
Lucas De Azevedo SantosVrije Universiteit Amsterdam | VU · Department of Chemistry and Pharmaceutical Sciences
Lucas De Azevedo Santos
PhD
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45
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Introduction
Additional affiliations
May 2017 - November 2021
May 2017 - November 2021
Education
May 2017 - November 2021
May 2017 - November 2021
March 2015 - March 2017
Publications
Publications (45)
Herein, we dismiss a recent proposal by Civiš, Hobza, andco-workers to modify the IUPAC definition of hydrogen bonds in orderto expand the scope from protonic Y−Hδ+ to hydridic Y−Hδ− hydrogen-bond donor fragments [J. Am. Chem. Soc. 2023, 145, 8550]. Based onaccurate Kohn−Sham molecular orbital (KS-MO) analyses, we falsify theconclusion that interac...
We have quantum chemically analyzed the closed-shell d8–d8 metallophilic interaction in dimers of square planar [M(CO)2X2] complexes (M = Ni, Pd, Pt; X = Cl, Br, I) using dispersion-corrected density...
Back cover showcasing research from the group of Professor
Célia Fonseca Guerra at the Vrije Universiteit Amsterdam,
The Netherlands The Fonseca Guerra Group studies the nature and
strength of weak chemical interactions in biological
and supramolecular self-assembled systems through
state-of-the-art quantum-chemical methods and analyses.
This work...
“The TheoCheM group develops sophisticated quantum mechanical models and techniques to uncover the physical principles behind the many incompletely (or supposedly) understood phenomena in chemistry. In the present work, we explain the physical mechanism behind the blueshift in the trifurcated hydrogen‐bonded X–•••H3C–Y complexes…” This and more abo...
We have quantum chemically investigated the boron‐boron bonds in B2, diborynes B2L2, and diborenes B2H2L2 (L=none, OH2, NH3) using dispersion‐corrected relativistic density functional theory at ZORA‐BLYP‐D3(BJ)/TZ2P. B2 has effectively a single B−B bond provided by two half π bonds, whereas B2H2 has effectively a double B=B bond provided by two hal...
Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulati...
We have quantum chemically investigated the origin of the atypical blueshift of the H−C bond stretching frequency in the hydrogen‐bonded complex X⁻•••H3C−Y (X, Y=F, Cl, Br, I), as compared to the corresponding redshift occurring in Cl⁻•••H3N and Cl⁻•••H3C−H, using relativistic density functional theory (DFT) at ZORA‐BLYP‐D3(BJ)/QZ4P. Previously, th...
Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal FmZ⋅⋅⋅F⁻ complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA‐M06/QZ4P. Quantitative Kohn‐Sham MO and energy decomposition analyses (EDA) show that...
The synthesis of the selenium‐based ligand L¹SeSeL¹ (2,2’‐diselanediylbis(N,N‐bis(pyridin‐2‐ylmethyl)ethan‐1‐amine) is described along with its reactivity with cobalt(II) salts. The cobalt(II)‐diselenide complex [Co2(L¹SeSeL¹)Cl4] was obtained in good yield, and its spectroscopic properties closely resemble that of its sulfur analog. Reaction of L¹...
The gauche conformer in 1-X,2-Y-disubstituted ethanes, that is, the staggered orientation in which X and Y are in closer contact, is only favored for relatively small substituents that do not give rise to large X···Y steric repulsion. For more diffuse substituents, weakly attractive orbital interactions between antiperiplanar bonds (i.e., hyperconj...
The formation of Co(III)-thiolate complexes from Co(II)-disulfide complexes using the anionic ligand 8-quinolinolate (quin-) has been studied experimentally and quantum chemically. Two Co(II)-disulfide complexes [Co2(LxSSLx)(Cl)4] (x = 1 or 2; L1SSL1 = 2,2'-disulfanediylbis(N,N-bis(pyridin-2-ylmethyl)ethan-1-amine; L2SSL2 = 2,2'-disulfanedylbis (N-...
The redox-conversion reaction of cobalt(II)-disulfide to cobalt(III)-thiolate complexes triggered by addition of the bidentate ligand 2,2'-bipyridine has been investigated. Reaction of the cobalt(II)-disulfide complex [Co2(L1SSL1)(X)4] (L1SSL1 = di-2-(bis(2-pyridylmethyl)amino)-ethyldisulfide; X = Cl or Br) [1X] with 2,2'-bipyridine (bpy) resulted...
Phosphites have been used to control several soybean diseases, however, few studies have investigated the association between phosphites with fungicides in soybean. The objectives of this study were to assess the potential of potassium phosphite (Phi) in combination with fungicides for powdery mildew management, and Phi detection in the presence of...
Invited for this month's cover are collaborators from the TheoCheM group of the Vrije Universiteit Amsterdam and the University of Perugia. The cover picture shows a σ‐electron traveling through a hydrogen‐bonded squaramide linear chain. The charge transfer within the σ‐electronic system is the cause for the cooperativity in the investigated urea,...
The cover picture shows σ-electrons, which by traveling through the chain, strengthen the hydrogen bonds in squaramide linear chains. This increasing gain in stability becomes more pronounced when the chain elongates and originates from the donor–acceptor charge transfer interaction within the σ-electronic system. As the charge flows from one end o...
We have quantum chemically analyzed the cooperative effects and structural deformations of hydrogen‐bonded urea, deltamide, and squaramide linear chains using dispersion‐corrected density functional theory at BLYP‐D3(BJ)/TZ2P level of theory. Our purpose is twofold: (i) reveal the bonding mechanism of the studied systems that lead to their self‐ass...
The concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms and bonds are viewed as point charges and dipole moment vectors, respectively, is however oversimplified. To provide a causal model rooted in quantitative...
We have analyzed the structure and stability of archetypal pnictogen-bonded model complexes D3PnA- (Pn = N, P, As, Sb; D, A = F, Cl, Br) using state-of-the-art relativistic density functional calculations at the ZORA-M06/QZ4P level. We have accomplished two tasks: (i) to compute accurate trends in pnictogen-bond strength based on a set of consisten...
The cover image is based on the Full Paper Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study by Lucas de Azevedo Santos et al., https://doi.org/10.1002/jcc.26489.
Invited for this month's cover are the groups of Prof. Dr. Teodorico C. Ramalho (Federal University of Lavras and University Hradec Kralove) and Prof. Dr. F. Matthias Bickelhaupt (Vrije Universiteit Amsterdam and Radboud University). The cover picture shows the key message of their work, that is, the covalency of the chalcogen bonds, in an elegantl...
The Front Cover shows the key message of our work, that is, the covalency of the chalcogen bonds, in an elegantly simple and attractive manner. To that end, the chalcogen bonds are represented by schematic 3D structures of the bond donor D2Ch and the bond acceptor A–, and their attractive interaction in green. Then, a colorful molecular orbital (MO...
We have quantum chemically investigated the rotational isomerism of 1,2‐dihaloethanes XCH2CH2X (X = F, Cl, Br, I) at ZORA‐BP86‐D3(BJ)/QZ4P. Our Kohn‐Sham molecular orbital (KS‐MO) analyses reveal that hyperconjugative orbital interactions favor the gauche conformation in all cases (X = F−I), not only for X = F as in the current model of this so‐cal...
We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) t...
We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-S...
The Lewis acid/base interaction is a cornerstone of chemistry and is teaching material for every undergraduate chemistry student. Thus, a set of simple and intuitive rules to rationalize the strength of these interactions are desired. This article provides just that! The bond dissociation energy of X3B–NY3 Lewis pairs increases along X,Y=F, Cl, Br,...
We have quantum chemically investigated the bonding between archetypical Lewis acids and bases. Our state‐of‐the‐art computations on the X3B−NY3 Lewis pairs have revealed the origin behind the systematic increase in B−N bond strength as X and Y are varied from F to Cl, Br, I, H. For H3B−NY3, the bonding trend is driven by the commonly accepted mech...
Halogen bonds are highly important in medicinal chemistry as halogenation of drugs, generally, improves both selectivity and efficacy towards protein active sites. However, accurate modeling of halogen bond interactions remains a challenge, since a thorough theoretical investigation of the bonding mechanism, focusing on the realistic complexity of...
For the synthesis of magnetic molecularly imprinted polymers (MMIPs), quinoline was used as a template molecule, methacrylic acid (MAA) as a functional monomer, ethylene glycol dimethacrylate (EGDMA) as a cross-linking agent and toluene as porogenic solvent, adding magnetic character with nanoparticles of maghemite (γ-Fe2O3). The solvents for extra...
Essential to understanding life, the biomolecular phenomena have been an important subject in science, therefore a necessary path to be covered to make progress in human knowledge. To fully comprehend these processes, the non-covalent interactions are the key. In this review, we discuss how specific protein-ligand interactions can be efficiently de...
The structure of bioactive compounds inside their biological target is mainly dictated by the intermolecular interactions present in the binding side, whereas intramolecular interactions are responsible for the structure of an isolated molecule. Accordingly, this work reports the relative significance of these interactions for the bioactive conform...
The aim of this work was to study the synthesis of molecularly imprinted polymers (MIPs) for the selective adsorption of β-estradiol (E2). For this, six solvents with different polarities were tested and the results indicated that, for obtaining a good E2 adsorbent, the solvent should be moderately polar to favor the formation of a monomer-template...
The effects of solvent on the synthesis of molecularly imprinted polymers (MIPs) for the selective adsorption
of quinoline were evaluated in this work. The MIPs were synthesized by the “bulk” method using the
quinoline molecule (IQ) as a template in different solvents, such as toluene (MIPT) and chloroform
(MIPC). The adsorbents were characterized...
Several rare or orphan diseases have been characterized that singly affect low numbers of people, but cumulatively reach ∼6% - 10% of the population in Europe and in the United States. Human genetics has shown to be broadly effective when evaluating subjacent genetic defects such as orphan genetic diseases, but on the other hand, a modest progress...
A thermodynamic study about the stability of intermediates in the reaction of 5‐hydroxymethylfurfural (HMF) over Preyssler heteropolyacids (HPA‐Preyssler) was performed to explain the self‐etherification or oxidation of HMF. Although the product of etherification forms in higher proportion when a heteropolyacid is used, other oxidation products are...
The 2,2'-((5-(4-bromophenyl)furan-2-yl)methylene) bis (5,5-dimethylcyclohexane-1,3-dione) (3) and 2,2'-((5-(4-chlorophenyl)furan-2-yl)methylene) bis (5,5-dimethylcyclohexane-1,3-dione) (4) were prepared in, respectively, 63% and 59% yield, via ZrOCl2⋅8H2O catalyzed condensation reactions between dimedone and appropriate aldehydes. Their structures...
Pyran moiety containing heterocyclic compounds have the capability for binding to either side to cyclohex-2-enone rings and to form xanthene derivatives (1,8-dioxooctahydroxanthenes also known as xanthenodiones). These xanthene derivatives display a wide range of biological activities and find applications in laser technologies and photodynamic the...
Levulinic acid (LA) transformation to different pyrrolidones via reductive amination was studied using an Ir/SiO2-SO3H catalyst in liquid phase. The effects of solvent, amine concentration, H2 partial pressure, catalyst mass, and reuse were studied. The spent catalysts were evaluated by DRIFTS to obtain evidence of the interaction of levulinic acid...
The electronic effects in supramolecular systems are a great challenge for computational chemistry, and the understanding of ligand-protein interactions driven by Halogen Bonds can be limited by Molecular Mechanics point of view. In fact, the variations of the Halogen Bond acceptors, such as an aromatic ring and electrons lone pairs, restrict the c...
Stacking interactions between substituted buckybowls (corannulene and sumanene) with fullerenes (C60 and C70) were studied at the B97-D2/TZVP level. Corannulene and sumanene monomers were substituted with five and six Br, Cl, CH3, C2H or CN units, respectively. A comprehensive study was conducted, analyzing the interaction of corannulenes and suman...
b Stacking p/p interactions of ring-annelated corannulenes with fullerenes C 60 and C 70 were studied at the B97-D level. For this purpose three-, four-, and five-membered rings (saturated and unsaturated) were annelated to the five rim bonds of corannulene. Substitution effects with NH, O and S units on each one of the five saturated five-membered...
Understanding the molecular recognition process of nucleobases is one of the greatest challenges for both computational chemistry and biophysics fields. In fact, our results point out that it is a hard task to take into account the hydrophobic interactions, such as π−π and T-stacking interactions, by theoretical calculations using conven-tional for...
Stacking interactions between substituted buckybowls (corannulene and sumanene) with fullerenes (C 60 and C 70) were studied at the B97-D2/TZVP level. Corannulene and sumanene monomers were substituted with five and six Br, Cl, CH 3, C 2H or CN units, respectively. This work was carried out for supplement our previous work of the study of substitue...