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5. Basis Sets for Heavy Atoms

Author

Paschoal, Diego Fernando da Silva, Gomes, Mariana da Silva, Machado, Larissa Pereira Nogueira, Dos Santos, Hélio Ferreira, Carpenter, Barry, Series Editor, Ceroni, Paola, Series Editor, Landfester, Katharina, Series Editor, Leszczynski, Jerzy, Series Editor, Luh, Tien-Yau, Series Editor, Perlt, Eva, Series Editor, Polfer, Nicolas C., Series Editor, and Salzer, Reiner, Series Editor

Published
2021
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15. Microwave-assisted synthesis, spectral characterization and DFT studies of Zn(II) complexes based on N-acylhydrazone ligands: stability and antioxidant activity

Author

Santos, Daniela Corrêa, primary, Henriques, Ruan Roberto, additional, Lopes Jr, Marcos Antonio Abreu, additional, Maia, Paulo José Sousa, additional, Silva, Andreza Miranda Barata, additional, Paschoal, Diego Fernando Silva, additional, and Souza, Andréa Luzia Ferreira, additional

Published
2023
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16. Assessment of a Computational Protocol for Predicting Co-59 NMR Chemical Shift.

Author

Gomes, Matheus G. R., De Souza, Andréa L. F., Dos Santos, Hélio F., De Almeida, Wagner B., and Paschoal, Diego F. S.

Subjects
CHEMICAL shift (Nuclear magnetic resonance), DENSITY functional theory, ORGANIC solvents
Abstract

In the present study, we benchmark computational protocols for predicting Co-59 NMR chemical shift. Quantum mechanical calculations based on density functional theory were used, in conjunction with our NMR-DKH basis sets for all atoms, including Co, which were developed in the present study. The best protocol included the geometry optimization at BLYP/def2-SVP/def2-SVP/IEF-PCM(UFF) and shielding constant calculation at GIAO-LC-ωPBE/NMR-DKH/IEF-PCM(UFF). This computational scheme was applied to a set of 34 Co(III) complexes, in which, Co-59 NMR chemical shift ranges from +1162 ppm to +15,100 ppm, and these were obtained in distinct solvents (water and organic solvents). The resulting mean absolute deviation (MAD), mean relative deviation (MRD), and coefficient of determination (R2) were 158 ppm, 3.0%, and 0.9966, respectively, suggesting an excellent alternative for studying Co-59 NMR. [ABSTRACT FROM AUTHOR]

Published
2023
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34. Predicting Pt-195 NMR Chemical Shift and ¹J(195Pt-31P) Coupling Constant for Pt(0) Complexes Using the NMR-DKH Basis Sets.

Author

e Silva, Joyce H. C., Dos Santos, Hélio F., and Paschoal, Diego F. S.

Subjects
NUCLEAR magnetic resonance, CHEMICAL shift (Nuclear magnetic resonance), HYDROSILYLATION, CATALYSIS, ALKENES, COUPLING constants
Abstract

Pt(0) complexes have been widely used as catalysts for important reactions, such as the hydrosilylation of olefins. In this context, nuclear magnetic resonance (NMR) spectroscopy plays an important role in characterising of new structures and elucidating reaction mechanisms. In particular, the Pt-195 NMR is fundamental, as it is very sensitive to the ligand type and the oxidation state of the metal. In the present study, quantum mechanics computational schemes are proposed for the theoretical prediction of the Pt-195 NMR chemical shift and ¹J(195Pt-31P) in Pt(0) complexes. The protocols were constructed using the B3LYP/LANL2DZ/def2-SVP/IEF-PCM(UFF) level for geometry optimization and the GIAO-PBE/NMR-DKH/IEF-PCM(UFF) level for NMR calculation. The NMR fundamental quantities were then scaled by empirical procedures using linear correlations. For a set of 30 Pt(0) complexes, the results showed a mean absolute deviation (MAD) and mean relative deviation (MRD) of only 107 ppm and 2.3%, respectively, for the Pt-195 NMR chemical shift. When the coupling constant is taken into account, the MAD and MRD for a set of 33 coupling constants in 26 Pt(0) complexes were of 127 Hz and 3.3%, respectively. In addition, the models were validated for a group of 17 Pt(0) complexes not included in the original group that had MAD/MRD of 92 ppm/1.7% for the Pt-195 NMR chemical shift and 146 Hz/3.6% for the ¹J(195Pt-31P). [ABSTRACT FROM AUTHOR]

Published
2021
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35. Predicting the structure and NMR coupling constant 1J(129Xe–19F) of XeF6 using quantum mechanics methods.

Author

Paschoal, Diego F. S. and Dos Santos, Hélio F.

Abstract

The XeF6 molecule exists as a monomer in the gas phase and as the (XeF6)4 tetramer in solution. Herein we used distinct quantum mechanics methods to study the conformational equilibrium for the XeF6 monomer, which is represented mainly by Oh and C3v symmetric geometries, and for the (XeF6)4 structure found in condensate phases. The NMR 1J(129Xe–19F) coupling constant is predicted using our own NMR-DKH basis set, designed for NMR properties. The C3v conformer of XeF6 was stable only with HF, CCSD, and hybrid DFT functionals with at least 28% exact HF exchange. Increasing the % of HF exchange improves the description of the geometry and the Oh → C3v equilibrium. The BMK, BHandHLYP and LC-ωPBE functionals produce results in excellent agreement with experiments and high-level calculations for the XeF6 molecule. When it comes to the 1J(129Xe–19F) coupling constant, the (XeF6)4 structure must be considered. For that compound, BHandHLYP leads to the best structure, and BMK leads to the best coupling constant; therefore, the generalized protocol BMK/NMR-DKH//BHandHLYP/def2-SVP is recommended to study the XeF6 molecule in the gas phase and solution. [ABSTRACT FROM AUTHOR]

Published
2021
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37. Ajuste de funções de base atômicas para o cálculo de propriedades moleculares

Author

Paschoal, Diego Fernando da Silva, Santos, Hélio Ferreira dos, Jorge, Francisco Elias, Custódio, Rogério, Rezende, Stella Maris, and Furones, Maikel Yusat Ballester

Subjects
Deslocamento químico, Nonlinear optics, Reatividade, Chemical shift, Reactivity, CIENCIAS EXATAS E DA TERRA::QUIMICA [CNPQ], Primeira hiperpolarizabilidade, Óptica não-linear, Complexos de Pt(II) e Pd(II), Função de base, First hyperpolarizability, Pt(II) and Pd(II) complexes, Basis set
Abstract

CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Um estudo sistemático a respeito da importância do nível de teoria e do conjunto de funções de base no cálculo de propriedades moleculares foi conduzido. Foram realizados estudos a respeito das propriedades ópticas lineares (OL) e não-lineares (ONL) de moléculas diatômicas, pequenas moléculas poliatômicas e moléculas orgânicas conjugadas com grupos doadores e retiradores de elétrons. Além disso, foi avaliada a estrutura e reatividade de complexos de Pt(II) e Pd(II). Por fim, um estudo a respeito do deslocamento químico de 195Pt foi conduzido, onde diversos parâmetros que influenciam em tal propriedade foram extensivamente analisados. Para cada trabalho proposto um novo conjunto de funções de base foi desenvolvido. Foram propostas as bases D10 (BH), P3 (CO), F3 (CS), J5 (N2), NLO (H,C,N,O,F,S), NLO-X (X=I,II,III,V,aV) (H,B-F,Si-Cl), mDZP (Pd,Pt), kPd-ADZP(Pd) e NMR-TZPP-DKH (H-He, Li-Ne, Na-Ar, K-Ca, Ga-Kr, Rb-Sr, In-Xe e Pt). Previsões das propriedades OL e ONL de diversas moléculas foram realizadas. Para um conjunto de moléculas com valores de primeira hiperpolarizabilidade (β) variando de 0 a 190 esu um desvio médio absoluto de 13,2 esu foi encontrado no nível cam-B3LYP/NLO-V em comparação com um desvio de 27,2 esu com a base da literatura 6-31G(2d). Além disso, foram realizados estudos de estrutura e reatividade da cisplatina e do cispaládio. Para a reação de hidrólise da cDDPt foi prevista uma barreira de energia no nível B3LYP/mDZP/6-31+G(d) de 22,8 kcal.mol-1 que está em excelente acordo com o valor experimental de 22,±0,4 kcal.mol-1. Considerando a mesma reação, porém para o análogo de Pd, um valor de 17,11 kcal.mol-1 no nível B3LYP/mDZP/6-31+G(d) e de 16,94 kcal.mol-1 no nível B3LYP/kPd-ADZP/6-31+G(d) foram previstos e estão em bom acordo com o valor esperado de 16,34 kcal.mol-1. Somado a isso, uma análise a respeito do deslocamento químico de 195Pt foi abordada, onde para uma ampla faixa de 73 complexos de Pt(II) um desvio absoluto médio de apenas 156 ppm foi encontrado no nível GIAO-B3LYP(DKHSO)/NMR-TZPP-DKH/IEFPCM-UFF. Todas as bases aqui propostas foram testadas de forma sistemática e, no geral, bons resultados foram encontrados para as propriedades analisadas e com custos computacionais altamente acessíveis. A systematic study about the importance of the level of theory and the basis sets in the calculation of molecular properties was conducted. It performed studies on the linear and nonlinear optical properties of diatomic molecules, small polyatomic molecules and conjugated donor/acceptor organic molecules. In addition, the structure and reactivity of Pt(II) and Pd(II) complexes were evaluated. Finally, a study about the 195Pt chemical shift was conducted, where various parameters that influence such property have been extensively analyzed. For each work proposed a new basis set was developed. The following basis sets were proposed: D10 (BH), P3 (CO), F3 (CS), J5 (N2), NLO (H,C,N,O,F,S), NLO-X (X=I,II,III,V,aV) (H,B-F,Si-Cl), mDZP (Pd,Pt), kPd-ADZP(Pd) and NMR-TZPP-DKH (H-He, Li-Ne, Na-Ar, K-Ca, Ga-Kr, Rb-Sr, In-Xe e Pt). Estimates of L-NLO properties of several molecules were performed. For a set of molecules with values of first hyperpolarizability (β) ranging from 0 to 190 esu, an average absolute deviation of 13,2 esu was found at cam-B3LYP/NLO-V level compared with 27,2 esu with the standard basis set 6-31G(2d). Furthermore, studies of structure and reactivity of cisplatin and cispalladium were performed. For the aquation reaction of cisplatin an energy barrier of 22.8 kcal.mol-1 was predicted at B3LYP/mDZP/6-31+G(d) level, which it is in excellent agreement with the experimental value of 22.9±0.4 kcal.mol-1. Considering the same reaction, but for Pd analogous, a value of 17.11 kcal.mol-1 at B3LYP/mDZP/6-31+G(d) level and 16.94 kcal.mol-1 at B3LYP/kPd-ADZP/6-31+G(d) level were predicted and these values are in good agreement with the expected value of 16.34 kcal.mol-1. Added to this, an analysis about the 195Pt chemical shift was addressed, where for a wide range of 73 Pt(II) complexes and average absolute deviation of only 156 ppm was found at GIAO-B3LYP(DKHSO)/NMR-TZPP-DKH/IEFPCM-UFF level. All basis sets proposed here were systematically tested and, in general, good results were found for the properties of interest and highly affordable computational costs.

Published
2014

47. Non-centrosymmetric crystals of new N-benzylideneaniline derivatives as potential materials for non-linear optics.

Author

Souza, Talita Evelyn, Rosa, Iara Maria Landre, Legendre, Alexandre Oliveira, Paschoal, Diego, Maia, Lauro J. Q., Dos Santos, Hélio F., Martins, Felipe Terra, and Doriguetto, Antonio Carlos

Subjects
CRYSTAL structure research, NONLINEAR optical techniques, INTRAMOLECULAR charge transfer, MOLECULAR conformation, X-ray diffraction
Abstract

Three new N-benzylideneaniline derivatives [ p-nitrobenzylidene- p-phenylamineaniline (I), 2,4-dinitrobenzylidene- p-phenylamineaniline (II) and p-dinitrobenzylidene- p-diethylamineaniline (III)] containing electron-push-pull groups have been prepared. They present a planar N-benzylideneaniline core and neighbouring functional atoms, which are related through an efficient intramolecular charge transfer (CT). Two of the derivatives crystallize in non-centrosymmetric space groups, a necessary condition for non-linear optical (NLO) responses. The NLO properties were calculated for the molecular conformations determined by single-crystal X-ray diffraction as well as for the four molecules packed into each corresponding unit cell, using a quantum-chemical method at the cam-B3LYP/NLO-V level of theory. As expected from antiparallel face-to-face stacking through centrosymmetry, the main NLO descriptors - namely, the first hyperpolarizability (βtot) and its projection on the dipole moment direction (βvec) - are almost zero for the tetramer of derivative III. Interestingly, the calculated first hyperpolarizability decreases in the non-centrosymmetric unit-cell content of derivative II when compared to its single molecule, which may be related to its molecular pillaring, similar to that observed in derivative III. On the other hand, a desirable magnification of the NLO properties was found for packed units of derivative I, which may be a consequence of its parallel face-to-tail stacking with the CT vectors of all molecules pointing in the same direction. Moreover, the CT vector of compound I makes an angle of θ = 33.6° with its crystal polar axis, resulting in a higher-order parameter (cos3θ = 0.6) compared with the other derivatives. This is in line with the higher macroscopic second-order NLO response predicted for derivative I, βtot = 120.4 × 10−30 e.s.u. [ABSTRACT FROM AUTHOR]

Published
2015
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48. Exploring the PotentialEnergy Surface for the Interaction of Sterically Hindered Trichloro(diethylenetriamine)gold(III)Complexes with Water.

Author

Dos Santos, Hélio F., Paschoal, Diego, and Burda, JaroslavV.

Subjects
*POTENTIAL energy surfaces, *DIETHYLENETRIAMINE, *ORGANOGOLD compounds, *TRANSITION metal complexes, *WATER, *REACTIVITY (Chemistry)
Abstract

The reactivity of gold(III) complexes is analyzed fora series of derivatives of 3-azapentane-1,5-diamine (dien) tridentateligand that can contain some bulky substituents. Two distinct seriesof compounds are considered where the dien ligand is either deprotonated(R-dien-H) or protonated (R-dien) at the secondary amine where R= ethyl (Et) or methyl (Me). While the deprotonated specieswill occur in neutral and basic solutions, the protonated forms arelikely to be present in acidic environment. Hydration reaction (water/Cl–ligand exchange) of 14 complexes is modeled with quantumchemical calculations. Our calculations predict that the reactivitydecreases with the increase in the molecular volume of the substituteddien ligand, and the calculated rate constants are in satisfactoryagreement with experimental results. In addition, quantitative structure/reactivitymodels are proposed where the angle between the entering and leavinggroups in the transition state structure (the reactivity angle) isused as a molecular descriptor. These models explain the trend ofthe relative reactivity of these complexes and can be used to designnew ligands for gold(III) complexes aiming to adjust the reactivityof the complex. [ABSTRACT FROM AUTHOR]

Published
2012
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49. Gaussian basis sets for ab initio calculation of NLO properties of polyatomic molecules.

Author

Maroulis, G., Bancewicz, T., Champagne, B., Buckingham, A.D., Paschoal, Diego, Costa, Marcello F., Junqueira, Georgia M.A., and Dos Santos, Hélio F.

Subjects
GAUSSIAN beams, POLYATOMIC molecules, DIATOMIC molecules, DIPOLE moments, POLARIZABILITY (Electricity), BENZENE, ELECTRON donor-acceptor complexes, NITROANILINE
Abstract

In this paper, basis sets for H, C, N and O atoms were adjusted to obtain electric properties of diatomic molecules. The dipole moment, polarizability and first-order hyperpolarizability were calculated for H_{2}, CH^{+}, CN^{-} and CO molecules and the basis sets modified to reproduce the reference data available. A sequential methodology was used, where the basis set for H is firstly adjusted and then used to fit the basis set for C in the CH^{+} molecule and so on. The final basis sets were (7s2p1d)→[3s2p1d] for H and (9s5p2d)→ [5s3p2d] for C and O. In the case of N atom, the best basis set was found to be (9s5p1d)→[5s3p1d], where only one set of d polarization functions was needed. The atomic basis sets fitted were further utilized for calculation of geometry and electric properties of 36 benzene derivatives mono- and di-substituted by electron donor and acceptor groups attached at ortho, meta and para positions. The results were satisfactory for most of molecules. For instance, in the case of p-nitroaniline, an important push-pull benzene derivative, the first hyperpolarizability was predicted to be 9.4 × 10^{-30} e.s.u. in excellent agreement with experimental value, 9.2 × 10^{-30} e.s.u.. Besides electric properties, our basis sets also gave good geometries for polyatomic molecules at reasonable computational cost. Therefore, the results reported in the present paper suggest the use of our modified basis sets for calculation of geometry and electric properties (linear and non-linear) of push-pull benzene derivatives like molecules. [ABSTRACT FROM AUTHOR]

Published
2010

50. Influência do ambiente enzimático na reatividade de complexos anticâncer de ouro(iii)

Author

Sánchez Delgado, Giset Yuliana, Santos, Hélio Ferreira dos, Paschoal, Diego Fernando da Silva, Nascimento Junior, Clebio Soares, Scarpellini, Marciela, Andrade, Gustavo Fernandes Souza, and Costa, Luiz Antônio Sodré

Subjects
Potencial de redução, Volume buried, Complexos de ouro(III), Reduction potential, Phosphines, Tiorredoxina redutase, CIENCIAS EXATAS E DA TERRA::QUIMICA [CNPQ], DFT, Buried volume, Thioredoxin reductase, Fosfinas, Gold(III) complexes
Abstract

CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Complexos de ouro(III) são compostos promissores para a quimioterapia do câncer com mecanismos de ação que envolvem etapas dependentes de sua estabilidade redox. A escolha do ligante é crucial para ajustar a reatividade e atividade biológica destes mesmos. Fosfinas terciárias (PR3) estão entre os ligantes auxiliares mais usados nestes compostos. A estabilidade redox dos complexos [AuIII(C^N^C)PR3] + (C^N^C=2,6-difenilpiridina) (A) e [AuIII(N^N^N)PR3] 3+ (N^N^N=2,2′:6′,2″-terpiridina) (B) foi investigada para um conjunto de 41 fosfinas, usando o potencial padrão de redução (Eo ) para o sistema eletroquímico Au3+→Au1+ como referência. Para os compostos (A), Eo variou numa faixa de 829 mV com valores negativos; para os compostos (B) os valores de Eo foram positivos numa faixa de 507 mV. As fosfinas com alto impacto estérico diminuem a estabilidade do complexo apesar de serem fortes doadores σ. Propriedades estéricas e eletrônicas foram usadas para construir modelos quantitativos de relação estrutura-propriedade (QSPR – Quantitative Structure-Properties Relationship), sendo o volume buried o principal fator na estabilidade dos compostos estudados. No caso dos compostos (B), o impacto estérico é mais pronunciado nas espécies de ouro(I). A capacidade de doação de elétrons das fosfinas possui maior peso na estabilidade redox dos compostos (B) em relação aos compostos (A). Posteriormente, quinze compostos com diferentes ligantes bidentados (bident) e tridentados (trident), mantendo fixo o cloreto como ligante auxiliar ([AuIII(bident)Cl2] 3+n (bident = do tipo N^N e C^N) e [AuIII(trident)Cl]3+n (trident = do tipo N^N^N, C^N^N, C^C^N, C^N^C e N^C^N)), foram estudados. Os valores de Eo calculados abrangeram uma ampla faixa de 2600 mV. Os compostos do tipo [AuIII(C^C^N)Cl] mostraram a maior estabilidade com Eo de aproximadamente -1,60 V em solução aquosa. A análise de orbitais naturais e o E o indicaram que a inclusão da ligação Au-C é menos eficiente para a estabilização do composto na posição lateral comparada à central. O posicionamento consecutivo de dois ligantes piridina desfavorece a redução dos complexos de ouro(III). No caso do composto [AuIII(C^N^N)Cl], o ligante bipy (N^N) se comporta como um ligante redox não-inocente, participando ativamente do processo de redução sem uma mudança estrutural significativa após redução. Os resultados reportados ajudam na previsão da estabilidade redox de complexos de ouro(III), a qual afeta sua reatividade química frente a importantes alvos biológicos. Finalmente, modelos moleculares foram propostos para o aduto [AuIII(C^N^C)(SHCysR)]+ , com a fração [AuIII(C^N^C)]+ ligada ao resíduo Cys498 da TrxR, que representa o produto 6 da primeira reação de troca de ligante. O composto original [AuIII(C^N^C)Cl] apresentou E° = -1,20 V, aumentado para ⁓ +0,30 V nos modelos estudados do aduto, mostrando que Eo é principalmente influenciado pela troca do ligante auxiliar (por exemplo, Clpor S-R) com um pequeno efeito da estrutura da enzima. Além disso, foi abordada reação final de substituição C^N^C/Cys497, a qual se mostrou dependente do estado de protonação da Cys497. Estudos termodinâmicos e cinéticos sugerem que esta reação é exergônica, exibindo uma barreira de energia de 20,2 kcal mol-1 . A transferência completa do íon Au para o sítio ativo da enzima levaria à inibição total da sua atividade, causando a morte das células cancerígenas. Gold(III) complexes are promising compounds for cancer chemotherapy with mechanisms of action that involve steps dependent on their redox stability. The choice of the ligand is crucial to adjust their reactivity and biological activity. Tertiary phosphines (PR3) are among the most used auxiliary ligands in these compounds. The redox stability of [AuIII(C^N^C)(PR3)]+ (C^N^C=2,6-diphenylpyridine) (A) and [AuIII(N^N^N)(PR3)]3+ (N^N^N=2,2′:6′,2″-terpyridine) (B) complexes was herein investigated for a set of 41 phosphines, using the predicted standard reduction potential (Eo ) for Au3+/Au1+ electrochemical system as reference. For complexes (A), E o spread over 829 mV and all values were negative; for complexes (B), the E o values were positive and covered a narrower range of 507 mV. Phosphines with high steric impact decrease the complex stability despite being strong σdonors. Steric and electronic properties were used to build quantitative structure-property relationship models (QSPR), with the volume buried being the main factor in the stability of the studied compounds. In the case of compounds (B), the steric impact is more pronounced in gold(I) species. The electron-donating ability of phosphines has greater weight in the redox stability of compounds (B) compared to compounds (A). Later, fifteen compounds with different bidentate (bident) and tridentate (trident) ligands, keeping the chloride fixed as an auxiliary ligand ([AuIII(bident)Cl2] 3+n (bident = N^N and C^N) and [AuIII(trident)Cl]3+n (trident = N^N^N, C^N^N, C^C^N, C^N^C and N^C^N)), were studied. The calculated Eo values covered a wide range of 2600 mV. The compounds of the type [AuIII(C^C^N)Cl] showed the greatest stability with Eo of approximately -1.60 V in aqueous solution. The analysis of natural orbitals and Eo indicated that the inclusion of the AuC bond is less efficient for stabilizing the compound in the lateral position compared to the central position. The consecutive positioning of two pyridine ligands disfavors the reduction of gold(III) complexes. In the case of the compound [AuIII(C^N^N)Cl], the bipy ligand (N^N) behaves as a non-innocent redox ligand, actively participating in the reduction process without a significant structural change after reduction. The reported results help predict the redox stability of gold(III) complexes, which affects their chemical reactivity against important biological targets. Finally, molecular models were proposed for [AuIII(C^N^C)(SHCys-R)]+ adduct, with the [AuIII(C^N^C)]+ moiety bonded to residue Cys498 of TrxR, which represents the product of the first ligand exchange reaction. The original compound [AuIII(C^N^C)Cl] showed E° = - 8 1.20 V, which enlarges to ⁓ +0.30 V for the studied models of the adduct, showing that Eo is mainly influenced by auxiliary ligand exchange (eg: Clby SR) with a small effect of the enzyme structure. Furthermore, the final C^N^C/Cys497 substitution reaction was addressed, which showed to be dependent on the protonation state of Cys497. Thermodynamic and kinetic studies suggest that this reaction is exergonic, exhibiting an energy barrier of 20.2 kcal mol-1 . The complete transfer of the Au ion to the enzyme's active site would lead to the total inhibition of its activity, causing cancer cell death.

Published
2021

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