Dihedral Angle Research Articles

Exploring the Theoretical Foundations of Thermally Activated Delayed Fluorescence (TADF) Emission: A Comprehensive TD-DFT Study on Phenothiazine Systems.

This study conducts a thorough theoretical investigation of Thermally Activated Delayed Fluorescence (TADF) in phenothiazine-based systems, examining ten molecular configurations recognized experimentally as TADF-active. Employing Time-Dependent Density Functional Theory (TD-DFT), our analysis spans the investigation of singlet-triplet energy gaps (ΔEST), spin-orbit coupling, and excitation characteristics using Multiwfn. This approach not only validates the adherence to El Sayed's rule across these systems but also provides a detailed understanding of charge transfer dynamics, as visualized through heat maps. A significant aspect of our study is the exploration of different oxidation states of sulfur and site substitutions on phenothiazine. This systematic variation aims to identify additional TADF-active compounds, drawing parallels with properties characterizing other known TADF emitters. Our investigation into Reverse Intersystem Crossing (rISC) rates and the analysis of dihedral angles in relation to ΔEST values offer nuanced insights into the TADF behaviours of these molecules. By integrating rigorous computational analysis with practical implications, we provide a foundational understanding that enhances the design and optimization of phenothiazine-based materials for optoelectronic applications. This work not only advances our theoretical understanding of TADF in phenothiazine derivatives but also serves as a guide for experimentalists and industry professionals in the strategic design of new TADF materials.

Structural Equilibrium Configuration of Benzene and Aniline: A First-Principles Study

The present work describes the equilibrium configuration of aromatic compounds like benzene and aniline molecules using the first principle (ab initio) calculation method implemented by the Gaussian 98 programs. The ground state energy for benzene and aniline molecules obtained using the DFT (B3LYP) calculation is lower than that obtained with the HF+MP2 method which, in turn, is lower than that obtained with the HF calculation. The calculated values of bond length, bond angle, and dihedral angle for these molecules with HF, HF+MP2, and DFT (B3LYP) levels of calculation agree with each other within 2%. The calculated C-C and C-H bond lengths of the benzene molecule are 1.394 Å and 1.084 Å at DFT (B3LYP) calculation and these values agree well with the experimental value of 1.395 Å and 1.084 Å for C-C and C-H bond. Also, the calculated value of bond angles and dihedral angles for benzene molecule are 120° and 180° respectively. For aniline molecule, the C-N and N-H bond lengths are found 1.378 Å and 1.003 Å respectively at DFT (B3LYP) calculation, which agrees with the experimental value of C-N and N-H bond lengths with values of 1.475 Å and 1.008 Å within 7% respectively. For the benzene molecule, there is a symmetrical charge distribution. The total dipole moment of the benzene molecule is zero, indicating that the centers of positive and negative charge coincide with each other such that the benzene molecule is non-polar whereas aniline is a polar molecule with a dipole moment of 1.9828 Debye

Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics.

NMR chemical shifts provide a sensitive probe of protein structure and dynamics but remain challenging to predict and interpret. We examine the effect of protein conformational distributions on 15N chemical shifts for dihydrofolate reductase (DHFR), comparing QM/MM predicted shifts with experimental shifts in solution as well as frozen distributions. Representative snapshots from MD trajectories exhibit variation in predicted 15N chemical shifts of up to 25 ppm. The average over the fluctuations is in significantly better agreement with room temperature solution experimental values than the prediction for any single optimal conformations. Meanwhile, solid-state NMR (SSNMR) measurements of frozen solutions at 105 K exhibit broad lines whose widths agree well with the widths of distributions of predicted shifts for samples from the trajectory. The backbone torsion angle ψi-1 varies over 60° on the picosecond time scale, compensated by φi. These fluctuations can explain much of the shift variation.

Comparative experimental study of the biomechanical properties of retrograde tibial nailing and distal tibia plate in distal tibia fracture.

Objective: A biomechanical comparative analysis was conducted to evaluate the retrograde tibial nailing (RTN) and distal tibia plate techniques for the treatment of distal tibia fractures. Methods: Fourteen fresh adult tibia specimens were selected, consisting of seven males and seven females aged 34-55years. The specimens were randomly divided into two groups (Group A and Group B) using a numerical table method, with seven specimens in each group. Group A underwent internal fixation of distal tibial fractures using RTN, while Group B received internal fixation using a plate. The axial compression properties of the specimens were tested in the neutral positions under pressures of 100, 200, 300, 400, and 500N. Additionally, the torsional resistance of the two groups was assessed by subjecting the specimens to torques of 1.0, 2.0, 3.0, 4.0, and 5.0Nm. Results: At pressures of 400 and 500N, the axial compression displacement in Group A (1.11 ± 0.06, 1.24 ± 0.05) mm was significantly smaller than that in Group B (1.21 ± 0.08, 1.37 ± 0.11) mm (p = 0.023, 0.019). Moreover, at a pressure of 500N, the axial compression stiffness in Group A (389.24 ± 17.79) N/mm was significantly higher than that of the control group (362.37 ± 14.44) N/mm (p = 0.010). When subjected to torques of 4 and 5Nm, the torsion angle in Group A (2.97° ± 0.23°, 3.41° ± 0.17°) was significantly smaller compared to Group B (3.31° ± 0.28°, 3.76° ± 0.20°) (p = 0.035, 0.004). Furthermore, at a torque of 5Nm, the torsional stiffness in Group A (1.48 ± 0.07) Nm/° was significantly higher than that in Group B (1.36 ± 0.06) N·m/° (p = 0.003). Conclusion: The results obtained from the study demonstrate that the biomechanical performance of RTN outperforms that of the distal tibial plate, providing valuable biomechanical data to support the clinical implementation of RTN.

Multifunctional tension–compression conversion sensing structure inspired by rotating stairs

Developing sensors that combine sensitivity and range while detecting multiple physical stimuli is crucial for advancing human–computer interaction. To create a sensor that combines high sensitivity and wide detection range, and can respond to multiple signals, we designed a tension–compression conversion structure (TCS) inspired by the rotating stairs and used the stretchable strain sensor as the sensing unit to realize the detection of pressure and torsion signals. The performance of the multifunctional sensing structure can be designed and predicted by theoretical calculations. The variable stiffness design strategy enables the sensing structure to have satisfactory sensitivity (2.27 N−1) and detection range (0.003 ∼ 25.55 N). In addition, the sensing structure can detect the torsion angle within 30° and the torque within 86.4 N·mm, and can work stably in the underwater environment. This tension–compression conversion sensing structure inspired by rotating stairs will provide new ideas for developing multifunctional sensors with both sensitivity and range.

Pyrene-Based Deep-Blue Fluorophores with Narrow-Band Emission.

High-efficiency narrow-band luminescent materials have attracted intense interest, resulting in their great colorimetric purity. This has led to a variety of high-tech applications in high-definition displays, spectral analysis, and biomedicine. In this study, a rigid pyrene core was employed as the molecular backbone, and four narrow-band pyrene-based blue emitters were synthesized using various synthetic methods (such as Lewis-acid catalyzed cyclization domino reactions, Pd-catalyzed coupling reactions like Suzuki-Miyaura and Sonogashira). Due to the steric effect of the hydroxy group at the 2-position, the target compounds exhibit deep blue emission (<429 nm, CIEy < 0.08) with full width at half-maximum (FWHM) less than 33 nm both in solution and when solidified. The experimental and theoretical results indicated that the substituents at the 1- and 3-positions afford a large dihedral angle with the pyrene core, and the molecular motion is almost fixed by multiple intra- and intermolecular hydrogen bonding interactions in the crystallized state, leading to a suppression of the vibrational relaxation of the molecular structure. Moreover, we observed that the suppression of the vibrational relaxation in the molecular structures and the construction of rigid conjugated structures can help develop narrow-band organic light-emitting materials.

Forest Canopy Height Estimation by Integrating Structural Equation Modeling and Multiple Weighted Regression

As an important component of forest parameters, forest canopy height is of great significance to the study of forest carbon stocks and carbon cycle status. There is an increasing interest in obtaining large-scale forest canopy height quickly and accurately. Therefore, many studies have aimed to address this issue by proposing machine learning models that accurately invert forest canopy height. However, most of the these approaches feature PolSAR observations from a data-driven viewpoint in the feature selection part of the machine learning model, without taking into account the intrinsic mechanisms of PolSAR polarization observation variables. In this work, we evaluated the correlations between eight polarization observation variables, namely, T11, T22, T33, total backscattered power (SPAN), radar vegetation index (RVI), the surface scattering component (Ps), dihedral angle scattering component (Pd), and body scattering component (Pv) of Freeman-Durden three-component decomposition, and the height of the forest canopy. On this basis, a weighted inversion method for determining forest canopy height under the view of structural equation modeling was proposed. In this study, the direct and indirect contributions of the above eight polarization observation variables to the forest canopy height inversion task were estimated based on structural equation modeling. Among them, the indirect contributions were generated by the interactions between the variables and ultimately had an impact on the forest canopy height inversion. In this study, the covariance matrix between polarization variables and forest canopy height was calculated based on structural equation modeling, the weights of the variables were calculated by combining with the Mahalanobis distance, and the weighted inversion of forest canopy height was carried out using PSO-SVR. In this study, some experiments were carried out using three Gaofen-3 satellite (GF-3) images and ICESat-2 forest canopy height data for some forest areas of Gaofeng Ridge, Baisha Lizu Autonomous County, Hainan Province, China. The results showed that T11, T33, and total backscattered power (SPAN) are highly correlated with forest canopy height. In addition, this study showed that determining the weights of different polarization observation variables contributes positively to the accurate estimation of forest canopy height. The forest canopy height-weighted inversion method proposed in this paper was shown to be superior to the multiple regression model, with a 26% improvement in r and a 0.88 m reduction in the root-mean-square error (RMSE).

In silico drug derivatives for KRAS-G12D: free-energy surfaces in aqueous solution by well-tempered metadynamics simulations

KRAS oncogenes are the largest family of mutated RAS isoforms, participating in about 30% of all cancers. Due to their paramount medical importance, enormous effort is being devoted to the development of inhibitors using clinical tests, wet-lab experiments and drug design, being this a preliminary step in the process of creating new drugs, prior to synthesis and clinical testing. One central aspect in the development of new drugs is the characterisation of all species that can be used for treatment. In this aim, we propose a computational framework based on combined all-atom molecular dynamics and metadynamics simulations in order to accurately access the most stable conformational variants for several derivatives of a recently proposed small-molecule, called DBD15-21-22. Free energy calculations are essential to unveil mechanisms at the atomic scale like binding affinities or dynamics of stable states. Considering specific atom-atom distances and torsional angles as reliable reaction coordinates we have obtained free-energy landscapes by well-tempered metadynamics simulations, revealing local and global minima of the free-energy hypersurface. We have observed that a variety of stable states together with transition states are clearly detected depending on the particular species, leading to predictions on the behaviour of such compounds in ionic aqueous solution.

1-Ethyl-3,3-di-methyl-spiro-[indoline-2,8'-phenaleno[1,9-fg]chromene

The title pyrene-fused spiro-pyran derivative, C30H25NO, crystallizes with two mol-ecules in the asymmetric unit with dihedral angles between their fused-ring sub units of 76.20 (8) and 89.38 (9)°. In the crystal, weak C-H⋯π inter-actions link the mol-ecules into a three-dimensional network.

Structural Insights and Influence of Terahertz Waves in Midinfrared Region on Kv1.2 Channel Selectivity Filter.

Potassium ion channels are the structural basis for excitation transmission, heartbeat, and other biological processes. The selectivity filter is a critical structural component of potassium ion channels, whose structure is crucial to realizing their function. As biomolecules vibrate and rotate at frequencies in the terahertz band, potassium ion channels are sensitive to terahertz waves. Therefore, it is worthwhile to investigate how the terahertz wave influences the selectivity filter of the potassium channels. In this study, we investigate the structure of the selectivity filter of Kv1.2 potassium ion channels using molecular dynamics simulations. The effect of an electric field on the channel has been examined at four different resonant frequencies of the carbonyl group in SF: 36.75 37.06, 37.68, and 38.2 THz. As indicated by the results, 376GLY appears to be the critical residue in the selectivity filter of the Kv1.2 channel. Its dihedral angle torsion is detrimental to the channel structural stability and the transmembrane movement of potassium ions. 36.75 THz is the resonance frequency of the carbonyl group of 376GLY. Among all four frequencies explored, the applied terahertz electric field of this frequency has the most significant impact on the channel structure, negatively impacting the channel stability and reducing the ion permeability by 20.2% compared to the absence of fields. In this study, we simulate that terahertz waves in the mid-infrared frequency region can significantly alter the structure and function of potassium ion channels and that the effects of terahertz waves differ greatly based on frequency.

Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures

While low-temperature Nuclear Magnetic Resonance (NMR) holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here, we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) in Escherichia coli Dihydrofolate Reductase (DHFR) at 105 K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of Ni+1 to Ψi. With selective 15N and 13C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in 13C'-15N correlation spectrum. For this unique amide, we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin: 114 ± 7° for the major peak and 150 ± 8° and 164 ± 16° for the minor peaks as contrasted with 118° for the X-ray crystal structure (and 118° to 130° for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low-temperature NMR spectra.

A new theoretical method for torsional-flexural vibrations response of thin-walled beams with closed cross-sections under uniform distributed moving load

This article presents a new theoretical method for the torsional-flexural vibration response of a thin-walled beam with closed cross sections under a uniformly distributed moving load. Based on Vlasov’s theory and restrained torsion theory, a comprehensive equation of motion for torsional flexural vibration is established by considering the effects of additional torque caused by the change of the shear center and the center of mass and the warpage coefficient. Using the Fourier transform, Laplace transform, and their inverse transformations, the torsional-flexural vibration response expression of thin-walled beams with closed cross-sections under a uniformly distributed moving load was derived. The results calculated by the analytical solutions in this study were compared with those from finite element method, demonstrating the reliability and superiority of the analytical solutions. Compared with the method that ignores the warpage coefficient, the lateral displacement and torsion angle of the beam calculated by the proposed theoretical method decreased by more than 12.00%. The effect of the cross-sectional properties on the natural frequency of the torsional-flexural vibration of thin-walled beams is analyzed, and the results show that the moment of inertia and mass per unit length have a considerable influence on the torsional-flexural frequency, which increases with the moment of inertia and decreases with an increase in the mass per unit length. The influences of the load magnitude, load velocity, and load eccentricity on the dynamic response were further investigated. According to the results, the lateral displacement of the beam increased significantly with increases in the load eccentricity and load magnitude. In practical engineering, the conclusions of this study can be used to limit the torsional-flexural vibration response of simple maglev support bridges to ensure the safety of vehicles and passengers.

Vacuum pendulum test for a modified Kaluza–Klein theory

Experiments were performed in vacuum to examine a modified Kaluza–Klein theory. Originally proposed by Mbelek and Lachièze-Rey, the 5D Kaluza–Klein-[Formula: see text] theory includes an external scalar field [Formula: see text] to couple gravitational and electromagnetic fields and can be used to explain some misunderstood phenomena in physics. The theory predicts that a pendulum will experience detectable forces exceeding predictions from classical electromagnetism when interacting with a scalar field. In this experiment, a dielectric mirror is hung as a pendulum inside a vacuum chamber and its oscillations are examined with two laser interferometers. In proximity to the pendulum, different solenoids and toroids will induce magnetic fields that can also be shielded to a great extent using a Gauss chamber. The experiments were conducted in a vacuum chamber to allow the measurement of torsion angles as low as 0.1[Formula: see text]arcsec above the noise, as well as 0.1[Formula: see text][Formula: see text]m translations of the pendulum. The phenomenon observed differs from what was observed by Mbelek at ambient pressure in both magnitude and behavior. Dummy test results hint at the presence of convection effects to explain the pendulum’s rotation, which was eliminated under higher vacuum and by placing a wall between the solenoid and pendulum. In the presence of stronger magnetic fields, the pendulum’s translation was observed to agree with effects predicted by a consideration of diamagnetic effects.

Time dependent dihedral angle oscillations of the spike protein of SARS-CoV-2 reveal favored frequencies of dihedral angle rotations

The spike protein of SARS-CoV-2 is critical to viral infection of human host cells which ultimately results in COVID-19. In this study we analyzed the behavior of dihedral angles (phi and psi) of the wild-type spike protein over time from molecular dynamics and identified that their oscillations are dominated by a few discrete, relatively low frequencies in the 23–63 MHz range with 42.969 MHz being the most prevalent frequency sampled by the oscillations. We thus observed the spike protein to favor certain frequencies more than others. Gaps in the tally of all observed frequencies for low-abundance amino acids also suggests that the frequency components of dihedral angle oscillations may be a function of position in the primary structure since relatively more abundant amino acids lacked gaps. Lastly, certain residues identified in the literature as constituting the inside of a druggable pocket, as well as others identified as allosteric sites, are observed in our data to have distinctive time domain profiles. This motivated us to propose additional residues with similar time domain profiles, which may be of potential interest to the vaccine and drug design communities for further investigation. Thus these findings indicate that there is a particular frequency domain profile for the spike protein hidden within the time domain data and this information, perhaps with the suggested residues, might provide additional insight into therapeutic development strategies for COVID-19 and beyond.

Syn-Aminoauration versus Anti-Aminoauration of Alkynes in Au(I)/Au(III) Catalysis: Understanding the Origin of Selectivity.

There is no experimental evidence of whether such gold-catalyzed aminoauration reactions follow the anti- and/or syn-pathway, and hence, to understand the origin of the selectivity in Au(I)- and Au(III)-catalyzed reactions of alkynes, a thorough mechanistic study was performed using DFT methods. The NBO and ASM analyses provided significant information about the structure-stability-reactivity of the pathway-determining states (PDS). This study further reveals that the oxidation states and geometries of gold, the steric bulk, and the dihedral angles of the PDS direct the mechanistic pathways and control the turnover frequency.

Deep Spectral Meshes: Multi-Frequency Facial Mesh Processing with Graph Neural Networks

With the rising popularity of virtual worlds, the importance of data-driven parametric models of 3D meshes has grown rapidly. Numerous applications, such as computer vision, procedural generation, and mesh editing, vastly rely on these models. However, current approaches do not allow for independent editing of deformations at different frequency levels. They also do not benefit from representing deformations at different frequencies with dedicated representations, which would better expose their properties and improve the generated meshes’ geometric and perceptual quality. In this work, spectral meshes are introduced as a method to decompose mesh deformations into low-frequency and high-frequency deformations. These features of low- and high-frequency deformations are used for representation learning with graph convolutional networks. A parametric model for 3D facial mesh synthesis is built upon the proposed framework, exposing user parameters that control disentangled high- and low-frequency deformations. Independent control of deformations at different frequencies and generation of plausible synthetic examples are mutually exclusive objectives. A Conditioning Factor is introduced to leverage these objectives. Our model takes further advantage of spectral partitioning by representing different frequency levels with disparate, more suitable representations. Low frequencies are represented with standardised Euclidean coordinates, and high frequencies with a normalised deformation representation (DR). This paper investigates applications of our proposed approach in mesh reconstruction, mesh interpolation, and multi-frequency editing. It is demonstrated that our method improves the overall quality of generated meshes on most datasets when considering both the L1 norm and perceptual Dihedral Angle Mesh Error (DAME) metrics.

A Theoretical Method for Calculating the Internal Contact Pressure of Parallel Wire Cable during Fretting Wear

Fretting wear of the stay cable is an important factor affecting the service life of the cable. To accurately calculate the extent of fretting wear, it is necessary to calculate the internal contact pressure in the cable. Although there are many theories and experiments on the contact behavior between wires, there are still no theoretical formulations for calculating the distribution of contact pressure in stay cables. In this paper, by studying the transfer effect of contact pressure in the cable, the PIC (parallel wire cable internal point contact pressure) model for calculating the contact pressure in the parallel wire cable is proposed, considering the effects of wire twisting, sheath compression, and cable bending on the contact pressure. A finite element model corresponding to the contact mode between steel wires is established, and the effectiveness of the PIC model is verified through numerical simulation analysis and a comparison of the existing contact models. The results indicate that contact pressure caused by wire twisting (CWT) is superimposed layer by layer inwards, with the contact pressure increasing closer to the inner layers, and its magnitude is mainly related to the axial tension and twist angle. Simultaneously, on the same layer, contact points along the diagonal experience the greatest contact pressure. Contact pressure caused by sheath compression (CSC) is assumed to conform to the Boussinesq distribution, with the outer layers exhibiting greater contact pressure compared to the inner layers. Contact pressure caused by cable bending (CCB) conforms to the two-dimensional closely arranged contact force transmission model, has a clear layering phenomenon, and the contact pressure within the same layer does not change significantly. The magnitude of the contact pressure is exponentially related to the curvature of the cable and proportional to the tension of the cable, which explains the reason why the slip occurs later for the cables with high tensile forces. Among these three types of contact pressure, CWT is the greatest, followed by CCB, while CSC is the smallest. The theoretical analysis results show that factors such as wire radius, tension, torsion angle, and wire position have an impact on contact pressure. Contact pressure is transmitted along force chains within the cable, following the superposition law between layers. It is uncertain whether slip occurs in the neutral axis or in the outermost layer because of the different distributions of tangential force and interlayer frictional resistance between the layers of wires. Fretting wear simulations of two wires demonstrate that contact pressure has a significant influence on wear patterns, and the “averaging” of contact pressure is a major reason for achieving uniform interface wear. While the contact width increases proportionally with the contact pressure, excessive contact pressure can complicate the problem by changing the contact mode from gross slip to partial slip. This study provides a theoretical method for calculating contact pressures at any contact point within the cables in engineering practice.

Crystal structure and Hirshfeld surface analysis of a salt of antineoplastic kinase inhibitor vandetanib.

A salt of vandetanib, namely, 4-({4-[(4-bromo-2-fluorophenyl)amino]-6-methoxyquinazolin-7-yl}methoxy)-1-methylpiperazin-1-ium 2-(butylamino)-4-phenoxy-6-sulfamoylbenzoate acetonitrile monosolvate, C22H25BrFN4O2+·C17H19N2O5S-·C2H3N, composed of kinase inhibitor vandetanib and sulfamyl diuretic bumetanide in a 1:1 molar ratio, is reported. There is proton transfer between the piperidine ring of vandetanib and the carboxyl group of bumetanide to form the salt. In the vandetanib cation, the arene and pyrimidine rings are not coplanar, their planes subtending a dihedral angle of 60.47 (14)°. The roles of the intermolecular interactions in the crystal packing were clarified using Hirshfeld surface analysis, and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H...H (40.5%), O...H/H...C (20.7%), C...H/ H...C (18.8%) and N...C/C...N (9.0%) contacts.

Virtual indentation of the empty capsid of the minute virus of mice using a minimal coarse-grained model.

A minimal coarse-grained model for T=1 viral capsids assembled from 20 protein rigid trimers has been designed by extending a previously proposed form of the interaction energy written as a sum of anisotropic pairwise interactions between the trimeric capsomers. The extension of the model has been performed to properly account for the coupling between two internal coordinates: the one that measures the intercapsomer distance and the other that gives the intercapsomer dihedral angle. The model has been able to fit with less than a 10% error the atomic force microscopy (AFM) indentation experimental data for the empty capsid of the minute virus of mice (MVM), providing in this way an admissible picture of the main mechanisms behind the capsid deformations. In this scenario, the bending of the intercapsomer dihedral angle is the angular internal coordinate that can support larger deformations away from its equilibrium values, determining important features of the AFM indentation experiments as the elastic constants along the three symmetry axes of the capsid and the critical indentations. From the value of one of the parameters of our model, we conclude that trimers in the MVM must be quite oblate tops, in excellent agreement with their known structure. The transition from the linear to the nonlinear regimes sampled in the indentation process appears to be an interesting topic for future research in physical virology.

Dynamic Insights into DNA Conformational Changes and the Impact of Magnesium Ions on Topoisomerase IA Enzymes: A Molecular Dynamics Simulation Study

Molecular dynamics simulations were employed to scrutinize the conformational changes in DNA strands and elucidate the influence of magnesium ions on Topoisomerase IA enzymes. Through the computation of Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), hydrogen bond distances, dihedral angles, and Solvated Accessible Surface Area (SASA), we meticulously examined the structural dynamics. The results reveal intricate patterns of DNA strand alterations, showcasing the profound role of magnesium ions in modulating the behavior of Topoisomerase IA enzymes. This study contributes essential insights into the molecular mechanisms governing DNA conformational changes, offering a foundation for further understanding the biochemical intricacies of Topoisomerase IA enzyme function.