Helder Marques - Academia.edu (original) (raw)

Papers by Helder Marques

Inorganics, 2022

An attempt was made, using computational methods, to understand whether the intermolecular intera... more An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some a...

There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules... more There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown here that these views are not necessarily true since the attractive energy between the oxygen atom of some molecules and several electron-rich anionic bases examined in a series of 34 ion-molecule complexes varied from the weak (ca-2.30 kcal mol-1) to the ultra-strong (-90.10 kcal mol-1). The [MP2 /aug-cc-pVTZ] binding energies for several of these complexes were found to be comparable to or significantly larger than that of the well-known hydrogen bond complex [FH•••F]-(~ 40 kcal mol-1). The nature of the intermolecular interactions was examined using the quantum theory of atoms in molecules, second-order natural bond orbital and symmetric adaptive perturbation theory energy decomposition analyses. It was found that many of these interactions comprise mixed bonding character (ionic and covalent), especially manifest in the moderate to strongly bound complexes. All these can be explained by an n (lone-pair bonding orbital) ® s* (anti-bonding orbital) donor-acceptor charge transfer delocalization. This study, therefore, demonstrates that the covalently bound oxygen atom in molecules can have a significant ability to act as an unusually strong chalcogen bond donor.

Inorganics, 2019

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper... more In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specifi...

Computation, 2018

The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry... more The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry in molecular assemblies are presented in a brief review of the field. Emphasis has been placed to show that type-I and -II halogen-centered F···F long-ranged intermolecular distances viable between the entirely negative fluorine atoms in some fluoro-substituted dimers of C6H6 can be regarded as the consequence of significant non-covalent attractive interactions. Such attractive interactions observed in the solid-state structures of C6F6 and other similar fluorine-substituted aromatic compounds have frequently been underappreciated. While these are often ascribed to crystal packing effects, we show using first-principles level calculations that these are much more fundamental in nature. The stability and reliability of these interactions are supported by their negative binding energies that emerge from a supermolecular procedure using MP2 (second-order Møller-Plesset perturbation theory)...

Journal of Computational Chemistry, 2019

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design pro... more The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C 3 F 6), upon its interaction with another same molecule to form (C 3 F 6) 2 dimers. The existence of σand π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C 3 F 6 itself and the (C 3 F 6) 2 dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C 3 F 6) 2 dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C 3 F 6) 2 dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt,

Inorganics, 2022

An attempt was made, using computational methods, to understand whether the intermolecular intera... more An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some a...

There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules... more There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown here that these views are not necessarily true since the attractive energy between the oxygen atom of some molecules and several electron-rich anionic bases examined in a series of 34 ion-molecule complexes varied from the weak (ca-2.30 kcal mol-1) to the ultra-strong (-90.10 kcal mol-1). The [MP2 /aug-cc-pVTZ] binding energies for several of these complexes were found to be comparable to or significantly larger than that of the well-known hydrogen bond complex [FH•••F]-(~ 40 kcal mol-1). The nature of the intermolecular interactions was examined using the quantum theory of atoms in molecules, second-order natural bond orbital and symmetric adaptive perturbation theory energy decomposition analyses. It was found that many of these interactions comprise mixed bonding character (ionic and covalent), especially manifest in the moderate to strongly bound complexes. All these can be explained by an n (lone-pair bonding orbital) ® s* (anti-bonding orbital) donor-acceptor charge transfer delocalization. This study, therefore, demonstrates that the covalently bound oxygen atom in molecules can have a significant ability to act as an unusually strong chalcogen bond donor.

Inorganics, 2019

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper... more In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specifi...

Computation, 2018

The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry... more The divergence of fluorine-based systems and significance of their nascent non-covalent chemistry in molecular assemblies are presented in a brief review of the field. Emphasis has been placed to show that type-I and -II halogen-centered F···F long-ranged intermolecular distances viable between the entirely negative fluorine atoms in some fluoro-substituted dimers of C6H6 can be regarded as the consequence of significant non-covalent attractive interactions. Such attractive interactions observed in the solid-state structures of C6F6 and other similar fluorine-substituted aromatic compounds have frequently been underappreciated. While these are often ascribed to crystal packing effects, we show using first-principles level calculations that these are much more fundamental in nature. The stability and reliability of these interactions are supported by their negative binding energies that emerge from a supermolecular procedure using MP2 (second-order Møller-Plesset perturbation theory)...

Journal of Computational Chemistry, 2019

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design pro... more The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C 3 F 6), upon its interaction with another same molecule to form (C 3 F 6) 2 dimers. The existence of σand π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C 3 F 6 itself and the (C 3 F 6) 2 dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C 3 F 6) 2 dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C 3 F 6) 2 dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt,