Gerd B. Rocha

RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I

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 · 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° is only slightly higher than the AM1 figure of 5.88°, and both are much smaller than the PM3 and PM5 figures of 6.98° and 9.83°, 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.

Sparkle/PM3 for the modeling of europium(III), gadolinium(III), and terbium(III) complexes

O modelo Sparkle/PM3 e parametrizado para complexos de europio (III), gadolinio (III) e terbio (III). A validacao do modelo foi realizada utilizando noventa e seis complexos de Eu(III), setenta complexos de Gd(III) e quarenta e dois complexos de Tb(III); todos a partir de estruturas cristalograficas de alta qualidade, com fator R < 5%. Os erros medios absolutos, obtidos com o modelo Sparkle/PM3, considerando todas as distâncias interatomicas do tipo lantanideo-atomo ligante, foram 0,080 A para Eu(III), 0,063 A para Gd(III) e 0,070 A para Tb(III). Estes valores medios sao similares aos obtidos com o modelo Sparkle/AM1 (0,082 A, 0,061 A, e 0,068 A, respectivamente). Alem disso, a exatidao em reproduzir o poliedro de coordenacao de complexos de Eu(III), Gd(III) e Tb(III) e similar a obtida utilizando metodos ab initio com potenciais efetivos de caroco. Finalmente, com o objetivo de avaliar se as geometrias preditas com o modelo Sparkle/PM3 sao confiaveis, escolhemos um dos complexos de Eu(III), BAFZEO, para o qual geramos centenas de diferentes geometrias iniciais, onde variamos de forma aleatoria as distâncias e ângulos entre os ligantes e o ion Eu(III). Em seguida, todas essas geometrias iniciais foram otimizadas usando o modelo Sparkle/PM3. Como resultado, observamos uma tendencia significativa onde a geometria que apresentou o menor erro medio absoluto apresentou tambem a energia total mais baixa, o que reforca a validade do modelo Sparkle. The Sparkle/PM3 model is extended to europium(III), gadolinium(III), and terbium(III) complexes. The validation procedure was carried out using only high quality crystallographic structures, for a total of ninety-six Eu(III) complexes, seventy Gd(III) complexes, and forty-two Tb(III) complexes. The Sparkle/PM3 unsigned mean error, for all interatomic distances between the trivalent lanthanide ion and the ligand atoms of the first sphere of coordination, is: 0.080 A for Eu(III); 0.063 A for Gd(III); and 0.070 A for Tb(III). These figures are similar to the Sparkle/AM1 ones of 0.082 A, 0.061 A, and 0.068 A respectively, indicating they are all comparable parameterizations. Moreover, their accuracy is similar to what can be obtained by present-day ab initio effective core potential full geometry optimization calculations on such lanthanide complexes. Finally, we report a preliminary attempt to show that Sparkle/PM3 geometry predictions are reliable. For one of the Eu(III) complexes, BAFZEO, we created hundreds of different input geometries by randomly varying the distances and angles of the ligands to the central Eu(III) ion, which were all subsequently fully optimized. A significant trend was unveiled, indicating that more accurate local minima geometries cluster at lower total energies, thus reinforcing the validity of sparkle model calculations.

On the charge factors of the simple overlap model for the ligand field in lanthanide coordination compounds

Abstract In this Letter, we propose a semi-empirical procedure through which the charge factors, appearing in the simple overlap model (SOM) for the ligand field in lanthanide compounds, can be obtained. The idea is based on the concept of bond valence and bond strength introduced by Pauling in the 1920s. The charge factors thus obtained are used in the calculation of the so-called ligand field parameters, B q k s, and, subsequently, in the prediction of the Stark levels of the 7 F J manifolds ( J =1,2,3 and 4) of the Eu 3+ ion in coordination compounds with mixed ligands. Comparison with experiment shows that the results are quite satisfactory.

Sparkle/RM1 parameters for the semiempirical quantum chemical calculation of lanthanide complexes

In this article, we present Sparkle Model parameters to be used with RM1, presently one of the most accurate and widely used semiempirical molecular orbital models based exclusively on monoatomic parameters, for systems containing H, C, N, O, P, S, F, Cl, Br, and I. Accordingly, we used the geometries of 169 high quality crystallographic structures of complexes for the training set, and 435 more for the validation of the parameterization for the whole lanthanide series, from La(III) to Lu(III). The distance deviations appear to be random around a mean for all lanthanides. The average unsigned error for Sparkle/RM1 for the distances between the metal ion and its coordinating atoms is 0.065 A for all lanthanides, ranging from a minimum of 0.056 A for Pm(III) to 0.074 A for Ce(III), making Sparkle/RM1 a balanced method across the lanthanide series. Moreover, a detailed analysis of all results indicates that Sparkle/RM1 is particularly accurate in the prediction of lanthanide cation-coordinating atom distances, making it a suitable method for the design of luminescent lanthanide complexes. We illustrate the potential of Sparkle/RM1 by carrying out a Sparkle/RM1 full geometry optimization of a tetramer complex of europium with 181 atoms. Sparkle/RM1 may be used for the prediction of geometries of large complexes, metal–organic frameworks, etc., to useful accuracy.

Efficient synthesis of 16 aromatic Morita-Baylis-Hillman adducts: Biological evaluation on Leishmania amazonensis and Leishmania chagasi.

Sixteen aromatic Morita-Baylis-Hillman adducts (MBHA) 1-16 were efficiently synthesized in a one step Morita-Baylis-Hillman reaction (MBHR) involving commercial aldehydes with methyl acrylate or acrylonitrile (81-100% yields) without the formation of side products on DABCO catalysis and at low temperature (0°C). The toxicities of these compounds were assessed against promastigote form of Leishmania amazonensis and Leishmania chagasi. The low synthetic cost of these MBHA, green synthetic protocols, easy one-step synthesis from commercially available and cheap reagents as well as the very good antileishmanial activity obtained for 14 and 16 (IC₅₀ values of 6.88μgmL⁻¹ and 11.06μgmL⁻¹ respectively on L. amazonensis; 9.58μgmL⁻¹ and 14.34μgmL⁻¹ respectively on L. chagasi) indicates that these MBHA can be a novel and promising class of anti-parasitic compounds.

3-Hydroxy-2-methylene-3-(4-nitrophenylpropanenitrile): A new highly active compound against epimastigote and trypomastigote form of Trypanosoma cruzi

We have synthesized the Morita-Baylis-Hillman adduct (MBHA) 3-hydroxy-2-methylene-3-(4-nitrophenyl)-propanenitrile (3) in quantitative yield and evaluated on Trypanosoma cruzi epimastigote and bloodstream trypomastigote forms. Compound 3 strongly inhibited epimastigote growth, with IC(50)/72hof 28.5 microM and also caused intense trypomastigotes lysis, with an IC(50)/24h of 25.5 microM. Ultrastructural analysis showed significant morphological changes on both parasite forms treated with 3, including increase of cell volume and rounding of cell body as well as intense intracellular disorganization. Morphological changes indicative of apoptosis, autophagy or necrosis were observed in most affected cells. Docking calculations of 1, 2 and 3 pointed out the possibility of T. cruzi Farnesyl Pyrophosphate Synthase (TcFPPS) enzyme inhibition in 3 mechanism of action.

RM1 Model for the Prediction of Geometries of Complexes of the Trications of Eu, Gd, and Tb

All versions of our previous Sparkle Model were very accurate in predicting lanthanide-lanthanide distances in complexes where the two lanthanide ions directly face each other, and mainly lanthanide-oxygen, and lanthanide-nitrogen distances, which are by far the most common ones in lanthanide complexes. In this article, we are advancing for the first time the RM1 model for lanthanides. Designed to be a much more general NDDO model, the RM1 model for lanthanides is capable of predicting geometries of lanthanide complexes for the cases when the central lanthanide trication is directly coordinated to any other atoms, not only oxygen or nitrogen. The RM1 model for lanthanides is defined by three important attributes: (a) the orbitals, the lanthanide ion has now three electrons and a NDDO basis set made of 5d, 6s, and 6p functions; (b) the parametrization, via cluster analysis and an adequate sampling; and (c), the statistical validation of the parameters to make sure the errors behave as random around a mean. All three aspects are described in detail in the article. Results indicate that the RM1 model does extend the accuracy of the previous Sparkle Models to types of coordinating bonds other than Ln-O and Ln-N; the most common ones for Eu, Gd, and Tb, being Ln-C, Ln-S, Ln-Cl, and Ln-Br. Overall, these other coordinating bonds are now predicted within 0.06 Å of their correct values. Therefore, the RM1 model here presented is capable of predicting geometries of lanthanide complexes, materials, metal-organic frameworks, etc., with useful accuracy.

Revisiting the Origin of the Preferential p-p Stacking Conformation of the (+)-8-Phenylmenthyl Acrylate

1 H NMR experimental data which show the stacking conformation of 2 (2S) is more stable that trans conformation (2T) and the stacking conformation of 3 (3S) is less stable that trans conformation (3T). After that, geometrical and energetic features of the intermolecular complex benzene…methylacrylate (4) have also been studied using MPW1B95 method. From our results, we have noticed that both steric and dispersion effects play a key role in the conformational equilibrium of 2.

Cerium (III) Complexes Modeling with Sparkle/PM3

The Sparkle/PM3 model is extended to cerium(III) complexes. The validation procedure was carried out using only high quality crystallographic structures (R factor < 0.05A), for a total of thirty-seven Ce(III) complexes. The Sparkle/PM3 unsigned mean error, for all interatomic distances between the Ce(III) ion and the directly coordinating oxygen or nitrogen atoms, is 0.080A, a level of accuracy equivalent to the Sparkle/AM1 figure of 0.083A. Moreover, their accuracy is similar to what can be obtained by present-day ab initio effective core potential full geometry optimization calculations on such lanthanide complexes.

1,3-thiazolium-5-thiolates mesoionic compounds: semiempirical evaluation of their first static hyperpolarizabilities and synthesis of new examples

Calculos semi-empiricos do tipo AM1-TDHF para a primeira hiperpolarizabilidade estatica, b(0), de dezesseis compostos mesoionicos do sistema 1,3-tiazolio-5-tiolato foram realizados. Com base nos resultados obtidos, dois novos compostos mesoionicos, 2-(4-nitrofenil)-3-metil-4- (metilfenil)-1,3-tiazolio-5-tiolato e 2-(4-nitrofenil)-3-metil-4-(metoxifenil)-1,3-tiazolio-5-tiolato, foram sintetizados e caracterizados por metodos espectroscopicos e analiticos. Semiempirical AM1-TDHF calculations of the static first hyperpolarizabilities, b(0), of 1,3-thiazolium-5-thiolate mesoionic derivatives were performed. Guided by these results, two new mesoionic compounds - 2-(4-nitrophenyl)-3-methyl-4-(methylphenyl)-1,3-thiazolium-5-thiolate and 2-(4-nitrophenyl)-3-methyl-4-(methoxyphenyl)-1,3-thiazolium-5-thiolate - were synthesized and characterized by analytical and spectroscopic means.