Icosahedral B12, macropolyhedral boranes, β-rhombohedral boron and boron-rich solids

The preference for icosahedral B₁₂ amongst polyhedral boranes and elemental boron is explained based on an optimization of overlap model. The ingenious ways in which elemental boron and boron-rich solids achieve icosahedron-related structures are explained by a fragment approach. The Jemmis mno rules are used to get the electron requirements. The extra occupancies and vacancies in β-rhombohedral structures are shown to be inevitable results of electron requirements. The detailed understanding of the structure suggests ways of doping β-rhombohedral boron with metals for desired properties. Theoretical studies of model β-rhombohedral solids with metal dopings provide support for the analysis.     

Thermodynamic stability of boron: the role of defects and zero point motion

Its low weight, high melting point, and large degree of hardness make elemental boron a technologically interesting material. The large number of allotropes, mostly containing over a hundred atoms in the unit cell, and their difficult characterization challenge both experimentalists and theoreticians. Even the ground state of this element is still under discussion. For over 30 years, scientists have attempted to determine the relative stability of alpha- and beta-rhombohedral boron. We use density functional calculations in the generalized gradient approximation to study a broad range of possible beta-rhombohedral structures containing interstitial atoms and partially occupied sites within a 105 atoms framework. The two most stable structures are practically degenerate in energy and semiconducting. One contains the experimental 320 atoms in the hexagonal unit cell, and the other contains 106 atoms in the triclinic unit cell. When populated with the experimental 320 electrons, the 106 atom structure exhibits a band gap of 1.4 eV and an in-gap hole trap at 0.35 eV above the valence band, consistent with known experiments. The total energy of these two structures is 23 meV/B lower than the original 105 atom framework, but it is still 1 meV/B above the alpha phase. Adding zero point energies finally makes the beta phase the ground state of elemental boron by 3 meV/B. At finite temperatures, the difference becomes even larger.     

Structural paradigms in macropolyhedral boranes

Macropolyhedral borane clusters are concave polyhedra constituting fused convex simple polyhedra. They are formally obtained by condensation of simple polyhedral boranes under elimination of between one and four BH(3) or isoelectronic units. The number of eliminated vertexes from simple polyhedra equals the number of shared vertexes in macropolyhedral boranes. For each of the eight classes with general formulae ranging from B(n)H(n-4) to B(n)H(n+10), more than one structure type is possible, differing in the number of shared vertexes and in the types of the two combined cluster fragments. However, only one type of "potential structures" is represented by experimentally known examples and is found to be favored by theoretical calculations. A sophisticated system exists among the favored macropolyhedral borane structures. For each class of macropolyhedral boranes, the number of skeletal electron pairs is directly related to the general formula, the number of shared vertexes and the type of fused cluster fragments. In order to predict the distribution of vertexes among the fused fragments, we propose the concept of preferred fragments. Preferred fragments are those usually present in the thermodynamically most stable structure of a given class of macropolyhedral boranes and are also frequently observed in the experimentally known structures. This allows us to completely predict the cluster framework of the thermodynamically most stable macropolyhedral borane isomers.     

Structural relationships among two vertex sharing macropolyhedral boranes

Various two vertex sharing macropolyhedral boranes were computed at the B3LYP/6-311 + G**//B3LYP/6-31G* level of theory to determine the preferred fragments for the thermodynamically most stable isomers. These are nido-10 and arachno-9 vertex fragments for neutral macropolyhedral boranes. The thermodynamically most stable isomers of the nido:nido-, arachno:nido- and arachno:arachno-macropolyhedral borane classes are structurally related to each other by the successive removal of one open face vertex as in the case of simple polyhedral boranes. For these classes, the stabilities of the thermodynamically most stable macropolyhedra relative to isomeric simple polyhedra follow similar trends with respect to the number of skeletal electrons.     

Which nido:nido-macropolyhedral boranes are most stable?

A comparison of the relative stabilities computed at RB3LYP/6-311+G(d,p)//RB3LYP/6-31G(d)+ZPE of the neutral nido-single clusters and two vertex-sharing macropolyhedral nido:nido-clusters shows single-cluster nido-boranes with up to 11 vertexes to be energetically more favorable than isomeric macropolyhedral boranes. Extra hydrogen atoms at the open face have a significant influence on the relative stabilities of the single cluster nido-boranes vs nido:nido-macropolyhedral boranes. For anionic species, a clear-cut turning point for macropolyhedral preference is shifted to no less than 17 vertexes. Thermodynamically most stable neutral and anionic nido:nido-macropolyhedral boranes usually consist of a nido-10-vertex and a nido-11-vertex unit, respectively. The relative stabilities of isomeric neutral macropolyhedra reflect the patterns exhibited by the sum of thermodynamic stabilities of the individual clusters.     

A unifying electron-counting rule for macropolyhedral boranes, metallaboranes, and metallocenes.

A generally applicable electron-counting rule-the mno rule-that integrates macropolyhedral boranes, metallaboranes, and metallocenes and any combination thereof is presented. According to this rule, m + n + o number of electron pairs are necessary for a macropolyhedral system to be stable. Here, m is the number of polyhedra, n is the number of vertices, and o is the number of single-vertex-sharing condensations. For nido and arachno arrangements, one and two additional pairs of electrons are required. Wade's n + 1 rule is a special case of the mno rule, where m = 1 and o = 0. B20H16, for example has m = 2 and n = 20, leading to 22 electron pairs. Ferrocene, with two nido polyhedral fragments, has m = 2, n = 11, and o = 1, making the total 2 + 11 + 1 + 2 = 16. The generality of the mno rule is demonstrated by applying it to a variety of known macropolyhedral boranes and heteroboranes. We also enumerate the various pathways for condensation by taking icosahedral B12 as the model. The origin of the mno rule is explored by using fragment molecular orbitals. This clearly shows that the number of skeletal bonding molecular orbitals of two polyhedral fragments remains unaltered during exohedral interactions. This is true even when a single vertex is shared, provided the common vertex is large enough to avoid nonbonding interactions of adjacent vertices on either side. But the presence of more than one common vertex results in the sharing of surface orbitals thereby, reducing the electronic requirements.     

Determinants of cyanuric acid and melamine assembly in water

While the recognition of cyanuric acid (CA) by melamine (M) and their derivatives has been known to occur in both water and organic solvents for some time, analysis of CA/M assembly in water has not been reported (Ranganathan, A.; Pedireddi, V. R.; Rao, C. N. R. J. Am. Chem. Soc.1999, 121, 1752-1753; Mathias, J. P.; Simanek, E. E.; Seto, C. T.; Whitesides, G. M. Macromol. Symp.1994, 77, 157-166; Zerkowski, J. A.; MacDonald, J. C.; Seto, C. T.; Wierda, D. A.; Whitesides, G. M. J. Am. Chem. Soc.1994, 116, 2382-2391; Mathias, J. P.; Seto, C. T.; Whitesides, G. M. Polym. Prepr.1993, 34, 92-93; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1993, 115, 905-916; Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1992, 114, 5473-5475; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc.1990, 112, 6409-6411; Wang, Y.; Wei, B.; Wang, Q. J. Chem. Cryst.1990, 20, 79-84; ten Cate, M. G. J.; Huskens, J.; Crego-Calama, M.; Reinhoudt, D. N. Chem.-Eur. J.2004, 10, 3632-3639). We have examined assembly of CA/M, as well as assembly of soluble trivalent CA and M derivatives (TCA/TM), in aqueous solvent, using a combination of solution phase NMR, isothermal titration and differential scanning calorimetry (ITC/DSC), cryo-transmission electron microscopy (cryo-TEM), and synthetic chemistry. While the parent heterocycles coprecipitate in water, the trivalent system displays more controlled and cooperative assembly that occurs at lower concentrations than the parent and yields a stable nanoparticle suspension. The assembly of both parent and trivalent systems is rigorously 1:1 and proceeds as an exothermic, proton-transfer coupled process in neutral pH water. Though CA and M are considered canonical hydrogen-bonding motifs in organic solvents, we find that their assembly in water is driven in large part by enthalpically favorable surface-area burial, similar to what is observed with nucleic acid recognition. There are currently few synthetic systems capable of robust molecular recognition in water that do not rely on native recognition motifs, possibly due to an incomplete understanding of recognition processes in water. This study establishes a detailed conceptual framework for considering CA/M heterocycle recognition in water which enables the future design of molecular recognition systems that function in water.     

Electron-deficient bonding in rhomboid rings

The bonding environment of boron is usually thought about in terms of localized 2c-2e/3c-2e bonding (as in diborane) or completely delocalized polyhedral bonding (as in B(12)H(12)(2)(-)). Recently, a number of boron compounds having a rhomboidal B(4) framework have been synthesized; these show an amazing variation in their skeletal electron count, one that cannot be interpreted in familiar ways. In this report, we systematically explore the origin of the range of electron counts in these compounds. We find that four skeletal MOs are primarily responsible for keeping the B(4) skeleton together. As a subunit in a macropolyhedral environment, termed rhombo-B(4), such an arrangement of B atoms deviates from Wade's rule by three electron pairs (if treated as a distorted arachno system derived from B(6)H(6)(2)(-)). Aided by this analysis, we examine the nature of bonding in Na(3)B(20), where the rhombo-B(4) unit forms linear chains fusing closo-B(7) units. Theory suggests that this structure requires one more electron per formula unit for optimal bonding. Finally, we study the nature of bonding in beta-SiB(3), where silicon atoms also adopt the rhomboid framework.     

Can undoped calcium tetraborides exist? An answer from the comparison of its density functional theory electronic structure with that of rare-earth metal tetraboride

Periodic density functional theory calculations are used to discuss the existence of metal tetraborides MB4 with divalent metals. Tetraborides which contain metal atoms inserted in a three-dimensional boron network made of B6 octahedra and B2 dumbbells exhibit a pseudo energy gap for a count of 60 valence electrons per M4(B6)2(B2)2 formula unit. Such a count satisfies the stability electron requirement for B6(2-) (20 electrons) octahedra and B2(2-) (8 electrons) units and allows the filling of two supplementary low-lying bands deriving from the valence metallic d atomic orbitals. This favored electron count is not reached for CaB4 which is then formally deficient by one electron per metal atom. This indicates that CaB4 is unlikely to exist without n-doping.     

Conserved mechanism of copper binding and transfer. A comparison of the copper-resistance proteins PcoC from Escherichia coli and CopC from Pseudomonas syringae

The copper-resistance proteins PcoC from Escherichia coli and CopC from Pseudomonas syringae exhibit 67% sequence identity, but the chemistry reported for PcoC (Peariso, K.; Huffman, D. L.; Penner-Hahn, J. E.; O'Halloran, T. V. J. Am. Chem. Soc. 2003, 125, 342-343) was distinctly different from that reported for CopC (Zhang, L.; Koay, M.; Maher, M. J.; Xiao, Z.; Wedd, A. G. J. Am. Chem. Soc. 2006, 128, 5834-5850). The source of the inconsistency has been identified, and His1 is confirmed as an unprecedented bidentate ligand in each protein. Access to a bona fide wild-type PcoC protein allowed unequivocal observation of intermediates involved in intermolecular redox copper transfer reactions.     

Synthesis design and structure of a multipore zeolite with interconnected 12- and 10-MR channels

A new molecular sieve, ITQ-38, containing interconnected large and medium pores in its structure has been synthesized. The rational combination of dicationic piperidine-derivative molecules as organic structure directing agents (OSDAs) with germanium and boron atoms in alkaline media has allowed the synthesis of ITQ-38 zeolite. High-resolution transmission electron microscopy (HRTEM) has been used to elucidate the framework topology of ITQ-38, revealing the presence of domains of perfect ITQ-38 crystals as well as very small areas containing nanosized ITQ-38/ITQ-22 intergrowths. The structure of ITQ-38 is highly related to ITQ-22 and the recently described polymorph C of ITQ-39 zeolite. It shares a common building layer with ITQ-22 and contains the same building unit as the polymorph C of ITQ-39. All three structures present similar framework density, 16.1 T atoms/1000 ?(3).     

Copper chemistry of beta-diketiminate ligands: monomer/dimer equilibria and a new class of bis(mu-oxo)dicopper compounds

A series of Cu(I) and Cu(II) complexes of a variety of beta-diketiminate ligands (L(-)) with a range of substitution patterns were prepared and characterized by spectroscopic, electrochemical, and, in several cases, X-ray crystallographic methods. Specifically, complexes of the general formula [LCuCl](2) were structurally characterized and their magnetic properties assessed through EPR spectroscopy of solutions and, in one instance, by variable-temperature SQUID magnetization measurements on a powder sample. UV-vis spectra indicated reversible dissociation to 3-coordinate monomers LCuCl in solution at temperatures above -55 degrees C. The Cu(I) complexes LCu(MeCN) exhibited reversible Cu(I)/Cu(II) redox couples with E(1/2) values between +300 and +520 mV versus NHE (cyclic voltammetry, MeCN solutions). These complexes were highly reactive with O(2), yielding intermediates that were identified as rare examples of neutral bis(mu-oxo)dicopper complexes on the basis of their EPR silence, diagnostic UV-vis absorption data, and O-isotope-sensitive resonance Raman spectroscopic features. The structural features of the compounds [LCuCl](2) and LCu(MeCN) as well as the proclivity to form bis(mu-oxo)dicopper products upon oxygenation of the Cu(I) complexes are compared to data previously reported for complexes of more sterically hindered beta-diketiminate ligands (Aboelella, N. W.; Lewis, E. A.; Reynolds, A. M.; Brennessel, W. W.; Cramer, C. J.; Tolman, W. B. J. Am. Chem. Soc. 2002, 124, 10600. Spencer, D. J. E.; Aboelella, N. W.; Reynolds, A. M.; Holland, P. L.; Tolman, W. B. J. Am. Chem. Soc. 2002, 124, 2108. Holland, P. L.; Tolman, W. B. J. Am. Chem. Soc. 1999, 121, 7270). The observed structural and reactivity differences are rationalized by considering the steric influences of both the substituents on the flanking aromatic rings and those present on the beta-diketiminate backbone.     

Theoretical evidence for C-F bond activation by a fluoro-calix[4]pyrrole-tert-amine macrocycle

Density functional theory as well as highly correlated ab initio molecular orbital theory was used to explore the possibility of activating C-F bonds in fluoroalkanes by organic macrocycles. The results indicate that the reaction between fluoro-calix [4]pyrrole-tert-amine and CH3F via a Menshutkin displacement mechanism is highly favorable and competitive from a thermochemical point of view with the very efficient C-Cl activation by a simple macrocyclic amine recently reported in the literature (Stanger, L. J.; Noll, B. C.; Gonzalez, C.; Marquez, M.; Smith, B. D. J. Am. Chem. Soc. 2005, 127, 4184).     

Metal ion binding by a bicyclic diamide: deep UV Raman spectroscopic characterization

Deep UV resonance Raman spectroscopy was used for characterizing ligand-metal ion complexes. The obtained results demonstrated a strong intrinsic sensitivity and selectivity of a Raman spectroscopic signature of a bicyclic diamide, a novel chelating agent for lanthanides and actinides (Lumetta, G. J.; Rapko, B. M.; Garza, P. A.; Hay, B. P.; Gilbertson, R. D.; Weakley, T. J. R.; Hutchison, J. E. J. Am. Chem. Soc. 2002, 124, 5644). Molecular modeling, which included structure optimization and calculation of Raman frequencies and resonance intensities, allowed for assigning all strong Raman bands of the bicyclic diamide as well as predicting the band shifts observed because of complex formation with metal ions. A comparative analysis of Raman spectra and the results of the molecular modeling could be used for elucidating the structure of complexes in solution.     

Searching for the second oxidant in the catalytic cycle of cytochrome P450: a theoretical investigation of the iron(III)-hydroperoxo species and its epoxidation pathways

Iron(III)-hydroperoxo, [Por(CysS)Fe(III)-OOH](-), a key species in the catalytic cycle of cytochrome P450, was recently identified by EPR/ENDOR spectroscopies (Davydov, R.; Makris, T. M.; Kofman, V.; Werst, D. E.; Sligar, S. G.; Hoffman, B. M. J. Am. Chem. Soc. 2001, 123, 1403-1415). It constitutes the last station of the preparative steps of the enzyme before oxidation of an organic compound and is implicated as the second oxidant capable of olefin epoxidation (Vaz, A. D. N.; McGinnity, D. F.; Coon, M. J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 3555-3560), in addition to the penultimate active species, Compound I (Groves, J. T.; Han, Y.-Z. In Cytochrome P450: Structure, Mechanism and Biochemistry, 2nd ed.; Ortiz de Montellano, P. R., Ed.; Plenum Press: New York, 1995; pp 3-48). In response, we present a density functional study of a model species and its ethylene epoxidation pathways. The study characterizes a variety of properties of iron(III)-hydroperoxo, such as the O-O bonding, the Fe-S bonding, Fe-O and Fe-S stretching frequencies, its electron attachment, and ionization energies. Wherever possible these properties are compared with those of Compound I. The proton affinities for protonation on the proximal and distal oxygen atoms of iron(III)-hydroperoxo, and the effect of the thiolate ligand thereof, are determined. In accordance with previous results (Harris, D. L.; Loew, G. H. J. Am. Chem. Soc. 1998, 120, 8941-8948), iron(III)-hydroperoxo is a strong base (as compared with water), and its distal protonation leads to a barrier-free formation of Compound I. The origins of this barrier-free process are discussed using a valence bond approach. It is shown that the presence of the thiolate is essential for this process, in line with the "push effect" deduced by experimentalists (Sono, M.; Roach, M. P.; Coulter, E. D.; Dawson, J. H. Chem. Rev. 1996, 96, 2841-2887). Finally, four epoxidation pathways of iron(III)-hydroxperoxo are located, in which the species transfers oxygen to ethylene either from the proximal or from the distal sites, in both concerted and stepwise manners. The barriers for the four mechanisms are 37-53 kcal/mol, in comparison with 14 kcal/mol for epoxidation by Compound I. It is therefore concluded that iron(III)-hydroperoxo, as such, cannot be a second oxidant, in line with its significant basicity and poor electron-accepting capability. Possible versions of a second oxidant are discussed.     

Rapid phosphine exchange on 1.5-nm gold nanoparticles

Triphenylphosphine-cappped, 1.5-nm gold nanoparticles "Au(101)(PPh(3))(21)Cl(5)" prepared following Hutchison's procedure (Weare, W. W.; Reed, S. M.; Warner, M. G.; Hutchison, J. E. J. Am. Chem. Soc. 2000, 122, 12890) undergo rapid exchange of capping ligand phosphine with dissociated and added phosphine in dichloromethane solvent at 298 K. Remarkably, while the (1)H NMR spectrum resonances of the attached phosphine are broad, characteristic of a range of incompletely averaged environments, the (31)P NMR spectrum (observable only at 213 K and below) exhibits a single, narrow resonance indicating that all of the phosphorus atoms are magnetically equivalent.     

Origin of the nonplanarity of tetrafluoro cyclobutadiene, C4F4

Density functional theory as well as M?ller-Plesset investigations has been carried out on tetrafluoro cyclobutadiene, C4F4, to explore the origin of its nonplanarity. Although Petersson et al. (Petersson, E. J.; Fanuele, J. C.; Nimlos, M. R.; Lemal, D. M.; Ellison, G. B.; Radziszewski, J. G. J. Am. Chem. Soc. 1997, 119, 11122-11123) had earlier predicted a nonplanar geometry of this compound on the basis of spectral and bond orbital analysis, the explanation of the same from a more fundamental point of view is still missing. In the present study, we provide a heuristic explanation for the origin of nonplanarity of C4F4. The two major driving forces behind this nonplanar geometry are the unusual aromaticity of this cyclic homoatomic 4pi electron system and the second-order Jahn-Teller effect (SOJTE). These driving forces can well be explained by various energy and density parameters and also by nucleus-independent chemical shift (NICS) values. Aromaticity of a cyclic homoatomic 4pi electron system is quite remarkable. The enhancement of pi- delocalization as evidenced from molecular orbital analysis may be attributed to s-ppi mixing in nonplanar C4F4.     

Red light in chemiluminescence and yellow-green light in bioluminescence: color-tuning mechanism of firefly, Photinus pyralis, studied by the symmetry-adapted cluster-configuration interaction method

The yellow-green luminescence from firefly luciferase has long been understood to be the emission from enol-oxyluciferin. However, a recent experiment showed that an oxyluciferin constrained to the keto form produced a yellow-green emission in luciferase (Branchini, B. R.; Murtiashaw, M. H.; Magyar, R. A.; Portier, N. C.; Ruggiero, M. C.; Stroh, J. G. J. Am. Chem. Soc. 2002, 124, 2112-2113). The present quantum mechanical/molecular mechanical and symmetry-adapted cluster-configuration interaction (SAC-CI) theoretical study supports the keto-form to be the yellow-green bioluminescence state in luciferase. We give the theoretically optimized structure of the excited state of oxyluciferin within luciferase, which gives luminescence calculated by the SAC-CI method that is close to the experimental value. Coulombic interactions with neighboring residues, in particular Arg218 and the phosphate group of AMP, play important roles in the color-tuning mechanism. Transformation to the enol form is energetically unfavorable in the luciferase environment. The twisted intramolecular charge-transfer (TICT) state is meta stable and would be easily relaxed to the co-planer structure. Further analyses were performed to verify the spectral-tuning mechanism based on the protonation state and the resonance structure of oxyluciferin.     

Rules for macropolyhedral boranes

Based on extensive computational studies, rules to derive the thermodynamically most stable macropolyhedral borane for any formula between B_nH_n−4 to B_nH_n+8 were identified. Formally, the macropolyhedral boranes may be obtained by condensing regular convex borane clusters where as many BH₃ moieties are eliminated as vertexes are shared in the macropolyhedral framework. Macropolyhedral boranes consisting of two cluster fragments may be classified according to their general formulae ranging from B_nH_n−4 to B_nH_n+8. For each of these formulae, various structure types are conceivable differing in the number of shared vertexes and in the types of combined cluster fragments. However, for each general formula, only one structure type is known experimentally and this one is also computationally found to be thermodynamically preferred! For each class of macropolyhedral B_nH_m boranes, a preferred number of shared vertexes is identified, and this determines the number of skeletal electron pairs. With this knowledge, the type of fused clusters, i.e. the most favourable framework, may be predicted. The concept of preferred fragments may be applied to even predict the distribution of vertexes among the fused fragments in the thermodynamically most stable isomers. When there is at least one closo fragment it has 12-vertexes. Without any closo fragment the most stable macropolyhedral borane has a nido 10-vertex cluster fragment.     

Controlled excitations of the Belousov-Zhabotinsky reaction: Experimental procedures

The purpose of this research was to explore the unstirred, ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction as an experimental model for the response of excitable media to small perturbations (slightly larger than the threshold for excitations). Following Showalter et al. (Showalter, K.; Noyes, R. M.; Turner, H. J.Am. Chem. Soc. 1979, 101, 7463-69), we used a positively biased silver electrode to release silver ions into a BZ reaction mixture, removing bromide ions and causing an excitation if sufficient bromide was removed. We found (1) a scaling region in which the delay before activation increased linearly as the size of the perturbation decreased, qualitatively consistent with but not fully explained by the Oregonator of Field et al. (Field, R. J.; K?r?s, E.; Noyes, R. M. J. Am. Chem. Soc. 1972, 94, 8649-64); (2) evidence for a 10 s oligomerization time scale; and (3) that activations were always delayed until after the end of a pulse of current, with the delay essentially constant for sufficiently long pulses, an effect not seen in simple ODE models but consistent with the anomalously large current apparently required for activation (Showalter, K.; Noyes, R. M. J. Am. Chem. Soc. 1976, 98, 3730-31) and explainable by bromide transport. Overall, the BZ system appeared to be well-suited as an experimental prototype, despite its complexity.