On the structural, electronic, and optical properties of L-histidine crystal: a DFT study.

CONTEXT: The monoclinic L-histidine crystal is critical for protein structure and function and is also found in the myelin of brain nerve cells. This study numerically examines its structural, electronic, and optical properties. Our findings indicate that the L-histidine crystal has an insulating band gap of approximately 4.38 eV. Additionally, electron and hole effective masses range between 3.92[Formula: see text]-15.33[Formula: see text] and 4.16[Formula: see text]-7.53[Formula: see text], respectively. Furthermore, our investigation suggests that the L-histidine crystal is an excellent UV collector due to its strong optical absorption activity for photon energies exceeding 3.5 eV. METHODS: To investigate the structural, electronic, and optical properties of L-histidine crystals, we used the Biovia Materials Studio software to conduct Density Functional Theory (DFT) simulations as implemented in the CASTEP code. Our DFT calculations were performed using the generalized gradient approximation (GGA) as parameterized by the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional, with an additional dispersion energy correction (PBE [Formula: see text] TS) based on the model proposed by Tkatchenko and Scheffler to describe van der Waals interactions. Additionally, we employed the norm-conserving pseudopotential to treat core electrons.

New ethionamide boosters and EthR2: structural and energetic analysis.

Ethionamide (ETH) is a high-profile drug for the treatment of patients with multidrug-resistant Mycobacterium tuberculosis and, in order to produce its inhibitory effects, it needs to be bioactivated by monooxygenase EthA. This process is under the control of the transcriptional repressors EthR and EthR2, so that their inhibition results in the boosting of ethionamide activation. Herein, through crystallographic data and computer simulations, we calculated the interaction binding energies of four inhibitors with improved in vitro potency, namely BDM76060 (PDB ID: 6HS1), BDM72201 (PDB ID: 6HRX), BDM76150 (PDB ID: 6HS2) and BDM72719 (PDB ID: 6HRY), in complexes with the transcriptional repressor EthR2, using density functional theory (DFT) within the molecular fractionation with conjugated caps (MFCC) approach. It was observed that these ligands share the same binding site within a 10.0 Å radius of the EthR2 protein; however, their structural particularities have a significant impact on the global energies of systems. The BDM72201 and BDM72719 components are weakly attached to the binding site, while BDM76060 and BDM76150 components produce stronger bonds, corroborating with experimental studies demonstrating that BDM76060 and BDM76150 are more successful in producing inhibitory effects. BDM76060 and BDM76150 have many functional groups that increase the contact surface with the protein and attract a more significant number of amino acid residues, being able to produce polarities that generate stronger interactions. In the current scenario of a growing number of cases of bacterial resistance, the obtained data can be used to guide clinical trials of these inhibitors and other inhibitors that act on the alternative EthR2 pathway, focusing on improving the activity of ethionamide, its effectiveness, a reduction in the treatment time and exposure to cytotoxic effects.

Computational structural, electronic and optical properties of the palmitic acid in its C form.

In this work, we report a theoretical study of the structural, electronic, and optical properties of palmitic acid crystal in its C form under DFT calculations level. Palmitic acid is a fatty acid that constitutes the large majority of vegetable oils with recognized potential applications in medicine, pharmaceuticals, cosmetics technology, foods, and fuel. As a main result, we have found that the electronic bandstructure reveals an indirect gap given by 3.713 eV (E→B andE→Γ), as a main bandgap, while the secondary bandgaps found were 4.175 eV (γ1→Γ) and 4.172 eV (γ2→B). It behaves like a wide bandgap semiconductor, which points to potential applications in optoelectronic devices.

In silico approach of modified melanoma peptides and their immunotherapeutic potential.

Melanoma is a type of skin cancer with increasing incidence worldwide and high lethality. Conventional forms of treatment are not effective in advanced cancer stages. Hence, immunotherapeutic approaches have been tested to modulate immune response against tumor cells. Some vaccine models using tumor-associated antigens (TAAs) such as glycoprotein 100 (gp100) have been studied, but their expected effectiveness has not been shown until now. Antigen immunogenicity is a crucial point to improve the immune response, and therefore mutations are inserted in peptide sequences. It is possible to understand the interactions which occur between peptides and immune system molecules through computer simulation, and this is essential in order to guide efficient vaccine models. In this work, we have calculated the interaction binding energies of crystallographic data based on modified gp100 peptides and HLA-A*0201 using density functional theory (DFT) and the molecular fractionation with conjugated caps (MFCC) approach. Our results show the most relevant residue-residue interactions, the impact of three mutations in their binding sites, and the main HLA-A*0201 amino acids for peptide-HLA binding.

Betaine-loaded CaCO3 microparticles improve survival of vitrified feline preantral follicles through higher mitochondrial activity and decreased reactive oxygen species.

Ovary fragments from six sexually mature cats were vitrified in the presence or absence of betaine or ascorbic acid, loaded (7.4 or 74µM betaine; 20 or 200µM ascorbic acid) or not (1mM betaine or 0.3mM ascorbic acid) into CaCO3 microparticles, and assessed for follicular morphology, oxidative stress and mitochondrial activity Feline ovarian tissue was successfully preserved after vitrification in the presence of 74µM betaine loaded in CaCO3 microparticles, as confirmed by morphological analysis and the density of preantral follicles and stromal cells, as well as by the increased mitochondrial activity and decreased production of reactive oxygen species.

Rose Bengal incorporated to α-cyclodextrin microparticles for photodynamic therapy against the cariogenic microorganism Streptococcus mutans.

Rose Bengal@α-cyclodextrin (RB@α-CD) microparticles (µPs) were prepared and the RB inclusion in α-CD was experimentally demonstrated through infrared, UV-VIS absorption spectroscopy and cyclic voltammetry. The RB inclusion in α-CD was theoretically investigated using classical molecular mechanics calculations, the simulation results showing that RB can be included in both the narrow and wide apertures of the α-cyclodextrin ring with configurations exhibiting average binding energies of about 27 kcal mol-1. The prepared RB@α-CD microparticles were characterized through Scanning Electron Microscopy (SEM) and it was demonstrated that they are highly efficient in the photodynamic therapy against a Streptococcus mutans (the main bacteria of cariogenic dental plaque) suspension, as a concentration of RB@α-CD µPs 10 times smaller than the usual concentration of pure RB is still capable to produce significant antibacterial activity.

Vibrational Modes and Phonon and Thermodynamic Properties of the Metaboric Acid Polymorphs α-, ß-, and γ-(BOH)3O3 within a Density Functional Theory Framework.

A combined study of vibrational and thermodynamic properties of metaboric acid (BOH)3O3 crystal polymorphs α, ß, and γ were obtained through density functional theory (DFT) calculations in an attempt to resolve the conflicting assignments that currently exist in the literature for them. A complete correlation between the normal-mode assignment and vibrational signatures to distinguish particular features of each metaboric acid polymorph, in particular, those related to motions of the planar layers in α-(BOH)3O3, with a level of detail surpassing essays based on previous published experimental works has been achieved. Besides, no DFT-based research work was published early on the (BOH)3O3 polymorph vibrational properties, and our DFT-simulated infrared and Raman spectra for all metaboric acid polymorphs agree very well with experiment. Comparison of the previously published experimental IR and Raman spectroscopic results with predictions from higher levels DFT calculations allows identification of the in-plane and out-of-plane B-O bending modes. For example, the strongest measured (DFT-calculated) Raman modes of α-(BOH)3O3 at 591 and 797 cm-1 (599 and 810 cm-1) are identified as vibrational signatures of breathing B3O3/Ag in-plane modes, while the shoulder in the lattice modes region at 135 (143) cm-1 is the vibrational signature of the bending B3O3/B1g out-of-plane mode. Phonon-dispersion bands and their respective phonon densities of states were also evaluated for each system, as well as temperature-dependent curves for entropy, enthalpy, free energy, heat capacity, and Debye temperature. Phonon dispersion curves are singular for each (BOH)3O3 species, and a consistent gap decrease between the lowest and highest frequency vibrational bands was observed. The DFT-based calculations also revealed that the noncovalent interactions prevalent in the α and ß crystals lead to significant differences with respect to the thermodynamic properties in comparison with the γ phase.

Vibrational Properties of Bulk Boric Acid 2A and 3T Polymorphs and Their Two-Dimensional Layers: Measurements and Density Functional Theory Calculations.

Boric acid (H3BO3) is being used effectively nowadays in traps/baits for the management of Aedes aegypti L. and Aedes albopictus Skuse species of mosquitoes, which are the main spreading vectors worldwide for diseases such as malaria, dengue, and zika. Previously, we published results on the structural, electronic, and optical properties of its molecular triclinic H3BO3-2A and trigonal H3BO3-3T polymorphs within the framework of density functional theory (DFT). Because of the renewed importance of these materials, the focus of this work is on the vibrational properties of the bulk boric acid 2A and 3T polymorphs. We measured the infrared and Raman spectra of the former, which was accompanied and interpreted through state-of-the-art DFT calculations, supplemented by computations regarding the H3BO3 molecule and two-dimensional layers based on the bulk structures. We identify/assign their normal modes and find vibrational signatures for each polymorph as well as in- and out-of-plane motions and molecular vibrations, unveiling a nice agreement between the DFT level of theory employed and our improved spectroscopic measurements in the wavenumber ranges of 400-2000 cm-1 (infrared) and 0-1500 cm-1 (Raman). We show that a dispersion-corrected DFT functional within the generalized gradient approximation (GGA) can be very accurate in describing the vibrational properties of the boric acid polymorphs. Besides, several issues left open/not clearly resolved in previously published works on the vibrational mode assignments of the bulk and 2D sheets of boric acid are explained satisfactorily. Finally, phonon dispersions and associated densities of states were also evaluated for each polymorph along with their temperature-dependent DFT-calculated entropy, enthalpy, free energy, heat capacity, and Debye temperature. In particular, our DFT calculations suggest a possible way to differentiate the 2A and 3T boric acid polymorphs through Raman spectroscopy and heat capacity measurements.

Vibrational Spectroscopy and Phonon-Related Properties of the L-Aspartic Acid Anhydrous Monoclinic Crystal.

The infrared absorption and Raman scattering spectra of the monoclinic P21 l-aspartic acid anhydrous crystal were recorded and interpreted with the help of density functional theory (DFT) calculations. The effect of dispersive forces was taken into account, and the optimized unit cells allowed us to obtain the vibrational normal modes. The computed data exhibits good agreement with the measurements for low wavenumbers, allowing for a very good assignment of the infrared and Raman spectral features. The vibrational spectra of the two lowest energy conformers of the l-aspartic molecule were also evaluated using the hybrid B3LYP functional for the sake of comparison, showing that the molecular calculations give a limited description of the measured IR and Raman spectra of the l-aspartic acid crystal for wavenumbers below 1000 cm(-1). The results obtained reinforce the need to use solid-state calculations to describe the vibrational properties of molecular crystals instead of calculations for a single isolated molecule picture even for wavenumbers beyond the range usually associated with lattice modes (200 cm(-1) < ω < 1000 cm(-1)).

Antimicrobial effect of Dinoponera quadriceps (Hymenoptera: Formicidae) venom against Staphylococcus aureus strains.

AIMS: Dinoponera quadriceps venom (DqV) was examined to evaluate the antibacterial activity and its bactericidal action mechanism against Staphylococcus aureus. METHODS AND RESULTS: DqV was tested against a standard strain of methicillin-sensitive Staphylococcus aureus (MSSA), Staph. aureus ATCC 6538P and two standard strains of methicillin-resistant Staphylococcus aureus (MRSA), Staph. aureus ATCC 33591 and Staph. aureus CCBH 5330. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC), the rate of kill and pH sensitivity of the DqV were determined by microdilution tests. Bactericidal and inhibitory concentrations of DqV were tested to check its action on Staph. aureus membrane permeability and cell morphology. The MIC and MBC of DqV were 6·25 and 12·5 µg ml(-1) for Staph. aureus ATCC 6538P, 12·5 and 50 µg ml(-1) for Staph. aureus CCBH 5330 and 100 and 100 µg ml(-1) for Staph. aureus ATCC 33591, respectively. Complete bacterial growth inhibition was observed after 4 h of incubation with the MBC of DqV. A lowest MIC was observed in alkaline pH. Alteration in membrane permeability was observed through the increase in crystal violet uptake, genetic material release and morphology in atomic force microscopy. CONCLUSIONS: The results suggest antibacterial activity of DqV against Staph. aureus and that the venom acts in the cell membrane. SIGNIFICANCE AND IMPACT OF THE STUDY: Alteration in membrane permeability may be associated with the antimicrobial activity of hymenopteran venoms.

L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations.

Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → ß transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.

Anhydrous crystals of DNA bases are wide gap semiconductors.

We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

Structural, electronic and optical properties of ilmenite and perovskite CdSnO3 from DFT calculations.

CdSnO(3) ilmenite and perovskite crystals were investigated using both the local density and generalized gradient approximations, LDA and GGA, respectively, of the density functional theory (DFT). The electronic band structures, densities of states, dielectric functions, optical absorption and reflectivity spectra related to electronic transitions were obtained, as well as the infrared absorption spectra after computing the vibrational modes of the crystals at q = 0. Dielectric optical permittivities and polarizabilities at ω = 0 and ∞ were also calculated. The results show that GGA-optimized geometries are more accurate than LDA ones, and the Kohn-Sham band structures obtained for the CdSnO(3) polymorphs confirm that ilmenite has an indirect band gap, while perovskite has a direct band gap, both being semiconductors. Effective masses for both crystals are obtained for the first time, being highly isotropic for electrons and anisotropic for holes. The optical properties reveal a very small degree of anisotropy of both crystals with respect to different polarization planes of incident light. The phonon calculation at q = 0 for perovskite CdSnO(3) does not show any imaginary frequencies, in contrast to a previous report suggesting the existence of a more stable crystal of perovskite CdSnO(3) with ferroelectric properties.

C60-derived nanobaskets: stability, vibrational signatures, and molecular trapping.

C(60)-derived nanobaskets, with chemical formulae (symmetry point group) C(40)H(10) (C(5v)), C(39)H(12) (C(3v)), C(46)H(12) (C(2v)), were investigated. Molecular dynamic simulations (MDSs) indicate that the molecules preserve their bonding frame for temperatures up to 300 K (simulation time 100 ps), and maintain atomic cohesion for at least 4 ps at temperatures up to 3500 K. The infrared spectra of the C(60)-derived nanobaskets were simulated through density functional theory (DFT) calculations, allowing for the attribution of infrared signatures specific to each carbon nanobasket. The possibility of using C(60)-derived nanobaskets as molecular containers is demonstrated by performing a DFT study of their bonding to hydrogen, water, and L-alanine. The carbon nanostructures presented here show a higher bonding energy (approximately 1.0 eV), suggesting that a family of nanostructures, C(n)-derived (n = 60,70,76,80, etc) nanobaskets, could work as molecular containers, paving the way for future developments such as tunable traps for complex molecular systems.

Defects in graphene-based twisted nanoribbons: structural, electronic, and optical properties.

We present some computational simulations of graphene-based nanoribbons with a number of half-twists varying from 0 to 4 and two types of defects obtained by removing a single carbon atom from two different sites. Optimized geometries are found by using a mix of classical quantum semiempirical computations. According with the simulations results, the local curvature of the nanoribbons increases at the defect sites, especially for a higher number of half-twists. The HOMO-LUMO energy gap of the nanostructures has significant variation when the number of half-twists increases for the defective nanoribbons. At the quantum semiempirical level, the first optically active transitions and oscillator strengths are calculated using the full configuration interaction (CI) framework, and the optical absorption in the UV/vis range (electronic transitions) and in the infrared (vibrational transitions) are achieved. Distinct nanoribbons show unique spectral signatures in the UV/vis range, with the first absorption peaks in wavelengths ranging from the orange to the violet. Strong absorption is observed in the ultraviolet region, although differences in their infrared spectra are hardly discernible.

Adsorption of ascorbic acid on the C60 fullerene.

Adsorption of ascorbic acid (AsA) on C60 is investigated using classical molecular mechanics and density functional theory (DFT). Classical annealing was performed to explore the space of molecular configurations of ascorbic acid adsorbed on C60, searching for optimal geometries. From the structure with the smallest total energy, 10 initial configurations were prepared by applying rotations of 90 degrees about three orthogonal axes. Each one of these configurations was optimized using DFT (for both LDA and GGA exchange-correlation functionals), and an estimate of their total and adsorption energies was found. Different configurations have minimal adsorption energies (defined here as the total energy of the adsorbate minus the total energy of the separate molecules) from -0.54 to -0.10 eV, with distinct optimal distances between the AsA and C60 centers of mass. According to a Hirshfeld population analysis, AsA is, in general, an acceptor of electrons from C60. Our results demonstrate the feasibility of noncovalent functionalization of C60 with AsA and provide minimal energy values for the several different configurations investigated. These results should be considered in reactions as a possible way to prevent against the oxidative damage and toxicity of C60. The beneficial effects of using AsA-C60 includes its action when administered together with levodopa, against the neurotoxicity generated by levodopa isolated, which opens new strategies for the Parkinson's disease treatment.

Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins.

The legume lectins from the subtribe Diocleinae, often referred to as concanavalin A-like lectins, are a typical example of highly similar proteins that show distinct biological activities. The pH-dependent oligomerization that some of these lectins undergo and the relative position of amino acids within the carbohydrate-binding site are factors that have been reported to contribute to these differences in the activities of Diocleinae lectins. In the present work, we determined the amino acid sequence and the crystal structure of the lectin of Dioclea rostrata seeds (DRL), with the aim of investigating the structural bases of the different behavior displayed by this lectin in comparison to other Diocleinae lectins and determining the reason for the distinct pH-dependent dimer-tetramer equilibrium. In addition, we discovered a novel multimeric arrangement for this lectin.

Möbius and twisted graphene nanoribbons: stability, geometry, and electronic properties.

Results of classical force field geometry optimizations for twisted graphene nanoribbons with a number of twists N(t) varying from 0 to 7 (the case N(t)=1 corresponds to a half-twist Möbius nanoribbon) are presented in this work. Their structural stability was investigated using the Brenner reactive force field. The best classical molecular geometries were used as input for semiempirical calculations, from which the electronic properties (energy levels, HOMO, LUMO orbitals) were computed for each structure. CI wavefunctions were also calculated in the complete active space framework taking into account eigenstates from HOMO-4 to LUMO+4, as well as the oscillator strengths corresponding to the first optical transitions in the UV-VIS range. The lowest energy molecules were found less symmetric than initial configurations, and the HOMO-LUMO energy gaps are larger than the value found for the nanographene used to build them due to electronic localization effects created by the twisting. A high number of twists leads to a sharp increase of the HOMO-->LUMO transition energy. We suggest that some twisted nanoribbons could form crystals stabilized by dipolar interactions.

Identification of lamivudine conformers by Raman scattering measurements and quantum chemical calculations.

Characterization of nucleoside and non-nucleoside human immunodeficiency virus (HIV) reverse transcriptase inhibitors conformers, NRTIs and NNRTIs, respectively, is fundamental for an improved treatment of infected individuals. Three conformers in lamivudine I powder are quickly identified in this work by assignment of some Raman peaks to their vibrational frequencies, as obtained by first principles quantum chemical calculations. The method is proposed as a practical procedure for non-destructive identification, analysis, and process monitoring of NRTIs and NNRTIs conformers.