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Supramolecular systems may be used to stabilize otherwise unstable isomers to find alternative synthetic pathways. It has been reported that cucurbit[8]uril can stabilize trans-I and trans-II Cu II cyclam, whereas trans-III is the only non-substituted trans Cu II cyclam diastereoisomer found outside of the host molecule experimentally. Quantum chemistry methods can provide valuable insight into the intermolecular interactions involved in these inclusion complexes. All five possible trans diastereoisomers of Cu II cyclam were studied within the host molecule to calculate the interaction energy and free energy of association for each complex. The relative free energies of the five free cyclams confirm that trans-I and trans-II are the most energetically accessible diastereoisomers from the initial trans-III starting point. Energy decomposition analysis was used to identify the attractive and repulsive interactions between cyclam and cucurbit[8]uril and showed that trans-II encounters repulsive forces almost three times greater than trans-I, which may explain the 7:3 ratio of trans-I to trans-II within cucurbit[8]uril that occurs experimentally. Optimized complex geometries with trans-III, IV, and V show that the cyclams protrude out of cucurbit[8]uril, whereas trans-I and trans-II become more encapsulated and elongate the host, suggesting that the position of the cyclam is extremely important when forming non-covalent interactions. Our results agree with the experimental findings and provide greater insight into why the most stable isolated cyclam diastereoisomer, trans-III, does not form a complex. [ABSTRACT FROM AUTHOR]

Accurate determination of intermolecular non-covalent-bonded or non-bonded interactions is the key to potentially useful molecular dynamics simulations of polymer systems. However, it is challenging to balance both the accuracy and computational cost in force field modelling. One of the main difficulties is properly representing the calculated energy data as a continuous force function. In this paper, we employ well-developed machine learning techniques to construct a general purpose intermolecular non-bonded interaction force field for organic polymers. The original ab initio dataset SOFG-31 was calculated by us and has been well documented, and here we use it as our training set. The CLIFF kernel type machine learning scheme is used for predicting the interaction energies of heterodimers selected from the SOFG-31 dataset. Our test results show that the overall errors are well below the chemical accuracy of about 1 kcal/mol, thus demonstrating the promising feasibility of machine learning techniques in force field modelling. [ABSTRACT FROM AUTHOR]

Benzothiazole derivatives were synthesized and their antidiabetic potential evaluated using α-glucosidase, α-amylase, non-enzymatic glycosylation of hemoglobin and advanced glycation end product inhibition assays. Compound 3l showed low IC values of 0.31, 0.98, 0.59 and 0.19 mM in α-amylase, α-glucosidase, non-enzymatic glycosylation of hemoglobin and AGE inhibition assays, respectively, and outperformed the standard acarbose. Enzyme kinetic studies revealed that it has a K of 0.39 and 1.5 mM for α-amylase and α-glucosidase, respectively. The non-bonded interactions of 3l with α-amylase (3OLD) and α-glucosidase (2ZE0) showed that it binds in the active site pocket and is surrounded by residues Asp197, Glu233, Asp300 in 3OLD and Asp199, Glu256, Asp326 in 2ZE0. [ABSTRACT FROM AUTHOR]

A long standing problem in normal mode analysis is identifying the right internal coordinates given only the cartesian coordinates, the masses of the atoms and the cartesian force constants without using any other additional chemical information. A possible solution is suggested here as drawing the normal modes obtained from the mass weighted cartesian force constant matrix and identifying the correct bonds and angles from the normal mode pictures. If chosen properly, the internal coordinates will have minimum mixing in the normal mode representation. This can in principle lead to an automation algorithm. A complete basis of internal coordinates is defined as the minimum number of valence internal coordinates that describe all the normal modes as completely as possible. It was shown in the literature that the relaxed force constants could be used as a measure of bond order in all atom-atom distance coordinates. Some of the bonded and non-bonded atom pairs can have similar values of the relaxed force constants and hence to use the relaxed force constant as a measure of bond order we need to separate the bonded pairs from the non-bonded ones. This needs extra chemical information of which pairs are bonded. The new definition of complete basis of non-redundant valence internal coordinates helps to identify the bonded pairs effectively without extra information. The hydrogen bonded water clusters (HO), n = 2-6, methane dimer and methane-water complex are used as examples to verify that the relaxed force constants of bonded pairs are indeed a measure of bond order. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

SUMMARY This paper analyses the buckling behaviour of single-walled and double-walled carbon nanotubes. The total potential of the atomic structure consists of the bonded energy and the non-bonded energy, both resulting from interatomic potentials, as well as the energy of external contributions. In particular, the influence of the in-layer and inter-layer non-bonded interactions is investigated. These non-bonded interactions are important to avoid the nanotubes from self-intersection or penetration and govern the morphology of the buckled tubes. The simulation model is based on a molecular statics approach embedded in the finite element framework. The search for equilibrium configurations of the structure leads to a non-linear system of equations, which is linearised and solved iteratively. Therefore, the model relies on the fully non-linear description of the interatomic potential and the atomic kinematics. Stability points of the loaded carbon nanotubes are detected by an accompanying eigenvalue analysis in combination with a bisection algorithm. By means of branch switching, the continuation of the non-linear load-deformation path in the postbuckling regime is enabled. With this framework, the buckling characteristics of carbon nanotubes in consequence of different loading conditions is studied. Results of numerical simulations are given for carbon nanotubes under torsion, axial compression and bending. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

For 12 acetylacetonates of the composition M(acac) ( n = 2, 3, or 4) and M(acac)(CH) (M is a metal) the total area ( S) of the faces of Voronoi-Dirichlet polyhedra (VDP) corresponding to all intermolecular contacts of one molecule in the crystal structure and the total volume of pyramids ( V), whose bases are formed of such faces and the vertices are occupied by the nuclei of atoms participating in intermolecular contacts, are determined. The key features of non-bonded interactions are considered. The existence of a linear dependence of the sublimation enthalpy of acetylacetonates on the S or V parameters of their molecular VDP is revealed. It is shown that the sublimation enthalpy of Ga(acac) requires the refinement and theoretically should be 124 kJ/mol. [ABSTRACT FROM AUTHOR]

Ab initio and density-functional theory (DFT) modeling have proven to be important tools in the determination of the properties and reactivity of selenium with respect to biological activity. In this review, we address recent applications of quantum chemistry in three areas of interest to selenium chemistry: theoretical 77Se chemical shifts, analysis of Se...N,O interactions important to redox chemistry and mechanistic determinations for selenoenzymes and small selenium molecules. High-performance computing and DFT have allowed for large-scale calculations of both the enzyme active site and solution-phase reactivity. The latter development is important for understanding the complex mechanisms of small molecule GPx mimics. Application of solvent-assisted proton exchange to the redox scavenging mechanism of PhSeH by our research group is highlighted. [ABSTRACT FROM AUTHOR]

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs. [ABSTRACT FROM AUTHOR]

We compare experimental melting curves of short heterogeneous DNA oligomers with theoretical curves derived from statistical mechanics. Partition functions are computed with the one-dimensional Peyrard-Bishop (PB) Hamiltonian, already used in the study of the melting of long DNA chains. Working with short chains we take into account, in the computations, not only the breaking of the interstrand hydrogen bonds, but also the complete dissociation of the double helix into separate single strands. Since this dissociation equilibrium is of general relevance, independent of the particular microscopic model, we give some details of its treatment. We discuss how the non bonded three-dimensional interactions, not explicitly considered in the one-dimensional PB model, are taken into account through the treatment of the dissociation equilibrium. We also evaluate the relevance of the dissociation as a function of the chain length. [ABSTRACT FROM AUTHOR]

This paper describes a (6-8) variant of the Lennard-Jones (6-12) potential,for computing the energy of non-bonded interactions in molecular mechanicscalculations, which combines the overall precision of the Buckingham (6-exp)potential with the computational efficiency of the standard Lennard-Jones(6-12) potential. There is also a note on the radius of convergence of thefull matrix Newton–Raphson optimization procedure. [ABSTRACT FROM AUTHOR]