: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Halogen bonding has been known in material science for decades, but until recently, halogen bonds in protein–ligand interactions were largely the result of serendipitous discovery rather than rational design. In this Perspective, we provide insights into the phenomenon of halogen bonding, with special focus on its role in drug discovery. We summarize the theoretical background defining its strength and directionality, provide a systematic analysis of its occurrence and interaction geometries in protein–ligand complexes, and give recent examples where halogen bonding has been successfully harnessed for lead identification and optimization. In light of these data, we discuss the potential and limitations of exploiting halogen bonds for molecular recognition and rational drug design.

Principles and applications of halogen bonding in medicinal chemistry and chemical biology.

The research on 1,2,3-triazoles has been lively and ever-growing since its stimulation by the advent of click chemistry The attractiveness of 1H-1,2,3-triazoles and their derivatives originates from their unique combination of facile accessibility via click chemistry and truly diverse supramolecular interactions, which enabled myriads of applications in supramolecular and coordination chemistry The nitrogen-rich triazole features a highly polarized carbon atom allowing the complexation of anions by hydrogen and halogen bonding or, in the case of the triazolium salts, via charge-assisted hydrogen and halogen bonds On the other hand, the triazole offers several N-coordination modes including coordination via anionic and cationic nitrogen donors of triazolate and triazolium ions, respectively After CH-deprotonation of the triazole and the triazolium, powerful carbanionic and mesoionic carbene donors, respectively, are available The latter coordination mode even features non-innocent ligand behavior Moreover, these supramolecular interactions can be combined, eg, in ion-pair recognition, preorganization by intramolecular hydrogen bond donation and acceptance, and in bimetallic complexes Ultimately, by clicking two building blocks into place, the triazole emerges as a most versatile functional unit allowing very successful applications, eg, in anion recognition, catalysis, and photochemistry, thus going far beyond the original purpose of click chemistry It is the intention of this review to provide a detailed analysis of the various supramolecular interactions of triazoles in comparison to established functional units, which may serve as guidelines for further applications

Beyond click chemistry - supramolecular interactions of 1,2,3-triazoles.

Halogen bonding is a noncovalent interaction that is receiving rapidly increasing attention because of its significance in biological systems and its importance in the design of new materials in a variety of areas, for example, electronics, nonlinear optical activity, and pharmaceuticals. The interactions can be understood in terms of electrostatics/polarization and dispersion; they involve a region of positive electrostatic potential on a covalently bonded halogen and a negative site, such as the lone pair of a Lewis base. The positive potential, labeled a σ hole, is on the extension of the covalent bond to the halogen, which accounts for the characteristic near-linearity of halogen bonding. In many instances, the lateral sides of the halogen have negative electrostatic potentials, allowing it to also interact favorably with positive sites. In this discussion, after looking at some of the experimental observations of halogen bonding, we address the origins of σ holes, the factors that govern the magnitudes of their electrostatic potentials, and the properties of the resulting complexes with negative sites. The relationship of halogen and hydrogen bonding is examined. We also point out that σ-hole interactions are not limited to halogens, but can also involve covalently bonded atoms of Groups IV-VI. Examples of applications in biological/medicinal chemistry and in crystal engineering are mentioned, taking note that halogen bonding can be "tuned" to fit various requirements, that is, strength of interaction, steric factors, and so forth.

Halogen Bonding: An Interim Discussion

Although recognized in small molecules for quite some time, the implications of halogen bonding in biomolecular systems are only now coming to light. In this study, several systems of proteins in complex with halogenated ligands have been investigated by using a two-layer QM/MM ONIOM methodology. In all cases, the halogen−oxygen distances are shown to be much less than the van der Waals radius sums. Single-point energy calculations unveil that the interaction becomes comparable in magnitude to classical hydrogen bonding. Furthermore, we found that the strength of the interactions attenuates in the order H ≈ I > Br > Cl. These results agree well with the characteristics discovered within small model halogen-bonded systems. A detailed analysis of the interactions reveals that halogen bonding interactions are responsible for the different conformation of the molecules in the active site. This study would help to establish such interaction as a potential and effective tool in the context of drug design.

Halogen bonding--a novel interaction for rational drug design?

A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods.

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods

The Knoevenagel condensation of diethylmalonate and various aldehydes catalyzed by proline in a common ionic liquid was achieved. Mild reaction conditions, enhanced rates, improved yields, recyclability of ionic liquids containing proline, and reagents’ reactivity which is different from that in conventional organic solvents are the remarkable features observed in ionic liquids. The ionic liquid containing catalyst was recycled in four subsequent runs with no decrease in activity. In addition, the results of calculations with the Gaussian 98 suite of program are in good accordance with the experimental outcomes.

Synthetic and theoretical study on proline-catalyzed Knoevenagel condensation in ionic liquid

The binding of pefloxacin mesylate (PFLX) to bovine lactoferrin (BLf) and human serum albumin (HSA) in dilute aqueous solution was studied using fluorescence spectra and absorbance spectra. The binding constant K and the binding sites n were obtained by fluorescence quenching method. The binding distance r and energy-transfer efficiency E between pefloxacin mesylate and bovine lactoferrin as well as human serum albumin were also obtained according to the mechanism of Forster-type dipole-dipole nonradiative energy-transfer. The effects of pefloxacin mesylate on the conformations of bovine lactoferrin and human serum albumin were also analyzed using synchronous fluorescence spectroscopy.

Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin.

Polyethylene Glycol as a Nonionic Liquid Solvent for the Synthesis of N-Alkyl and N-Arylimides

The tautomers of thymine are systematically calculated using various methods. The order of the relative stability, dipole moment as well as solvent effect of the 13 isomers are investigated. The one-step transition process by proton transfer in gas phase and in solution (H2O or CH3OH), which acts as both proton donor and acceptor, are exhaustively studied, meanwhile, the internal rotation between two related isomers in the gas phase is also investigated. Furthermore, the energy barrier of each transition is calculated and the results show that both H2O and CH3OH could reduce the energy barrier. Comparisons between the activation energies of all the producing processes of each tautomer as well as temperature effect on the producing processes are made. The calculation results also indicated that the diketo is the most stable isomer both in gas phase and in solution, additionally, it is thermodynamically as well as dynamically favored.

Ji-Cai Fan

Papers

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods

Synthetic and theoretical study on proline-catalyzed Knoevenagel condensation in ionic liquid

Binding interactions of pefloxacin mesylate with bovine lactoferrin and human serum albumin.

Polyethylene Glycol as a Nonionic Liquid Solvent for the Synthesis of N-Alkyl and N-Arylimides

Systematic theoretical investigations on the tautomers of thymine in gas phase and solution