Novel graph-theoretical approach to estimating the relative importance of individual Kekulé valence structures. I. Simple catacondensed systems

A novel graph-theoretical approach for ordering Kekulé valence structures of benzenoid hydrocarbons is presented. The approach involves the transformation of the Kekulé structures into the subspaces of their individual double bonds. The submolecules generated in this way [H. Joela, Theor. Chim. Acta 39 , 241 (1975)] are ordered according to suitable connectivity indices. The resulting orders parallel those predicted from the so called Kekulé indices [A. Graocvac, I. Gutman, M. Randi?, and N. Trinajst?, J. Am. Chem. Soc. 95 , 6267 (1973)]. A relation is thus illustrated between VB and MO theories. The method is new and allows the prediction of the relative stabilities of structures from purely combinatorial vent without resort to computer.     

Novel graph-theoretical approach to estimating the relative importance of individual Kekulé valence structures. III. Nonalternate and nonbenzenoid hydrocarbons

Molecular connectivities of submolecules [H. Joela, Theor. Chim. Acta 39 , 241 (1975)] corresponding to Kekulé structures of nine nonalternate hydrocarbons and four nonbenzenoid hydrocarbons containing four-membered rings are correlated with their Kekulé indices. In the latter class of compounds it was observed that the corresponding submolecules contain cut vertices and bridges in contrast to submolecules of benzenoid hydrocarbons which are devoid of such bridges. It was observed, furthermore, that the branching index goes up with the number of bridges in the submolecule. The results present an application to the abstract relation [D. Cvetkovi?, I. Gutman, and N. Trinajsti?, J. Chem. Phys. 61 , 2700 (1974)] between resonance and MO theories.     

Ordering of Kekulé structures using nonadjacent numbers

Kekulé indices and conjugated circuits are computed for 36 Kekulé structures, together with two VB quantities associated with the corresponding factor graphs (previously called submolecules). These latter quantitites are nonadjacent numbers of Hosoya and the reciprocal of the connectivity indices of Randi?. It was found that the index of Hosoya successfully orders a set of Kekulé structures belonging to the same hydrocarbon in a parallel order as their Kekulé indices and branching indices. This substantiates the relation between VB and MO theories. A code is derived by summing contributions of nonadjacent numbers in all Kekulé stuctures of a hydrocarbon. The order of the resulting codes is found to be identical to the order of the molecular properties (resonance energies, π-energies, and eigenvalues) of the hydrocarbons.     

Computing the Kekulé structure count for alternant hydrocarbons

A fast computer algorithm brings computation of the permanents of sparse matrices, specifically, molecular adjacency matrices. Examples and results are presented, along with a discussion of the relationship of the permanent to the Kekulé structure count. A simple method is presented for determining the Kekulé structure count of alternant hydrocarbons. For these hydrocarbons, the square of the Kekulé structure count is equal to the permanent of the adjacency matrix. In addition, for alternant structures the adjacency matrix for N atoms can be written in such a way that only an N/2 × N/2 matrix need be evaluated. The Kekulé structure count correlates with topological indices. The inclusion of the number of cycles improves the fit. When comparing with previous results, the variance decreases 74%. The calculated standard heat of formation correlates with the logarithm of the Kekulé structure count. This heat increments 349 kJ/mol each time the Kekulé structure count increases by one order of magnitude. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Computation of the pseudorotation matrix to satisfy the Eckart axis conditions

A general solution for satisfying the Eckart axis conditions [C. Eckart, Phys. Rev. 47, 552 (1935)] is presented. The goal is to find such a pseudorotation matrix T that the vector product between the reference molecular conformation R and another transformed conformation r' is zero [ summation operator(a)m(a) r(a) 'xRa=0; r(a) '=Tr(a)]. Our solution avoids the limitations of the earlier one [H. M. Pickett and H. L. Strauss, J. Am. Chem. Soc. 92, 7281 (1970)], which fails when one of the involved intermediate matrices is singular. We also discuss how to choose among the always nonunique pseudorotation matrices T the one that represents a true rotation for situations when an alignment of the two conformations is desired.     

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.     

Diversity-oriented fluorescence library approach (DOFLA) to the discovery of chymotrypsin sensor

The diversity-oriented fluorescence library approach (DOFLA) has emerged and found applications in various fields to meet the acute demands for novel fluorescence sensors. The power of this approach has been demonstrated with the impressive discoveries of novel sensors for polymers such as DNA and heparin or for small molecules such as GTP and glutathione ( J. Am. Chem. Soc. 2003, 125, 1130- 1131 ; J. Am. Chem. Soc. 2006, 128, 10380- 10381 ; J. Am. Chem. Soc. 2007, 129, 4510- 4511 ; Chem. Commun. [Online early access]. DOI: 10.1039/b717058k. Published online Dec 11, 2008. http://www.rsc.org/publishing/journals/CC/article.asp?doi=b717058k ). Herein we report the application of this approach on quinaldinium fluorescent dye library synthesis on solid support and novel chymotrypsin sensor discovery. The new sensors are not only selective to chymotrypsin over other proteins but also only to the active conformation of chymotrypsin.     

Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones.

We report an accurate computational study of the role of water in transfer hydrogenation of formaldehyde with a ruthenium‐based catalyst using a water‐specific model. Our results suggest that the reaction mechanism in aqueous solution is significantly different from that in the gas phase or in methanol solution. Previous theoretical studies have shown a concerted hydride and proton transfer in the gas phase (M. Yamakawa, H. Ito, R. Noyori, J. Am. Chem. Soc. 2000 , 122, 1466–1478;J.‐W. Handgraaf, J. N. H. Reek, E. J. Meijer, Organometallics 2003 , 22, 3150–3157; D. A. Alonso, P. Brandt, S. J. M. Nordin, P. G. Andersson, J. Am. Chem. Soc. 1999 , 121, 9580–9588; D. G. I. Petra, J. N. H. Reek, J.‐W. Handgraaf, E. J. Meijer, P. Dierkes, P. C. J. Kamer, J. Brussee, H. E. Schoemaker, P. W. N. M. van Leeuwen, Chem. Eur. J. 2000 , 6, 2818–2829), whereas a delayed, solvent‐mediated proton transfer has been observed in methanol solution (J.‐W. Handgraaf, E. J. Meijer, J. Am. Chem. Soc. 2007 , 129, 3099–3103). In aqueous solution, a concerted transition state is observed, as in the previous studies. However, only the hydride is transferred at that point, whereas the proton is transferred later by a water molecule instead of the catalyst.     

Mechanistic aspects of proton chain transfer in the green fluorescent protein. Part II. A comparison of minimal quantum chemical models

In this paper we report the results of extensive quantum chemical reaction pathway calculations for the electronic ground state of several different cluster models that mimic the proton chain transfer path within the green fluorescent protein (GFP). Our principal objective is to establish the robustness with respect to variations in the model of our recent mechanistic inferences for the ground state proton chain transfer [S. Wang and S. C. Smith, J. Phys. Chem. B, 2006, 110, 5084]. Additionally, comparison of our ground state results with the excited state proton transfer (ESPT) study by Vendrell et al. [O. Vendrell, R. Gelabert, M. Moreno and J. M. Lluch, J. Am. Chem. Soc., 2006, 128, 3564] leads to the conclusion that the mechanism of proton chain transfer may be expected to be analogous in ground and excited states, principally because in both cases the loss of the chromophore's phenolic proton contributes strongly to the reaction coordinate only late in the reaction path.     

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.     

Mathematical studies of Kekulé structures

The perfect matching vector and forcing and the Kekulé-vector of cata-benzenoids are defined. Two theorems are given which set the sufficient and necessary conditions for HKZ-vector (Harary et al. J Math Chem 6:295, 1991) and Kekulé-vector in cata-benzenoids. Additional two theorems are obtained which give sharp bounds for the modules of HKZ- and Kekulé vectors. Dedicated to Professor Tadeusz Marek Krygowski on the happy occasion of his 70th birthday.     

A structural model for cyanine dyes templated into the minor groove of DNA

3,3-Diethylthiadicarbocyanine (DiSC₂(5)) is a monocationic dye which forms cofacial dimers that insert into the minor groove of DNA [J. Seifert, R. Conner, S. Kushon, M. Wang, B. Armitage, J. Am. Chem. Soc. 121 (1999) 2987]. These dyes self-assemble into long helical aggregates in AT-rich regions with the dimers aligned in an end-to-end fashion. A model is presented that allows for the construction of large helical aggregates with continuously variable structural parameters. The spectra or excited states are computed using a direct intermediate neglect of differential overlap (INDO) single configuration interaction (SCI) method. Results are reported for both H- and J-type aggregates ranging in size from 2 to 6 dimers. A more approximate model based on transition charge densities enables calculations of larger aggregates. These models are used to derive structural parameters of both H- and J-type aggregates from the available spectral data, resulting in a new structural model for J-type aggregation in these systems.     

Local hardness equalization: exploiting the ambiguity

In the density-functional theory of chemical reactivity, the local hardness is known to be an ambiguous concept. The mathematical structure associated with this problematic situation is elaborated and three common definitions for the local hardness are critically examined: the frontier local hardness [S. K. Ghosh, Chem. Phys. Lett. 172, 77 (1990)], the total local hardness [S. K. Ghosh and M. Berkowitz, J. Chem. Phys. 83, 2976 (1985)], and the unconstrained local hardness [P. W. Ayers and R. G. Parr, J. Am. Chem. Soc. 122, 2010 (2000)]. The frontier local hardness has particularly nice properties: (a) it has smaller norm than most, if not all, other choices of the local hardness and (b) it is "unbiased" in an information-theoretic sense. For the ground electronic state of a molecular system, the frontier local hardness is equal to the global hardness. For an electronic system in its ground state, both the chemical potential and the frontier local hardness are equalized. The frontier local hardness equalization principle provides a computational approach for designing reagents with desirable chemical reactivity profiles.     

3D superposition of chemical fragments for N‐membered rings: application to conformational analysis

In this paper a procedure is suggested for the 3D superposition of chemical fragments, which is specifically designed for rings molecules and can be combined with statistical multivariate procedures to extract useful conformational information. The procedure relies on the plane introduced by Cremer and Pople ‘A general definition of ring puckering coordinates. J. Am. Chem. Soc. 1975; 97 (6): 1354–1358’ to define the celebrated puckering coordinates, and provides a measure of distance between two geometrical conformations. Real datasets are analyzed to illustrate how it can be used as input to agglomerative clustering methods, multidimensional scaling analysis and allows to compute the centroid of a group of fragments. Copyright © 2010 John Wiley & Sons, Ltd.     

Ketone methylenation without epimerization: Total synthesis of (±) laurene

A total synthesis of the sesquiterpene hydrocarbon laurene, incorporating a non-epimerizing method of ketone methylenation, has been achieved. It is shown that both the phosphonic acid bis(dimethylamide) method of Corey and Kwiatkowski and the phosphite pyrolysis method of Kuwajima are non-epimerizing. For the present case however, the recently published method of Coates [J. Am. Chem. Soc. 94, 4758 (1972)] is preferable.     

Electronic structure, excited states, and photoelectron spectra of uranium, thorium, and zirconium bis(Ketimido) complexes (C5R5)2M[-NCPh2]2 (M = Th, U, Zr; R = H, CH3)

Organometallic actinide bis(ketimide) complexes (C5Me5)2An[-N=C(Ph)(R)]2 (where R = Ph, Me, and CH2Ph) of thorium(IV) and uranium(IV) have recently been synthesized that exhibit chemical, structural, and spectroscopic (UV-Visible, resonance-enhanced Raman) evidence for unusual actinide-ligand bonding. [Da Re et al., J. Am. Chem. Soc., 2005, 127, 682; Jantunen et al., Organometallics, 2004, 23, 4682; Morris et al., Organometallics, 2004, 23, 5142.] Similar evidence has been observed for the group 4 analogue (C5H5)2Zr[-N=CPh2]2. [Da Re et al., J. Am. Chem. Soc., 2005, 127, 682.] These compounds have important implications for the development of new heavy-element systems that possess novel electronic and magnetic properties. Here, we have investigated M-ketimido bonding (M = Th, U, Zr), as well as the spectroscopic properties of the highly colored bis-ketimido complexes, using density functional theory (DFT). Photoelectron spectroscopy (PES) has been used to experimentally elucidate the ground-state electronic structure of the thorium and uranium systems. Careful examination of the ground-state electronic structure, as well as a detailed modeling of the photoelectron spectra, reveals similar bonding interactions between the thorium and uranium compounds. Using time-dependent DFT (TDDFT), we have assigned the bands in the previously reported UV-Visible spectra for (C5Me5)2Th[-N=CPh2]2, (C5Me5)2U[-N=CPh2]2, and (C5H5)2Zr[-N=CPh2]2. The low-energy transitions are attributed to ligand-localized N p --> C=N pi excitations. These excited states may be either localized on a single ketimido unit or may be of the ligand-ligand charge-transfer type. Higher-energy transitions are cyclopentadienyl pi --> CN pi or cyclopentadienyl pi --> phenyl pi in character. The lowest-energy excitation in the (C5Me5)2U[-N=Ph2]2 compound is attributed to f-f and metal-ligand charge-transfer transitions that are not available in the thorium and zirconium analogues. Geometry optimization and vibrational analysis of the lowest-energy triplet state of the zirconium and thorium compounds also aids in the assignment and understanding of the resonance-enhanced Raman data that has recently been reported. [Da Re et al., J. Am. Chem. Soc., 2005, 127, 682.].     

The triplet-state lifetime of indole in aqueous and viscous environments: significance to the interpretation of room temperature phosphorescence in proteins

The interpretation of room temperature phosphorescence studies of proteins requires an understanding of the mechanisms governing the tryptophan triplet-state lifetimes of residues fully exposed to solvent and those deeply buried in the hydrophobic core of proteins. Since solvents exposed tryptophans are expected to behave similarly to indole free in solution, it is important to have an accurate measure of the triplet state lifetime of indole in aqueous solution. Using photon counting techniques and low optical fluence (J/cm(2)), we observed the triplet-state lifetime of aqueous, deoxygenated indole and several indole derivatives to be approximately 40 micros, closely matching the previous reports by Bent and Hayon based on flash photolysis (12 micros; Bent, D. V.; Hayon, E. J. Am. Chem. Soc. 1975, 97, 2612-2619) but much shorter than the 1.2 ms lifetime observed more recently (Strambini, G. B.; Gonnelli, M. J. Am. Chem. Soc. 1995, 117, 7646-7651). However, we have now been able to reproduce the long lifetime reported by the latter workers for aqueous indole solutions and show that it likely arises from geminate recombination of the indole radical cation and solvated electron, a conclusion based on studies of the indole radical cation in water (Bent and Hayon, 1975). The evidence for this comes from a fast rise in the phosphorescence emission and measurements of a corresponding enhanced quantum yield in unbuffered solutions. This species can be readily quenched, and the corresponding fast rise disappears, leaving a monoexponential 40 micros decay, which we argue is the true indole triplet lifetime. The work is put in the context of room temperature phosphorescence studies of proteins.     

Four-coordinate iron(II) porphyrinates: electronic configuration change by intermolecular interaction

The syntheses and structures of three four-coordinate iron(II) porphyrinates are reported. The three derivatives are tetraarylporphyrin species, where the aryl is either phenyl, p-methylphenyl, or p-methoxyphenyl. One of these derivatives, that of tetraphenylporphyrin, Fe(TPP), is a new crystalline phase that is distinct from the earlier reported phase (Collman, J. P.; et al. J. Am. Chem. Soc. 1975, 97, 2676). This new phase of Fe(TPP) has a very saddled porphyrin core; the prior phase was ruffled. The iron atom has close interactions (approximately 3.10 A) with two pyrrole Cb-Cb bonds above and below the porphyrin plane. M?ssbauer spectra and magnetic susceptibility measurements, different for the two phases, provide strong evidence that the two phases of Fe(TPP) have distinct electronic structures that originate from intermolecular interactions.