Conformational, spectroscopic, and molecular dynamics DFT study of precursors for new potential antibacterial fluoroquinolone drugs

SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu3 metal cluster

The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV-Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range -17.08 to -58.52 kcal/mol in vacuum and -53.34 to -93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV-Vis of ABP is in agreement with theoretically predicted ones.

Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido-N-phenylmaleimide

The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.

Exploration for the Optical Properties and Fluorescent Prediction of Nitrotriazole and Nitrofurazan: First-Principles and TD-DFT Calculations

High-energy materials containing azole and furazan have revealed numerous properties; however, the underlying optical properties need to be solved. Meanwhile, the uncertainty for the choice of fluorescent matrix materials and the flexible situational conditions prompted us to estimate the optical and fluorescent properties of 5,5'-dinitro-2H,2H'-3,3'-bi-1,2,4-triazole (DNBT), 4,4'-dinitroazolefurazan (DNAF), and 4,4'-dinitro-3,3'-4,3'-ter-1,2,5-oxadiazole (DNTO). The first-principles calculation with improved dispersion correction terms and time-dependent density functional theory were utilized to calculate the absorbance and excitation energy of DNBT, DNAF, and DNTO, as well as characterization for their crystal structure, electronic structure, molecular orbitals, and so forth, synchronously. In this work, the absorbance anisotropy of DNBT and DNTO is stronger than that of DNAF. The absorbance for each of the (0,0,1) crystal planes in the three compounds is greater than that of the other two crystal planes. Moreover, DNBT has the maximum absorbance on the (0,0,1) crystal plane. The N-N-H from DNBT and N-O-N from DNTO and DNAF are responsible for these results, while N=N in DNAF weakens the performance of N-O-N. UV-vis spectra show that the maximum absorption wavelengths λ_max for DNBT, DNAF, and DNTO are 225, 228, and 201 nm, respectively. The number of five-membered rings and the coplanarity of groups in the intermolecular non-conjugation interaction potentially improve this ability due to the results from the crystal diffraction analysis. In addition, the polarization rate DNBT > DNTO > DNAF based on the molecular orbital analysis and the electrostatic potential calculation implies that the excitation energy of DNBT is less than DNTO, and the excitation energy of DNTO is less than DNAF. This work is beneficial to the expansion of energetic materials into the optical field and the accelerated application process of the related industry.

Probing the Site-Specific Reactivity and Catalytic Activity of Ag n (n = 15-20) Silver Clusters

Density functional theory calculations within the framework of generalized gradient approximation (GGA), meta-GGA, and local functionals were carried out to investigate the reactivity and catalytic activity of Ag _n (n = 15-20) clusters. Our results reveal that all the Ag _n clusters in this size range, except Ag₂₀, adsorb O₂ preferably in the bridged mode with enhanced binding energy as compared to the atop mode. The O₂ binding energies range from 0.77 to 0.29 in the bridged mode and from 0.36 to 0.15 eV in the atop mode of O₂ adsorption. The strong binding in the case of the bridged mode of O₂ adsorption is also reflected in the increase in O-O bond distance. Natural bond orbital charge analysis and vibrational frequency calculations reveal that enhanced charge transfer occurs to the O₂ molecule and there is significant red shift in the stretching frequency of O-O bond in the case of the bridged mode of O₂ adsorption on the clusters, thereby confirming the above results. Moreover, the simulated CO oxidation reaction pathways show that the oxidation of the CO molecule is highly facile on Ag₁₆ and Ag₁₈ clusters involving small kinetic barriers and higher heats toward CO₂ formation.

Cubic Nanogrids for Counterbalance Contradiction among Reorganization Energy, Strain Energy, and Wide Bandgap

Molecular cross-scale gridization and polygridization of organic π-backbones make it possible to install 0/1/2/3-dimensional organic wide-bandgap semiconductors (OWBGSs) with potentially ZnO-like fascinating multifunctionality such as optoelectronic and piezoelectronic features. However, gridization effects are limited to uncover, because the establishment of gridochemistry still requires a long time, which offers a chance to understand the effects with a theoretical method, together with data statistics and machine learning. Herein, we demonstrate a state-of-the-art 3D cubic nanogridon with a size of ∼2 × 2 × 1.5 nm³ to examine its multigridization of π-segments on the bandgap, molecular strain energy (MSE), as well as reorganization energy (ROE). A cubic gridon (CG) consists of a four-armed bifluorene skeleton and a thiophene-containing fused arene plane with the Csp³ spiro-linkage, which can be deinstalled into face-on or edge-on monogrids. As a result, multigridization does not significantly reduce bandgaps (E_g ≥ 4.03 eV), while the MSE increases gradually from 4.72 to 23.83 kcal/mol. Very importantly, the ROE of a CG exhibits an extreme reduction down to ∼28 meV (λ⁺) that is near the thermal fluctuation energy (∼26 meV). Our multigridization results break through the limitation of the basic positively proportional relationship between reorganization energies and bandgaps in organic semiconductors. Furthermore, multigridization makes it possible to keep the ROE small under the condition of a high MSE in OWBGS that will guide the cross-scale design of multifunctional OWBGSs with both inorganics' optoelectronic performance and organics' mechanical flexibility.

Assessment of time-dependent density functionals for the electronic excitation energies of organic dyes used in DSSCs

The absorption spectra modeled as the vertical excitation energies of 13 dye sensitizers used in dye-sensitized solar cells (DSSCs) are benchmarked by means of time-dependent (TD)-DFT, using 36 functionals from different DFT rungs.

Effects of Magnesium, Calcium, and Aluminum Chelation on Fluoroquinolone Absorption Rate and Bioavailability: A Computational Study

Fluoroquinolones (FQs) are a widespread class of broad-spectrum antibiotics prescribed as a first line of defense, and, in some cases, as the only treatment against bacterial infection. However, when administered orally, reduced absorption and bioavailability can occur due to chelation in the gastrointestinal tract (GIT) with multivalent metal cations acquired from diet, coadministered compounds (sucralfate, didanosine), or drug formulation. Predicting the extent to which this interaction reduces in vivo antibiotic absorption and systemic exposure remains desirable yet challenging. In this study, we focus on quinolone interactions with magnesium, calcium and aluminum as found in dietary supplements, antacids (Maalox) orally administered therapies (sucralfate, didanosine). The effect of FQ-metal complexation on absorption rate was investigated through a combined molecular and pharmacokinetic (PK) modeling study. Quantum mechanical calculations elucidated FQ-metal binding energies, which were leveraged to predict the magnitude of reduced bioavailability via a quantitative structure-property relationship (QSPR). This work will help inform clinical FQ formulation design, alert to possible dietary effects, and shed light on drug-drug interactions resulting from coadministration at an earlier stage in the drug development pipeline.

One-Pot Synthesis of 3-Substituted 4H-Quinolizin-4-ones via Alkyne Substrate Control Strategy

Three-substituted 4H-quinolizin-4-ones were obtained via a facile method with good selectivity and high efficiency. On the basis of alkyne substrate control, the mild and cost-efficient reaction has a broad substrate scope (20 examples, up to 93% yield) and is also easy to scale up. Active sites on the products allow for further modifications. The alkyne substrate control strategy could be further extended to achieve more complex three-substituted 4H-quinolizin-4-one skeletons.

Conformational dynamics of aqueous hydrogen peroxide from first principles molecular dynamics simulations

We performed first principles molecular dynamics simulations of a relatively dilute aqueous hydrogen peroxide (H2O2) solution to examine its structural alterations and relevant dynamics upon solvation. The internal rotation of the OH groups about the O-O bond facilitates the flexible structure of H2O2. Structural calculations reveal dihedral angle fluctuations in the aqueous solution. Water molecules make stronger hydrogen bonds through the hydrogen atom of the solute than the oxygen atom leading to distinct hydrogen bonding configurations inside the first solvation shell. Time-dependent dihedral angle alterations result in conformational changes and the normalized dihedral angle distribution plot displays characteristic peaks at ∼100-120° and ∼230°, illustrating various conformational states. Within the simulation time, flexibility-induced interconversion of hydrogen peroxide gives rise to several cisoid and transoid conformers. In this study, we examine the relative population of the associated conformational states and the lifetime of the cisoid and transoid conformers from the torsion angle variations. We also determine the free energy landscape of the rotational isomerization process in H2O2 and explore two distinct energy barriers during such interconversion.

Formation of metal-radical species upon reduction of late transition metal complexes with heteroleptic ligands: an experimental and theoretical study

Three novel transition metal complexes with selenadiazoloquinolones as potential broad spectrum antibiotics in clinical praxis.

Computational studies of 2-(4-oxo-3-phenylthiazolidin-2-ylidene)malononitrile

The molecular structure of the 2-(4-oxo-3-phenylthiazolidin-2-ylidene) malononitrile (3) is calculated using DFT B3LYP/6-311G(d, p) method. The calculated geometric parameters are in good agreement with the experimental data. The NBO calculations were performed to predict the natural atomic charges at the different atomic sites and study the different intramolecular charge transfer (ICT) interactions occurring in the studied system. The BD(2)C17-C19 → BD*(2)C14-C15, LP(2)O2 → BD*(1)N5-C9 and LP(1)N5 → BD*(2)C10-C11 ICT interactions causing stabilization of the system by 23.30, 30.63 and 52.48 kcal/mol, respectively. The two intense electronic transition bands observed experimentally at 249 nm and 296 nm are predicted using the TD-DFT calculations at 237.9 nm (f = 0.1618) and 276.4 nm (f = 0.3408), respectively. These electronic transitions are due to H-3 → L (94%) and H → L (95%) excitations, respectively.