Terms Of Interaction Energies Research Articles

Molecular energies from an incremental fragmentation method

The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

Influence of methoxy-substituents on the strength of Br … Br type II halogen bonds in bromobenzoic acid

4-bromo-3,5-di(methoxy)benzoic acid (I) crystallizes in the monoclinic C2/c space group, a = 22.3405 (6) Å, b = 4.85142 (14) Å, c = 18.1583 (5) Å, β = 93.086 (2)°. The crystal structure shows head-to-head dimeric units linked via type II Br … Br interactions as well as Br … π and weak H-bonding interactions. The whole structure exhibits features similar to those of the parent 4-bromobenzoic acid (II), most notably the overall geometrical features involved in the Br … Br type II interactions. Both structures display comparable C–Br … Br angles (θ1 = 98.3 and 91.6° and θ2 = 163.0 and 163.5° for (I) and (II) respectively), but the Br … Br distance is significantly shorter in (I) (3.58 Å) than in (II) (3.81 Å). QM computations provide the magnitude of the intermolecular interactions present in both (I) and (II), and allow disclosing the individual covalent and electrostatic contributions to the Br⋯Br halogen bond in terms of interaction energies, electrostatic potentials, and a molecular orbital (MO) analysis.

Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis.

Two very different quantum mechanically based energy decomposition analyses (EDA) schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS) based on the Amsterdam Density Functional (ADF) package and the other is natural EDA (NEDA) based in the General Atomic and Molecular Electronic Structure System (GAMESS) package. It reveals that in addition to the model (theory and basis set), the fragmentation channels more significantly affect the interaction energy terms (ΔE) between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative) polarization (POL) and charge transfer (CL) energies prefers the eclipsed ferrocene. The repulsive (positive) deformation (DEF) energy, which is dominated by the cyclopentadienyle (Cp) rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO) analysis indicates that all NBO energies, total Lewis (no Fe) and lone pair (LP) deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP) of the Fe atom and the acceptor antibond (BD*) NBOs of all C–C and C–H bonds in the ligand, LP(Fe)-BD*(C–C & C–H), which strongly stabilizes the eclipsed (D5h) conformation by −457.6 kcal·mol−1.

Interplay between tetrel and triel bonds in RC6H4CN⋯MF3CN⋯BX3 complexes: A combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study.

Intermolecular ternary complexes composed of: (1) the centrally placed trifluoroacetonitrile or its higher analogs with central carbon exchanged by silicon or germanium (M = C, Si, Ge), (2) the benzonitrile molecule or its para derivatives on one side, and (3) the boron trifluoride of trichloride molecule (X = F, Cl) on the opposite side as well as the corresponding intermolecular tetrel- and triel-bonded binary complexes, were investigated by symmetry-adapted perturbation theory (SAPT) and the supermolecular Møller-Plesset method (MP2) at the complete basis set limit for optimized geometries. A character of interactions was studied by quantum theory of atoms-in-molecules (QTAIM). A comparison of interaction energies and QTAIM bond descriptors for dimers and trimers reveals that tetrel and triel bonds increase in their strength if present together in the trimer. For the triel-bonded complex, this growth leads to a change of the bond character from closed-shell to partly covalent for Si or Ge tetrel atoms, so the resulting bonding scheme corresponds to a preliminary stage of the SN2 reaction. Limitations of the Lewis theory of acids and bases were shown by its failure in predicting the stability order of the triel complexes. The necessity of including interaction energy terms beyond the electrostatic component for an elucidation of the nature of σ- and π-holes was presented by a SAPT energy decomposition and by a study of differences in monomer electrostatic potentials obtained either from isolated monomer densities, or from densities resulting from a perturbation with the effective field of another monomer.

Synergistic and diminutive effects between halogen bond and lithium bond in complexes involving aromatic compounds.

Quantum chemical calculations have been performed to study the interplay between halogen bond and lithium bond in the ternary systems FX-C6H5CN-LiF, FLi-C6H5CN-XF, and FLi-C6H5X-NH3 (X = Cl, Br, and I) involving aromatic compounds. This effect was studied in terms of interaction energy, electron density, charge transfer, and orbital interaction. The results showed that both FX-C6H5CN-LiF and FLi-C6H5CN-XF exhibit diminutive effects with the weakening of halogen bond and lithium bond, while FLi-C6H5X-NH3 displays synergistic effects with the strengthening of halogen bond and lithium bond. The nature of halogen bond and lithium bond in the corresponding binary complexes has been unveiled by the quantum theory of atoms in molecules methodology and energy decomposition analysis.

THEORETICAL STUDY OF CO2:N2 ADSORPTION IN FAUJASITE IMPREGNATED WITH MONOETHANOLAMINE

Many efforts have been made to develop amine-based solid adsorbents for capture of CO2 by adsorption. Compared with the traditional process of absorption in aqueous solutions of amines, the adsorbents with amine immobilized in solids generally result in processes with lower capital and energy costs. The literature contains some experimental studies of CO2 adsorption in impregnated materials; however, few studies are devoted to the theoretical interpretation of this system in terms of CO2 capture for post-combustion (N2 mixture with a low partial pressure of CO2). Therefore, this study investigates the adsorption of a CO2:N2 mixture on zeolite NaX impregnated with monoethanolamine (MEA), using molecular simulation. A model of NaX impregnated with MEA was proposed and the adsorption of a 15:85 (CO2:N2) mixture was investigated based on the Monte Carlo method. The simulation of the MEA impregnated zeolite at 25 ˚C predicted higher CO2 selectivity and significant improvement in the heat of adsorption. Unfortunately, the adsorption heat improvement did not translate into corresponding increases in the amount of adsorbed CO2. Moreover, MEA concentrations higher than 12 wt% hindered the adsorption of CO2 molecules. An explanation for the results in terms of occupied volumes and interaction energies is presented.

Dynamical equations for the period vectors in a periodic system under constant external stress

The purpose of this paper is to derive the dynamical equations for the period vectors of a periodic system under constant external stress. The explicit starting point is Newton’s second law applied to halves of the system. Later statistics over indistinguishable translated states and forces associated with transport of momentum are applied to the resulting dynamical equations. In the final expressions, the period vectors are driven by the imbalance between internal and external stresses. The internal stress is shown to have both full interaction and kinetic energy terms.

Accurate modeling of cation–π interactions in enzymes: a case study on the CDPCho:phosphocholine cytidylyltransferase complex

Cation–π interactions are functionally relevant, strong secondary interactions that play versatile roles in a variety of chemical and biological systems. Therefore, it is very important to be able to describe accurately and reliably these interactions. In this study, we propose a methodology for the accurate modeling of cation–π interactions in proteins using QM/MM calculations. We developed a methodology for computing the many-body interaction energy terms and tested the effect of various factors on the accuracy of the binding energy. We found that once well-equilibrated structures were reached in the MD simulations, very similar results can be obtained for the various snapshots taken from the trajectory. The calculated interaction energies were only slightly influenced by electrostatic embedding of the point charges in the QM/MM calculations and by QM/MM geometry optimization. The calculated molecular mechanics interaction energies were off by 50 % for cation–π interactions. Instead, we suggest the calibration of force fields based on fragment-based QM calculations on geometries obtained from MD simulations to yield reliable binding energies at reduced computational cost.

Theoretical Investigation of Proton Transfer in Thiazolidine-2-thione and Oxazolidine-2-thione via Direct Transition and Self-Assisted and Water-Assisted Tautomerization

Thione–thiol transformation of thiazolidine-2-thione and oxazolidine-2-thione via direct transition, as well as self-assisted and water-assisted tautomerization was investigated using the quantum-chemical calculations. The thione complexes are more stable than the corresponding thiols. The calculations revealed that the proton transfer energy barriers are significantly lower in the presence of water molecules. Direct transition is more difficult than the water-assisted and self-assisted processes. The cooperative effects in terms of additive interaction energies and cooperativity factors of the clusters are measured and discussed. The electronic properties of the complexes are analyzed using parameters derived from atoms-in-molecules and natural bond orbital methodologies. Also, the influence of the hydrogen bond on the molecular and topological properties, as well as nuclear magnetic resonance one- and two-bond spin–spin coupling constants are investigated.

Does single-electron chalcogen bond exist? Some theoretical insights.

Ab initio calculations have been carried out to investigate the σ-hole interaction in XHY···CH3 and XHY···CH2CH3 complexes, where X = F, Cl, Br and Y = S, Se. This interaction, termed "single-electron chalcogen bond interaction" was analyzed in terms of geometric, interaction energies and electronic features of the complexes. This interaction is a weak one, with an interaction energy that varies from a minimum of -1.7 kcal mol(-1) for BrHS···CH3 to -6.0 kcal mol(-1) for FHSe···CH2CH3 at the CCSD(T)/aug-cc-pVTZ level of theory. Energy decomposition analysis indicated that the dominant attraction energy originates in the electrostatic term which is larger for the Se complexes than for the S counterparts. However, the attractive polarization and dispersion components also make an important contribution to the interaction energy for the single-electron chalcogen bond interactions.

Exploring σ-hole bonding in XH3Si···HMY (X=H, F, CN; M=Be, Mg; Y=H, F, CH3) complexes: a "tetrel-hydride" interaction.

In this work, a σ-hole interaction is predicted theoretically in XH3Si···HMY complexes, where X=H, F, CN; M=Be, Mg and Y=H, F, CH3. The properties of this interaction, termed "tetrel-hydride" interaction, are investigated in terms of geometric, interaction energies, and electronic features of the complexes. The geometry of these complexes is obtained using the second-order Møller-Plesset perturbation theory (MP2) with aug-cc-pVTZ basis set. For each XH3Si···HMY complex, a tetrel-hydride bond is formed between the negatively charged H atom of HMY molecule and the positively charged Si atom of XH3Si molecule. The CCSD(T)/aug-cc-pVTZ interaction energies of this type of σ-hole bonding range from -0.6 to -3.8 kcal mol(-1). The stability of XH3Si···HMY complexes is attributed mainly to electrostatic and correlation effects. The nature of tetrel-hydride interaction is analyzed with atoms in molecules (AIM) and natural bond orbital (NBO) theories.

Thermodynamic Insights in the Separation of Cellulose/Hemicellulose Components from Lignocellulosic Biomass Using Ionic Liquids

This work reports on the ionic liquid (IL) based separation of cellulose/hemicellulose from lignocellulosic biomass, by means of macroscale predictions using the COnductor like Screening MOdel for Real Solvents (COSMO-RS) model that is based on a statistical mechanical framework. For the benchmarking studies the experimental infinite dilution activity coefficient values for 13 components were predicted in 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulphonyl}imide with an average absolute deviation (%AAD) of 15 %. Further, the solid–liquid equilibria of glucose, fructose, galactose, and xylose in [EMIM][EtSO4] and Aliquat®336 were predicted successfully with 15 % root-mean-square deviation. Afterwards, the selectivities were predicted at infinite dilution for cellulose/hemicellulose in 1,156 ILs with a combination of 34 cations and 34 anions. Based on these values, the ammonium-based ILs 1-methyl-4-aminotriazolium hexafluorophosphate [14MATAZ][PF6] and 4-aminotriazolium bis(oxalato(2)borate) [4ATAZ][BOB] were found to be good candidates for cellulose and hemicellulose extraction, respectively. The ILs selected using the COSMO-RS methodology were then studied qualitatively in terms of interaction energies and HOMO–LUMO energy gap. The binding energy for [1-methyl-4-aminotriazolium][PF6] + cellulose and [4-aminotriazolium][BOB] + cellulose systems are higher as compared with IL + cellulose + hemicellulose, indicating greater stability.

Tryptophan-[Re6Se8I6]3− Cluster Interaction: A Computational Study

The interaction between tryptophan (Trp) and the [Re6Se8I6]3− cluster is studied here using density functional theory calculations including relativistic scalar interactions via the zero-order regular approximation and solvent effects, which we describe in terms of interaction energies, Mulliken charge analysis and molecular orbitals. In the indole functional groups of the Trp-[Re6Se8I6]3− cluster conjugates, modification of the molecular orbitals associated with Trp occurs because states associated with the [Re6Se8I6]3− cluster and the hybrid orbitals have a mixed metal–molecule character, which is attributed to the stronger than expected π interactions facilitated by the indole group in Trp. Here, we find that the energy transfer from hybrid states of Trp-[Re6Se8I6]3− to clusters could reduce intrinsic fluorescence intensity of Trp in the conjugated system.

Homology-Based Prediction of Potential Protein-Protein Interactions between Human Erythrocytes and Plasmodium falciparum.

Plasmodium falciparum, a causative agent of malaria, is a well-characterized obligate intracellular parasite known for its ability to remodel host cells, particularly erythrocytes, to successfully persist in the host environment. However, the current levels of understanding from the laboratory experiments on the host–parasite interactions and the strategies pursued by the parasite to remodel host erythrocytes are modest. Several computational means developed in the recent past to predict host–parasite/pathogen interactions have generated testable hypotheses on feasible protein–protein interactions. We demonstrate the utility of protein structure-based protocol in the recognition of potential interacting proteins across P. falciparum and host erythrocytes. In concert with the information on the expression and subcellular localization of host and parasite proteins, we have identified 208 biologically feasible interactions potentially brought about by 59 P. falciparum and 30 host erythrocyte proteins. For selected cases, we have evaluated the physicochemical viability of the predicted interactions in terms of surface complementarity, electrostatic complementarity, and interaction energies at protein interface regions. Such careful inspection of molecular and mechanistic details generates high confidence on the predicted host–parasite protein–protein interactions. The predicted host–parasite interactions generate many experimentally testable hypotheses that can contribute to the understanding of possible mechanisms undertaken by the parasite in host erythrocyte remodeling. Thus, the key protein players recognized in P. falciparum can be explored for their usefulness as targets for chemotherapeutic intervention.

Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin.

The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.

New group contribution estimation of solvent activity in polymer solutions

A new group contribution method (GCM) approach, based upon the combination of a thermodynamic model and molecular simulation (MS) is introduced. While other conventional GCMs require fitting with experimental data to determine group parameter values, proposed model calculates them directly using the pairwise interaction energy of functional groups (FG), obtained from MS. The solvent activities of a large variety of polymer solutions were estimated using the Helmholtz energy of mixing, based on the modified double lattice (MDL) model. For each polymer/solvent system, the interaction energy term within the Helmholtz energy expression is determined using the aforementioned group parameter derived from MS combined GCM (MS–GCM). From a number of polymer and solvent molecules, eleven FGs are defined. As considering FG connectivity, dummy atoms are introduced at the first adjacent positions in order to prevent impossible configurations during interaction energy calculation. The molecule disassembling method and dummy atom selection for each FG are carefully investigated. Newly proposed approach of MS–GCM could reduce the number of parameter much less than conventional GCMs but successfully predicted solvent activity. Its total deviation average of solvent activity estimation is 3.9%. Although it is little bit higher than previous work of Hu et al. but still remains in acceptable level.

From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen.

The understanding of protein-protein interactions is indispensable in comprehending most of the biological processes in a cell. Small-scale experiments as well as large-scale high-throughput techniques over the past few decades have facilitated identification and analysis of protein-protein interactions which form the basis of much of our knowledge on functional and regulatory aspects of proteins. However, such rich catalog of interaction data should be used with caution when establishing protein-protein interactions in silico, as the high-throughput datasets are prone to false positives. Numerous computational means developed to pursue genome-wide studies on protein-protein interactions at times overlook the mechanistic and molecular details, thus questioning the reliability of predicted protein-protein interactions. We review the development, advantages, and shortcomings of varied approaches and demonstrate that by providing a structural viewpoint in terms of shape complementarity and interaction energies at protein-protein interfaces coupled with information on expression and localization of proteins homologous to an interacting pair, it is possible to assess the credibility of predicted interactions in biological context. With a focus on human pathogen Mycobacterium tuberculosis H37Rv, we show that such scrupulous use of details at the molecular level can predict physicochemically viable protein-protein interactions across host and pathogen. Such predicted interactions have the potential to provide molecular basis of probable mechanisms of pathogenesis and hence open up ways to explore their usefulness as targets in the light of drug discovery.

Influence of magnetic field and Rashba spin–orbit coupling on strong-coupling magnetopolarons in quantum disks

On the basis of Lee–Low–Pines (LLP) unitary transformation, the influence of external magnetic field, Rashba spin–orbit coupling and quantum size effect on the ground-state interaction energy of strong-coupling magnetopolarons in quantum disks (QDs) is studied by using the Tokuda improved linear combine operator method. The results show that the ground-state interaction energy of magnetopolarons consists of four parts: the energy caused by the confinement potential of QDs, interaction energy between the electron and external magnetic field, electron and longitudinal-optical (LO) phonon interaction energy and additional term of Rashba effect originating from phonons. The electron–LO phonon interaction energy Ee- ph and additional term of Rashba effect are always negative; the absolute value |Ee- ph | increases with increasing transverse confinement strength ω0, cyclotron frequency of external magnetic field ωc and electron–LO phonon coupling strength α, but decreases with increasing the thickness of QDs L; the state properties of magnetopolarons are closely linked with the sign of the ground-state interaction energy of magnetopolarons E int and change of E int with ωc, ω0, α and L. In addition, the vibration frequency of magnetopolarons λ increases with increasing ωc, ω0 and α, but decreases with increasing L. For the ground state of magnetopolarons in QDs, the electron–LO phonon interaction plays a significant role, meanwhile, the influence of Rashba spin–orbit coupling effect cannot be ignored.

Anisotropic adsorption of oleate on diaspore and kaolinite crystals: Implications for their flotation separation

Comparative studies of flotation of oleate on diaspore and kaolinite in different particle size fractions (0.075–0.038mm, 0.038–0.01mm, 0–0.01mm) are presented to investigate the influences of particle size. The flotation results show that the kaolinite recovery increases with a decrease in particle size, while the case of diaspore is the opposite. Chemisorptions of anionic oleate collector on the surface Al sites of the negatively charged diaspore and kaolinite are confirmed by zeta potential and FTIR measurements. Anisotropic surface broken bond densities are calculated based on surface crystal chemistry to characterize anisotropic wettability of mineral crystals. The increasing order of broken bond densities (Db) and hydrophobicity for different crystal planes of diaspore and kaolinite correlate well with increasing the number of broken AlO bonds. The anisotropic adsorption of oleate on different crystal planes of diaspore and kaolinite are studied in terms of interaction energies computed by molecular dynamics (MD) simulations. The oleate is adsorbed more readily on (010) than (001) for diaspore. As for kaolinite, the oleate adsorption is considerably less on (001) as compared to (110). The conclusions drawn from purely theoretical computations are in good agreement with our experimental contact angle results.

The Mechanism of Activated Sludge Flocculation under Al<sup>3+ </sup>Dosin

The mechanism governing activated sludge flocculation under Al3+ dosing was studied in this paper. Activated sludge was cultivated in sequencing batch reactors (SBR) at 22°C. Batch dosages of Al3+ were 0.00, 0.125, 0.5, 1 and 1.5meq/L respectively, and continuous dosage was 0.1meq/L. As batch dosage increased, the total interaction energy, zeta potential and turbidity tended to decline, which suggested that batch dosing promoted sludge flocculation. Under the equivalent dose, the zeta potential of continuous dosing was higher, while the LB-EPS content showed the opposite tendency and turbidity reduction was similar. Both batch and continuous dosing promoted flocculation performance: in terms of interaction energy, batch dosing was more effective; while in terms of EPS, it was on the contrary.