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We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn–Teller distortion ranges from 0.78 to 6.14 kcal mol−1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F−. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F− in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of −3.50 and −3.45 eV at CAM-B3LYP/6-311+G(d) and −3.61 and −3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis. [ABSTRACT FROM AUTHOR]

The nature of halogen bonding under different dielectric conditions remains underexplored, especially for inorganic systems. The structural and energetic properties of model halogen bonded complexes (R3M−I—NH3 for R=H and F, and M=C, Si, and Ge) are examined computationally for relative permittivities between 1 and 109 using an implicit solvent model. We confirm and assess the exceptionally high maximum potentials at the sigma hole on I (Vs,max) in F3Ge−I relative to cases where M=C or Si. In particular, Ge far outperforms Si in mediating inductive effects. Linear relationships, typically with R2 >0.97, are identified between Vs,max, the full point charge on I in R3M−I, and the interaction energy, and optimized I—N distance in the complexes. An anomalous trend is identified in which, for each M, F3M−I—NH3 becomes less stable as the optimized I—N distance gets shorter in different dielectric environments; it is explained using the F−I—NH3 complex as a reference. [ABSTRACT FROM AUTHOR]

Polarized-ion models—with and without dipole reaction fields and charge-quadrupole interaction—are evaluated in calculating atomization energies, bond angles, and bending force constants of groups 2 and 12 dihalides. A study of the sensitivity to changes in the input parameters reveals a strong dependence on dipole polarizabilities. The charge–quadrupole bending terms of a multipole expansion are important for quasi-linear molecules, where the preceding terms in the expansion tend to cancel each other. They normally stabilize the linear geometry, but enhance bent structures, if a certain criterion for the ratio of quadrupole polarizabilities of metal and halide ions is fulfilled. The models explain the bent alkaline earth halides, but fail spectacularly for the group 12 halides—HgBr[sub 2] and HgI[sub 2] are even calculated as unstable relative to the constituent atoms. The unexpected weakness of ionic bonds is related to the large increase of the ionization energies by relativistic effects and the lanthanide contraction. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Abstract Heteroarenes such as (aza and oxa)borines are increasingly important as synthetic targets and reagents. We map the intramolecular cyclization of saturated heterocyclic chains through dative bonding. A related set of planar unsaturated aza-, oxa-, and fluora- rings that feature dative σ bonding enhanced by π delocalization are identified. The systems have, in general, the formulae A′(CH 2) m D′ and A′(CH) m D′, where m = 3 and 4, and A′ and D′ are acceptor and donor sites, respectively. In each case, the ring isomers, achievable via A′←D' internal coordination (in the manner of Kekulé's ouroboros), are more stable than chains. Unsaturated aromatic rings examined herein include a oxadiborine with a hypervalent oxygen center and a dioxadiborine. They are isoelectronic with an azaborine, which was synthesized more recently, and benzene. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

Monovalent boron, free borylene species of the form B-R are notoriously unstable. Consequently, there are substantial gaps in the literature concerning the potential utility of those species in organic and inorganic synthesis either as ligands or as critical intermediates in reactions. We show that the relative stability of borylene complexes varies widely, depending on the electron donating ability of the R group. We find that borylenes can form, in the gas phase, weak sigma hole type interactions to saturated carbon centers and stronger dative bonds to tetravalent silicon and germanium. An insertion reaction of the form FH3M + BR → FH2MBHR competes against dative bonding, however, and the reaction is barrierless in several cases when M = Si and in a few cases when M = Ge. For M = C, the barriers are high enough to stabilize monovalent boron complexes. In each case, the barrier heights to M-H bond activation and BR insertion are very sensitive to the nucleophilicity of BR. We confirm, at the MP2(full) and CCSD(T) levels, a substantial preference in borylenes for the singlet over the triplet state. An account is provided at the B3LYP-D3 and MP2(full) levels for the facile insertion reaction on the singlet surface when M = Si and for the stability of FH3M·BR type complexes and the higher barriers to insertion when M = C and Ge. [ABSTRACT FROM AUTHOR]

A remarkable transition in the chemical bonding in (HgF2) n clusters as a function of n is identified and characterized. HgF2 is a fascinating material. Certain significant consequences of relativistic effects on the structure of the HgF2 molecule, dimer, and trimer disappear in the extended solid. Relativistic effects in Hg ensure that HgX2 molecules (X≡F, Cl, Br, and I) are linear, rigid, and form weakly bound dimers and trimers held together by weak electrostatic and van der Waals-type forces (unlike ZnX2 and CdX2 systems in which the intermonomer contacts are strong polar covalent bonds). For HgF2, the location and nature of an apparent transition from weak interactions in the smallest (HgF2) n clusters to ionic bonding in the (fluorite) HgF2 extended solid has remained a mystery. Computational evidence obtained at the M06-2X, B97D3, and MP2 levels of theory and reported herein indicate that polar covalent bonding in (HgF2) n begins as early as n=5. For n=2 through to n=13, the transition or switch from weak (primarily dipole-dipole-type) intermonomer interactions to a preference for polar covalent bonding occurs within the range 5< n≤9. Thermodynamic evidence for this transition is provided. Our results demonstrate a significant risk associated with crystal structure prediction from the ground up (i.e., based on bonding patterns in small clusters). The path from monomers through to extended solids may be punctuated at one or several points (as n increases) with transitions in structure and bonding that are not anticipated or betrayed by the bonding in small clusters. [ABSTRACT FROM AUTHOR]

Nobroadly applicable and well-defined measure for the inductiveeffects of substituents (outside of the context of substituted benzenes)exists. We assess the viability of two different forms of weak interactionsas tools for this purpose. The responses of interatomic (I···Nand Ge···N) separations in the halogen-bonded and dativecovalent complexes F3CI···Y and FH3Ge···Y, where Y = NH2R, afford a directordering of a diverse set of substituents, R, according to their influenceon the availability of the N lone pair in the base (NH2R) for bonding. Despite their structural and electronic differences,the two bonding modes that we consider show good qualitative agreementon the electron-withdrawing inductive tendencies of substituents becauseof their sensitivity to the electronic environment at the donor site(the N center, in this case) on the base. The choice of the monosubstituted(NH2R) base minimizes steric interactions, resonance, andother electronic effects that could interfere with the bonding betweenN and the I or Ge centers in the complexes. We find, moreover, thatthe inductive tendencies for substituents in these complexes are,in general, not additive. Depending on the identity of R, the trisubstitutedbase (NR3) may actually reverse rather than enhance changesin the acid–base interactions that are achieved going fromNH3to NH2R. These outcomes are observed atthe MP2(full) and the M06-2X levels of theory, for both halogen anddative bonding interactions. A conservative ordering of substituentsaccording to the observed inductive tendencies is presented. [ABSTRACT FROM AUTHOR]

Wefind for distinct classes of halogen bonded complexes (MF3X···Y) that the ab initio BSSE-correctedbinding energies (ΔE) andenthalpies (ΔH) are predictedby functions of the form y = A/rn+ C. Here X is a halogen atom, Y is a base, ris the X···Y separation, and A, n, and Care constants. The actualvalue of n(5.5 < n< 7.0for ΔE) for each class isdetermined evidently by the availability of the lone pairs on thebase and is insensitive to M such that all of the complexes of a givenbase fall on the same curve for yversus r. Remarkably, several bases show the same behavior in somecases such that just three curves account for 55 MF3I···Ycomplexes of 11 bases, where M = C, Si, Ge, Sn, and Pb. Two additionalbases, THF and NF3, which form especially strong and weakcomplexes, respectively, are in classes by themselves. Anomalous modesof halogen bonding are identified; in particular, furan forms sigma-holecomplexes via carbons 2 and 3 (through the π system) in thering in preference to the oxygen site. These results are in line withexperimental observations for furan–dihalogen complexes, andseveral other small MF3I···Y pairs are proposedin this work for experimental interrogation. Instead of halogen bonding,CF4tends to form weak sigma-hole bonds to bases via thepolarized central carbon atom, and new examples of such pro-dativeinteractions to carbon in CF4are identified in this work.We find that GeF3I and SnF3I form I···Yhalogen bonds of comparable energies to those formed by the smallerand better studied CF3I. PbF3I forms the strongesthalogen bond regardless of the identity of the base; SiF3I consistently forms the weakest link. [ABSTRACT FROM AUTHOR]

How short can a C−C single bond get? The bonding in a set of molecules that are related structurally to previously synthesized or theoretically examined systems with short C−C bonds is investigated. According to calculations, a single C−C bond could be compressed to 1.313 Å! To the best of our knowledge, this is the shortest single C−C bond reported to date. This shortening is a consequence of a change in the C−C−C bond angle, θ, to minimize strain in the cages and an effort to offset the tension in the surrounding bridges. [ABSTRACT FROM AUTHOR]

We examine the bonding possibilities of the bis(phenalenyl) MP[sub2] sandwich complexes of the divalent metals M = Be, Mg, Ca, Sr, Ba, Zn, Cd, and Hg, at the B3LYP level of theory. The outcome is an extraordinary diverse class of low symmetry bis(phenalenyl)metal complexes in which bonding preferences and binding enthalpies differ dramatically. The lowest energy group 2 metal MP[sub2] complexes include an intriguing η[sup1], η[sup3] Be P[sub2] structure, and bent η[sup6], η[sup6] systems for M = Ca, Sr, and Ba. The group 12 bis(phenalenyl) complexes are thermodynamically unusable η[sup1], η[sup1] slip-sandwich structures. To better understand changes in the structural preferences going from the (η[sup6], η[sup6]) group 2 to the (η[sup1], η[sup1]) group 12 complexes, we explored the bonding in the bis(phenalenyl) complexes of transition metals with stable +2 oxidations states between Ca and Zn in period 4. The computed binding enthalpies are large and negative for nearly all of the minimum energy bis(phenalenyl) complexes of the group 2 and the transition metals; they are tiny for MgP[sub2], and are quite positive for the group 12 systems. The structural preferences and stability of the complexes is a subtle negotiation of several influences: the (un)availability of (n - 1)d and np, orbitals for bonding, the cost of the rehybridization at carbon sites in the phenalenyl rings in preparation for bonding to the metals, and the (P—P) interaction between the phenalenyl radicals. [ABSTRACT FROM AUTHOR]

Keywords: dielectric environments; geminal polarization; group 14 elements; halogen bonding; sigma holes EN dielectric environments geminal polarization group 14 elements halogen bonding sigma holes 1359 1359 1 10/29/21 20211001 NES 211001 B The Cover Feature shows b the Group 14 elements M=C, Si, and Ge in order of the effective electron-withdrawing power of the -MF SB 3 sb fragment. Thus, polarized germanium halide sites in molecules and solids (but not Si alternatives) may form strong halogen bonds that are comparable to those formed by their organic analogues. [Extracted from the article]

The existence and persistence of five-fold (quintuple) bonding in isomers of model RMMR molecules of quite different geometry are examined theoretically. The molecules studied are RMMR, with R = H, F, Cl, Br, CN, and CH3; M = Cr, Mo, and W. The potential energy surface of these molecules is quite complex, containing two, three, even four local minima. The structural preferences in these molecules are rationalized, and electronic factors responsible for these preferences are elucidated. The linear geometry is always a minimum, but almost never the global minimum; there is a definite preference in RMMR for either a trans-bent conformation or perturbations of the trans-bent isomer with at least one of the R groups in a bridging position about the MM bond. The potential energy surface of these RMMR molecules is relatively flat, the lowest energy conformation being that which for a given molecule attains the best compromise between maximization of the MM bonding and minimization of orbital interactions that are MR antibonding. A surprising low-symmetry Cs structure is identified, which along with the trans-bent isomer is one of the two most popular choices for the global minimum. Regardless of what isomer of the RMMR molecule is preferred, the MM quintuple bond persists. [ABSTRACT FROM AUTHOR]

The link between structural preferences in the monomers, dimers, and extended solid-state structures of the group 2 dihalides (MX2: M = Be, Mg, Ca, Sr, Ba and X = F, Cl, Br, I) is examined theoretically. The question posed is how well are geometric properties of the gas-phase MX2 monomers and lower order oligomers "remembered" in the corresponding MX2 solids. Significant links between the bending in the MX2 monomers and the D2h/C3v M2X4 dimer structures are identified. At the B3LYP computational level, the monomers that are bent prefer the C3v, triply bridged geometry, while the rigid linear molecules prefer a D2h doubly bridged structure. Quasilinear or floppy monomers show, in general, only a weak preference for either the D2h or the C3v dimer structure. A frontier orbital perspective, looking at the interaction of monomer units as led by a donor-acceptor interaction, proves to be a useful way to think about the monomer-oligomer relationships. There is also a relationship between the structural trends in these two (MX2 and M2X4) series of molecular structures and the prevalent structure types in the group 2 dihalide solids. The most bent monomers condense to form the high coordination number fluorite and PbCl2 structure types. The rigidly linear monomers condense to form extended solids with low coordination numbers, 4 or 6. The reasons for these correlations are explored. [ABSTRACT FROM AUTHOR]

Abstract: A qualitative rationalization of bonding patterns in halosilanes and halogermanes (MH4-nXn, n=1–4; M=Si, Ge; X=F, Cl, Br) is presented. Geometrical and bonding properties in these molecules are discussed on the basis of ab initio molecular orbital calculations employing the natural bond orbital population analysis. The results have been compared with data derived previously for halomethanes. Differences in the n-dependence of the M–Cl and M–Br bond lengths for M=C, Si, Ge are explained by a significant reduction in the closed-shell repulsion between the halide atoms. As M gets larger, a continuous decrease in the X–M–X bond angle is observed. Small bond angles (for n=2, 3) are favoured by the p-rich M orbitals in the M–X bonds. They are opposed, however, by the X⋯X repulsion. As M gets larger, the X⋯X separation for a given bond angle increases. A reduction in the X–M–X bond angle is therefore accomplished without overcompensation due to the X⋯X repulsion energy. The variation in the charge density at M as a function of n has been rationalized by differences in the electronegativity of the terminal atoms H and X. Dipole moments have been computed for the molecules in the series. As in the fluoromethanes, a maximum in the dipole moments at n=2 is explained by a combination of geometric and electronic properties unique to the fluoro-compounds. These are, an n-independent charge density at the F sites and a significant decrease in the M–F bond distance as n increases. [Copyright &y& Elsevier]

Abstract: A qualitative rationalization of the structural anomalies in the series of halomethanes, (CH4-nXn n=1–4, X=F, Cl, Br), is presented. Factors influencing the geometry of these molecules, which have not been considered hitherto, are discussed on the basis of ab initio molecular orbital calculations using natural bond orbital analysis. The electrostatic attraction between the central carbon and the terminal sites and the repulsion between the terminal sites compete in their influence on the molecular geometry. Intra-molecular interactions between the H and F sites are proposed as one of the reasons for the large H–C–H bond angle in CH2F2. We find a correlation between the hybridization on the central atom and the terminal atoms. In this context, we have decoupled the influence of a variation in n and changes in the bond angles on charge distribution at the C and F sites. Decoupling these two influence parameters is the prerequisite to elucidate their role in directing rehybridization on the central carbon and the terminal halides. The maximum in the experimental dipole moment of the fluoromethanes at n=2 is explained by a point-charge approximation. A constant charge density at the F sites and a monotonous decrease in the C–F bond distance as n increases account for this variation. [Copyright &y& Elsevier]

We investigate the validity of employing a potential dependent polarizability in a model to determine atom in molecule (AIM) polarizabilities. It is found that the assumption of an electric potential dependent polarizability leads to a contravention of the principle of conservation of energy. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

DFT calculations (M06-2X, B97D3, and MP2) indicate that polar covalent bonding in (HgF2)n begins at n = 5. [ABSTRACT FROM AUTHOR]

Evidence is provided for a transition from weak noncovalent interactions among HgF2 monomers to stronger polar covalent interactions in mercury difluoride clusters, (HgF2)n, as the size of the cluster (the value of n) increases. This transition—the so ‐ called “ionic switch” that was predicted in an earlier article in this journal—is explained as a triumph of electrostatic interactions (which favor short and strong bonds) against the rigidity imposed on mercury dihalide molecules by relativistic effects in Hg. The observations afford some new insights into nucleation processes. The complete account can be found in the Full paper by K. J. Donald and colleagues on page 16848 ff. [ABSTRACT FROM AUTHOR]

The nature of the bonding and a definite preference for an eclipsed geometry in several substituted but-2-ynes, including certain novel derivatives are uncovered and examined. In particular, we consider the molecular species R3C-C-C-CR3 (where R= H, F, Cl, Br, I, and CN), their R3C-B-N-CR3 analogues, and a few novel exo-bridge systems with intramolecular hydrogen bonds running parallel to the C-C-C-C chain. In some cases, the potential energy surfaces are remarkably flat-so flat, in fact, that free rotation is predicted for those molecules at very low temperatures. A systematic investigation of the bonding in the halogenated butynes demonstrates that the eclipsed conformation actually becomes more stable relative to the staggered form as R becomes larger and less electron-withdrawing. The rotational barriers (the differences in energy between the eclipsed and staggered geometries) are magnified significantly, however, in a special case where selected R groups at the ends of the R3C-C-C-CR'3 molecule form hydrogen bonds parallel to the C-C-C-C core. In those systems, the hydrogen bonds serve as a weak locking mechanism that favors the eclipsed conformation. A comparison of HF and uncorrected DFT methods versus the MP2(full), CCSD(T), and other dispersion-corrected methods confirms that correlation accounts to a significant extent for barriers in substituted butyne compounds. In the hydrogen-bonded systems, the barriers are comparable to and larger in some cases than the barriers observed for the more extensively studied ethane molecule. [ABSTRACT FROM AUTHOR]

Halogen bonding (R—X⋯Y) is a qualitative analogue of hydrogen bonding that may prove useful in the rational design of artificial proteins and nucleotides. We explore halogen-bonded DNA base pairs containing modified guanine, cytosine, adenine and thymine nucleosides. The structures and stabilities of the halogenated systems are compared to the normal hydrogen bonded base pairs. In most cases, energetically stable, coplanar structures are identified. In the most favorable cases, halogenated base pair stabilities are within 2 kcal mol-1 of the hydrogen bonded analogues. Among the halogens X = Cl, Br, and I, bromine is best suited for inclusion in these biological systems because it possesses the best combination of polarizability and steric suitability. We find that the most stable structures result from a single substitution of a hydrogen bond for a halogen bond in dA:dT and dG:dC base pairs, which allows 1 or 2 hydrogen bonds, respectively, to complement the halogen bond. [ABSTRACT FROM AUTHOR]

We have explored the structural and energetic properties of a series of RMX3‐NH3 (M=Si, Ge; X=F, Cl; R=CH3, C6H5) complexes using density functional theory and low‐temperature infrared spectroscopy. In the minimum‐energy structures, the NH3 binds axially to the metal, opposite a halogen, while the organic group resides in an equatorial site. Remarkably, the primary mode of interaction in several of these systems seems to be hydrogen bonding (C‐H‐‐N) rather than a tetrel (N→M) interaction. This is particularly clear for the RMCl3‐NH3 complexes, and analyses of the charge distributions of the acid fragment corroborate this assessment. We also identified a set of metastable geometries in which the ammonia binds opposite the organic substituent in an axial orientation. Acid fragment charge analyses also provide a clear rationale as to why these configurations are less stable than the minimum‐energy structures. Matrix‐isolation infrared spectra provide clear evidence for the occurrence of the minimum‐energy form of CH3SiCl3–NH3, but analogous results for CH3GeCl3–NH3 are less conclusive. Computational scans of the M‐N distance potentials for CH3SiCl3–NH3 and CH3GeCl3–NH3, both in the gas phase and bulk dielectric media, reveal a great deal of anharmonicity and a propensity for condensed‐phase structural change. [ABSTRACT FROM AUTHOR]

The most stable forms of E5Li7+ (E=Ge, Sn, and Pb) have been explored by means of a stochastic search of their potential-energy surfaces by using the gradient embedded genetic algorithm (GEGA). The preferred isomer of the Ge5Li7+ ion is a slightly distorted analogue of the D5 h three-dimensional seven-pointed starlike structure adopted by the lighter C5Li7+ and Si5Li7+ clusters. In contrast, the preferred structures for Sn5Li7+ and Pb5Li7+ are quite different. By starting from the starlike arrangement, corresponding lowest-energy structures are generated by migration of one of the E atoms out of the plane with the a corresponding rearrangement of the Li atoms. To understand these structural preferences, we propose a new energy decomposition analysis based on isomerizations (isomerization energy decomposition analysis (IEDA)), which enable us to extract energetic information from isomerization between structures, mainly from highly charged fragments. [ABSTRACT FROM AUTHOR]

Abstract: The potential energy surfaces of the Si4Li n (n =1–7) systems have been explored in detail and the global minimum structures were identified. The stability and growth patterns of the title clusters is rationalized in terms of the phenomenological shell model in which the tetrahedral Si4Li4 cluster is a closed shell (20 valence electron) highly stable cluster. Given that the structures reported herein are global minima on their corresponding potential energy surfaces, we propose them as good candidates for experimental detection. [Copyright &y& Elsevier]

The B19- anion and other boron species have been dubbed 'Wankel motors' for the almost barrierless rotation of inner and outer concentric rings relative to each other in these compounds. A single substitution in B19- is shown to shut down the well-established fluxionality in the anion. A carbon atom substituted in the structure to give a neutral CB18 species is shown computationally to enforce bond localization. [ABSTRACT FROM AUTHOR]