Molecular polarizability in the structural studies of halogenated pyrimidines

Bond and molecular polarizabilities of 2-amino-4,6-dichloropyrimidine and 2,4,6-trifluoropyrimidine have been evaluated by quantum mechanical δ-function potential model and molecular vibration methods. The longitudinal bond polarizabilities of CC, CCl and CF bonds confirm the earlier view that the 2,4 and 6 carbon atoms of the pyrimidine molecule are aliphatic in nature while the carbon in position five, being in the meta position to each of the nuclear nitrogens, has a certain degree of aromatic character. The results are discussed fully in comparison with X-ray structural data, and chemical reactions.     

Bond orders and atomic properties of the highly deformed halogenated fullerenes C60F18 and C60Cl30 derived from their charge densities

The experimental charge densities of the halogenated C(60) fullerenes C(60)F(18) and C(60)Cl(30) were determined from high-resolution X-ray data sets measured with conventional Mo(Kalpha) radiation at 20 K for C(60)Cl(30) and with synchrotron radiation at 92 K for the fluorine compound. Bond topological and atomic properties were analyzed by using Bader's AIM theory. For the different C--C bonds, which vary in lengths between 1.35 and 1.70 A bond orders n between n=2 and significantly below n=1 were calculated from the bond topological properties at the bond critical points (BCP's). The low bond orders are seen for 5/6 bonds with each contributing carbon carrying a halogen atom. By integration over Bader's zero flux basins in the electron density gradient vector field atomic properties were also obtained. In contrast to free C(60), in which all carbon atoms have a uniform volume of 11 A(3) and zero charge, atomic volumes vary roughly between 5 and 10 A(3) in the halogenated compounds. Almost zero atomic charges are also found in the Cl derivative but a charge separation up to +/-0.8 e exists between C and F in C(60)F(18) due to the higher fluorine electronegativity, which is also seen in the electrostatic potential for which the electronegativity difference between carbon and fluorine, and the addition to one hemisphere of the fullerene cage leads to a strong potential gradient along the C(60)F(18) molecule. From the summation over all atomic volumes it follows that the halogen addition does not only lead to a dramatic distortion of the C(60) cage but also to a significant shrinkage of its volume.     

The concept of bond order

A method for obtaining precise charge densities in defined regions of space from ab initio molecular wavefunctions is employed to place the concept of bond order on a firm theoretical footing. The bond orders obtained for carboncarbon bonds in a range of organic compounds are assessed: those for buta-1,3-diene confirm that it consists of essentially localised double and single bonds.     

Halogen bonding: a theoretical study based on atomic multipoles derived from quantum theory of atoms in molecules

Atomic multipole moments derived from quantum theory of atoms in molecules are used to study halogen bonds in dihalogens (with general formula YX, in which X refers to the halogen directly interacted with the Lewis base) and some molecules containing C–X group. Multipole expansion is used to calculate the electrostatic potential in a vicinity of halogen atom (which is involved in halogen bonding) in terms of atomic monopole, dipole, and quadrupole moments. In all the cases, the zz component of atomic traceless quadrupole moments (where z axis taken along Y–X or C–X bonds) of the halogens plays a stabilizing role in halogen bond formation. The effects of atomic monopole and dipole moments on the formation of a halogen bond in YX molecules depend on Y and X atoms. In Br₂ and Cl₂, the monopole moment of halogens is zero and has no contribution in electrostatic potential and hence in halogen bonding, while in ClBr, FBr, and FCl it is positive and therefore stabilize the halogen bonds. On the other hand, the negative sign of dipole moment of X in all the YX molecules weakens the corresponding halogen bonds. In the C–X-containing molecules, monopole and dipole moments of X atom are negative and consequently destabilize the halogen bonds. So, in these molecules the quadrupole moment of X atom is the only electrostatic term which strengthens the halogen bonds. In addition, we found good linear correlations between halogen bonds strength and electrostatic potentials calculated from multipole expansion.     

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.     

NMR and density functional studies of the stereoselective palladium catalyzed cyclocarbonylation of (1R,4R)-isolimonene

Carbonylation of (1R,4R)-isolimonene, catalyzed by [HPd(SnCl₃)(dppf)], involves the exo- and endo-carboncarbon double bonds to provide a cyclopentanone containing two new stereogenic centers with d.e. of 69%. It was shown that this diastereoselectivity arose from the two stereogenic centers of the substrate. Calculations carried out on the cyclization step show that the metal center of the palladium–acyl species coordinates the endocyclic double bond in the endo-position exclusively. The net charge distribution over the palladium center, the acyl carbon atom and the two carbon atoms of the CC bond determines the two nucleophilic attacks in this step.     

Topological analysis of the molecular charge density and impact sensitivy models of energetic molecules

Important explosives of practical use are composed of nitroaromatic molecules. In this work, we optimized geometries and calculated the electron density of 17 nitroaromatic molecules using the Density Functional Theory (DFT) method. From the DFT one-electron density matrix, we computed the molecular charge densities, thus the electron densities, which were then decomposed into electric multipoles located at the atomic sites of the molecules using the distributed multipole analysis (DMA). The multipoles, which have a direct chemical interpretation, were then used to analyze in details the ground state charge structure of the molecules and to seek for correlations between charge properties and sensitivity of the corresponding energetic material. The DMA multipole moments do not present large variations when the size of the Gaussian basis set is changed; the largest variations occurred in the range 10-15% for the dipole and quadrupole moments of oxygen atoms. The charges on the carbon atoms of the aromatic ring of each molecule become more positive when the number of nitro groups increases and saturate when there are five and six nitro groups. The magnitude and the direction of the dipole moments of the carbon atoms, indicators of site polarization, also depend on the nature of adjacent groups, with the largest dipole value being for C-H bonds. The total magnitude of the quadrupole moment of the aromatic ring carbon atoms indicates a decrease in the delocalized electron density due to an electron-withdrawing effect. Three models for sensitivity of the materials based on the DMA multipoles were proposed. Explosives with large delocalized electron densities in the aromatic ring of the component molecule, expressed by large quadrupole values on the ring carbon atoms, correspond to more insensitive materials. Furthermore, the charges on the nitro groups also influence the impact sensitivity.     

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.     

Theoretical studies on the substitution effect of fluorine on ethylene

The substitution effect of fluorine on ethylene is investigated by means of studyingthe properties of the charge distribution at the bond critical points with the theory of atomsin molecules.It is found that fluorine atom acts not only as a σ electron acceptor,but also asa π electron donor,and these double effects are reflected in the quantity of ellipticity,Lap-lacian and the charge density of charge distribution at the bond critical points.For C—C,C—Fbonds,the major axis of elliptical contours is perpendicular to the molecular plane,but forC—H bond,it is parallel to the molecular plane.Other effects originating from the substi-tution have also been discussed.     

Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.     

On the representation of molecular quadrupole moments in terms of atomic moments

The magnitude and algebraic sign of the molecular quadrupole moments of the homonuclear diatomic molecules N2, O2, F2, P2, S2 and Cl2 are analyzed by expressing them as a sum of the quadrupole moments of the free atoms and an induced molecular quadrupole due to bond formation. This induced molecular quadrupole is further analyzed in terms of in situ atomic dipole and quadrupole moments constructed following the electron partitioning method suggested by Hirshfeld. These in situ moments are interpreted in terms of the sigma and pi character of the chemical bonds and are compared with those predicted by the DMA method of Stone (The Theory of Intermolecular Forces; Clarendon: Oxford, 1996).     

Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders

We present a computational approach, using quantum Monte Carlo, that provides some insight into the effect of electron correlation on chemical bonding between individual pairs of atoms. Our approach rests upon a recently suggested relation between the bond order and charge fluctuations with respect to atomic domains. Within the present implementation we have taken a compromise between conceptual rigour and computational simplicity. In a first step atomic domains were obtained from Hartree-Fock (HF) densities, using Bader’s definition of atoms in molecules. These domains were used in a second step in quantum Monte Carlo calculations to determine bond orders for pairs of atoms. Correlation effects have been studied by comparison of HF bond orders with those obtained from pure diffusion quantum Monte Carlo calculations. We illustrate this concept for C–O and C–S bonds in different molecular environments. Our results suggest an approximate linear relation between bond order and bond length for these kinds of bonds.     

Geometric and electronic properties of endohedral Si @ C74

The generalized gradient approximation based on density functional theory is used to analyze the geometric and electronic properties of Si @ C(74). It is found that among the five possible optimized geometries of Si @ C(74), the most favorable endohedral site of Si atom is under the center of a pentagon ring on the sigma(h) plane, i.e., Si @ C(74)-5, which is different from the center stable site for Si in C(74) calculated by the semiempirical molecular orbital calculations and molecular mechanics calculations, and it is also different from the stable site, i.e., under a [6, 6] bond along the C(2) axis on the sigma(h) plane in C(74) for metal atoms Ba, Ca, and Eu. The deformation charge density on the sigma(h) plane reveals that the Si-C bonds in Si @ C(74)-5 have covalent character, while the Mulliken charge analysis together with a longer Si-C bond length reveals that the Si-C bonds in Si @ C(74)-5 have ionic character. Therefore, we infer that Si-C bonds in Si @ C(74)-5 contain both covalent and ionic characters.     

Hydrogen bond dynamics and microscopic structure of confined water inside carbon nanotubes

We have investigated the density and temperature dependences of microscopic structure and hydrogen bond dynamics of water inside carbon nanotubes (CNTs) using molecular dynamics simulation. The CNTs are treated as rigid, and smoothly truncated extended simple point charge water model is adopted. The results show that as the overall density increases, the atomic density profiles of water inside CNTs become sharper, the peaks shift closer to the wall, and a new peak of hydrogen atomic density appears between the first (outermost) and second layer. The intermittent hydrogen bond correlation function C(HB)(t) of water inside CNTs decays slower than that of bulk water, and the rate of decay decreases as the tube diameter decreases. C(HB)(t) clearly decays more slowly for the first layer of water than for other regions inside CNTs. The C(HB)(t) of the interlayer hydrogen bonds decays faster than those of the other regions and even faster than that of the bulk water. On the other hand, the hydrogen bond lifetimes of the first layer are shorter than those of the inner layer(s). Interlayer hydrogen bond lifetimes are clearly shorter than those of the constituent layers. As a whole, the hydrogen bond lifetimes of water inside CNTs are shorter than those of bulk water, while the relaxation of C(HB)(t) is slower for the confined water than for bulk water. In other words, hydrogen bonds of water inside CNTs break more easily than those of bulk water, but the water molecules remain in each other's vicinity and can easily reform the bonds.     

Investigation of organosilicon radicals : I. Methylphenylsilane anion radicals

CNDO/2 calculations with an spd basis set have been carried out on methyl-phenylsilane anion radicals, and the calculated spin density values compared with the experimental hyperfine coupling constants. The CNDO method overestimates the role of d orbitals and the partial charges on hydrogen atoms attached to silicon atom. The partial charge distribution and the carbonsilicon bond order in the anion radicals and the corresponding neutral molecules are discussed. The equilibrium carbonsilicon bond distance in the trimethylphenylsilane molecule and corresponding anion radical have also been investigated.     

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.     

C-H bond activation by hyperconjugation with Al-C bonds and by chelating coordination of the hydride ion

On treating di(tert-butyl)butadiyne with dimethylaluminum hydride under different reaction conditions two unprecedented organoelement compounds, containing cationic carbon atoms stable in solution at room temperature, were obtained. A vinyl cation (2) in which the cationic carbon atom is part of a C=C double bond was produced from 3 equiv of the hydride, whereas a large excess of the hydride yielded an aliphatic carbocation (3) by complete hydroalumination of all C-C multiple bonds. Each compound is zwitterionic with the hydride counterion effectively coordinated in a chelating manner by two strongly Lewis acidic aluminum atoms. In agreement with quantum-chemical calculations the C-H bond activation and the stabilization of the cationic species are further supported by a strong hyperconjugation with Al-C single bonds. This considerably diminishes the effective positive charge at the respective cationic carbon atoms.     

How big are atoms in crystals?

Atoms and bonds are central concepts in structural chemistry, but neither are concepts that arise naturally from the physics of condensed phases. It is ironic that the internuclear distances in crystals that are readily measured depend on the sizes of atoms, but since atoms in crystals can be defined in many different ways, all of them arbitrary and often incompatible, there is no natural way to express atomic size. I propose a simple coherent picture of Atoms-in-Crystals which combines properties selected from three different physically sound definitions of atoms and bonds. The charge density of the free atom that is used to construct the procrystal is represented by a sphere of constant charge density having the quantum theory of atoms in molecules (QTAIM) bonded radius. The sum of these radii is equal to the bond length that correlates with the bond flux (bond valence) in the flux theory of the bond. The use of this model is illustrated by answering the question: How big are atoms in crystals? The QTAIM bonded radii are shown to be simple functions of two properties, the number of quantum shells in the atomic core and the flux of the bond that links neighbouring atoms. Various radii can be defined. The univalent bonded radius measures the intrinsic size of the atom and is the same for all cations in a given row of the periodic table, but the observed bonded radius depends also on the bond flux that reflects the chemical environment.     

Topology of charge density of flucytosine and related molecules and characteristics of their bond charge distributions

The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.