Identifying and Analyzing Intermolecular Bonding Interactions in van der Waals Molecules

The molecular properties of heterocyclic and homocyclic hydrogen-bonded complexes evaluated by DFT calculations and AIM densities

This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, the interaction energies and polarizabilities were also evaluated, as well as the infrared stretch frequencies and absorption intensities. In addition, by combining intermolecular criteria and charge density concepts, calculations of Bader's theory of atoms in molecules were used to determine the maxima and minima for electron density in order to measure the strength of the n...H and ppi...H hydrogen bonds. Finally, the possibility of an F...H(alpha) secondary interaction between the fluoride (F) of hydrogen fluoride and the axial hydrogen atoms (H(alpha)) of the C2H4O and C2H5N heterocyclic rings was explored.

Experimental bond critical point and local energy density properties determined for Mn-O, Fe-O, and Co-O bonded interactions for tephroite, Mn2SiO4, fayalite, Fe2SiO4, and Co2SiO4 olivine and selected organic metal complexes: comparison with properties calculated for non-transition and transition metal M-O bonded interactions for silicates and oxides

Bond critical point (bcp) and local energy density properties for the electron density (ED) distributions, calculated with first-principle quantum mechanical methods for divalent transition metal Mn-, Co-, and Fe-containing silicates and oxides are compared with experimental model ED properties for tephroite, Mn 2SiO 4, fayalite, Fe 2SiO 4, and Co 2SiO 4 olivine, each determined with high-energy synchrotron single-crystal X-ray diffraction data. Trends between the experimental bond lengths, R(M-O), (M = Mn, Fe, Co), and the calculated bcp properties are comparable with those observed for non-transition M-O bonded interactions. The bcp properties, local total energy density, H( r c), and bond length trends determined for the Mn-O, Co-O, and Fe-O interactions are also comparable. A comparison is also made with model experimental bcp properties determined for several Mn-O, Fe-O, and Co-O bonded interactions for selected organometallic complexes and several oxides. Despite the complexities of the structures of the organometallic complexes, the agreement between the calculated and model experimental bcp properties is fair to good in several cases. The G( r c)/rho( r c) versus R(M-O) trends established for non-transition metal M-O bonded interactions hold for the transition metal M-O bonded interactions with G( r c)/rho( r c) increasing in value as H( r c) becomes progressively more negative in value, indicating an increasing shared character of the interaction as G( r c)/rho( r c) increases in value. As observed for the non-transition metal M-O bonded interactions, the Laplacian, nabla (2)rho( r c), increases in value as rho( r c) increases and as H( r c) decreases and becomes progressive more negative in value. The Mn-O, Fe-O, and Co-O bonded interactions are indicated to be of intermediate character with a substantial component of closed-shell character compared with Fe-S and Ni-S bonded interactions, which show greater shared character based on the | V( r c)|/ G( r c) bond character indicator. The atomic charges conferred on the transition metal atoms for the three olivines decrease with increasing atomic number from Mn to Fe to Co as the average M-O bond lengths decrease from 2.219 to 2.168 to 2.128 A, respectively.

Bond paths as privileged exchange channels

Evidence that the bond paths of the quantum theory of atoms-in-molecules (QTAIM) signal preferred quantum-mechanical exchange channels is presented. We show how bond paths between an atom A and the atoms B in its environment appear to be determined by competition among the A-B exchange-correlation energies that always contribute to stabilize the A-B interactions. These pairwise additive stabilizations depend neither on the attractive or repulsive nature of the classical electrostatic interaction between the atoms' charge densities, nor on the change in the self energies of the atoms involved. These other terms may well cause an overall molecular-energy increase in spite of a possibly large A-B exchange-correlation stabilization. After our proposal, bond paths, both at and out of equilibrium geometries, are endowed with a specific energetic meaning that should contribute to reconcile the orthodox QTAIM interpretation with other widely accepted views, and to settle recent controversies questioning the meaning of hydrogen-hydrogen bonding and the nature of the so-called "steric interactions", the role of bond paths in endohedral complexes, and the generality of the results provided by the QTAIM. Implications for the nature of more general closed-shell interactions are also briefly discussed.

Computational Study of the Interaction between TIBO Inhibitors and Y181 (C181), K101, and Y188 Amino Acids

The non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are an important class of drugs employed in anti-HIV chemotherapy. TIBO compounds, which belong to the NNRTIs class, are potent inhibitors of the HIV-1 reverse transcriptase enzyme (HIV-1 RT). However, mutations in the amino acids present in the active site of these inhibitors limit their clinical use. In this work, the intermolecular interactions taking place between compounds of the TIBO family and Y181 (C181), K101, and Y188 amino acids are investigated. For this purpose the coordinates of three RT crystalline structures complexed with TIBO were taken from PDB database, and were analyzed by means of the B3LYP/6-31+G(d,p) model. The natural bond orbital (NBO) and atoms in molecules (AIM) methods indicate that not only does the Y181C mutation lead to loss of favorable interactions between the TIBO side chains and tyrosine, but it also affects the interaction between the inhibitor and K101 and Y188. Results also revealed that the interaction between TIBO and K101 is stabilized by N-H...O and N-H...S hydrogen bonds. This is the first time that the presence of the latter hydrogen bond (N-H...S) is reported to play an important role in the stabilization of the interaction between TIBO and K101. In addition the NBO and natural population analyses (NPA) indicate that the 8 Cl-TIBO inhibitor presents a more effective interaction with the Y181, K101, and Y188 than that of 9 Cl-TIBO.

Cadmium(II) and Zinc(II) Complexes of S-Confused Thiaporphyrin

The synthesis of 5,10,15,20-tetraphenyl-2-thia-21-carbaporphyrin [S-confused thiaporphyrin, (SCPH)H] was optimized. The formation of the phlorin was detected, which was saturated at the meso carbon adjacent to thiophene. Phlorin converted readily to (SCPH)H in the final oxidation process. Insertion of cadmium(II) and zinc(II) into S-confused thiaporphyrin yielded (SCPH)Cd(II)Cl and (SCPH)Zn(II)Cl complexes. The macrocycle acted as a monoanionic ligand. Three nitrogen atoms and the C(21)H fragment of the inverted thiophene occupied equatorial positions. The compensation of the metal charge required the apical chloride coordination. The characteristic C(21)H resonances of the inverted thiophene ring were located at 1.71 and 1.86 ppm in the 1H NMR spectra of (SCPH)Cd(II)Cl and (SCPH)Zn(II)Cl, respectively. The proximity of the thiophene fragment to the metal ion induced direct scalar couplings between the spin-active nucleus of the metal (111/113Cd) and the adjacent 1H nucleus (J(CdH) = 8.97 Hz). The interaction of the metal ion and C(21)H also was reflected by significant changes of C(21) chemical shifts: (SCPH)Zn(II)Cl, 92.9 ppm and (SCPH)Cd(II)Cl, 88.2 ppm (free ligand (SCPH)H, 123.7 ppm). The X-ray analysis performed for (SCPH)Cd(II)Cl confirmed the side-on cadmium-thiophene interaction. The Cd...C(21) distance (2.615(7) A) exceeded the typical Cd-C bond lengths, but was much shorter than the corresponding van der Waals contact. The density functional theory (DFT) was applied to model the molecular structures of zinc(II) and cadmium(II) complexes of S-confused thiaporphyrin. Subsequent AIM analysis demonstrated that the accumulation of electron density between the metal and thiophene, which is necessary to induce these couplings, was fairly small. A bond path linked the cadmium(II) ion to the proximate C(22) carbon of the thiophene.

Cooperative effects, strengths of hydrogen bonds, and intermolecular interactions in circular cis, trans-cyclotriazane clusters (n=3–8)

Based on Becke's three parameter functional [J. Chem. Phys. 98, 5648 (1993)] of density functional theory (DFT) with the correlation of Lee-Yang-Parr [Phys. Rev. B 37, 785 (1988)] (DFT/B3LYP), the natural bond orbital (NBO) analysis, the Bader's theory of atoms in molecule (AIM), our calculations indicate that as cluster size (n) increases, the n-dependent cooperative changes in the lengths of the N...H H bonds (HBs) and N-H bonds, the N-H stretching frequencies and intensities, and the n(N)-->sigma*(N-H) charge transfers are observed to be pervasive in the circular cis, trans-cyclotriazane clusters (n = 3-8), which is very different from the linear cis, trans-cyclotriazane clusters reported in previous work. According to the NBO and AIM theories, the cooperativity of the intermolecular n(N)-->sigma*(N-H) interaction leads to the n-dependent N...H contractions. In this way, the stronger N...H bond is formed, as reflected in the increase in their rho(r(cp)) values. This increased electron density is translated into the improved capacity to concentrate electrons at the HB bond critical point (BCP), i.e., a higher potential energy V(r(cp)). On the other hand, stronger repulsion is also activated to counteract the contraction, which is reflected in the increased G(r(cp)) value that gives the tendency of the system to dilute electrons at the HB BCP. In terms of the three-body symmetry-adapted perturbation theory (three-body SAPT), the induction nonadditivity accounts for up to 97% of the nonadditive energy in the circular trimer. It can believed that the marked cooperativity of the n(N)-->sigma*(N-H) interactions is of nonadditive induction in nature. The N...H formation and nature of cooperativity in the circular clusters differ from those in the linear clusters that have been reported previously. According to the SAPT(DFT) method which is a combination of SAPT with the asymptotically corrected DFT, the cis, trans-cyclotriazane systems should contain remarkable dispersion interactions. However, the short-range dispersion cannot be reproduced thoroughly by DFT/B3LYP. A quantum cluster equilibrium model illustrates the neglected dispersion energies and the nonadditive energies can affect markedly the properties of the liquid consisting of the circular clusters.

Quantum Theory of Atoms in Molecules Analysis on the Conformational Preferences of Vinyl Alcohol and Related Ethers

Vinyl alcohol, methyl vinyl ether, and tert-butyl vinyl ether were studied within the framework of the quantum theory of atoms in molecules at the B3LYP/6-311++G(2d,2p) level. Local and integrated properties of the charge density indicate that the anti conformational preference of the tert-butyl derivative is not due to a differing resonance contribution with regard to the less bulky vinyl ethers but to steric effects. There is a small delocalization of charge density, either total or pi, between oxygen and the terminal vinyl carbon, which does not support the resonance picture of vinyl compounds.

On the nature of bonding in HCOOH...Ar and HCOOH...Kr complexes

The chemical interaction in HCOOH...Ng (Ng=Ar, Kr) complex was analyzed by topological analysis of the electron density based on Atoms-In-Molecules theory. For all computationally stable equilibrium structures of 1:1 HCOOH...Ng complexes, an intermolecular bond path with a "bond" critical point was found and perturbation of formic acid (FA) atomic basins and electron density was observed. The intermolecular interaction between the two complex subunits can be classified, according to its nature, as a closed-shell van der Waals type of interaction. However, one of the computed structures (complex II), pictures a noble gas atom attached linearly to the acidic O-H tail of FA. In this particular case, the electron density at the intermolecular bond critical point was found to resemble a hydrogen-bonded system and thus, may be termed a hydrogen-bond-like interaction. This change in the nature of the interaction is also shown by large perturbations of the FA properties found for this complex structure. The structural and vibrational perturbations are larger than for the other three structures and they increase for the Kr complexes compared to the Ar complex. [Figure: see text]. Electron density analysis of HCOOH...Ng (Ng=Ar,Kr) complex.

Hydrogen Bonding in Phenol, Water, and Phenol−Water Clusters

Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and density functional theoretical (DFT) methods and using various topological features of electron density. Calculated interaction energies at MP2/6-31G level for clusters with similar hydrogen-bonding pattern reveal that intermolecular interaction in phenol clusters is slightly stronger than in water clusters. However, fusion of phenol and water clusters leads to stability that is akin to that of H(2)O clusters. The presence of hydrogen bond critical points (HBCP) and the values of rho(r(c)) and nabla(2)rho(r(c)) at the HBCPs provide an insight into the nature of closed shell interaction in hydrogen-bonded clusters. It is shown that the calculated values of total rho(r(c)) and nabla(2)rho(r(c)) of all the clusters vary linearly with the interaction energy.

Si-E (E = N, O, F) bonding in a hexacoordinated silicon complex: new facts from experimental and theoretical charge density studies

The concept of hypervalency in molecules, which hold more than eight valence electrons at the central atom, still is a topic of constant debate. There is general interest in silicon compounds with more than four substituents at the central silicon atom. The dispute, whether this silicon is hypervalent or highly coordinated, is enlightened by the first experimental charge density determination and subsequent topological analysis of three different highly polar Si-E (E = N, O, F) bonds in a hexacoordinated compound. The experiment reveals predominantly ionic bonding and much less covalent contribution than commonly anticipated. For comparison gas-phase ab initio calculations were performed on this compound. The results of the theoretical calculations underline the findings of the experiment.

Cadmium(II) and Nickel(II) Complexes of Benziporphyrins. A Study of Weak Intramolecular Metal−Arene Interactions

Weak metal-arene interactions have been investigated in Zn, Cd, Hg, and Ni complexes of meso-tetraaryl m- and p-benziporphyrin (1 and 2) and of the new compound, m-benziporphodimethene (3). Compounds 1-3 incorporate the phenylene moiety into a macrocyclic structure so as to facilitate the interaction between the arene and coordinated metal ion. X-ray studies performed on Cd(II) and Ni(II) complexes show that the arene fragment approaches the ion at a distance much shorter than the sum of van der Waals radii. In chloronickel(II) m-benziporphyrin, a weak agostic bond is actually formed. In the NMR spectra of the Cd(II) and Hg(II) species, unusual (1)H-M and (13)C-M scalar couplings have been observed that are transmitted directly between the metal and the arene. DFT calculations performed for two Cd(II) species and subsequent AIM analysis show that the accumulation of electron density between the metal and arene necessary to induce these couplings is fairly small and the interaction is steric in nature. In the paramagnetic Ni(II) complexes of 1 and 3, the agostic proton of the m-phenylene exhibits large downfield (1)H NMR shifts (386 and 208 ppm at 298 K, respectively). An agostic mechanism of spin density transfer is proposed to explain these shifts as resulting from electron donation from the CH bond to the metal. In chloronickel(II) p-benziporphyrin, the inner protons of the p-phenylene have a contrastingly small shift (0.0 ppm at 298 K), indicating that in this case the agostic interaction is inefficient, in agreement with the X-ray data.

Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding

Although the two hydroxyl groups in 1,2-diols interact as evidenced by NMR and IR spectroscopic shifts, electron density topological analysis has shown a bond critical point (BCP) and atomic bond path to be absent (Klein, R. A.; J Comp Chem 2002, 23, 585-599; J Am Chem Soc 2002, 124, 13931-13937), indicating that no intramolecular hydrogen bond is formed. Here, we demonstrate that small NMR or IR shifts are neither necessarily diagnostic nor sufficient as indicators of hydrogen bond formation; moreover, modified van der Waals atomic radii are needed for estimating maximum nuclear interaction distances and nuclear interpenetration.