The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses

The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-F_ax and C4-F_eq epimines presented here.     

Effects of substituting a OH group by a F atom in D-glucose. Ab initio and DFT analysis.

High-level ab initio and DFT methods up to MP2/6-311++G//B3LYP/6-31G and B3LYP/6-311++G//B3LYP/6-31G levels have been used to assess the relative energies of 17 different structures of D-glucose and 13 different structures of 4-deoxy-4-fluoro-D-glucose. The structures were confirmed to correspond to minima on the potential energy surface at the RHF/6-31G level. Solvation Model 5.4/AM1 was used to calculate the effects of aqueous solution. The substitution of a OH group by a F atom does not much change the shape and electrostatic potential around corresponding conformers, but in the gas phase it destabilizes the cooperative network of intramolecular hydrogen bonds. This destabilization mostly affects structures with a chain of intramolecular hydrogen bonds oriented counterclockwise, as fluorine is unable to donate a hydrogen bond and therefore causes a gap in the chain. In contrast, for clockwise-oriented networks of hydrogen bonds, the fluorine can act as an acceptor at the end of a chain of cooperative hydrogen bonds. A slightly higher energy of anomeric and exo-anomeric stabilization is another effect of substituting the fourth hydroxyl group by a fluorine atom in D-glucose, observed both in the gas phase and in aqueous solution. For this reason, the alpha anomers contribute more to the equilibrium population of structures of 4-deoxy-4-fluoro-D-glucose than D-glucose. In aqueous solution, both D-glucose and its 4-deoxy-4-fluoro analogue are present as a mixture of mainly three corresponding structures. This indicates that 4-deoxy-4-fluoro-D-glucose is a good substitute for D-glucose in terms of its biochemical and biological activity. Moreover, this suggests that, for molecules with limited conformational freedom, the substitution of a OH group by a F atom is very likely to lead to a potential new drug. In contrast, it had already been shown that, for conformationally labile aliphatic compounds, replacement of a hydroxyl by a fluorine increases conformational diversity, so the fluorine-containing aliphatic molecules were not likely to be an example of a successful drug design. On the other hand, this work shows that, among molecules with limited conformational freedom, such as cyclic compounds, one is very likely to find targets for a successful rational drug design.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Ring opening reaction of protonated polyfluorinated benzenes in the gas phase. A theoretical MNDO study

The MNDO calculations of protonated polyfluorobenzenes [Ph-F_n]H⁺ indicate the possibility of a relatively free migration of the hydrogen proton with energy barriers of 125–145 kJ mol^?1. At a higher degree of substitution (n) the protonation of the ipso carbon atom occupied by fluorine becomes energetically feasible, along with analogous migrations of fluorine, which, however, are energetically the most advantageous (ΔE_a ～ 230 kJ mol^?1). In addition to bridged fluoronium ions, relatively stable cyclic intermediates were also found, which make possible a rearrangement to the difluoromethylenecyclopentadienyl cation and thus the elimination of CF₂ observed in collision-induced dissociation mass spectra.     

Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue

The effects of modifying the electronic characteristics of nonpolar base analogues substituted at positions involved in stacking interactions between SL2 RNA and the U1A protein are described. A surprisingly large difference in the stability between complexes formed with base analogues that differ only in the position of substitution of a single fluorine atom is observed. The results of high-level ab initio calculations of the interactions between the nonpolar base analogue and the amino acid side chain correlate with the experimentally observed trends in complex stability, which suggests that changes in stacking interactions that result from varying the position and degree of fluorine substitution contribute to the effects of fluorine substitution on the stability of the U1A-SL2 RNA complex.     

Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical

The conformational potential energy surfaces for mono- and difluoromethyl formate have been determined by using a modified G2(MP2) level of calculations. The structures and vibrational frequencies for the conformers of mono- and difluoromethyl formate have been reported. The hydrogen abstraction reaction channels between these two formates and OH radicals have been studied at the same level of theory. Using the standard transition state theory and taking into account the effect of tunneling across the reaction barrier, we have estimated the rate constant for hydrogen abstraction by OH radical. The effect of successive fluorine substitution for methyl hydrogen on the conformational stability and on the hydrogen abstraction rate has been analyzed.     

Selective electrophilic monofluorination on rings of various sizes using elemental fluorine

Elemental fluorine substitutes tertiary unactivated hydrogens in an electrophilic mode. This unorthodox substitution depends on the atomic charge density, on the hydrogen atom and on the p-orbital contribution on the CH bond. This is demonstrated by reacting F₂ with tertiary CH bonds located on rings of various sizes, producing the corresponding tertiary fluorine derivatives.     

Rotational spectroscopy and molecular structure of 1,1,2-trifluoroethylene and the 1,1,2-trifluoroethylene-hydrogen fluoride complex

Fourier transform microwave rotational spectra in the 6-22 GHz region are obtained for the complex formed between 1,1,2-trifluoroethylene and hydrogen fluoride, including the normal isotopomer, the two singly substituted 13C species, and the complex obtained with DF. A unique planar structure for the complex is determined from a combined analysis of the rotational constants derived from the spectra and atomic positions obtained using Kraitchman [Am. J. Phys. 21, 17 (1953)] substitution coordinates. Consistent with this structure, no hyperfine splitting of rotational lines due to the nuclear quadrupole coupling interaction is observed for the D-containing species. Although the primary interaction in the complex is a hydrogen-fluorine hydrogen bond, as is the case for all previously studied Lewis acid-fluoroethylene complexes, the CF2CHF-HF complex adopts a distinctly different geometry in which both the primary and secondary interactions occur between the HF molecule and a F atom and a H atom, respectively, bonded to the same carbon of CF2CHF. The 2.020(41) A hydrogen bond has hydrogen fluoride as the donor and 1,1,2-trifluoroethylene as the acceptor and forms a 109.0(13) degrees C-F...H angle. The secondary interaction between the hydrogen fluoride F atom and the H atom geminal to the acceptor F atom causes the hydrogen bond to deviate 41.6(51) degrees from linearity. Structural comparisons with analogous complexes formed with mono- and difluorinated ethylenes suggest that the primary hydrogen bond strength and the fluoroethylene fluorine atom basicity both decrease with increasing fluorine substitution. In the course of this work, it was necessary to obtain additional rotational spectra for the 1,1,2-trifluroethylene monomer and to improve the precision of the values of the structural parameters for this molecule.     

Effects of Electronic Structure of Adjacent Carbon on the Strength of C─F⋯H─F Organofluorine Hydrogen Bonds

We investigate the effects of the electronic structure of carbon atom on the organofluorine hydrogen bonds, C─F⋯H─F. Our results show that we can modulate the strength of organofluorine hydrogen bonds by adjusting the volume of fluorine atom in C─F via changing the electronic structure of adjacent carbon atoms. Different with the conventional hydrogen bonds, we found that instead of carbon rehybridization and hyperconjugative effects, the magnitude of fluorine atomic volume plays important roles in determining the strength of the C─F⋯H─F organofluorine hydrogen bonds. The lone pair electrons at both the proximal and the vicinal carbon dramatically reinforce the strength of C─F⋯H─F organofluorine hydrogen bond with its interaction energy in the range of about 15–25 kcal/mol, that is, the carbanion-mediated organofluorine hydrogen bond could be very strong. Due to the high electronegativity of fluorine atom, it easily attracts the excess electron from the proximal and vicinal carbon, which results in the increase of its volume and negative charge. The enhanced volume of fluorine atom gives rise to the large polarization energy, and its enhanced negative charge favors the large electrostatic interaction, both of which substantially contribute to making the organofluorine hydrogen bonds strong. © 2019 Wiley Periodicals, Inc.     

When,in the context of drug design,can a fluorine atom successfully substitute a hydroxyl group?

In this article, we deal with the question of whether a fluorine atom can substitute a hydroxyl group in such a way that will lead to a compound showing a desired biologic activity, that is, a potential new drug. It is obvious that a fluorine atom differs from a hydroxyl group, as it cannot donate hydrogen bonds. However, it can accept them. Moreover, both fluorine and oxygen are of similar size and are the most electronegative elements. Therefore, a fluorine atom is thought to be a good substitute for a hydroxyl group. However, it was shown that for conformationally labile aliphatic compounds a replacement of a hydroxyl by a fluorine increases conformational diversity, so the fluorine‐containing aliphatic molecules are present in equilibrium at room temperature as a mixture of several different conformers. In contrast, for cyclic compounds the substitution of an OH group by an F atom does not much change shape and electrostatic potential around corresponding conformers. Moreover, these compounds are present in equilibrium at room temperature in aqueous solution as a mixture of the same most favored structures. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Reductive Transformations of Organofluorine Compounds: III. Hydrodefluorination of Perfluoroalkylbenzenes Effected by Zn(Cu). The Unusual Behavior of Compounds Containing Perfluorinated tert-Butyl Group

Perfluoroalkylbenzenes under a treatment of a system Zn(Cu)-DMF-H₂O-electrolyte give rise in high yield to products of fluorine substitution by hydrogen in position 4. In perfluoro-tert-butylbenzene are substituted by hydrogen the fluorine atoms in positions 2 and 4; here the DMF-water ratio affects the regioselectivity of the process. In the perfluoro-4-tert-butyltoluene is mainly substituted the fluorine in the ortho-position to the C(CF₃)₃ group.     

Influence of the spatial position of a trifluoromethyl group on the 13C chemical shifts in the cyclohexane series

The influence of the introduction of a trifluoromethyl group on the 13C chemical shifts in cyclohexane was examined. The two main effects observed are located at the alpha and gamma positions relative to the carbon bearing the fluorine atoms. By comparison of the collected data it was possible to calculate the increments corresponding to the substitution of a hydrogen atom by a CF3 group at axial or equatorial positions on the cyclohexane ring.     

Association of Haloforms in Condensed and Gas Phases. Ir Spectroscopy and Dft Calculations

Fourier-transform infrared (FTIR) spectra are recorded for the haloforms of fluorine, chlorine, and bromine atoms in gas and liquid phases, as well as for their low-temperature films at 20–200 K. The molecules of these compounds are shown to be connected by hydrogen bonds associated with the transfer of a hydrogen atom. According to ab initio DFT calculations, chloroform demonstrates two types of associated structures, one with the chlorine atom and the other with the central carbon atom binding as the proton acceptor in the intermolecular interaction. At the same time, calculations predict only one form of bonding for two other haloforms, namely, between the hydrogen atom and the fluorine atom for fluoroform, and between the hydrogen atom and the carbon atom for bromoform.     

Real-time study of the adiabatic energy loss in an atomic collision with a metal cluster

Gas-phase hydrogen atoms are accelerated towards metallic surfaces in their vicinity. As it approaches the surface, the velocity of an atom increases and this motion excites the metallic electrons, causing energy loss to the atom. This dissipative dynamics is frequently described as atomic motion under friction, where the friction coefficient is obtained from ab initio calculations assuming a weak interaction and slow atom. This paper tests the aforementioned approach by comparing to a real-time Ehrenfest molecular dynamics simulation of such a process. The electrons are treated realistically using standard approximations to time-dependent density functional theory. We find indeed that the electronic excitations produce a friction-like force on the atom. However, the friction coefficient strongly depends on the direction of the motion of the atom: it is large when the atom is moving towards the cluster and much smaller when the atom is moving away. It is concluded that a revision of the model for energy dissipation at metallic surfaces, at least for clusters, may be necessary.     

THEORETICAL STUDIES ON THE SUBSTITUTION EFFECT OF FLUORINE ON ETHANE

<正> The substitution effect of fluorine on ethane has been investigated by means of studying the properties of the charge distribution at the bond critical points with the theory of atoms in molecule.It is found that the major substitution effects of fluorine atom are positive a inductive and polarity effect.At the same time,fluorine atom partially provides π electrons to other chemical bonds by means of hy-perconjugation in molecules with two fluorine atoms and one or two carbon atoms in the same plane,and these effects are reflected in the quantity of bond ellipticity,Laplacian and the charge density of charge distribution at the bond critical points.The substitution of hydrogen by fluorine in ethane strengthens all the bonds in substituted ethanes.Other effects originating from the substitution of hydrogen by fluorine have also been discussed.     

A further test of the shape and anisotropy of the F---H2 interaction potential

A recently proposed anisotropic potential model for the interaction of a fluorine atom with a hydrogen molecule treated as a rigid rotor analysed by carrying out exact quantum calculations of elastic and rotationally inelastic differential cross sections for comparison with previoully reported F---H₂ and newly measured F---D₂ state selected measurements. The sensitivity of the cross sections to changes of the potential anisotropy and to isotopic substitution is examined. The results provide specific indications on the features of the best potential energy surface in terms of its average ‘size’ and its most likely anisotropy responsible for inelastic rotational excitations occuring at collision energies of about 85 meV.     

Thiourea-Catalyzed C−F Bond Activation: Amination of Benzylic Fluorides

We describe the first thiourea-catalyzed C−F bond activation. The use of a thiourea catalyst and Ti(OiPr)₄ as a fluoride scavenger allows the amination of benzylic fluorides to proceed in moderate to excellent yields. Preliminary results with S- and O-based nucleophiles are also presented. DFT calculations reveal the importance of hydrogen bonds between the catalyst and the fluorine atom of the substrate to lower the activation energy during the transition state.     

Conformational analysis of cis-2-halocyclohexanols; solvent effects by NMR and theoretical calculations

Conformational problems often involve very small energy differences, even low as 0.5 kcal mol(-1). This accuracy can be achieved by theoretical methods in the gas phase with the appropriate accounting of electron correlation. The solution behavior, on the other hand, comprises a much greater challenge. In this study, we conduct and analysis for cis-2-fluoro-, cis-2-chloro-, and cis-2-bromocyclohexanol using low temperature NMR experiments and theoretical calculations (DFT, perturbation theory, and classical molecular dynamics simulations). In the experimental part, the conformers' populations were measured at 193 K in CD(2)Cl(2), acetone-d(6), and methanol-d(4) solutions; the preferred conformer has the hydroxyl group in the equatorial and the halogen in the axial position (ea), and its population stays at about 60-70%, no matter the solvent or the halogen. Theoretical calculations, on the other hand, put the ae conformer at a lower energy in the gas phase (MP2/6-311++G(3df,2p)). Moreover, the theoretical calculations predict a markedly increase in the conformational energy on going from fluorine to bromine, which is not observed experimentally. The solvation models IEF-PCM and C-PCM were tested with two different approaches for defining the atomic radii used to build the molecular cavity, from which it was found that only with explicit consideration of hydrogens can the conformational preference be properly described. Molecular dynamic simulations in combination with ab initio calculations showed that the ea conformer is slightly favored by hydrogen bonding.     

Substitution effect on the intermolecular halogen and hydrogen bonds of the σ‐bonded fluorinated pyridine···XY/HX complexes (XY = F2, Cl2, ClF; HX = HF,HCl)

Optimal structures, electronic and thermodynamic properties of the title complexes are presented. The stability of the hydrogen bonded systems is enhanced by the increasing dipole moments whereas in the halogen bonded systems it is also affected by the atom size in the diatomics. The consecutive addition of fluorine atoms to the pyridine moiety results in the decrease of the interaction energy for both types of the investigated bonds. The substitution on the meta sites in pyridine leads to more stable complexes than the substitution in the ortho position. The role of substitution on electric polarization and electrostatic forces is estimated by the symmetry‐adapted perturbation theory energy decomposition. The predicted Gibbs free energies of the complexes of mono fluorinated pyridines with HCl, HF, and ClF are from ?12 to ?22 kJ mol^?1 at 200 K. The possible experimental identification of the complexes with respect to the vibrational modes is discussed. © 2014 Wiley Periodicals, Inc.