Intermolecular charge transfer and hydrogen bonding in solid furan

The calculated structures of furan as a monomer, a dimer that was isolated from the crystal structure, and the full crystal structure have been thoroughly investigated by a combination of density functional theory (DFT) calculations and inelastic neutron scattering (INS) measurements. To improve our understanding of the nature and magnitude of the intermolecular interactions in the solid, the atoms in molecules (AIM) theory has been applied to the dimer and a cluster of eight monomers. After a careful topological study of the theoretical charge density and of its Laplacian, we have established the existence of C-H...pi, C-H...O, and H...H interactions between adjacent molecules in solid furan. The electron distribution has also been analyzed by performing natural bond orbital (NBO) calculations for the monomer and a H-bonded dimer. When the hydrogen bond is established between two adjacent furan rings, some electron charge is transferred from the pi electronic system of one furan ring to the other molecule in the dimer. This result provides a model of the interaction between end groups of neighboring chains of polyfuran and could be applicable to other conjugated polymers where the pi system is responsible for their conducting properties. To determine how the intermolecular bonds in the solid affect the vibrational dynamics in the periodic system, INS data were analyzed by performing molecular and periodic density functional calculations. Reasonable agreement is achieved, although we note that the poorest agreement is for modes involving hydrogen atoms.     

The role of quantum-mechanical interference and quasi-classical effects in conjugated hydrocarbons

The nature of the chemical bond in conjugated hydrocarbons is analyzed through the generalized product function energy partitioning (GPF-EP) method, which allows the calculation of the quantum-mechanical interference and quasi-classical contributions to the energy. The method is applied to investigate the differences between the chemical bonding in conjugated and non-conjugated hydrocarbon isomers and to evaluate the contribution from the energy components to the stabilization of the molecules. It is shown that in all cases quantum-mechanical interference has the effect of concentrating π electron density between the two carbon atoms directly involved in the (C-C)π bonds. For the conjugated isomers, this effect is accompanied by a substantial reduction of electron density in the π space of the neighbouring (C-C)σ bond. On the other hand, quasi-classical effects are shown to be responsible for the extra stabilization of the conjugated isomers, in which a decrease of the π space kinetic reference energy seems to play an important role. Finally, it is shown that the polarization of p-like orbitals in compounds with alternating single and double bonds ultimately increases electron density in the π space of the neighbouring (C-C)σ bond. Therefore, quasi-classical effects, rather than covalent ones, seem to be responsible for several properties of conjugated molecules, such as thermodynamic stability, planarity and (C-C)σ bond shortening. The shortcomings of the delocalization concept are discussed.     

Single‐electron halogen bond: Ab initio study

Ab initio calculations have been performed on single‐electron halogen bonds between methyl radical and bromine‐containing molecules to gain a deeper insight into the nature of such noncovalent interactions. Bader's atoms in molecules (AIM) theory have also been applied to the analysis of the linking of the single‐electron halogen bond. Various characteristics of the R? Br…CH₃ interaction, i.e., binding energies, geometrical parameters and topological properties of the electron density have been determined. The presence of the bond critical points (BCPs) between the bromine atom and methyl radical and the values of electron density and Laplacian of electron density at these BCPs indicate the closed‐shell interactions in the complexes. The single‐electron halogen bonds, which are significantly weaker than the normal halogen bonds, exhibit equally bond strength as compared to the single‐electron hydrogen bond. It has been also found that plotting of the binding energies versus topological properties of the electron density at the BCPs gives two straight lines. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Transfer of electron density as a result of hydrogen bond formation— A case of charged complexes

Previous investigation of transfer of electron density accompanying hydrogen bond formation has been extended to complexes between positively charged donors and neutral acceptors, as well as to the complexes between a neutral donor and a negatively charged acceptor molecules. The amount of transferred electron density from acceptor to donor for the charged complexes may be adequately described by the same exponential dependence on the equilibrium distance between the hydrogen atom and the nearest atom of the acceptor molecule as it was found for neutral complexes. Relation of the H‐bond energy to electron density at the H‐bond critical point was dependent on the sign of Laplacian of the electron density. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Electron distribution on an intramolecular hydrogen bond: A semiempirical AM1 study

Dipole moments of seven molecules were studied by AM1, each containing an intramolecular hydrogen bond between a hydroxyl group and a carbonyl or nitro group as hydrogen acceptors. The hydrogen bond causes two electron shifts: from H to O within the hydroxyl group and from C to O within the carbonyl group. The latter is accompanied by withdrawal of electrons from even more distant atoms. If the total electron density change is expressed as a vector, its direction is close to the direction of the O-H bond. This electron redistribution is in agreement with the previous, somewhat, puzzling experimental results. However, it differs from the commonly accepted picture according to which electron density changes on the hydrogen acceptor moiety are less important than those on the O-H bond.Dedicated to Professor Viktor Gutmann on the occasion of his 70th birthday.     

Excited-State Hydrogen Bonding Dynamics of Hydrogen-Bonded Clusters Formed by of Coumarin Derivatives in Aqueous Solution: A Time-Dependent Density Functional Theory Study

The time-dependent density functional theory and the density functional theory are used to investigate the nature of hydrogen bonds formed by the derivative of the coumarin (TFKC) and the water molecules. The ground-state geometry optimizations, electronic excited energies and corresponding oscillation strengths for the TFKC monomer, the hydrogen-bonded TFKC–Water (HBA) dimer, TFKC–Water (HBB) dimer and TFKC–2Water complex are calculated. We find that, upon photoexcitation, the weaker hydrogen bond in the ground state will be affected by the relatively large impact for TFKC in the water. For better understanding the properties of the hydrogen bonds in the excited states, the frontier molecular orbitals of the S0 and S1 states are shown, and we find the obvious electron density transitions form the water molecules to the TFKC monomer. The electron transfer is expected to be the reason the hydrogen bond dynamics happens.     

Electronic structure,geometry, and energetics of carbanion and carbocation of [1.1]ferrocenophane: An INDO study

INDO-SCF calculations with constrained geometry optimization have been performed to determine the bridge geometries in [1.1]ferrocenophane and its carbocation and carbanion to address the question of possible C-H-C hydrogen bonding in the carbanion derivative. In the equilibrium geometry of the carbanion, the endo-hydrogen is bonded to one of the bridge carbon atoms and the calculated distance between the two bridge carbons seems too large to accommodate a stable C-H-C hydrogen bond. The results indicate that the observed proton NMR spectrum of carbanion should be interpreted in terms of rapid proton exchange between two bridge carbon atoms rather than a symmetric hydrogen bond. The ground state charge distributions show that the ionic bridges in both carbanion and carbocation are highly conjugated and most of the ionic charge in both molecules is distributed over the ferrocene ring system. The charge on the iron varies only slightly among the three molecules and the formal oxidation state of iron remains +2. The role of the iron seems to be that of a conduit for charge transfer between ferrocene rings upon conjugation.     

INDO calculations on the sigmatropic [1, 5] H-Shift in 1,3-cyclohexadiene and 1,3,5-cycloheptatriene A homo-cyclopentadienyl transition state model

INDO calculations have been performed for the activated complex of the [1, 5] H.-shift in 1,3-cyclohexadiene and 1,3,5-cycloheptatriene. During the migration in the cyclohexadiene system a homoconjugation was calculated between the carbon atoms C₁ and C₅. For cycloheptatriene it could be demonstrated that one double bond does not participate in the reaction. Activation enthalpies are related to (homo)conjugation in the transition state of the reaction for cyclic conjugated dienes and trienes. The electron density on the migrating hydrogen can be related to the electron affinity of the ring system in the transition state.[/p]     

Structural properties and the effect of 2,6‐diaminoanthraquinone on G‐tetrad,non‐G‐tetrads,and mixed tetrads—A density functional theory study

Telomerase inhibitor causes the attrition of telomere length and consequently leading to senescence which require a lag period for cancer cells to stop proliferating. Telomeric sequences form quadruplex structures stabilized by tetrads. The structural and electronic properties related with interaction of 2,6‐diaminoanthraquinone and tetrads are the key step to elucidate the anticancer activity. The present study has been focused on the stability of the isolated tetrads and the effect of interaction of 2,6‐diaminoanthraquinone with G‐tetrad, non‐G‐tetrads, and mixed tetrads using density functional theory method in both gas and aqueous phases. The solvent interaction with the molecular systems has increased the stability of the isolated tetrads and complexes. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The atoms in molecules theory and natural bond orbital analysis have been performed to study the nature of hydrogen bonds in the inhibitor interacting complexes. The linear correlation is shown between electron density [ρ(r)], and its Laplacian [(²ρ(r)] at the bond critical points. The strong binding nature of 2,6‐diaminoanthraquinone with studied tetrads reveals that this inhibitor is suitable to stabilize the above tetrads and inhibit the telomerase activity. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Large dielectric susceptibility associated with proton transfer in a supramolecular structure of chloranilic acid and 5,5'-dimethyl-2,2'-bipyridine

A 1:1 adduct of chloranilic acid with 5,5'-dimethyl-2,2'-bipyridine, in which two kinds of molecules are connected by infinite hydrogen bond chains, exhibits a distinct dielectric phase transition when cooled. Below T(c)(=318 K) the hydrogen atoms participating in hydrogen bonding undergo long-range ordering and form an antiferroelectric-like state, taking a single minimum potential in the high-temperature phase (T>T(c)) due to the bifurcate hydrogen bond system. The proton-transfer phenomenon was clearly observed by electron density distribution analysis using a maximum entropy method of synchrotron x-ray diffraction data.     

Electron density based characterization of π bonds in planar molecules

A new method has been developed to detect and analyze molecular π systems. The concept of bonding critical point is generalized to electronic π systems, and it is shown how a π bond can be characterized via the corresponding bond critical point (BCP) in planar molecules. In this context, charge density and its Laplacian at the BCP(π) of a strongly delocalized π system can be distinguished from that of a localized one. The presented formalism is applied to three types of nanoconductors as conjugated polyenes, which revealed the alternative pattern of the double bonds. Also, several cyclic conjugated molecules are considered to explore their π electronic structure and aromaticity.     

Factors controlling extremely strong AAA-DDD triply hydrogen-bonded complexes

Triply hydrogen-bonded complexes of the form AAA-DDD are shown to have the strongest interaction when the complex is substituted with electron withdrawing groups on the donor molecule (DDD) and electron donating groups on the acceptor molecule (AAA). In particular, the largest effects are observed when the withdrawing groups act through resonance. This serves to flatten the entire system resulting in more linear, and consequently stronger, hydrogen bonds. Furthermore, the present calculations show that the binding energy correlates with the electron density at the bond critical points and inversely with the hydrogen bond lengths.     

Can BB double bond be as potential proton acceptor: A UB3LYP and UMP2 theoretical study on unusual intermolecular T-shaped XH…π interactions between the triplet state HBBH and HF, HCl, HCN or H2C2

The unusual weak T-shaped XH…π hydrogen bonds are found between the BB double bond of the triplet state HBBH and the acid hydrogen of HF, HCl, HCN and H₂C₂ using UMP2 and UB3LYP methods at 6-311++G(2df,2p) and aug-cc-pVTZ levels. The binding energies follow the order of HBBH…HF > HBBH…HCl > HBBH…HCN > HBBH…H₂C₂, and the hydrogen-bonded interactions in the triplet state complexes HBBH…HX (³B₁) are found to be weaker than those in HCCH…HX and OCBBCO…HX. The analyses of natural bond orbital (NBO) and the electron density shifts reveal that the nature of the T-shaped XH…π hydrogen-bonded interaction is that the lost density from the π-orbital of BB bond is shifted toward the hydrogen atom of HX, leading to the electron density accumulation and the formation of the hydrogen bond. The atoms in molecules (AIM) theory has been also applied to characterize bond critical points and confirm that it is difficult for the ground electronic state of HBBH to be as the hydrogen-bond proton acceptor, perhaps due to the nature of electron-deficient BB double bond.     

Molybdenum oxides versus molybdenum sulfides: geometric and electronic structures of Mo₃X(y)⁻ (X = O, S and y = 6, 9) clusters

We have conducted a comparative computational investigation of the molecular structure and water adsorption properties of molybdenum oxide and sulfide clusters using density functional theory methods. We have found that while Mo?O?? and Mo?S?? assume very similar ring-type isomers, Mo?O?? and Mo?S?? clusters are very different with Mo?O?? having a ring-type structure and Mo?S?? having a more open, linear-type geometry. The more rigid ∠(Mo-S-Mo) bond angle is the primary geometric property responsible for producing such different lowest energy isomers. By computing molecular complexation energies, it is observed that water is found to adsorb more strongly to Mo?O?? than to Mo?S??, due to a stronger oxide-water hydrogen bond, although dispersion effects reduce this difference when molybdenum centers contribute to the binding. Investigating the energetics of dissociative water addition to Mo?X?? clusters, we find that, while the oxide cluster shows kinetic site-selectivity (bridging position vs terminal position), the sulfide cluster exhibits thermodynamic site-selectivity.     

Application of Bader’s atoms in molecules theory to the description of coordination bonds in the complex compounds of Ca2+ and Mg2+ with methylidene rhodanine and its anion

In the framework of Bader??s atoms in molecules theory a complete analysis of the distribution function of electron density in molecules of complexes of Ca²⁺ and Mg²⁺ with methylidene rhodanine and its anion was carried out. The role of mutual polarization of the metal cation and the ligand in the formation of coordination bonds was demonstrated. The accumulation of electron density in the interatomic space of coordination bonds is assumed to be a consequence of the deformation of the ligand electron shell under the influence of the cation electric field. Based on the magnitude and sign of the Laplacian and the electron energy density at the critical points of coordination bonds the interactions were classified the in terms of the atoms in molecules theory. The energy of the coordination bonds was evaluated using the Espinoza??s formula. The stability of metal-containing rings was considered basing on the values of the bond ellipticity.     

Experimental and theoretical charge density distribution in a host-guest system: synthetic terephthaloyl receptor complexed to adipic acid

The experimental charge density distributions in a host-guest complex have been determined. The host, 1,4-bis[[(6-methylpyrid-2-yl)amino]carbonyl]benzene (1) and guest, adipic acid (2). The molecular geometries of 1 and 2 are controlled by the presence in the complex of intermolecular hydrogen bonding interactions and the presence in the host 1 of intramolecular hydrogen bonding motifs. This system therefore serves as an excellent model for studying noncovalent interactions and their effects on structure and electron density, and the transferability of electron distribution properties between closely related molecules. For the complex, high resolution X-ray diffraction data created the basis for a charge density refinement using a pseudoatomic multipolar expansion (Hansen-Coppens formalism) against extensive low-temperature (T = 100 K) single-crystal X-ray diffraction data and compared with a selection of theoretical DFT calculations on the same complex. The molecules crystallize in the noncentrosymmetric space group P2(1)2(1)2(1) with two independent molecules in the asymmetric unit. A topological analysis of the resulting density distribution using the atoms in molecules methodology is presented along with multipole populations, showing that the host and guest structures are relatively unaltered by the geometry changes on complexation. Three separate refinement protocols were adopted to determine the effects of the inclusion of calculated hydrogen atom anisotropic displacement parameters on hydrogen bond strengths. For the isotropic model, the total hydrogen bond energy differs from the DFT calculated value by ca. 70 kJ mol(-1), whereas the inclusion of higher multipole expansion levels on anisotropic hydrogen atoms this difference is reduced to ca. 20 kJ mol(-l), highlighting the usefulness of this protocol when describing H-bond energetics.     

Does the molecular structure of CaH2 affect the dihydrogen bonding in CaH2 … HY (Y = CH3, C2H3, C2H, CN, and NC) complexes? A quantum chemistry study using MP2 and B3LYP methods

Second-order M ller-Plesset(MP2) and density functional theory(DFT) calculations have been carried out in order to investigate the structures and properties of dihydrogen-bonded CaH 2 HY(Y = CH 3,C 2 H 3,C 2 H,CN,and NC) complexes.Our calculations revealed two possible structures for CaH 2 in CaH 2 HY complexes:linear(I) and bent(II).The bond lengths,interaction energies,and strengths for H H interactions obtained by both MP2 and B3LYP methods are quite close to each other.It was found that the interaction energy decreases with increasing electron density at the Ca-H bond critical point.Atom-in-molecule(AIM) results show that for all of Ca-H H-Y interactions considered here,the Laplacian of the electron density at the H H bond critical point is positive,indicating the electrostatic nature of these Ca-H H-Y dihydrogen bonded systems.