Andre Silva Pimentel

Infrared Spectroscopy of Anionic, Cationic, and Zwitterionic Surfactants

This paper describes the ordering degree of anionic, cationic, and zwitterionic surfactants with the increase of their packing density on Ge substrate by using Fourier transform infrared-attenuated total reflection (FTIR-ATR) spectroscopy. This work shows new insights on the conformational order of sodium dodecyl sulfate (SDS), N-hexadecyl-N-N-dimethyl-3-ammonio-1-propane-sulfonate (HPS), hexadecyl-trimethylammonium bromide (CTAB), and dodecyl trimethylammonium bromide (DTAB). DFT and semiempirical calculations are also performed in order to evaluate the effect of headgroup hydration and counterion. The CH2 asymmetric and symmetric stretching bands for the SDS molecule show a shift of 1.7 and 0.9 cm−1 to higher frequencies as the packing density increases, while it is observed a shift of 2.6 and 2.7 cm−1 for the HPS molecule, respectively. The DTAB molecule shows a shift of 4.5 cm−1 to lower frequencies for both CH2 asymmetric and symmetric stretching bands as the packing density increases, indicating the decrease of gauche conformations and the increase of all-trans conformations over the aliphatic chain.

A Theoretical and Experimental Study of Positive and Neutral LiF Clusters Produced by Fast Ion Impact on a Polycrystalline LiF Target

The positive and neutral clusters produced by the impact of approximately 60 MeV (252)Cf fission fragments on a LiF polycrystalline target are analyzed. The positive ion spectrum is dominated by the (LiF)(n)Li(+) series, n = 0-7, exhibiting a total yield 2 orders of magnitude higher than that of the (LiF)(n)(+) series. The yield for the dominant (LiF)(n)Li(+) series decreases roughly as exp(-kn), where k approximately 0.9 for n = 0-3 and k approximately 0.6 for the heavier clusters (n = 4-9), while the yield of the (LiF)(n)(+) series also decreases exponentially as n increases with k approximately 0.6. Theoretical calculations were performed for the (LiF)(n)Li(0), (LiF)(n)Li(+), and (LiF)(n)(0) series for n up to 9. For the smaller clusters the structures first obtained with a genetic algorithm generator were further optimized at the DFT/B3LYP/6-311+G(3df), DFT/B3LYP/LACV3P*, and MP2/LACV3P* levels of theory. An energy criterion is used for a proper taxonomic description of the optimized cluster isomers. Cluster properties such as fragmentation energy and stability are discussed for the proposed configurations. The results show that for all three series the most stable isomers present a linear structure for small cluster size (n = 1-3), while cubic cells or polyhedral structures are preferred for larger cluster sizes (n = 4-9). Fragmentation energy results suggest that a desorbed excited (LiF)(n)Li(+) ion preferentially dissociates via a cascade of (LiF)(n)(0) units, in agreement with the slope modification in the exponential decay of the (LiF)(n)Li(+) ion abundances for n > or = 3.

New Insights in the Atmospheric HONO Formation: New Pathways for N2O4 Isomerization and NO2 Dimerization in the Presence of Water

Isomerization of N(2)O(4) and dimerization of NO(2) in thin water films on surfaces are believed to be key steps in the hydrolysis of NO(2), which generates HONO, a significant precursor to the OH free radical in lower atmosphere and high-energy materials. Born-Oppenheimer molecular dynamics simulations using the density functional theory are carried out for NO(2)(H(2)O)(m), m ≤ 4, and N(2)O(4)(H(2)O)(n) clusters, n ≤ 7, used to mimic the surface reaction, to investigate the mechanism around room temperature. The results are (i) the NO(2) dimerization and N(2)O(4) isomerization reactions occur via two possible pathways, the non-water-assisted and water-assisted mechanisms; (ii) the NO(2) dimerization in the presence of water yields either ONONO(2)(H(2)O)(m) or NO(3)(-)NO(+)(H(2)O)(m) clusters, but it is also possible to form the HNO(3)(NO(2)(-))(H(3)O(+))(H(2)O)(m-2) transition state to form HONO and HNO(3), directly; (iii) the N(2)O(4) isomerization yields the NO(3)(-)NO(+)(H(2)O)(n) cluster, but it does not hydrolyze faster than the NO(2)(+)NO(2)(-)(H(2)O)(n) hydrolysis to directly form the HONO and HNO(3). New insights for hydrolysis of oxides of nitrogen in and on thin water films on surfaces in the atmosphere are discussed.

Antimalarial activity and mechanisms of action of two novel 4-aminoquinolines against chloroquine-resistant parasites

Chloroquine (CQ) is a cost effective antimalarial drug with a relatively good safety profile (or therapeutic index). However, CQ is no longer used alone to treat patients with Plasmodium falciparum due to the emergence and spread of CQ-resistant strains, also reported for P. vivax. Despite CQ resistance, novel drug candidates based on the structure of CQ continue to be considered, as in the present work. One CQ analog was synthesized as monoquinoline (MAQ) and compared with a previously synthesized bisquinoline (BAQ), both tested against P. falciparum in vitro and against P. berghei in mice, then evaluated in vitro for their cytotoxicity and ability to inhibit hemozoin formation. Their interactions with residues present in the NADH binding site of P falciparum lactate dehydrogenase were evaluated using docking analysis software. Both compounds were active in the nanomolar range evaluated through the HRPII and hypoxanthine tests. MAQ and BAQ derivatives were not toxic, and both compounds significantly inhibited hemozoin formation, in a dose-dependent manner. MAQ had a higher selectivity index than BAQ and both compounds were weak PfLDH inhibitors, a result previously reported also for CQ. Taken together, the two CQ analogues represent promising molecules which seem to act in a crucial point for the parasite, inhibiting hemozoin formation.

Adsorption of Sodium Dodecyl Sulfate on Ge Substrate: The Effect of a Low-Polarity Solvent

This paper describes the adsorption of sodium dodecyl sulfate (SDS) molecules in a low polar solvent on Ge substrate by using Fourier transform infrared-attenuated total reflection (FTIR-ATR) spectroscopy and atomic force microscopy (AFM). The maximum SDS amount adsorbed is (5.0 ± 0.3) × 1014 molecules cm−2 in CHCl3, while with the use of CCl4 as subphase the ability of SDS adsorbed is 48% lower. AFM images show that depositions are highly disordered over the interface, and it was possible to establish that the size of the SDS deposition is around 30–40 nm over the Ge surface. A complete description of the infrared spectroscopic bands for the head and tail groups in the SDS molecule is also provided.

Theoretical and experimental study of negative LiF clusters produced by fast ion impact on a polycrystalline 7LiF target.

The emission of negative cluster ions produced by the impact of approximately 60 MeV (252)Cf fission fragments on a (7)LiF polycrystalline target is analyzed. The negative ion mass spectrum is dominated by the ((7)LiF)(n)F(-) series, n = 1 to approximately 30. The desorption yield distribution of the ((7)LiF)(n)F(-) members has a maximum at n = 2 and then decreases as the sum of two exponentials whose decay parameters are k(Fast) = 0.9 and k(Slow) = 0.08. These k values are the same as those observed for the positive series and close to others obtained for condensed gas targets. Relative cluster ion stabilities, deduced from the experimental ion abundances for the (LiF)(n)F(-) series, are proposed to be correlated with theoretical structures according to their internal energy by using the deviation plot (D-plot) methodology. A pool of candidate cluster structures was generated using a genetic algorithm and further analyzed and optimized using density functional theory (DFT) with the hybrid functional B3LYP (DFT/B3LYP) and Moller-Plesset perturbation theory (MP2). For the small clusters (n = 1 to 2), the most stable structures are found to be linear, whereas the larger clusters (n = 4 to 6) present cubic or polyhedral structures. Fragmentation energies, ionization potentials, and relative stabilities are reported for the most abundant families of the (LiF)(n)F(-) and (LiF)(n)(-) series.

New Insight into the Formation of Nitrogen Sulfide: A Quantum Chemical Study

We studied the chemical mechanism for the formation of (2)NS in the interstellar medium was by using the CCSD/6-311++G(d,p) and CCSD(T)/6-311++G(3df,3pd) levels of theory. To the best of our knowledge, this is the first detailed study of the chemical mechanism for the formation of (2)NS. Several reactions proposed in this article are spin-forbidden. They were treated with the Landau-Zener theory and by the MRCI methodology. The following reactions paths proposed in this article are energetically favorable: (1) (1)NH + (2)SH --> cis-(2)HNSH --> TS1 --> trans-(2)HNSH --> TS2 --> (2)H(2)NS --> TS3 --> (2)NS + H(2) and (2) (4)N + (1)SH --> (1)NSH --> TS13 --> (1)HNS --> (2)NS + (2)H. However, the latter reaction, (4)N + (1)SH --> (1)NSH, is spin-forbidden, and its probability of occuring (p(sh)) is zero. The chemical mechanism for the formation of (2)NS in the interstellar medium is now presented in more detail, which is of great importance.

Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment

Epigenetic pathways are involved in a wide range of diseases, including cancer and neurological disorders. Specifically, histone modifying and reading processes are the most broadly studied and are targeted by several licensed drugs. Although there have been significant advances in understanding the mechanistic aspects underlying epigenetic regulation, the development of selective small-molecule inhibitors remains a challenge. Experimentally, it is generally difficult to elucidate the atomistic basis for substrate recognition, as well as the sequence of events involved in binding and the subsequent chemical processes. In this regard, computational modelling is particularly valuable, since it can provide structural features (including transition state structures along with kinetic and thermodynamic parameters) that enable both qualitative and quantitative evaluation of the mechanistic details involved. Here, we summarize knowledge gained from computational modelling studies elucidating the role of the protein environment in histone-lysine modifying and reading mechanisms. We give a perspective on the importance of calculations to aid and advance the understanding of these processes and for the future development of selective inhibitors for epigenetic regulators.

Theoretical and experimental studies of new modified isoflavonoids as potential inhibitors of topoisomerase I from Plasmodium falciparum.

DNA topoisomerase I from Plasmodium falciparum (PfTopoI), a potential selective target for chemotherapy and drug development against malaria, is used here, together with human Topo I (HssTopoI), for docking, molecular dynamics (MD) studies and experimental assays. Six synthetic isoflavonoid derivatives and the known PfTopoI inhibitors camptothecin and topotecan were evaluated in parallel. Theoretical results suggest that these compounds dock in the binding site of camptothecin and topotecan inside both enzymes and that LQB223 binds selectively in PfTopoI. In vitro tests against P. falciparum blood parasites corroborated the theoretical findings. The selectivity index (SI) of LQB223 ≥98 suggests that this molecule is the most promising in the group of compounds tested. In vivo experiments in mice infected with P. berghei showed that LQB223 has an antimalarial activity similar to that of chloroquine.

Docking and molecular dynamics studies of new potential inhibitors of the human epidermal receptor 2

Compounds similar to lapatinib and gefitinib have been investigated as potential inhibitors of the intracellular receptor tyrosine kinase (RTK) domain of the human epidermal receptor 2 (HER2), which is a promising molecular target to the drug design of new chemotherapies for breast, lung, ovarian and colorectal cancers. In this study, we have searched potential HER2 inhibitors used for treatment of other illnesses such as hepatitis, bacterial infections and sexual impotence screened in the DrugBank. The compounds selected were subjected to virtual screening docking in order to evaluate the main interactions between them and the RTK domain of HER2. The selected compounds were investigated by flexible docking, molecular dynamics studies and ΔG bind calculations. The results suggest that antrafenine, saprisartan, reserpine, irinotecan and udenafil are potential candidates to inhibit the RTK domain of HER2.