No abstract

Twenty years ago, the landmark AM1 was introduced, and has since had an increasingly wide following among chemists due to its consistently good results and time-tested reliability--being presently available in countless computational quantum chemistry programs. However, semiempirical molecular orbital models still are of limited accuracy and need to be improved if the full potential of new linear scaling techniques, such as MOZYME and LocalSCF, is to be realized. Accordingly, in this article we present RM1 (Recife Model 1): a reparameterization of AM1. As before, the properties used in the parameterization procedure were: heats of formation, dipole moments, ionization potentials and geometric variables (bond lengths and angles). Considering that the vast majority of molecules of importance to life can be assembled by using only six elements: C, H, N, O, P, and S, and that by adding the halogens we can now build most molecules of importance to pharmaceutical research, our training set consisted of 1736 molecules, representative of organic and biochemistry, containing C, H, N, O, P, S, F, Cl, Br, and I atoms. Unlike AM1, and similar to PM3, all RM1 parameters have been optimized. For enthalpies of formation, dipole moments, ionization potentials, and interatomic distances, the average errors in RM1, for the 1736 molecules, are less than those for AM1, PM3, and PM5. Indeed, the average errors in kcal x mol(-1) of the enthalpies of formation for AM1, PM3, and PM5 are 11.15, 7.98, and 6.03, whereas for RM1 this value is 5.77. The errors, in Debye, of the dipole moments for AM1, PM3, PM5, and RM1 are, respectively, 0.37, 0.38, 0.50, and 0.34. Likewise, the respective errors for the ionization potentials, in eV, are 0.60, 0.55, 0.48, and 0.45, and the respective errors, in angstroms, for the interatomic distances are 0.036, 0.029, 0.037, and 0.027. The RM1 average error in bond angles of 6.82 degrees is only slightly higher than the AM1 figure of 5.88 degrees, and both are much smaller than the PM3 and PM5 figures of 6.98 degrees and 9.83 degrees, respectively. Moreover, a known error in PM3 nitrogen charges is corrected in RM1. Therefore, RM1 represents an improvement over AM1 and its similar successor PM3, and is probably very competitive with PM5, which is a somewhat different model, and not fully disclosed. RM1 possesses the same analytical construct and the same number of parameters for each atom as AM1, and, therefore, can be easily implemented in any software that already has AM1, not requiring any change in any line of code, with the sole exception of the values of the parameters themselves.

Our previously defined Sparkle model (Inorg. Chem. 2004, 43, 2346) has been reparameterized for Eu(III) as well as newly parameterized for Gd(III) and Tb(III). The parameterizations have been carried out in a much more extensive manner, aimed at producing a new, more accurate model called Sparkle/AM1, mainly for the vast majority of all Eu(III), Gd(III), and Tb(III) complexes, which possess oxygen or nitrogen as coordinating atoms. All such complexes, which comprise 80% of all geometries present in the Cambridge Structural Database for each of the three ions, were classified into seven groups. These were regarded as a "basis" of chemical ambiance around a lanthanide, which could span the various types of ligand environments the lanthanide ion could be subjected to in any arbitrary complex where the lanthanide ion is coordinated to nitrogen or oxygen atoms. From these seven groups, 15 complexes were selected, which were defined as the parameterization set and then were used with a numerical multidimensional nonlinear optimization to find the best parameter set for reproducing chemical properties. The new parameterizations yielded an unsigned mean error for all interatomic distances between the Eu(III) ion and the ligand atoms of the first sphere of coordination (for the 96 complexes considered in the present paper) of 0.09 A, an improvement over the value of 0.28 A for the previous model and the value of 0.68 A for the first model (Chem. Phys. Lett. 1994, 227, 349). Similar accuracies have been achieved for Gd(III) (0.07 A, 70 complexes) and Tb(III) (0.07 A, 42 complexes). Qualitative improvements have been obtained as well; nitrates now coordinate correctly as bidentate ligands. The results, therefore, indicate that Eu(III), Gd(III), and Tb(III) Sparkle/AM1 calculations possess geometry prediction accuracies for lanthanide complexes with oxygen or nitrogen atoms in the coordination polyhedron that are competitive with present day ab initio/effective core potential calculations, while being hundreds of times faster.

No abstract

The Laplacian of the spherically averaged charge density ∇2ρ̄(r) has been computed from nonrelativistic SCF wave functions for the neutral atoms from hydrogen to uranium, and the singly positive ions, from helium to barium and lutetium to radium, in order to examine the shell structure. ∇2ρ̄(r) exhibits a number of extremal points and zeros with the absolute value of the function becoming smaller at each successive extremal point. The zeros, in particular the odd numbered zeros, are shown to exhibit good correlation with the Bohr theory of an atom while the extremal points correlate to a lesser extent. At most five shells are seen in the studied atomic cases based on the fact that the odd numbered zeros are the topological feature of ∇2ρ̄(r) most indicative of a shell.

We advance the concept that tautomerism is crucial for the understanding of the chemical behavior of tetracycline. Indeed, considering four deprotonations, there are 64 different possible tautomers to be considered for tetracycline. Our results indicate that tetracycline is a very adaptive molecule, capable of easily modifying itself through tautomerism in response to various chemical environments. Indeed, its situation in solution can be more accurately pictured as an equilibrium among a diversity of tautomeric species-an equilibrium that can be easily displaced depending on the various possible chemical perturbations, such as varying the pH or the dielectric constant of the solvent. Moreover, we also show that tetracycline could undergo four deprotonations and predict for it a fourth pKa of 13 and refer to our experimental determination of this parameter, which yielded the value of 12. We conclude that tautomerism is essential to the comprehension of the chemical behavior of tetracycline as determined by the semiempirical method AM1 as well as by the self-consistent reaction field method, which estimates the effects of the solvent on the tautomers. All tautomers in their different conformations have been fully optimized for each of the possible degrees of protonation of this molecule. Thus, the relative stabilities of the different tautomeric species have been computed.

In the present work, we sought to improve our sparkle model for the calculation of lanthanide complexes, SMLC,in various ways: (i) inclusion of the europium atomic mass, (ii) reparametrization of the model within AM1 from a new response function including all distances of the coordination polyhedron for tris(acetylacetonate)(1,10-phenanthroline) europium(III), (iii) implementation of the model in the software package MOPAC93r2, and (iv) inclusion of spherical Gaussian functions in the expression which computes the core-core repulsion energy. The parametrization results indicate that SMLC II is superior to the previous version of the model because Gaussian functions proved essential if one requires a better description of the geometries of the complexes. In order to validate our parametrization, we carried out calculations on 96 europium(III) complexes, selected from Cambridge Structural Database 2003, and compared our predicted ground state geometries with the experimental ones. Our results show that this new parametrization of the SMLC model, with the inclusion of spherical Gaussian functions in the core-core repulsion energy, is better capable of predicting the Eu-ligand distances than the previous version. The unsigned mean error for all interatomic distances Eu-L, in all 96 complexes, which, for the original SMLC is 0.3564 A, is lowered to 0.1993 A when the model was parametrized with the inclusion of two Gaussian functions. Our results also indicate that this model is more applicable to europium complexes with beta-diketone ligands. As such, we conclude that this improved model can be considered a powerful tool for the study of lanthanide complexes and their applications, such as the modeling of light conversion molecular devices.

PM6 is the first semiempirical method to be released already parametrized for the elements of the periodic table, from hydrogen to bismuth (Z = 83), with the exception of the lanthanides from cerium (Z = 58) to ytterbium (Z = 70). In order to fill this gap, we present in this article a generalization of our Sparkle Model for the quantum chemical semiempirical calculation of lanthanide complexes to PM6. Accordingly, we present Sparkle/PM6 parameters for all lanthanide trications from La(III) to Lu(III). The validation procedure again considered only high-quality crystallographic structures and included 633 complexes. Sparkle/PM6 unsigned mean errors UME(Ln-L)s, corresponding to all the interatomic distances between the lanthanide ion and the atoms directly coordinated to it, range from 0.066 to 0.086 Å for Gd(III) and Ce(III), respectively. These minimum and maximum UME(Ln-L)s across the lanthanide series are comparable to the Sparkle/AM1 values of 0.054 and 0.085 Å for Ho(III) and Pr(III), respectively, as well as to the values for Sparkle/PM3 of 0.064 and 0.093 Å for Gd(III) and Pr(III), respectively. Moreover, for all 15 lanthanide ions, these interatomic distance deviations follow a γ distribution within a 95% level of confidence, indicating that these errors appear to be random around a mean, freeing the model of systematic errors, at least within the validation set. Sparkle/PM6 presented here, therefore, broadens the range of applicability of PM6 to the coordination compounds of the rare earth metals.