Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes.

Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.

Remarkable Nonlinear Properties of a Novel Quinolidone Derivative: Joint Synthesis and Molecular Modeling.

A novel 4(1H) quinolinone derivative (QBCP) was synthesized and characterized with single crystal X-ray diffraction. Hirshfeld surfaces (HS) analyses were employed as a complementary tool to evaluate the crystal intermolecular interactions. The molecular global reactivity parameters of QBCP were studied using HOMO and LUMO energies. In addition, the molecular electrostatic potential (MEP) and the UV-Vis absorption and emission spectra were obtained and analyzed. The supermolecule (SM) approach was employed to build a bulk with 474,552 atoms to simulate the crystalline environment polarization effect on the asymmetric unit of the compound. The nonlinear optical properties were investigated using the density functional method (DFT/CAM-B3LYP) with the Pople's 6-311++G(d,p) basis set. The quantum DFT results of the linear polarizability, the average second-order hyperpolarizability and the third-order nonlinear susceptibility values were computed and analyzed. The results showed that the organic compound (QBCP) has great potential for application as a third-order nonlinear optical material.

Second-order nonlinear optical properties of two chalcone derivatives: insights from sum-over-states.

In this study, a combined experimental and theoretical study of the nonlinear optical properties (NLO) of two chalcone derivatives, (E)-3-(2-methoxyphenyl)-1-(2-(phenylsulfonylamine)phenyl)prop-2-en-1-one (MPSP) and (E)-3-(3-nitrophenyl)-1-(2-(phenylsulfonylamine)phenyl)prop-2-en-1-one (NPSP), in DMSO is reported. The single crystal structures of the compounds, which differ only by the type and position of one substituent, were grown using the slow evaporation technique, and the main structural differences are discussed. The two-photon absorption and first-order hyperpolarizability measurements were performed via the Z-scan technique and hyper-Rayleigh scattering experiment in DMSO. The theoretical calculations were performed using the Density Functional Theory (DFT) at the CAM-B3LYP/6-311++G(d,p) level, and the sum-over-states (SOS) approach in both static and dynamic cases. Besides the electron conjugation achieved by the aromatic rings, olefins, and carbonyl groups, both compounds have a nearly flat chalcone backbone, which is believed to contribute to the nonlinear optical properties. MPSP and NPSP have different positions, even though they have roughly the same conformation and form C-HO interactions. For several studied frequencies, the HRS first hyperpolarizability values for MPSP are greater than those for NPSP, indicating that in most cases the NLO properties of MPSP are better. The comparison among the theoretical and experimental HRS first hyperpolarizability results showed a good agreement. In addition, the two-dimensional second order nonlinear optical spectra obtained from the sum-over-states model indicate good second-order NLO responses of the two chalcone derivatives under external fields. Our findings are important not only to show the potential nonlinear optical application of the two new compounds but also to gain an insight into how different chemical compositions might affect the crystal structures and physico-chemical properties.

Using the Supermolecule Approach To Predict the Nonlinear Optics Potential of a Novel Asymmetric Azine.

Organic molecules with electron acceptors or withdrawal substituents terminal at π-conjugated system are promising candidates to be explored as materials with high linear and nonlinear optical properties. On the basis of these features, a novel asymmetric azine ( 7E, 8E)-2-(3-methoxy-4-hydroxy-benzylidene)-1-(4-nitrobenzylidene)hydrazineC15H13N3O4 (NMZ) was synthesized. The molecular structure of NMZ was elucidated by X-ray crystallography and the supramolecular arrangement was analyzed from Hirshfeld surface methodology. An iterative electrostatic scheme using a super molecule approach, where neighboring molecules are represented by charge points, was employed to investigate optical dipole moment (µ), the linear polarization (α) and the first (ß) and second (γ) hyperpolarizabilities. The NMZ crystallized in the centrosymetric space group P21/n and packs via combined O-H···O, C-H···O, and N···π interactions. The macroscopic property of third order χ(3) found for the NMZ is 298.62 times greater than values reported for chalcone derivative (2 E)-1-(3-bromophenyl)-3-[4 (methylsulfanyl)phenyl]prop-2-en-1-one. The results for NMZ indicate a good nonlinear optical effect.

A new quinolinone-chalcone hybrid with potential antibacterial and herbicidal properties using in silico approaches.

Quinolinone-chalcones are hybrid compounds consisting of chalcone and quinolone moieties with biological activity related to their hybrid structure. This work seeks to describe the structural and theoretical parameters related to the physicochemical properties and biological activity of a new quinolinone-chalcone. The synthesis, structural characterization by X-ray diffraction, molecular topology by Hirshfeld surfaces and QTAIM, molecular electronic calculations, and pharmacophore analysis were described. The weak interactions C-H…O, C-H…π, and C-H…Br were responsible for crystal growth and stabilized the crystalline state. The DFT analysis shows that the sulfonamide group region is susceptible to observed interactions, and the frontier molecular orbitals indicate high kinetic stability. Also, pharmacophore analysis revealed potential antibacterial and herbicidal activity; by docking within the active site of TtgR, a transcription regulator for the efflux pump TtgABC from the highly resistant Pseudomonas putida (P. putida) strain DOT-TIE, we showed that the activation of TtgR relies upon the binding of aromatic-harboring compounds, which plays a crucial role in bacterial evasion. In this context, a new quinolinone-chalcone has a higher binding affinity than tetracycline, which suggests it might be a better effector for TtgR.

Cyclohexanone-Based Chalcones as Alternatives for Fuel Additives.

The use of small molecules, such as chalcones and their derivatives, for more efficient fuels is in increasing demand due to environmental factors. Here, three crystal structures (BH I, II, and III) of cyclohexanone-based chalcones were synthesized and described by single-crystal X-ray diffraction and Hirshfeld surface analysis. The supramolecular modeling analysis on the hyperconjugative interaction energies and QTAIM analysis at the ωB97XD/6-311++G(d,p) level of theory were carried out to analyze the intermolecular interactions in the solid-state. The structure-property relationship, frontier molecular orbital, molecular electrostatic potential, and the experimental calorific value analysis show that the three compounds are a good alternative to be used as an additive for some fuels. Our findings represent a further step forward in the development of cheaper and more efficient fuel additives and pose an opportunity for further investigation on similar analogues.

Structural insights into the biological activity of a thioxopyrimidine derivative.

Bacterial resistance to the main widespread antibiotics, such as those based on quinolones, is a concern of the scientific community, leading to the search for new classes of molecules that can be used as an alternative. Here, we investigate the crystalline and chemical characteristics of a thioxopyrimide to understand its demonstrated biological activity and to identify which portion of the molecule can be used as a framework to develop new antibiotics. For this purpose, structural studies of ethyl 4-methyl-2-phenyl-6-thioxo-1,6-dihydro-5-pyrimidinecarboxylate were carried out aided by Hirshfeld surface analysis, as well as theoretical calculations on frontier molecular orbitals, molecular electrostatic potential, and conformational stability, in addition to docking studies targeting topoisomerase IV. The docking results show a reasonable accommodation of the molecule at the topoisomerase IV binding site and interact mainly by hydrogen bonds between the thioxopyrimidine portion with Glu198, Thr292, and Gly225, aided by hydrophobic interactions involving the rest of the molecule. These results suggest a relationship between the antibacterial activity shown mainly with the 4-thioxopyrimidine portion, leading to the investigation of new compounds that use this scaffold.

Halogen bonds on substituted dibromonitrobenzene derivatives.

Halogen bonding is a noncovalent interaction that has attracted great attention because of its importance in several areas, such as photonics, nonlinear optics, pharmaceutical products, supramolecular engineering, biochemistry, protein-ligand complexes, and polymer interactions. In this context, we describe the synthesis, molecular structure, supramolecular arrangement, and theoretical calculations of five dibromonitrobenzene derivatives, which present different halogen atoms substituted. The solid-state characterization was carried out by X-ray diffraction with the contribution of Hirshfeld surfaces for analysis of molecular interactions. The frontier molecular orbital, molecular electrostatic potential, and quantum theory of atoms in molecules were carried out at the M06-2X/6-311+G(d,p) level of theory. Those observed halogen interactions indicate the crystalline solid-state stabilization for the dibromonitrobenzene derivatives.

Experimental and molecular modeling study of a novel arylsulfonamide chalcone.

Chalcones have been reported to present biological activities that are potentialized when a sulfonamide group is attached. A comprehensive structural study was performed for arylsulfonamide chalcone N-(2-(3-4-methoxyphenyl-propanoyl)-phenyl)-benzene-sulfonamide in order to describe its supramolecular arrangement and its physicochemical properties. The molecular packing arrangement was described by X-ray diffraction and Hirshfeld surfaces (HS). Theoretical calculations were performed using density functional theory (DFT), molecular electrostatic potential (MEP) mapping, ab initio Car-Parrinelo molecular dynamics (CPMD) and the quantum theory of atoms in molecules (QTAIM). The solid-state arrangement is stabilized by C- H⋯O and C-H⋯π interactions observed on HS and MEP map. The topological analysis was evaluated by QTAIM.

Conformation analysis of a novel fluorinated chalcone.

Chalcones are an important class of natural compounds that exhibit numerous biological activities. In this paper, we report the synthesis and characterization of new fluorinated chalcone (FCH). The molecular geometry was determined by means of single crystal X-ray diffraction, and density functional theory (DFT) at B3LYP, M06-2X functionals and MP2 method, with the 6-311++G(d,p) basis set, was applied to optimize the ground state geometry and to study the molecular conformational stability. The molecular electrostatic potential (MEP) was also investigated at the same level of theory in order to identify and quantify the possible reactive sites. The FCH crystallizes in the centrossymmetric space group [Formula: see text] with two independent conformers (α and ß) in the asymmetric unit cell. The α conformer is arranged in planar layer whereas the ß creates a layer of non-classical dimer along c axis, that differ from α in about 11° in the orientation of phenyl groups. The stabilization of the ß conformer is achieved by C-H···π arrangement. The small energy difference between the conformers (0.086 kcal mol-1) and the absence of activation energy indicates that the conversion between them can takes place at room temperature and the ß isomer is stable only in solid state. The FCH most electrophilic site occurs on the oxygen atom from the carboxyl group with absolute MEP value of about -52 kcal mol-1 whereas the MEP value calculated for F site is about -23 kcal mol-1.