Vibrational Energy Distribution Research Articles

Comprehensive analysis of 2,5-dimethyl-1-(naphthalen-1-yl)-1H-pyrrole: X-ray crystal structure, spectral, computational, molecular properties, docking studies, molecular dynamics, and MMPBSA

This study examines the features of 2,5-dimethyl-1-(naphthalen-1-yl)-1H-pyrrole (DN1HP) in terms of its structure, vibrations, electronic transition properties, biological activity, and thermodynamic characteristics. X-ray single crystal structure solved and analysed. With the use of spectroscopic methods like FT-IR and UV–vis, the compound has been described. These experimental findings were contrasted with information derived from DFT (B3LYP) computations with the basis set 6–311++G(d,p). Vibrational allocations and Potential energy distribution(PED) were computed after optimizing the DN1PH compound's shape. The outcome of every experiment matched the values predicted by theory. To further investigate the reactivity, stability and biological activity of the titular molecule, calculations were made for the electrophilicity index (3.053), energy gap (3.789 eV), EH (−5.2962 eV), and EL (−1.5069 eV). To determine the compound's electrophilic and nucleophilic locations, a Molecular electrostatic potential (MEP) diagram was established. Molecular docking experiments have demonstrated the potential of the molecule in question as an anti-HIV medication. The binding energies of the drug to the proteins 3MLU, 3QEG, 5DHZ, and 3MLY are −5.86, −5.04, −5.01 and −4.97 kcal/mol, respectively. To further investigate the relationship and reliability of the protein (3MLU) with DN1HP, molecular dynamics (MD) simulators were utilized

Comparative computational analysis of orthoconic antiferroelectric liquid crystals: DFT analysis.

The study undertakes a comparative analysis of four distinct semi-fluorinated chiral Organic Active Ferroelectric Liquid Crystals (OAFLCs). The comparative analysis of the compounds is done by using various parameters, including thermodynamic, non-linear optical, electrical, atomic charge distribution, and atomic orientations. We use optimization algorithms to look at chemical reactivity, electrical properties, intermolecular interactions, and static hyperpolarizability. Sample 4 is the best choice for a wide range of display applications. This research contributes to understanding the nuanced properties of semi-fluorinated chiral OAFLCs and highlights Sample 4's potential for novel applications in display technology, owing to its superior stability and optimized properties. This study helps to enhance our understanding of the comparative analysis of semi-fluorinated chiral OAFLCs for potential advancements in display technologies by incorporating findings from key studies. The simulations are performed using density functional theory (DFT) with the B3LYP functional for predicting molecular properties, and Vibrational Energy Distribution Analysis (VEDA) software is used to perform the vibrational analysis of the molecules.

Investigation of spectroscopic characterization, crystal structure, and antitumor activity of a novel 2ATP molecule

In this section, the spectroscopic characteristics of 2-amino-toysl-pyridine (2ATP) are fully examined, using both experimental and computational investigations guided by density functional theory (DFT). It will facilitate our computational research using the B3LYP approach to use the basis set 6–311++G(d,p). Comprehensive assignments of vibrational modes were obtained from the vibrational spectra, which comprised FT-Raman and FT-IR spectroscopy and were recorded in the region of 3500–400 cm−1 and 4000–500 cm-1, respectively, using the Vibrational Energy Distribution Analysis (VEDA) approach. The net atomic charges inside the molecule were ascertained by using Mulliken population analysis, natural atomic charges, and electrostatic potentials (CHELPG). The structural conformations of 2ATP were determined using NMR spectroscopy in a CDCl3 solvent. The donor-acceptor interactions of the 2ATP molecule at the 6–311++G(d,p) level were studied by means of a Natural Bond Orbital (NBO) study. Studies of the ultraviolet (UV) spectrum in ethanol were used to assess the effects of the solvent. An assessment was made of the energy difference between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) in order to understand charge transfer processes that suggest the molecule may have biological activity. Molecular electrostatic potential (MEP) surfaces were used to predict the nucleophilic and electrophilic sites in molecules. The non-covalent interactions were evaluated using the reduced density gradient (RDG) approach. The Multiwfn software was used to analyze the topological properties of the 2ATP, including the Localized Orbital Locator (LOL) and Electron Localization Function (ELF). Further attention was drawn to the compound's exceptional pharmacological potential when its ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) characteristics were evaluated. Not to add, molecular docking experiments were carried out to evaluate the feasibility of 2ATP as a bioactive material with possible uses in the pharmaceutical business.

A locally resonant metamaterial and its application in vibration isolation: Experimental and numerical investigations

AbstractVibration isolation metamaterial barrier has been extensively studied in mitigating the damage induced by vibration, while a deeper understanding of the vibration isolation characteristics based on laboratory experiments is still lacking. In this work, a locally resonant metamaterial barrier is proposed, and a large‐scale laboratory experiment was first designed to investigate the isolation mechanism of the proposed metamaterial barrier. The metamaterial vibration isolation barrier is assembled by arraying 5 × 5 resonators. To better explain the observations in experiments and unveil the underlying isolation mechanism, COMSOL Multiphysics was also employed to simulate the laboratory experiment. Subsequently, the vibration isolation effect is quantitatively analyzed by analyzing the acceleration amplitude reduction spectrum (ARS) of the ground surface. The vibration isolation mechanism is discussed by monitoring the acceleration field around the metamaterial barrier. The results indicate that two significant locally resonant attenuation domains are observed, which are induced by the first‐order and second‐order vertical resonance frequencies of the metamaterial. Another experimental scheme that simultaneously monitored the acceleration of the mass block and the bottom of resonators was implemented to investigate vibration in the resonator. The vibration energy distribution on the mass block and the bottom of the resonator is found to depend significantly on the vibration frequency. When the frequency is lower than a certain frequency, the locally resonant is dominant. Otherwise, the geometric scattering is dominant. The vibration isolation mechanism of the locally resonance metamaterial was investigated by laboratory experiments and provided an effective solving path for isolating the low‐frequency vibration.

Spectroscopic and computational methods in the characterization of deep eutectic solvent, Gallic acid, and Glycerol

Several researchers have shown experimentally that Gallic acid has antioxidant, anti-inflammatory, and anti-aging properties, signifying its value in skin care. Glycerol has properties, such as increasing skin hydration, softening skin, and reducing skin dryness. The present work aims to understand the vibrational and spectroscopic study of the interacting mechanism of Deep Eutectic solvent mixture of Gallic acid and Glycerol. The theoretical analysis is performed using the Density Functional Theory with B3LYP/6-311 + g(d,p) level of theory. The optimized structure and frequency of the monomers and their biomolecular complex are obtained using Gauss view 6.0 and Gaussian16. The vibrational analysis is carried out using Vibrational Energy Distribution Analysis. The Natural Bond Orbital, molecular docking of the Glycerol-Gallic acid complex, and the molecular dynamics simulation of the docked protein-ligand system are carried out to understand the mechanism better. The theoretical and experimental frequencies are found to agree with each other. The Molecular Dynamic simulation analysis predicts that the protein-ligand complexation is relatively stable.

Study on the Length of the Effective Vibration Area of the Catenary in a Pantograph–Catenary Interaction System

The effective vibration area includes most of the catenary vibration caused by pantograph–catenary interactions and is the basis of the real-time catenary model for hardware-in-the-loop simulation. However, while the length of the effective vibration area is one of the most important parameters of the real-time catenary model, it has not been fully studied at present. In this paper, the length of the effective vibration area is first investigated. A pantograph–catenary interaction model is developed based on the modal superposition method. After the validation of the model, the vibration energy distribution of the catenary is used to determine the length of the effective vibration area based on the converged total energy. The influence of vehicle velocity and contact wire tension on the vibration energy distribution and length of the effective vibration area is investigated. The obtained appropriate length of effective vibration area is validated by a real-time catenary model and online measurement data of the contact force. The investigation results show that the energy distribution of the catenary can accurately determine the length of effective vibration area, and it increases with increasing vehicle velocity but decreases with increasing contact wire tension. The appropriate length of effective vibration area should be at least 160 m (approximately three spans) in the pantograph–catenary system.

Density functional theory and spectroscopic analysis of stigmasterol from Garcinia wightii: Deciphering its inhibitory potential against drug-resistant tuberculosis via insilico molecular docking and molecular dynamics simulations

This study investigates the molecular structure and electronic properties of stigmasterol, isolated from Garcinia wightii, using density functional theory (DFT) alongside experimental techniques including FT-IR, FT-Raman, UV–Vis, 1H and 13C NMR spectroscopy. Theoretical predictions are compared with experimental results, facilitated by vibrational energy distribution analysis for unambiguous vibrational wavenumber assignments. Natural bond orbitalanalyzes reveal donor-acceptor bond energies and electron densities, while Fukui functions identify reactive sites susceptible to electrophilic and nucleophilic attacks. Electronic properties are further explored through various analyzes, unveiling reactive surface sites. Non-covalent interactions are examined using reduced density gradient analysis. Assessment of absorption, distribution, metabolism, and excretion attributes aids in drug discovery efforts. Molecular docking studies against 20 target proteins for antitubercular screening show a stable glide score of -9.52 kcal/mol for the protein 4FDO (Mycobacterium tuberculosis DprE1 in complex with CT319). Molecular dynamics simulations over 100 ns indicate the stability of the ligand-protein complex, suggesting its potential as an antituberculosis agent. Stigmasterol's structural, vibrational, electronic, and topological properties are thoroughly investigated, revealing its ring skeleton with a flexible isooctyl side chain, adhering to C1 point group symmetry. Steric and stereo electronic interactions play crucial roles in conformation and binding to target proteins. Theoretical and experimental analyzes align, confirming the compound's bioactive properties. This comprehensive investigation underscores stigmasterol's potential as a tuberculosis treatment option, providing valuable insights into its structural characteristics and therapeutic possibilities.

GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function.

G protein-coupled receptors (GPCRs) exemplify sophisticated allosteric communication, transducing extracellular signals through ligand-induced structural rearrangements that resonate through the molecular scaffold. Despite extensive study, the biophysical underpinnings of how conformational changes spread remain unclear. This work employs a novel physics-based framework to characterize the role of energy dissipation in directing intramolecular signaling pathways. By modeling each residue as a network of coupled oscillators, we generate a localization landscape depicting the vibrational energy distribution throughout the protein scaffold. Quantifying directional energy flux between residues reveals distinct pathways for energy and information transfer, illuminating sequences of allosteric communication. Our analysis of CB1 and CCR5 crystal structures unveils an anisotropic pattern of energy dissipation aligning with key functional dynamics, such as activation-related conformational changes. These anisotropic patterns of vibrational energy flow constitute pre-configured channels for allosteric signaling. Elucidating the relationship between structural topology and energy dissipation patterns provides key insights into the thermodynamic drivers of conformational signaling. This methodology significantly advances our mechanistic understanding of allostery in GPCRs and presents a broadly applicable approach for rationally dissecting allosteric communication pathways, with potential implications for structure-based drug design targeting these critical receptors.

Proton-Coupled Electron Transfer upon Oxidation of Tyrosine in a De Novo Protein: Analysis of Proton Acceptor Candidates.

Redox-active residues, such as tyrosine and tryptophan, play important roles in a wide range of biological processes. The α3Y de novo protein, which is composed of three α helices and a tyrosine residue Y32, provides a platform for investigating the redox properties of tyrosine in a well-defined protein environment. Herein, the proton-coupled electron transfer (PCET) reaction that occurs upon oxidation of tyrosine in this model protein by a ruthenium photosensitizer is studied by using a vibronically nonadiabatic PCET theory that includes hydrogen tunneling and excited vibronic states. The input quantities to the analytical nonadiabatic rate constant expression, such as the diabatic proton potential energy curves and associated proton vibrational wave functions, reorganization energy, and proton donor-acceptor distribution functions, are obtained from density functional theory calculations on model systems and molecular dynamics simulations of the solvated α3Y protein. Two possible proton acceptors, namely, water or a glutamate residue in the protein scaffold, are explored. The PCET rate constant is greater when glutamate is the proton acceptor, mainly due to the more favorable driving force and shorter equilibrium proton donor-acceptor distance, although contributions from excited vibronic states mitigate these effects. Nevertheless, water could be the dominant proton acceptor if its equilibrium constant associated with hydrogen bond formation is significantly greater than that for glutamate. Although these calculations do not definitively identify the proton acceptor for this PCET reaction, they elucidate the conditions under which each proton acceptor can be favored. These insights have implications for tyrosine-based PCET in a wide variety of biochemical processes.

Numerical and experimental investigations of proper orthogonal decomposition for vibration energy distribution analysis of a two-stage planetary gear system

Numerical and experimental investigations of proper orthogonal decomposition for vibration energy distribution analysis of a two-stage planetary gear system

Time-dependent dynamical energy analysis via convolution quadrature

Dynamical Energy Analysis was introduced in 2009 as a novel method for predicting high-frequency acoustic and vibrational energy distributions in complex engineering structures. In this paper we introduce the first time-dependent Dynamical Energy Analysis method. Time-domain models are important in numerous applications including sound simulation in room acoustics, predicting shock-responses in structural mechanics and modelling electromagnetic scattering from conductors. The first step is to reformulate Dynamical Energy Analysis in the time-domain by means of a convolution integral operator. We are then able to employ the Convolution Quadrature method to provide a link between the previous frequency-domain implementations of Dynamical Energy Analysis and fully time-dependent solutions by means of the Z-transform. By combining a modified multistep Convolution Quadrature approach for the time discretisation, together with Galerkin and Petrov-Galerkin methods for the space and momentum discretisations, respectively, we are able to accurately track the propagation of high-frequency transient signals through phase-space. The implementation here is detailed for finite two-dimensional spatial domains and we demonstrate the versatility of our approach by performing a range of numerical experiments for regular, non-convex and irregular geometries as well as different types of wave source.

Single crystal, conformational, quantum reactivity, hirshfeld surface, molecular interactions, ADMET, and molecular docking investigations on HIV-1 site of 3-isopropyldiphenyl-1-(2-(thiophen-2yl)acetyl)piperidin-4-one

The 3-isopropyl-2,6-diphenyl-1-(2-(thiophen-2yl)acetyl)piperidin-4-one (IPTP) single crystals were grown by slow evaporation method and the structure is confirmed through FT-IR, 1H NMR, and 13C NMR spectral analyses. Single crystal X-ray diffraction revealed that the title compound having chair conformation of the piperidine ring, with an axial orientation of phenyl rings at C-2 and C-6 positions and an isopropyl group at C-3. Hirshfeld surface analysis was employed to examine intermolecular contacts and strong and weak attractive, repulsive, and van der Waals interactions in the molecule were determined using the reduced density gradient method (RDG). The geometrical parameters obtained through Density Functional Theory are compared with experimental values and also conducted to optimize structural parameters, frontier molecular orbitals (FMOs), and molecular electrostatic potential surface analysis (MEPS). NBO calculations were employed to investigate intermolecular and intramolecular charge movement, as well as the molecule's stability. Vibrational Energy Distribution Analysis (VEDA) software facilitated potential energy decomposition (PED) analysis using FT-IR wave numbers. The title compound molecular docking data were compared with the markedly available FDA-approved anti-HIV drug of Nelfinavir and their results were discussed, ADME analysis studies were discussed concerning FDA-approved anti-HIV drugs, including Nelfinavir, Betulinic Acid, Haloperidol, and Donepezil.

A New centrosymmetric supramolecular Hybrid Antimony (III)-based material :X-ray characterization, vibrational studies, theoretical (DFT and TD-DFT) studies, thermal behavior, opto-electric properties and atomic Hirshfeld surface analysis.

The new centrosymmetric hybrid material (C8H12N)4[SbCl5]2 has been successfully elaborated at room temperature by slow evaporation in the centrosymmetric monoclinic space group P21/c with the following parameters: a = 29.0349(16) Å, b = 13.1241(7) Å, c = 12.0278(7) Å, β = 95.567(2) ° Z = 4 and V = 4561.7(4) Å3. The asymmetric unit consists of two isolated [Sb2Cl10]4- dimers and four protonated cations (C8H12N)+ was optimized d by density functional theory (DFT) using the B3LYP method. The cohesion of this supramolecular material was ensured by the means of N—H…Cl hydrogen-bonding interactions yield a three-dimensional network. The infrared IR and Raman studies which were performed at room temperature charge in the 4000–400 cm -1 and 10- 3000 cm -1 frequency regions, respectively, displayed the existence of vibrational modes that correspond to the organic and inorganic groups. The assignment of wavenumbers which were based on potential energy distribution (PED), were performed using Vibrational Energy Distribution Analysis (VEDA) software. Actually, the values obtained by the B3LYP/LanL2MB are in good agreement with the experimental data.Moreover, the Hirschfeld surfaces analysis which was employed to identify the different intermolecular interactions, showed that predominate interactions were H…Cl. The Thermogravimetric analysis (TGA) reveals the decomposition of the compound remains stable above 175 °C that confirms its great thermal stability. Furthermore, the optical property of the 0D hybrid Sb(III) based halide was studied with a focus on the band gap. Theoretical investigations on the electronic structure, Simulated UV–Visible spectrum, band gap, and frontier molecular orbitals (FMOs) were undertaken using density functional theory (DFT) and time-dependent DFT (TD-DFT). Therefore, our results indicate an acceptable consistency was found between calculations and experimental results leading to consistent vibrational and optical features assignments as well as the energy gap (Eg) and the chemical reactivity descriptors which are primarily linked to the ring of the organic cation and the inorganic anion.

Synthesis, characterization, and comprehensive computational analysis of aromatic hydrazone compounds: Unveiling quantum parameters, evaluating antioxidant activity, and investigating molecular docking interactions

This study presents a synergistic approach encompassing experimental synthesis, computational analysis, and antioxidant activity evaluation of two aromatic hydrazone compounds, namely 4-[(2E)-2-(2-nitrobenzylidene) hydrazinyl] benzoic acid (NBHZ) and 4-[(2E)-2-(2-hydroxybenzylidene) hydrazinyl] benzoic acid (HBHZ). Efficient synthesis yielded impressive quantities (70 % and 58 %, respectively), and structural characterization employed IR, UV–Vis, and NMR spectroscopy. Antioxidant potential was assessed using the DPPH free radical scavenging assay, revealing distinct capabilities of NBHZ and HBHZ, each featuring a nitro (NO2) and a hydroxy (OH) group, respectively, at the ortho position. HBHZ exhibited superior efficacy (IC50 = 1.15 μg/mL) compared to NBHZ (IC50 = 2.1 μg/mL) and the standard antioxidant BHT (IC50 = 1.83 μg/mL). Computational analyses using Gaussian 09 at the B3LYP/6–311 G(d,p) level elucidated electronic characteristics, molecular electrostatic potential (MEP), HOMO-LUMO energies, and global reactivity descriptors. VEDA 4 further investigated vibrational behavior and potential energy distribution (PED), topological analyses electron localization function (ELF), localized orbital locator (LOL), average localized ionization energy (ALIE), and reduced density gradient (RDG) were identified to evaluate their interactions. Thermochemical parameters explored antioxidant mechanisms (hydrogen atom transfer (HAT), single electron transfer–proton transfer (SET–PT), and sequential proton loss electron transfer (SPLET)). Molecular docking via iGEMDOCK revealed binding interactions with the target NADPH oxidase. These findings not only provide insights into the compounds' antioxidant potential but also underscore the impact of specific molecular features on their properties. This integrated approach contributes to advancing the understanding of hydrazone compounds, guiding the design of materials with tailored functionalities for applications in oxidative stress mitigation.

A wave model of high frequency vibrational energy transfer in a wedge-shaped combined plate structure

Wedge shaped combined plate structure (WCPS) is broadly applied in large-sized transport equipment such as aerospace and shipping. However, with the increase of equipment operating running, it is easy to cause high-frequency vibration of structure components. Therefore, studying the energy transfer and vibration response of high-frequency vibration in WCPS is significant for the structural design of aerospace and shipping. The promising method is energy finite element analysis (EFEA). However, the energy transfer coefficient at joint of WCPS is needed in EFEA. The current studies about the energy transfer coefficients are focus on the joint between two uniform thickness plate. But it is some different that getting the energy transfer coefficient for WCPS, because the near-field solve representation for wedge-shaped plate is complicated due to the non-uniform thickness of wedge-shaped plate member in WCPS. In this research, geometric acoustic approximation and an equilibrium equation on both ends of joints were used to derive the equation of the energy transfer coefficient for the WCPS. Then by setting coupling nodes, construction of a coupling matrix to characterize discontinuity of energy density at the coupling position of the WCPS and energy density governing equation of wedge-shaped plates were integrated. In doing so, the EFEA modeling of the WCPS was developed and the energy density distribution on each node of the WCPS could be obtained. Same-sized uniformly coupled structures is analyzed, the vibration energy distribution characteristics of two types of coupling structures were compared. The results show that the energy density value of the wedge plate member attenuate more slowly than that of the uniform plate member due to the acoustic black hole aggregation effect in the wedge plate part, and there is an abrupt change in the energy density value at the joint of WCPS. As a result, the factors influencing high-frequency vibration energy transfer were investigated.

Insights into the dynamic symphony: a comprehensive computational exploration of pure and fluorinated 6O.6 liquid crystals with the help of DFT analysis

ABSTRACT This article is based on the Density Functional Theory (DFT) simulations approach to examine the structural and vibrational behaviour of pure 6O.6 and fluorinated 6O.6 liquid crystalline compounds. The molecular interactions of the molecules were investigated by their optimised molecular structure. Identification of significant functional groups and their dynamic behaviours are made with the help of vibrational frequencies obtained through DFT calculations. Vibrational Energy Distribution Analysis (VEDA) software was used to perform the Potential Energy Distribution (PED) function of FT-IR and Raman spectra. Furthermore, changes in vibrational peaks provide insight into structural modifications. This investigation mainly focused on analysing the different reactivity, thermodynamic parameters and non-linear optical (NLO) properties of the compounds. This also helps to open a new path for further investigations into optoelectronic applications and molecular dynamics.

Quantification and visualization of vibration power flow in train-track-bridge coupled system under thermal effects

This paper presents an approach to investigate the effect of temperature on the transmission and distribution of vibration energy for train-track-bridge coupled systems. The vibration of the coupled system can be simulated by integrating the multi-body dynamics model of the train with the finite element models of the track and bridge. The transmission and distribution of vibration energy can be evaluated using a structural intensity method. This approach was implemented to investigate the vibration characteristics of a coupled system under extreme temperature conditions. The system consisted of a CRH2 high-speed train, a CRTS I double-block ballastless track, and an arch bridge. The results show that extreme temperature not only impacts the characteristics of vibration energy transmission in the coupled system but also affects vibration energy distribution. This research provides new insights into vibration control and optimization design for bridges in regions with significant temperature variations.

Molecular Dynamics Simulation of Thermal Nonequilibrium and Chemical Reaction Processes in Hydrogen Combustion.

Using reactive force field (ReaxFF) and molecular dynamics simulation, we investigate the combustion process of hydrogen-oxygen systems in initial thermal nonequilibrium states with different translational and rovibrational temperatures for oxygen. The system studied in this work contains 300 oxygen molecules and 700 hydrogen molecules with a density of 7 times the air density. For this system, the characteristic relaxation times of oxygen and hydrogen vibrational energies are 0.173 and 0.249 ns, respectively. 0.6% of hydrogen undergoes a chemical reaction with oxygen during the thermal nonequilibrium relaxation stage. For the distribution of translational energy and vibrational energy of oxygen in the thermal nonequilibrium state, the maximum mean error of the statistical distribution in the simulation and the Boltzmann distribution at temperature calculated from the average kinetic energy of molecules is about 2.25 × 10-5. At the same time, it was observed in the simulation that many-body interactions play a certain role in the combustion process. Furthermore, we compare the ignition time and temperature rise behavior of different combustion mechanisms and molecular dynamics simulations starting from the thermal equilibrium state. These results will provide meaningful references for the construction of thermal nonequilibrium combustion chemical reaction mechanisms.

Design, one-pot novel synthesis of substituted acridine derivatives: DFT, structural characterisation, ADME and anticancer DNA polymerase epsilon molecular docking studies

A novel type of reaction synthesis of an acridine derivative alkaloid of 9-chloro-1-methylacridine-4-carboxylic acid (CMAC) and structurally characterised. FT-IR, 1H NMR, 13C NMR, and GC-mass spectrometry were used. Density functional theory calculations were performed to understand the electronic properties of the molecular structures, including the frontier molecular orbital (FMO), molecular electrostatic potentials (MEP), NLO material properties, RDG studies, and global chemical reactivity descriptors. Furthermore, Theoretical IR, a vibrational wavenumber was obtained for the title compound by simulation and compared with the experimental wavenumbers. Vibrational energy distribution analysis (VEDA) software was used for potential energy decomposition (PED) analysis. Finally, the bioavailability of the title compound was examined by (ADME/Tox) absorption, distribution, metabolism, and excretion properties. DNA polymerase epsilon, which carries a P301R substitution (PDB ID: 6g0a), was used as the receptor for employing an in silico molecular docking process. The docking study revealed the significant interactions between the receptor active sites and the CMAC ligand.

Spectroscopic and computational study of Favipiravir-Adenine cocrystallization biomolecular complex

The research focuses on the structural investigation of biomolecules and biomolecular complexes using the DFT method, spectroscopic techniques, and determining cocrystal formation. The significant difficulties in making new drug products are low oral bioavailability and poor aqueous solubility. However, the co-crystallization of biomolecules can enhance their solubility without changing their pharmacological properties. The optimized structure of the molecules is obtained using the B3LYP/6–311++G(d,p) basis set within the framework of Density Functional Theory (DFT). Various vibrational techniques such as Fourier Transform Infrared (FTIR), Raman, and Surface-Enhanced Raman Spectroscopy (SERS) are employed to characterize the monomers and their interacting system. Possible vibrational assignments along with Potential energy distribution (PED) analysis are carried out using Vibrational Energy Distribution Analysis (VEDA). Natural Bond Orbital (NBO), Non-Linear Optical (NLO), Non-Covalent Interaction (NCI), and Atoms in Molecule (AIM) study are carried out to understand the interacting mechanism in the Favipiravir-Adenine biomolecular complex. The study shows that there is charge transfer through inter and intramolecular interaction in the complex. The binding energy of protein and Ligand is investigated using the Autodock tool for the molecular docking method and the negative value of binding energy – 4.36 kcal/mol of Favipiravir-Adenine biomolecular complex exclaims good binding affinity with the chosen protein 6LU7. Lipinski's criteria for druglikeness also claim that monomers and synthesized biomolecular complexes have the potential to influence drugs with good oral bioavailability. Cocrystal formation is confirmed by the X-ray diffraction pattern. The Protox II software claims that the toxicity of the drug and synthesized biomolecular complex is class IV.