Assessment of quantum‐chemical methods for electronic properties and geometry of signaling biomolecules

A reasonable balance between accuracy and feasibility of quantum‐chemical methods depends on the complexity of the molecular system and the scientific goals. Six series of indole‐, naphthalene‐, phenol‐, benzoic‐, phenoxy‐, other auxin‐derivatives, and a test set of similar organic molecules have been chosen for an assessment of 13 density functional and semi‐empirical molecular orbital methods with respect to electronic and structural properties. The accuracy and precision of HOMO/LUMO calculations are determined by comparison with experimental ionization potentials and electron affinities. Further comparison was performed at atomic level by covariance analysis. The methods KMLYP, MSINDO, and PM3 are precise and accurate for the whole set of molecules. The method AM1 offers comparable accuracy with the exception of electron affinities of indole derivatives, where significant deviations from experiment were observed. Geometrical properties were best reproduced with the semi‐empirical method MSINDO. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical study of tautomeric and ionizing effects of guanine,cytosine, and their methyl derivatives

The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of guanine and cytosine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre- and post-translational effects of guanine and cytosine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory B3LYP functional accompanied with 6-311G (d,p), 6-311+G (d,p), and 6-311++G (df,pd) basis sets. Our results reveal that the cytosine tautomer has a higher EA and IP than the guanine tautomers. The higher EA suggest that an electron that attaches to the GC base pair would predominately attach to the cytosine instead of guanine. The higher IP would suggest that an electron that is removed from the GC base pair would be predominately removed from the guanine within the base pair. Understanding how tautomerization, ionization, and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.     

The chalcone synthase superfamily of type III polyketide synthases

This review covers the functionally diverse type III polyketide synthase (PKS) superfamily of plant and bacterial biosynthetic enzymes. from the discovery of chalcone synthase (CHS) in the 1970s through the end of 2001. A broader perspective is achieved by a comparison of these CHS-like enzymes to mechanistically and evolutionarily related families of enzymes, including the type I and type II PKSs, as well as the thiolases and beta-ketoacyl synthases of fatty acid metabolism. As CHS is both the most frequently occurring and best studied type III PKS, this enzyme's structure and mechanism is examined in detail. The in vivo functions and biological activities of several classes of plant natural products derived from chalcones are also discussed. Evolutionary mechanisms of type III PKS divergence are considered, as are the biological functions and activities of each of the known and functionally divergent type III PKS enzymc families (currently twelve in plants and three in bacteria). A major focus of this review is the integration of information from genetic and biochemical studies with the unique insights gained from protein X-ray crystallography and homology modeling. This structural approach has generated a number of new predictions regarding both the importance and mechanistic role of various amino acid substitutions observed among functionally diverse type III PKS enzymes.     

The 3-21G(N*) basis set: An economical polarized basis set for ab initio studies on nitrogen-containing molecules

The 3-21G basis set shares with its older cousin, the 4-31G basis set, a tendency to overestimate valence angles at nitrogen atoms and to underestimate seriously barriers to inversion at such atoms. The 6-31G* basis set generally yields greatly improved results in these respects. It is here shown that, for a variety of molecules, supplementation of the 3-21G basis set at three- or two-coordinate nitrogen atoms with a set of six d-functions having exponent 1.0 leads to optimized geometries and inversion barriers at such nitrogen centers in good agreement with results obtained with the 6-31G* basis set. This supplemented basis set, designated as 3-21G(N*), also leads to calculated vibrational frequencies in good agreement with those calculated with the 6-31G* basis set. The 3-21G(N*) basis set offers an economical alternative to the 6-31G* basis set, particularly for molecules containing several first-row atoms other than nitrogen.     

The prediction of nucleophilic attacking sites via determinants of ‘active’ frontier and near-frontier orbitals

A method for computing the most favourable initial attacking site for a nucleophile on a transition metal complex is described, and applied to the nucleophilic substitution and addition reactions of fluoromethane, and the cationic complexes [BFe(CO)₃]⁺ (B = C₆H₇ and C₇H₉). The reactions considered are classified according to whether they are frontier or non-frontier orbitally or charge controlled. It is found that initial attack on the (polyenyl)M(CO)₃ cations is always predicted to occur at the M(CO)₃ moiety, in agreement with the experimental observation of intermediates in several such reactions and suggesting that the existence of these species is a general phenomenon.     

An investigation into the role of chloro-substituents in hydrogen-bonded crystals: The crystal structures of the dichlorophenols

A graphical analysis has been made of hydrogen-bonding patterns and non-bonded interactions in the crystal structures of the six dichlorophenols. This shows that hydrogen bonding is the primary interaction in stabilising all the isomers, and that C?C and Cl?Cl non-bonded interactions are also important in stabilising structures characterised by a short (≈ 4 Ã) axis.     

Toward templated metal-organic frameworks: synthesis, structures, thermal properties, and luminescence of three novel lanthanide-adipate frameworks

Three novel praseodymium-adipate frameworks were synthesized hydrothermally. GWMOF-3 ([Pr(2)(adipic acid)(3)(H(2)O)(4)].adipic acid.4H(2)O) and GWMOF-6 ([Pr(2)(adipic acid)(3)(H(2)O)(2)].4,4'-dipyridyl) formed three-dimensional structures, whereas GWMOF-4 ([Pr(2)(adipic acid)(3)(H(2)O)(2)].H(2)O) produced a more dense, two-dimensional topology. Single-crystal X-ray and powder diffraction, IR spectroscopy, fluorescence spectroscopy, thermogravimetric analysis, and elemental analysis were employed to characterize all samples. GWMOF-6 represents an innovative step forward in metal-organic framework synthesis where a neutral molecular species not used in the construction of the framework is utilized as a structure-directing agent, or template. Furthermore, this template molecule (4,4'-dipyridyl) is shown to sensitize the fluorescence of lanthanide metal centers in a europium analogue of GWMOF-6.     

A new smoothing-regularization approach for a maximum-likelihood estimation problem

We consider the problem min _i=1 ^m (aⁱ,x–b_iloga ⁱ, z) subject tox 0 which occurs as a maximum-likelihood estimation problem in several areas, and particularly in positron emission tomography. After noticing that this problem is equivalent to mind(b, Ax) subject tox 0, whered is the Kullback-Leibler information divergence andA, b are the matrix and vector with rows and entriesa ⁱ,b _i, respectively, we suggest a regularized problem mind(b, Ax) + d(v, Sx), where is the regularization parameter,S is a smoothing matrix, andv is a fixed vector. We present a computationally attractive algorithm for the regularized problem, establish its convergence, and show that the regularized solutions, as goes to 0, converge to the solution of the original problem which minimizes a convex function related tod(v, Sx). We give convergence-rate results both for the regularized solutions and for their functional values.The research of A. N. Iusem was partially supported by CNPq Grant No. 301280/86-MA.