Terms Of Interaction Energies Research Articles

Bacterial attachment to oxygen-functionalized graphenic surfaces.

In this work we have investigated the effect of oxygen plasma treatment of graphenic surfaces and the introduction of functional groups on changes in work function, wettability, surface free energy and bacterial adhesion. The plasma parameters were adjusted (generator power: <60W, exposure time: <20min) to limit the modifications to the surface without changing the bulk structure. The parent and modified graphenic surfaces were thoroughly characterized by μRaman spectroscopy, thermogravimetry, scanning electron microscopy, contact angle, X-ray photoelectron spectroscopy, work function and microbiological tests. It was found that even the short time of plasma modification results in a significant increase in work function, surface free energy and hydrophilicity. The changes in surface chemistry stimulate also substantial changes in bacterial adhesion. The strong relationship between work function and adhesion of bacteria was observed for all the investigated strains (Staphylococcus epidermidis, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli) whereas the bacterial colonization trend correlates with the bacterial zeta potential. The bacteria-graphenic surface interaction is discussed in terms of total interaction energy. The results point out the work function lowering of the graphenic biomaterial surface as an effective strategy for the infection risk limitation.

Toward Efficient Toxic-Gas Detectors: Exploring Molecular Interactions of Sarin and Dimethyl Methylphosphonate with Metal-Centered Phthalocyanine Structures.

The rapid and reliable detection of lethal agents such as sarin is of increasing importance. Here, density-functional theory (DFT) is used to compare the interaction of sarin with single-metal-centered phthalocyanine (MPc) and MPc layer structures to a benign model system, i.e., the adsorption of dimethyl methylphosphonate (DMMP). The calculations show that sarin and DMMP behave nearly identical to the various MPcs studied. Among NiPc, CuPc, CoPc, and zinc phthalocyanine (ZnPc), we find the interaction of both sarin and DMMP to be the strongest with ZnPc, both in terms of interaction energy and adsorption-induced work function changes. ZnPc is thus proposed as a promising sensor for sarin detection. Using X-ray photoelectron spectroscopy, the theoretically predicted charge transfer from DMMP to ZnPc is confirmed and identified as a key component in the sensing mechanism.

Unraveling the role of dipolar versus Dzyaloshinskii-Moriya interactions in stabilizing compact magnetic skyrmions

Magnetic skyrmions have been the subject of extensive experimental studies in ferromagnetic thin films and multilayers, revealing a diversity in their size, stability and internal structure. While the orthodox skyrmion theory focuses on the Dzyaloshinskii-Moryia interaction (DMI) and neglects higher-order energy terms, it is becoming clear that the full stray field energy needs to be taken into account to understand these recent observations. Here we present a micromagnetic study based on rigorous mathematical analysis which allows to account for the full stray field energy in the thin film and low DMI regime. In this regime, the skyrmion profile is close to a Belavin-Polyakov profile, which yields analytical expressions for the equilibrium skyrmion radius and energy. The obtained formulas provide a clear identification of Dzyaloshinskii-Moryia and long-range dipolar interactions as two physical mechanisms determining skyrmion size and stability, a consideration of importance for the optimization of skyrmion characteristics for spintronic applications.

Ab initio investigation of the formation mechanism of nano-interfaces between 3d-late transition-metals and ZrO2 nanoclusters.

Understanding the formation of nano-interfaces between metallic clusters and nanoscale metal-oxides is an important step towards using such systems for catalytic applications. Thus, in this work, we employ density functional theory calculations to study the TMn-(ZrO2)13 interactions, for TM = Fe, Co, Ni, or Cu, and n = 1, 4, and 8. We found a general trend for adsorption and interaction energies (ad/int) for all cluster sizes, with . In terms of size effects, both adsorption and interaction (frozen adsorbed structures) energies become stronger with increasing cluster sizes due to the increase in the number of TM atoms in direct contact with the (ZrO2)13 nanocluster. The structural and electronic properties change for each TMn/(ZrO2)13 system, indicating that these properties could be tuned through variables like the TM species, cluster size and morphology (isomers with different structures). The results also indicate that, from the studied TMs, Ni (Cu) should form the smallest (largest) clusters when supported on the (ZrO2)13 nanoclusters. These and other results discussed here help understand the formation of the nano-interface in the TM-ZrO2 systems, which can be useful in the development of new catalysts.

Coarse-grained molecular dynamic simulations of interactions of poly(amidoamine) with sodium octadecyl sulfate at the water/octane interface

This study investigated the interactions of poly(amidoamine) (PAMAM) and sodium octadecyl sulfate (SOS) molecules at the water/octane interface by analyzing spatial structures and interfacial properties of water/PAMAM/SOS/octane (oil) systems. Coarse-grained molecular dynamic simulations were performed to examine the dependence of the systems on interfacial coverage (IC, corresponding to the concentration of SOS molecules) and PAMAM concentration (CPAMAM) in terms of density profiles, interaction energy, interfacial thickness, order parameters (SCD), interfacial tension (γ), and area compressibility modulus (KA). Simulation results showed that the presence of PAMAM molecules had a stronger effect on SOS head groups and pushed the head groups toward the oil phase. The interaction energy between PAMAM and SOS molecules increased with increments of CPAMAM in a fixed IC. Interfacial thickness and SCD increased with increased CPAMAM. The γ value in the presence of PAMAM was lower compared with pure SOS solutions and decreased with increased CPAMAM. The area compressibility modulus (KA) of SOS monolayer increased with increased CPAMAM.

Recent developments in symmetry‐adapted perturbation theory

AbstractSymmetry‐adapted perturbation theory (SAPT) is a well‐established method to compute accurate intermolecular interaction energies in terms of physical effects such as electrostatics, induction (polarization), dispersion, and exchange. With many theory levels and variants, and several computer implementations available, closed‐shell SAPT has been applied to produce numerous intermolecular potential energy surfaces for complexes of experimental interest, and to elucidate the interactions in various complexes relevant to catalysis, organic synthesis, and biochemistry. In contrast, the development of SAPT for general open‐shell complexes is still a work in progress. In the last decade, new developments from several research groups, including the author's, have greatly enhanced the capabilities of SAPT. The new and emerging approaches are designed to make SAPT more widely applicable (including interactions involving multireference systems, complexes in arbitrary spin states, and intramolecular noncovalent interactions), more accurate (enhanced description of intramolecular correlation, a better account of exchange effects, relativistic SAPT, and explicitly correlated SAPT), and more efficient (enhanced density‐fitted implementations, linear‐scaling variants, empirical dispersion, and an implementation on graphics processing units). The new developments open up avenues for SAPT applications to an unprecedented variety of weakly interacting complexes.This article is categorized under: Electronic Structure Theory &gt; Ab Initio Electronic Structure Methods Electronic Structure Theory &gt; Density Functional Theory Molecular and Statistical Mechanics &gt; Molecular Interactions

Insights into Non‐Ideal Behavior of Double Salt Ionic Liquids with Common Cation: Volumetric Behaviour, Molecular Dynamics Simulations and NMR Experiments

AbstractThe designer concept of ionic liquid (ILs) allows combination of different types of cation with anion to manipulate desire sets of physico‐chemical properties. The additional degree of freedom to improve these properties is addition of second IL, i. e. mixture of two pure ILs, known as “Double Salt Ionic Liquids (DSILs)”. Depending on variation in physico chemical properties, DSILs could be ideal or non‐ideal solution. The present study was explores non‐ideal behaviour of three novel combination of imidazolium based DSILs using physico‐chemical properties. The proposed DSILs are homogeneous mixtures of two pure ILs with common cation and two different anions: ethylsulfate and bis(trifluoromethylsulfonyl)imide / trifluoromethanesulfonate / thiocyanate. The densities, ρ and speeds of sound, u for proposed DSILs were determined at different temperatures. The excess molar volumes VmE and excess molar isentropic compressibilities KS,mE were calculated and discussed in view of chemical structures of pure ILs, nature of anions and type of interaction between ions. The VmE were found to be positive for all cases, whereas positive or negative KS,mE were observed for studied DSILs. The behaviour of DSILs was explained by molecular dynamics simulations in terms of interaction energies and hydrogen bonds between components of DSILs as well as 1H NMR results. The results indicate random distribution of anions around imidazolium cation and structural changes during formulation of DSILs.

Effect of dissolved organic matter on adsorption of sediments to Oxytetracycline: An insight from zeta potential and DLVO theory.

To reveal the adsorption mechanism of sediment to antibiotics with the presence of dissolved organic matter (DOM), batch experiments were carried out by oxytetracycline (OTC) on sediments with decayed plants (PDOM) and composted chicken manure (MDOM), and the zeta potential in the system before and after adsorption was measured. Results showed that the PDOM promoted the adsorption process, while the MDOM inhibited the adsorption. Adding PDOM, the change of zeta potential (Δζ) increased by 40.08% for first terrace sediments (FT) and 63.98% for riverbed sediments (RB), respectively; meanwhile, MDOM decreased by 20.04% for FT and 28.39% for RB, respectively. The results of kinetic fitting models of replacing the adsorption amount with Δζ were consistent with the initial. It indicated that there was a positive correlation between the adsorption amount and Δζ, and the zeta potential can be used to quickly judge the degree of adsorption process. The Derjaguin-Landau-Verwey-Overbeek (DLVO) theory describes the interactions of sediment particles. In terms of adsorption amount, zeta potential (absolute value) and total interaction energy all followed the order: RB > FT, RB-PDOM > FT-PDOM, and RB-MDOM > FT-MDOM. The more negative the zeta potential is, the better the dispersion of the particles is. Stronger repulsion is more conducive to adsorbing positively charged OTC. The site energy distribution theory further explained that the distribution of adsorption site in the various states of sediments increased while adding the PDOM and decreased while adding the MDOM.

HFLD: A Nonempirical London Dispersion-Corrected Hartree-Fock Method for the Quantification and Analysis of Noncovalent Interaction Energies of Large Molecular Systems †.

A nonempirical quantum mechanical method for the efficient and accurate quantification and analysis of intermolecular interactions is presented and tested on existing benchmark sets. The leading idea here is to focus on the intermolecular part of the correlation energy that contains the all-important London dispersion (LD) interaction. To keep the cost of the method low, essentially at the level of a Hartree-Fock (HF) calculation, the intramolecular part of the correlation energy is neglected. We also neglect the nondispersive parts of the intermolecular correlation energy. This scheme that we denote as Hartree-Fock plus London dispersion (HFLD) can be readily realized on the basis of the recently reported multilevel implementation of the domain-based local pair natural orbital coupled-cluster (DLPNO-CC) theory in conjunction with the well-established local energy decomposition (LED) analysis. The accuracy and efficiency of the HFLD method are evaluated on rare gas dimers, on the S66 and L7 benchmark sets of noncovalent interactions, and on an additional set (LP14) consisting of bulky Lewis pairs held together by intermolecular interactions of various strengths, with interaction energies ranging from -8 to -107 kcal/mol. It is first shown that the LD energy calculated with this approach is essentially identical to that obtained from the full DLPNO-CCSD(T)/LED calculation, with a mean absolute error of 0.2 kcal/mol on the S66 benchmark set. Moreover, in terms of the overall interaction energies, the HFLD method shows an efficiency that is comparable to that of the HF method, while retaining an accuracy between that of the DLPNO-CCSD and DLPNO-CCSD(T) schemes. Since the underlying DLPNO-CCSD method is linear scaling with respect to the system size, the HFLD approach also does not lead to new bottlenecks for large systems. As an illustrative example of its efficiency, the HFLD scheme was applied to the interaction between the substrate and the residues in the active site of the cyclohexanone monooxygenase enzyme. The excellent cost/performance ratio indicates that the HFLD method opens new avenues for the accurate calculation and analysis of noncovalent interaction energies in large molecular systems.

Explicitly Correlated Dispersion and Exchange Dispersion Energies in Symmetry-Adapted Perturbation Theory.

The individual interaction energy terms in symmetry-adapted perturbation theory (SAPT) not only have different physical interpretations but also converge to their complete basis set (CBS) limit values at quite different rates. Dispersion energy is notoriously the slowest converging interaction energy contribution, and exchange dispersion energy, while smaller in absolute value, converges just as poorly in relative terms. To speed up the basis set convergence of the lowest-order SAPT dispersion and exchange dispersion energies, we borrow the techniques from explicitly correlated (F12) electronic structure theory and develop practical expressions for the closed-shell Edisp(20)-F12 and Eexch-disp(20)-F12 contributions. While the latter term has been derived and implemented for the first time, the former correction was recently proposed by Przybytek [ J. Chem. Theory Comput. 2018 , 14 , 5105 - 5117 ] using an Ansatz with a full optimization of the explicitly correlated amplitudes. In addition to reimplementing the fully optimized variant of Edisp(20)-F12, we propose three approximate Ansätze that substantially improve the scaling of the method and at the same time avoid the numerical instabilities of the unrestricted optimization. The performance of all four resulting flavors of Edisp(20)-F12 and Eexch-disp(20)-F12 is first tested on helium, neon, argon, water, and methane dimers, with orbital and auxiliary basis sets up to aug-cc-pV5Z and aug-cc-pV5Z-RI, respectively. The double- and triple-ζ basis set calculations are then extended to the entire A24 database of noncovalent interaction energies and compared with CBS estimates for Edisp(20) and Eexch-disp(20) computed using conventional SAPT with basis sets up to aug-cc-pV6Z with midbond functions. It is shown that the F12 treatment is highly successful in improving the basis set convergence of the SAPT terms, with the F12 calculations in an X-tuple ζ basis about as accurate as conventional calculations in bases with cardinal numbers (X + 2) for Edisp(20) and either (X + 1) or (X + 2) for Eexch-disp(20). While the full amplitude optimization affords the highest accuracy for both corrections, the much simpler and numerically stable optimized diagonal Ansatz is a very close second. We have also tested the performance of the simple F12 correction based on the second-order Møller-Plesset perturbation theory, SAPT-F12(MP2) [ Frey , J. A. ; Chem. Rev. 2016 , 116 , 5614 - 5641 ] and observed that it is also quite successful in speeding up the basis set convergence of conventional Edisp(20) + Eexch-disp(20), albeit with some outliers.

The electrostatic core of the outer membrane protein X from E. coli

Electrostatic side chain contacts can contribute substantial interaction energy terms to the stability of proteins. The impact of electrostatic interactions on the structure and architecture of outer membrane proteins is however not well studied compared to soluble proteins. Here, we report the results of a systematic study of all charged side chains of the E. coli outer membrane protein X (OmpX). The data identify three distinct salt-bridge clusters in the core of OmpX that contribute significantly to protein stability in dodecylphosphocholine detergent micelles. The three clusters form an “electrostatic core” of the membrane protein OmpX, corresponding in its architectural role to the hydrophobic core of soluble proteins. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.

Study of interactions energies between residues of the active site of Hsp90 and the geldanamycin analogues using Quantum Mechanics/Molecular Mechanics (QM/MM) methods

Background: (Hsp90) 90KDa heat shock proteins are molecular chaperone involved in process of cellular oncogenesis, hence its marked importance as a therapeutic target. An inhibitor of Hsp90 chaperone activity is the geldanamycin, a thready compound that has the power to bind to the binding of ATP in the N-terminal of Hsp90 domain site, however this reported in clinical trials hepatotoxic damage, which I pitting to its disuse. On the other hand, taking advantage that the geldanamycin joins successfully Hsp90, efforts have focused on the search for similar that they have the same or better effect and both exhibited lower effects than its predecessor, as it has been the case with the similar 17-AAG and 17-DMAG. Methods: In order to know the chemical factors influencing the growth or decay of the biological activity of such compounds have been evaluated different computational techniques such as docking and 3DQSAR, however it has not been considered in a quantitative way what happens within the active site represented in terms of interaction energy, as it has been evaluated in this work. Results: To evaluate interaction energies found that the Lys58 is essential for the union of the analogs to the active site of Hsp90, and that the activity of these will depend on if these have on the C-11 position of the macrocycle a group of small and at the same time attractor of electrons, as it is reflected with the series C-11 hydroxy and methoxy C-11. Conclusion: Theses outcomes were supported with Quantum Similarity and reactivity indices using the Density Funtional Theory in order to understand the non-covalent stabilization in the active site for theses compounds.

Statistical Distributions of Physical Characteristics of Molecules with Casimir Force in the Transfer of Admixtures in Nanoscale Volumes

In this work, we study the statistical properties of molecular systems of admixtures, which are placed in nanoscale volumes like cube or parallelepiped with impermeable surfaces on their walls. We simulate interactions of free motion of molecules of admixtures with molecules on the surfaces of walls: we modeled them in the form of atomic structure grid using SiO2 as a material. This type of substance allows us to take into account the manifestation of one of the important quantum effects: Casimir force. We used its general expression in terms of interaction energy, with the assumption of dependence on distance and projected area between atoms of the wall and atoms of the admixtures. To model surface roughness we used uniform random distribution function for surface heights (z coordinates). The results of computational experiments can be used to estimate the distribution of chemical bond lengths, valence, and dihedral angles lengths deviations in polyatomic molecules. Our model can be useful to determine the stable configuration properties of the system, to solve practical problems in the conditions of physical limitations of nanoscale devices, filtration of admixtures in highly dispersed systems, in the development of mechanisms in structures that have parallel plates or membranes, including porous structures. Also we compute radial distribution function for multicomponent admixtures including atoms of inert gases, water vapor, and ethanol. And we took into account the influence of Casimir force on admixtures for cube and parallelepiped type volumes. In results, we showed distributions of deviations of lengths from their equilibrium values.

Two- and three-body, and relaxation energy terms in water clusters: Application of the hierarchical BSSE corrected decomposition scheme

A detailed analysis of the two- and three-body interaction energy components in water clusters containing up to 30 water molecules is performed at the M05-2X/6-311G** level of theory, using the “hierarchical” basis set superposition error (BSSE)-corrected energy decomposition scheme, VMFC(3), of Valiron and Mayer. We showed that the average BSSE-corrected two- and three-body interaction energy terms are about 74 to 80 and 20 to 26%, respectively, of the total BSSE-corrected interaction energy for all investigated clusters. It was observed that the three-body interaction energy component is significantly negative/positive if there are two H-bonds and one attraction/repulsion interaction energy in the corresponding trimer, respectively. Our calculations also revealed that the deformation energy of water molecules is dependent on their H-bonded environment. To assess the accuracy of the calculations presented here, benchmark calculations were carried out at the high, LNO-CCSD(T)/CBS, level of theory.

In silico site-directed mutagenesis of neutralizing mAb 4C4 and analysis of its interaction with G-H loop of VP1 to explore its therapeutic applications against FMD

Investigating the behaviour of bio-molecules through computational mutagenesis is gaining interest to facilitate the development of new therapeutic solutions for infectious diseases. The antigenetically variant genotypes of foot and mouth disease virus (FMDV) and their subsequent infections are challenging to tackle with traditional vaccination. In such scenario, neutralizing antibodies might provide an alternate solution to manage the FMDV infection. Thus, we have analysed the interaction of the mAb 4C4 with a synthetic G-H loop of FMDV-VP1 through in silico mutagenesis and molecular modelling. Initially, a set of 25,434 mutants were designed and the mutants having better energetic stability than 4C4 were clustered based on sequence identity. The best mutant representing each cluster was selected and evaluated for its binding affinity with the antigen in terms of docking scores, interaction energy and binding energy. Six mutants have confirmed better binding affinities towards the antigen than 4C4. Further, interaction of these mutants with the natural G-H loop that is bound to mAb SD6 was also evaluated. One 4C4 variant having mutations at the positions 2034(N→L), 2096(N→C), 2098(D→Y), 2532(T→K) and 2599(A→G) has revealed better binding affinities towards both the synthetic and natural G-H loops than 4C4 and SD6, respectively. A molecular dynamic simulation for 50 ns was conducted for mutant and wild-type antibody structures which supported the pre-simulation results. Therefore, these mutations on mAb 4C4 are believed to provide a better antibody-based therapeutic option for FMD.Communicated by Ramaswamy H. Sarma

A density functional study on synthetic polymer–amino acid interaction

Interaction of four synthetic polymers viz., poly- $$\upvarepsilon $$ -caprolactone (PCL), polyglycolide (PGA), polylactic acid (PLA) and Poly(lactic-co-glycolic) acid (PLGA) used as protein delivery vectors with a few amino acids have been studied by using density functional theory. Association geometries of polymer–amino acid adduct are modelled in a vacuum and in four solvents. Nature and strength of interaction have been analyzed in terms of interaction energy and thermochemical parameters of adducts as well as vibrational frequency shifts upon adduct formation. Results suggest comprehensive stability of adducts in the gas phase. Progressive destabilization of adducts with increasing polarity of solvent is observed. Redshifts in vibrational frequencies of X-H bonds ( $$\hbox {X}= \hbox {H}$$ donor in hydrogen bonding) upon adduct formation are noticed. The study asserts the potentiality of the considered synthetic polymers as an amino acid carrier. Synopsis Synthetic polymers can form stable complexes with amino acids and are potential vectors for protein delivery.

Anticancer Agent Edelfosine Exhibits a High Affinity for Cholesterol and Disorganizes Liquid-Ordered Membrane Structures.

Edelfosine is an anticancer drug with an asymmetric structure because, being a derivative of glycerol, it possesses two hydrophobic substituents of very different lengths. We showed that edelfosine destabilizes liquid-ordered membranes formed by either 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine, sphingomyelin (SM), and cholesterol (1:1:1 molar ratio) or SM and cholesterol (2:1 molar ratio). This was observed by differential scanning calorimetry in which phase transition arises from either of these membrane systems after the addition of edelfosine. The alteration in the liquid-ordered domains was characterized by using a small-angle X-ray diffraction that revealed the formation of gel phases as a consequence of the addition of edelfosine at low temperatures and by a wide-angle X-ray diffraction that confirmed changes in the membranes, indicating the formation of these gel phases. The increase in phase transition derived by the edelfosine addition was further confirmed by Fourier-transform infrared spectroscopy. The effect of edelfosine was compared with that of structurally analogue lipids: platelet-activating factor and 1-palmitoyl-2-acetyl- sn-glycero-3-phosphocholine, which also have the capacity of destabilizing liquid-ordered domains, although they are less potent than edelfosine for this activity, and lysophosphatidylcholine, which lacks this capacity. It was concluded that edelfosine may be associated with cholesterol favorably competing with sphingomyelin, and that this sets sphingomyelin free to undergo a phase transition. Finally, the experimental observations can be described by molecular dynamics calculations in terms of intermolecular interaction energies in phospholipid-cholesterol membranes. Higher interaction energies between asymmetric phospholipids and cholesterol than between sphingomyelin and cholesterol were obtained. These results are interesting because they biophysically characterize one of the main molecular mechanisms to trigger apoptosis of the cancer cells.

Phase dilemma in natural orbital functional theory from the N-representability perspective

Any rigorous approach to first-order reduced density (1RDM) matrix functional theory faces the phase dilemma, that is, having to deal with a large number of possible combinations of signs in terms of the electron-electron interaction energy. This problem was discovered by reducing a ground-state energy generated from an approximate N-particle wavefunction into a functional of the 1RDM, known as the top-down method. Here, we show that the phase dilemma also appears in the bottom-up method, in which the functional E[1RDM] is generated by progressive inclusion of N-representability conditions on the reconstructed two-particle reduced density matrix. It is shown that an adequate choice of signs is essential to accurately describe model systems with strong non-dynamic (static) electron correlation, specifically, the one-dimensional Hubbard model with periodic boundary conditions and hydrogen rings. For the latter, the Piris natural orbital functional 7 (PNOF7), with phases equal to -1 for the inter-pair energy terms containing the exchange-time-inversion integrals, agrees with exact diagonalization results.

How many hydrogen molecules (H2) can be stored in a clathrate hydrate cage?

Storage of hydrogen gas (H2) in clathrate hydrate at ambient conditions has many potential applications, such as clean energy, environment and ecology protection, submarine, and space rocket. In this research article, the hydrogen gas hydrate is studied by using higher level quantum chemical methods such as MP2, CCSD, and CCSD(T). The interaction energy terms in the hydrate cage and the guest molecular cluster are calculated and analyzed. Some useful conclusion points are summarized as follows: (1) The capacity and stability of the hydrogen molecular clusters in hydrate cages are determined by three energy terms: the hydrogen bond energy (ΔEH-b) of water molecules, the interaction energy (ΔEcage-clst) between the hydrate cage and the guest molecular cluster, and the interaction energy (ΔEclst) of the guest molecular cluster in the cage. (2) The energy term ΔEclst of the hydrogen molecular cluster in the hydrate cage is the only repulsive energy contribution (positive values) to the stability of the gas-hydrate cages, which increases with the number of hydrogen molecules and decreases with the size of the cage volume. (3) The strong hydrogen bond energy ΔEH-b remains constant in a broad range of 2.74 Å to 2.86 Å, in which the change in ΔEH-b is less than ±5 kJmol−1. (4) Capacity of hydrogen molecules in the hydrate cage depends on the volume of the hydrate cages. When the side length RO-O is 2.82 Å, at most 4 hydrogen molecules can be stored in the 512 cage. In large hydrate cages (51262 and 51264), more hydrogen molecules can be stored.

Theoretical Investigation on Direct Vinylogous Aldol Reaction of Isatin Catalyzed by Chiral-N, N'-dioxide Sc(III) Complex

The mechanism and enantio- as well as diastereo-selectivity of asymmetric direct aldol reaction of isatin with α-angelica lactone catalyzed by chiral N, N'-dioxide-Sc(OTf)3 were studied at the B3LYP(SMD, THF)/6-31G(d,p) level. The calculations indicated that the reaction occurred along stepwise mechanism, that is, CC bond formation followed by H-transfer from α-angelica lactone to carbonyl group of isatin. The H-transfer step was predicted to be the rate-determining step(RDS), with the energy barrier of 23.3 ∼ 26.2 kcal mol−1 for four stereoisomeric products. The ortho-isopropyl groups of amide in ligand blocked the reacting site from re-face of isatin and induced the re-face of α-angelica lactone to approach to the si-face of isatin, leading to the predominant product with 3S, 2′S-configuration. In this asymmetric catalysis, the interaction energy term (ΔEint), especially stabilizing orbital energy (ΔEoi) and electrostatic energy (ΔVelstat), were the main contributors to the enantioselectivity of the reaction, while the activation strain energy (ΔEstrain) of α-angelica substrate enhanced the diastereodifferentiation of the two competing pathways, contributing to high diastereomeric ratio (d.r.). The turnover frequency (TOF) along the favorable si-face pathway was predicted to be 2.76 × 10−21 s−1, with the rate constant of k(T) = 7.5 × 10−2 exp(-108390/RT) dm3 mol−1 s−1 over 258.15 K ∼ 358.15 K temperature range. These results provided explanation for the good reactivity as well as excellent asymmetric induction of chiral N, N'-dioxide-Sc(OTf)3 in direct aldol reaction of isatin.