RESUMO

The 1-acyl thiourea family [R1C(O)NHC(S)NR2R3] exhibits the flexibility to incorporate a wide variety of substituents into their structure. The structural attributes of these compounds are intricately tied to the type and extent of substitution. In the case of 3-mono-substituted thioureas (R2=H), the conformational behavior is predominantly shaped by the presence of an intramolecular N-H ⋅ ⋅ ⋅ O=C hydrogen bond. This study delves into the structural consequences stemming from the inclusion of substituents possessing hydrogen-donor capabilities within four novel 1-acyl-3-mono-substituted thiourea derivatives. A comprehensive suite of analytical techniques, encompassing FTIR, Raman spectroscopy, multinuclear (1H and 13C) NMR spectroscopy, single-crystal X-ray diffraction, and supported by computational methods, notably NBO (Natural Bond Orbital) population analysis, Hirshfeld analysis, and QTAIM (Quantum Theory of Atoms in Molecules), was harnessed to scrutinize and characterize these compounds. In the crystalline state, these compounds exhibit an intricate interplay of intermolecular interactions, prominently featuring an expansive network of hydrogen bonds between the hydroxy (-OH) groups and the carbonyl and thiocarbonyl bonds within the 1-acyl thiourea fragment. Notably, the topological analysis underscores significant distinctions in the properties of the acyl thiourea fragment and the intramolecular >C=O ⋅ ⋅ ⋅ H-N bond when transitioning from the isolated molecule to the crystalline environment.

RESUMO

CONTEXT: In this work, we did a theoretical exploration of C8F8 (Ib) and its anion radical analogue (IIb) in this work. By investigating the thermochemistry of electron capture, we find that the free energy associated with the conversion of C8H8 (Ia) into its anion radical analogue IIa is of the order of + 92.83 kcal.mol-1, while the conversion of Ib into IIb is - 6.42 kcal.mol-1. Therefore, species IIb is thermodynamically more stable than its neutral analogue. Natural bond orbitals (NBO) analyses revealed that compound Ib exhibits a relative electronic stability as a function of intramolecular delocalisations of the type [Formula: see text] of the order of 2.70 kcal.mol-1. Similar delocalizations for Ia are energetically lower (1.45 kcal.mol-1). Topological analyses of compounds Ib and IIb indicate that the addition of an electron to Ib enhances the covalency of the C-C bond, as can be seen by the reduction in the ellipticity of the C-C bond. The opposite is observed for Ia, whose addition of the electron (leading to IIa) reduces the covalency of the C-C bond. By comparing the free and packaged forms of the species, it is found that, in the crystalline form, the system will present greater relative stability due to the dispersive interactions involved, as evidenced by non-covalent interactions (NCI) analysis. Finally, it was possible to verify that the manifestation of the current density with a lower paratropic and less antiaromatic character in Ib and IIb point to C8F8 as a strong candidate for electron capture. METHODS: Geometry optimization calculations were carried out, for all monomer structures using the hybrid functional B3LYP-D3 and the 6-31+G(d,p) basis set. To determine the formation thermochemistry of the ions, electronic energy corrections was performed using the DLPNO-CCSD(T)/aug-cc-pVTZ/C method. Starting from the optimised forms, shielding, nuclear magnetic resonance (NMR) spectra employing gauge-independent atomic orbital (GIAO), and NBO calculations were performed for these monomers, using the PBE0 functional and the pCSseg-2 atomic basis set. The magnetochemical analysis of ring currents was performed using the GIMIC formalism. For the topological analysis, it was applied the combination DLPNO-CCSD(T)/aug-cc-pVTZ/C, previously used for correcting the electronic energy.

RESUMO

CONTEXT AND RESULTS: This work aims to study the influence of the absence and presence of permanent charges on the electronic and dynamical properties of the non-covalent bound diatomic systems involving He and Li, Be as neutral and ionic partners. The charge displacement results suggest that in the formation of HeLi[Formula: see text], HeBe[Formula: see text], and HeBe[Formula: see text], the neutral He atom undergoes, in the electric field of the ion, a pronounced electronic polarization, and the natural bond order theoretical approach indicates that in the formation of the molecular orbital He acts as a weak electron donor. The energy decomposition analysis provides the dispersion and induction components as the attractive leading terms controlling the stability of all systems, confirming that the formed bond substantially maintains a non-covalent nature which is also supported by the Quantum Theory of Atoms in Molecules (QTAIM) analysis. Finally, it was found that the HeLi and HeBe neutral systems are unstable under any condition, HeLi[Formula: see text] and HeBe[Formula: see text] ionic systems are stable below 317K and 138K, respectively, while the HeBe[Formula: see text] system becomes unstable only after 3045K. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The potential energy curves and interactions in all systems were studied theoretically based on coupled-cluster singles and doubles method with perturbative inclusion of triples CCSD(T) method with an aug-cc-pV5Z basis set. More precisely, it was determined the potential energy curves describing the stability of the HeLi, HeLi[Formula: see text], HeBe, HeBe[Formula: see text], and HeBe[Formula: see text] systems, the charge displacement within the formed adducts, the decomposition of their total interaction energy, the topological analysis of their bonds, their rovibrational energies, their spectroscopic constants and lifetimes.

RESUMO

CONTEXT: Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well. METHODS: Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).

Assuntos

RESUMO

This work is focused on evaluating the performance of exchange-correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H2  â†” H2 CO, CO + H2 O â†” HCOOH, HCN â†” HNC, H + F2  â†” HF + F, H + N2  â†” HN2 , and H + CO â†” HCO. In general, the BB1K functional (hybrid-meta-generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%-55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.

RESUMO

An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-exchange contribution directly. Instead, weight factors are estimated to decompose the exact Vxc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first-order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.

RESUMO

The nature of the interaction between the molecules of the sodium dodecyl sulfate surfactant forming two crystal phases, one anhydrous, NaC12H25O4S and the other, NaC12H25O4S.H2O, hydrated with one water molecule for unit cell, has been studied in detail using the quantum theory of atoms in molecules and a localized electron detector function. It was found that for the anhydrous crystal, the head groups of the surfactant molecules are linked into a head-to-head pattern, by a bond path network of Na-O ionic bonds, where each Na+ atom is attached to four S O 4 - groups. For the hydrated crystal, in addition to these four bonds for Na+, two additional ones appear with the oxygen atoms of the water molecules, forming a bond paths network of ionic Na-O bonds, that link the Na+ atoms with the S O 4 - groups and the H2O molecules. Each H2O molecule is bonded to two S O 4 - groups via hydrogen bonds, while the S O 4 - groups are linked to a maximum of four Na+ atoms. The phenomenon of aggregation of the sodium dodecyl sulfate molecules at the liquid water/vacuum interface was studied using NVT molecular dynamics simulations. We have found that for surfactant aggregates, the Na+ ions are linked to a maximum of three SO4 - groups and three water molecules that form Na-O bonds. Unlike hydrated crystal, each of the O atoms that make these Na-O bonds is linked to only one Na+ ion. Despite these differences, like the crystal phases, the surfactant molecules tend to form a head-to-head network pattern of ionic Na-O bonds that link their heads. The present results indicate that the clustering of anionic surfactant at the water/vacuum interface is a consequence of the electrostatic alignment of the cationic and anionic groups as occurs in the crystalline phases of sodium dodecyl sulfate.

RESUMO

The chlordecone (CLD) and the ß-hexachlorocyclohexane (ß-HCH) are persistent organic pollutants with a great environmental stability that cause severe affectations to health. The concentration of these pesticides in the environment is low, which represent a problem for their determination, even for the modern analytical methods. The labeling of these compounds with an iodine radioisotope for their use as radiotracers is a potential solution to this problem. The present work studies the interaction of 1-iodochlordecone (I-CLD) and ß-1-iodo-pentachlorocyclohexane (I-ß-HCH) with cyclodextrins (CDs), during the formation of molecular inclusion complexes pesticide@CDs. The methodology of multiple minima hypersurfaces, quantic calculations based on density functional theory and a topologic study of electronic density were used to corroborate the stability of I-CLD@CDs and I-ß-HCH@CDs complexes. Three main types of guest-host complexes in relation to the occlusion grade were observed: with total occlusion, with partial occlusion and external interaction without occlusion. The more stable complexes are obtained when the γ-CD is the host molecule. The formed complexes with radiolabelled pollutants are analogous with the ones reported in previous works. These results confirm the utility of these complexes for the removal of organochlorine pesticides from polluted water and, also, demonstrate the possibility of using the I-CLD and the I-ß-HCH as possible radiotracers for these pollutants in further studies with environmental proposes.

Assuntos

RESUMO

The nature of the H-bonds between the human protein HLA-DR1 (DRB*0101) and the hemagglutinin peptide HA306-318 has been studied using the Quantum Theory of Atoms in Molecules for the first time. We have found four H-bond groups: one conventional CO··HN bond group and three nonconventional CO··HC, π··HC involving aromatic rings and HN··HCaliphatic groups. The calculated electron density at the determined H-bond critical points suggests the follow protein pocket binding trend: P1 (2,311) >> P9 (1.109) > P4 (0.950) > P6 (0.553) > P7 (0.213) which agrees and reveal the nature of experimental findings, showing that P1 produces by a long way the strongest binding of the HLA-DR1 human protein molecule with the peptide backbone as consequence of the vast number of H-bonds in the P1 area and at the same time the largest specific binding of the peptide Tyr308 residue with aromatic residues located at the binding groove floor. The present results suggest the topological analysis of the electronic density as a valuable tool that allows a non-arbitrary partition of the pockets binding energy via the calculated electron density at the determined critical points.

Assuntos

RESUMO

Mesoionic compounds belonging to the 1,3-oxazol-5-one, 1,3-diazole-4-thione and 1,3-thiazole-5-thione rings have been evaluated by a combination of Density Functional Theory, Quantum Theory of Atoms in Molecules, Electron Localization Function, Natural Bond Orbitals and Geodesic Electrostatic Potential Charge calculations. Atomic, bond, and ring properties have been considered to describe the electronic structure of mesoionic compounds. The results show that not only the ring type, but also the substituent groups have great influence on these properties. In addition, there is a significant and heterogeneous π-bonding contribution throughout the mesoionic rings. Finally, we conclude that some classical conceptions of charge localization and π-bonding contribution in these compounds are misleading or incomplete. © 2015 Wiley Periodicals, Inc.