The use of minimal topological differences to inspire the design of novel tetrahydroisoquinoline analogues with antimalarial activity.

A quantitative structure-activity relationship (QSAR) study was conducted using nineteen previously synthesized, and tested 1-aryl-6-hydroxy-1,2,3,4-tetrahydroisoquinolines with proven in vitro activities against Plasmodium falciparum. In order to computationally design and screen potent antimalarial agents, these compounds with known biological activity ranging from 0.697 to 35.978 µM were geometry optimized at the B3LYP/6-311 + G(d,p) level of theory, using the Gaussian 09W software. To calculate the topological differences, the series of the nineteen compounds was superimposed and a hypermolecule obtained with s ¯ = 17 and 20 vertices. Other molecular descriptors were considered in order to build a highly predictive QSAR model. These include the minimal topological differences (MTD), LogP, two dimensional polarity surface area (TDPSA), dipole moment (µ), chemical hardness (η), electrophilicity (ω), potential energy (Ep), electrostatic energy (Eele) and number of rotatable bonds (NRB). By using a training set composed of 15 randomly selected compounds from this series, several QSAR equations were derived. The QSAR equations obtained were then used to attempt to predict the IC50 values of 4 remaining compounds in a test (or validation) set. Ten analogues were proposed by a fragment search of a fragment library containing the pharmacophore model of the active compounds contained in the training set. The most active proposed analogue showed a predicted activity within the lower micromolar range.

Interactions of Nucleic Acid Bases with Temozolomide. Stacked, Perpendicular, and Coplanar Heterodimers.

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson-Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a dominating attractive force, largest for the stacked structures, and smallest for the coplanar dimers.

Catalysis of the Aza-Diels-Alder Reaction by Hydrogen and Halogen Bonds.

The combination of H2C═NH and cis-1,3-butadiene to form a six-membered ring was examined by quantum calculations. The energy barrier for this reaction is substantially lowered by the introduction of an imidazolium catalyst with either a H or halogen (X) atom in the 2-position, which acts via a H or halogen bond to the N atom of the imine, respectively. X = I has the largest effect, and Cl the smallest; Br and H are roughly equivalent. The catalyst retards the formation of the incipient N-C bond from imine to diene while simultaneously accelerating the C-C bond formation. The energy of the π* LUMO of the imine is lowered by the catalyst, which thereby enhances charge transfer from the diene to the imine. Assessment of free energies suggests catalytic rate acceleration by as much as 4-6 orders of magnitude.

Comparison of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and NH3.

In addition to the standard halogen bond formed when NH3 approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X-C bond. MP2/aug-cc-pVDZ calculations indicate the latter geometry is favored for X = F, and the σ-hole structure is preferred for the heavier halogens. The π-hole structure is stabilized by charge transfer from the NH3 lone pair into the π*(CN) antibonding orbital, and is characterized by a bond path from the N of NH3 to the C atom of XCN, a form of tetrel bond. The most stable 2 : 1 NH3/XCN heterotrimer for X = F and Cl is cyclic and contains a tetrel bond augmented by a pair of NHN H-bonds. For X = Br and I, the favored trimer is noncyclic, stabilized by a tetrel and a halogen bond.

Interactions between Thiourea and Imines. Prelude to Catalysis.

The interaction between thiourea and a series of imines was examined via high-level ab initio calculations. For each imine, there is a set of stable complexes that represent minima on the potential energy surface. One type is characterized by a pair of symmetric NH···N hydrogen bonds (HBs), with both NH groups of thiourea approaching the imine N from above and below its molecular plane. Another geometry category combines a linear NH···N with a CH···S HB. A third, which is less stable, has the S approaching the imine's CH2 group, and a stacking arrangement is present in the fourth. Interaction energies vary from ∼2 kcal/mol to a maximum of 13.5 kcal/mol. The formation of the complex tends to elongate the C-N bond within the imine by as much as 0.004 Å, but there are certain dimers that cause a small contraction of this bond.

S···π Chalcogen Bonds between SF2 or SF4 and C-C Multiple Bonds.

SF2 and SF4 were each paired with a series of unsaturated hydrocarbons including ethene, ethyne, 1,3-butadiene, and benzene, in each case forming a chalcogen bond between the S atom and the carbon π-system. MP2 ab initio calculations reveal that the S atom is situated directly above one specific C═C bond, even when more than one are present. The binding energies range between 3.3 and 6.6 kcal/mol. SF2 engages in a stronger, and shorter, noncovalent bond than does SF4 for all systems with the exception of benzene, to which SF4 is more tightly bound. cis-Butadiene complexes contain the shortest chalcogen bond, even if not necessarily the strongest. The internal S-F covalent bonds elongate upon formation of each chalcogen bond. The molecules are held together largely by charge transfer forces, particularly from the C═C π-bonds to the σ*(SF) antibonding orbitals. In the case of SF2, a sulfur lone pair can transfer charge into the π* MOs of the alkene, a back-transfer which is more difficult for SF4.

Intramolecular S···O chalcogen bond as stabilizing factor in geometry of substituted phenyl-SF3 molecules.

Density functional methods are used to examine the geometries and energetics of molecules containing a phenyl ring joined to the trigonal bipyramidal SF3 framework. The phenyl ring has a strong preference for an equatorial position. This preference remains when one or two ether -CH2OCH3 groups are added to the phenyl ring, ortho to SF3, wherein an apical structure lies nearly 30 kcal/mol higher in energy. Whether equatorial or apical, the molecule is stabilized by a S···O chalcogen bond, sometimes augmented by CH···F or CH···O H-bonds. The strength of the intramolecular S···O bond is estimated to lie in the range between 3 and 6 kcal/mol. A secondary effect of the S···O chalcogen bond is elongation of the S-F bonds. Solvation of the molecule strengthens the S···O interaction. Addition of substituents to the phenyl ring has only modest effects upon the S···O bond strength. A strengthening arises when an electron-withdrawing substituent is placed ortho to the ether and meta to SF3, while electron-releasing species produce an opposite effect.

Chalcogen bonding between tetravalent SF4 and amines.

The N···S chalcogen bond between SF4 and a series of alkyl and arylamines is examined via ab initio calculations. This bond is a strong one, with a binding energy that varies from a minimum of 7 kcal/mol for NH3 to 14 kcal/mol for trimethylamine. Its strength derives in large measure from charge transfer from the N lone pair into the σ*(SF) antibonding orbitals involving the two equatorial F atoms, one of which is disposed directly opposite the N atom. Decomposition of the total interaction energy reveals that the induction energy constitutes more than half of the total attraction. The positive region of the molecular electrostatic potential of SF4 that lies directly opposite the equatorial F atoms is attracted to the N lone pair, but the magnitude of this negative region on each amine is a poor predictor of the binding energy. The shortness and strength of the N···S bond in the dimethylamine···SF4 complex suggest it may better be described as a weak covalent bond.