pyridinium cation is not favored either in the gas phase or solution of P4AN in nonpolar solvent. In these cases, the proton favored to bond with one O-atom from the nitrate group. Second order interaction energies and Mayer bond order values revealed these results. The bond order of the NH bond is higher in polar solvents as well as at the experimental structure than either in the gas phase or non polar solvents. The topology parameters obtained from the atoms in molecules (AIM) analysis were used to describe the nature of the NH and OH bonds. The bond critical points (BCP) were found to be close to the H-atoms in case of stronger interaction.

Theoretical Study on the Extraction of Alkaline Earth Salts by 18-Crown-6: Roles of Counterions, Solvent Types and Extraction Temperatures

The roles of counterions, solvent types and extraction temperatures on the selectivity of 18-crown-6 (L) toward alkaline earth salts MX2 (M = Ca, Sr, Ba; X = Cl-, NO3-) have been studied by density functional method at B3LYP level of theory in gas and solvent phase. In gas phase, the chloride anion Cl- is the preference counterion than nitrate anion NO3-. This result is confirmed by the interaction energies, the second order interaction energies, charge transfers, energy difference between HOMO-LUMO and electrostatic potential maps. The presence of solvent reversed the gas phase trend. It is found that NO3- is the preference counterion in solvent phase. The calculated free energies demonstrate that the solvent types strongly change the strength of the complex formation. The free energies are exothermic in polar solvent while for the non polar solvent the free energies are endothermic. As the temperature changes the free energies also vary where the higher the temperatures the lower the free energy values. The calculated free energies are correlated well with the experimental stability constants. This theoretical study would have a strong contribution in planning the experimental conditions in terms of the preference counterions, solvent types and optimum extraction temperatures.

An Integrative Meta-analysis of MicroRNAs in Hepatocellular Carcinoma

We aimed to shed new light on the roles of microRNAs (miRNAs) in liver cancer using an integrative in silico bioinformatics analysis. A new protocol for target prediction and functional analysis is presented and applied to the 26 highly differentially deregulated miRNAs in hepatocellular carcinoma. This framework comprises: (1) the overlap of prediction results by four out of five target prediction tools, including TargetScan, PicTar, miRanda, DIANA-microT and miRDB (combining machine-learning, alignment, interaction energy and statistical tests in order to minimize false positives), (2) evidence from previous microarray analysis on the expression of these targets, (3) gene ontology (GO) and pathway enrichment analysis of the miRNA targets and their pathways and (4) linking these results to oncogenesis and cancer hallmarks. This yielded new insights into the roles of miRNAs in cancer hallmarks. Here we presented several key targets and hundreds of new targets that are significantly enriched in many new cancer-related hallmarks. In addition, we also revealed some known and new oncogenic pathways for liver cancer. These included the famous MAPK, TGFβ and cell cycle pathways. New insights were also provided into Wnt signaling, prostate cancer, axon guidance and oocyte meiosis pathways. These signaling and developmental pathways crosstalk to regulate stem cell transformation and implicate a role of miRNAs in hepatic stem cell deregulation and cancer development. By analyzing their complete interactome, we proposed new categorization for some of these miRNAs as either tumor-suppressors or oncomiRs with dual roles. Therefore some of these miRNAs may be addressed as therapeutic targets or used as therapeutic agents. Such dual roles thus expand the view of miRNAs as active maintainers of cellular homeostasis.

EXTRACTION OF STRONTIUM(II) BY CROWN ETHER: INSIGHTS FROM DENSITY FUNCTIONAL CALCULATION

The structures, energetic and thermodynamic parameters of crown ethers with different cavity size, electron donating/withdrawing substituent groups and donor atoms have been determined with density functional method at B3LYP level of theory in gas and solvent phase. Small core quasi-relativistic effective core potentials was used together with the accompanying SDD basis set for Sr2+ and DZP basis set was used for crown ether atoms. Natural bond orbital (NBO) analysis was evaluated to characterize the distribution of electrons on the complexes. The interaction energy is well correlated with the values of Strontium charge after complexation, the second order interaction energies (E2) and HOMO-LUMO energy gab (∆Egab). The interaction energy and thermodynamics parameters in gas phase are reduced in solvent phase as the solvent molecules weaken the metal-crown ether interaction. The thermodynamic parameters indicated that less feasibility to extract Sr2+ ion directly from pure water without presence of organic solvent. The theoretical values of extraction energy for Sr(NO3)2 salt from aqueous solution in different organic solvent is validated by the experimental trend. This study would have strong contribution in planning the experiments to the design of specific host ligand and screening of solvent for extraction of metal ion.

Pnicogen–π complexes: theoretical study and biological implications

The energetic and geometric features of pnicogen-π complexes involving different types of aromatic rings (benzene, trifluorobenzene, hexafluorobenzene and s-triazine) and the heavier pnicogenes (ECl(3), E = As, Sb, Bi) are investigated using theoretical methods (ab initio and DFT-D3). We have analyzed how the interaction energy is affected by the π-acidity of the aromatic moieties and the pnicogen used. In addition, we have found several examples in the Protein Databank where pnicogen-π interactions are present. This likely indicates the potential use of this interaction in the design and synthesis of potential inhibitors of enzymatic reactions. Moreover, in order to know the reliability of the latest version of dispersion termed corrected DFT-D3, we have also compared the energies obtained using the ab initio MP2 method with those obtained using BP86-D3. We have also computed and analyzed the dispersion contribution to the total interaction energy in order to know if it is crucial for the favourable binding. This allows a better understanding of the physical nature of the interaction. Finally, we have used the Bader's theory of "atoms-in-molecules" to demonstrate that the electron density computed at the bond critical point that emerges upon complexation can be used as a measure of bond order in this noncovalent interaction.

Nanoparticle-Based Surface Templating

This study is focused on making molds with micrometer-sized feature arrays, studying high solids loading nanoparticle suspension for nanoparticle-based templating, and cast forming of surface-templated materials. Polydimethylsiloxane (PDMS) and silicone molds with micrometer-sized feature arrays are made using mold cores templated by a focused ion beam microscope. Al2O3 nanoparticle suspensions are evaluated based on nanoparticle interaction energy and suspension flowability in order to obtain stable and high solids loading suspensions. Templated feature transfer ability is compared for the PDMS and silicon molds under ambient and freeze-drying conditions. This work provides a new approach for surface templating of nanoparticle-based materials.

Testing Assumptions about Solute Concentration Dependence in Liquid Crystal NMR

The NMR spectra of four solutes, used as probes of liquid crystal orientational order, were analyzed. For each solute, samples were prepared at different solute concentrations, and the concentration dependence was used to extrapolate zero-concentration properties. The mean-field (Maier-Saupe) model when applied to solutes neglects solute-solute interactions and assumes all solutes in a mixed-solute sample see the same average environment. The first assumption is only valid as one approaches zero concentration, while experiments are typically carried out at concentrations between 0 and 10 mol %. The solute concentration dependence has in the past been "scaled out" using an internal solute reference as an orientational standard. We measured the concentration dependence of the orientational order parameter and calculate the corresponding interaction energies based on a mean-field interaction potential for a solute. We find agreement at the 3% level between experiments for different solutes while using (i) the zero-concentration values as solute-dependent orientational references and (ii) scaling to either order parameters or interaction energies; these two scalings gave equivalent but not identical results. We find, too, that errors inherent in the experiment and the calculations will limit attempts to refine the theory to push the comparisons beyond the 2% level.

Prediction of the Solubility, Activity Coefficient and Liquid/Liquid Partition Coefficient of Organic Compounds

AbstractSolvation models, based on fundamental chemical structure theory, were developed in the SPARC mechanistic tool box to predict a large array of physical properties of organic compounds in water and in non‐aqueous solvents strictly from molecular structure. The SPARC self‐interaction solvation models that describe the intermolecular interaction between like molecules (solute‐solute or solvent‐solvent) were extended to quantify solute‐solvent interaction energy in order to estimate the activity coefficient in almost any solvent. Solvation models that include dispersion, induction, dipole‐dipole and hydrogen bonding interactions are used to describe the intermolecular interaction upon placing an organic solute molecule in any single or mixed solvent system. In addition to estimation of the activity coefficient for 2674 organic compounds, these solvation models were validated on solubility and liquid/liquid distribution coefficient in more than 163 solvents including water. The RMS deviations of the calculated versus observed activity coefficients, solubilities and liquid/liquid distribution coefficients were 0.272 log mole fraction, 0.487 log mole fraction and 0.44 log units, respectively.

Polymer–polymer miscibility: generalized double lattice model

We generalize the modified double lattice model (mDLM) to investigate the miscibility of polymer blend systems. We re-define model parameters, Cβ and Cγ, as functions of chain length of polymer and interaction energy. Cβ corrects the degree of asymmetry between two molecules. Cγ reduces the mathematical defects originated from the truncation of higher order interaction energy terms. We correlate Cβ and Cγ with Ryu et al.'s numerical data for polymer blends with various chain lengths. In addition, associated interactions between polymer segments are considered based on the secondary lattice concept. In comparison with experimental data, the calculated coexistence curves and critical points by the proposed model show better agreements than those of mDLM.

Through space hyperconjugation in half-cage alcohols

Previous theoretical studies indicate that hyperconjugation and through-space interactions of a steric or electronic nature are mainly responsible for conformational effects in half-cage systems, influencing bond lengths, bond angles and dihedral angles as well as charge distributions. As chemical shieldings are likewise affected, it is of much interest to evaluate their contributions in order to use them for structure elucidation purposes (calculating chemical shifts for individual rotamers has the advantage of detecting effects that would otherwise appear as averages in observed spectra). Half-cage systems provide interesting models due to their rigid molecular framework. On rotation of the single C–O bond of half-cage alcohol derivatives, different groups are forced into close proximity. In our investigation of conformational effects on chemical shifts of “inside” and “outside” half-cage alcohols we found that certain positions on the inside (2) isomer did not reproduce effects observed for the outside (1) isomer. To probe interactions between lone pairs on oxygen and the C9–H9s bond, we used DFT B3LYP/6-31g(d) methodology to optimize geometries and to calculate the second order interaction energy and chemical shifts at 30° intervals. We found that not only is strong hyperconjugation through space present but, besides the oxygen p orbital, there is also a considerable contribution from the oxygen sp orbital. Although this result is not unexpected given the spatial proximity of the orbitals that are involved, to our knowledge the literature on hyperconjugation has, so far, been limited to participation by p orbitals on oxygen.

Phase behaviors of symmetric polymer blend systems

AbstractThe modified double‐lattice model is extended to polymer blend systems. We redefine Cγ as a new universal function of interaction energy to reduce the mathematical defects that originate from the truncation of higher order interaction energy terms. We correlate Cγ with Ryu et al.'s numerical results for symmetric polymer blends with various chain lengths (r1 = r2 = 8, 20, 50, or 100). In addition, oriented interactions between polymer segments are considered with respect to the secondary lattice concept. The proposed model shows a good agreement with the experimental data. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1532–1538, 2004

Hierarchy of the Interaction Energy Distribution in the Spatial Structure of Globular Proteins and the Problem of Domain Definition

An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared with available data. The method is based on entirely physical model of van der Waals interactions that reflects as illustrated in this work the distribution of electron density. Various levels of hierarchy in the protein spatial structure are discerned by analysis of the energy interaction between structural units of different scales. Thus the level of energy hierarchy plays role of sole parameter, and the method obviates the use of complicated geometrical criteria with numerous fitting parameters. The algorithm readily and accurately locates domains formed by continuous segments of the protein chain as well as those comprising non-sequential segments, sets no limit to the number of segments in a domain. We have analyzed 309 protein structures. Among 277 structures for which our results could be compared with the domain definitions made in other works, 243 showed complete or partial coincidence, and only in 34 cases the domain structures proved substantially different. The domains delineated with our approach may coincide with reference definition at different levels of the globule hierarchy. Along with defining the domain structure, our approach allows one to consider the protein spatial structure in terms of the spatial distribution of the interaction energy in order to establish the correspondence between the hierarchy of energy distribution and the hierarchy of structural elements.

Electronic and physical properties of Al3VxTi1−x (x=1, 0.875, and 0) alloys

In this article, the electronic structure of Al3VxTi1−x (x=1, 0.875, and 0) alloys with and without planar faults has been investigated. The results for the bond order integral and interaction energy between atoms, the local density of states, and the energies of the planar faults (i.e., antiphase boundary and stacking fault) are presented for the alloys. The results show that the directional bonding of the p orbital of Al in the Al3V alloy leads to the brittleness of the alloy, whereas, in the Al3V0.875Ti0.125 alloy, the p orbital bonding characteristic of Al is partly weakened and the s orbital bonding characteristic of Al is partly increased. This may change the structure of the dislocation core. The results of the local density of states (LDOS) of the atoms on the planar faults in the alloys demonstrate that the planar faults make the peaks of the LDOS of Ti and Al on the planar faults shift toward higher energy regions, and thus may increase the structural energies of Ti and Al on the planar faults. With Ti partially replacing V in Al3V, the effect of the planar faults on the LDOS of Ti is weakened, which may decrease the energy of the planar faults. This is confirmed by the result of the energy of the planar faults for Al3VxTi1−x (x=1, 0.875, and 0) alloys. The result of the energies of the planar faults for Al3VxTi1−x (x=1, 0.875, and 0) also shows that the 〈111〉 directional stacking fault is stable in Al3Ti and that the 〈001〉 directional antiphase boundary is stable in Al3V. With Ti partially replacing V in Al3V, the energies of the planar faults decrease and the activity of deformation twining and type 〈110〉 superdislocation increase. This may provide more than five independent slip systems for the Al3V0.875Ti0.125 alloy and may improve the ductility of the Al3V alloy.

Conformational Analysis of Poly(propylene oxide) and Its Model Compound 1,2-Dimethoxypropane

Conformational characteristics of poly(propylene oxide) (PPO) and its model compound, 1,2-dimethoxypropane (1,2-DMP), have been investigated. For 1,2-DMP, ab initio molecular orbital (MO) calculations at the MP2/6-31+G*, MP2/6-311+G*, and MP4/6-31+G* levels were carried out, and the free energies and dipole moments of all the possible conformers were evaluated. The bond conformations and the average dipole moments were calculated from the MO data and compared with the corresponding experimental values. The MO calculations, in general, reproduced the observations quite well. The unknown parameters in the Karplus equation expressing the dihedral-angle dependence of the vicinal coupling constant 3 J COCH were determined by comparison of the 3 J COCH values observed for 1,2-DMP with those calculated from the MO results. The free energies were broken down into conformational energy contributions corresponding to first-, second-, and third-order intramolecular interactions. All the first-order-interaction energies were found to be positive. On the other hand, the second-(E ω1 and E ω2 ) and third-(E χ ) order-interaction energies, which reflect nonbonded C-HO...D contacts, were found to be negative ; for example, the E ω1 , E ω2 , and E χ values determined for gaseous 1,2-DMP at the MP2/6-31+G* level are -1.236, -1.884, and -1.266 kcal mol -1 , respectively. As pointed out for 1,2-dimethoxyethane, the gauche stability of the C-C bond in the O-C-C-O sequence appears to arise from the nonbonded C-H...0 interactions. Using the rotational isomeric state (RIS) scheme with up to third-order interactions, the characteristic ratio and dipole moment ratio of isotactic PPO were calculated and found to be in good agreement with the observations.

Quantum Ashkin-Teller model near the decoupling limit

The critical properties and the spectrum of the quantum Ashkin-Teller chain are investigated by perturbation expansion around the exactly soluble Ising decoupling limit. The critical exponents are found to satisfy the hyperscaling relation and they are consistent with the conjectured values. The critical Hamiltonian in the finite-size scaling limit is transformed into a two-band spin-1/2 Fermi system, where the interaction energy in first order is the product of the band magnetizations. The complete spectrum is shown to exhibit a conformal structure with infinite primary operators, the anomalous dimensions of which are consistent with a Gaussian form.

Conformal invariance and the spectrum of the quantum Ashkin-Teller chain near the decoupling point

The complete spectrum of the critical quantum Ashkin-Teller chain is solved exactly in the finite size scaling limit near the Ising decoupling point. The model is transformed into two spin 1 2 fermion systems, where the interaction energy in first order is proportional to the product of the subsystem magnetizations. The spectrum of the model consists of infinitely many conformal towers, and the anomalous dimensions of the different operators are consistent with the Gaussian form.