Molecular Energetics Research Articles

Anti-proliferative 2,3-dihydro-1,3,4-thiadiazoles targeting VEGFR-2: Design, synthesis, in vitro, and in silico studies

In this study, we present the design, synthesis, and evaluation of six new thiadiazole derivatives designed as VEGFR-2 inhibitors. The most promising compound, 18b, demonstrated promising inhibitory activity against VEGFR-2, with an IC50 value of 0.165 µg/mL. The in vitro assessments on MCF-7 and HepG2 cell lines revealed the superior anti-proliferative effects of compound 18b, exhibiting IC50 values of 0.06 and 0.17 µM, respectively. Further investigations into the cell cycle distribution of compound 18b on MCF-7 cells exhibited a cell cycle arrest at the S phase (52.96 %) and significantly reducing the percentage of cells in the G0-G1 and G2/M phases. Additionally, compound 18b demonstrated a remarkable pro-apoptotic effect, with 45.29 % total apoptosis, characterized by both early and late apoptosis, and minimal necrosis. These findings were corroborated by RT-PCR analysis, revealing a significant downregulation of the anti-apoptotic gene Bcl2 and upregulation of the pro-apoptotic gene BAX in compound 18b-treated cells compared to control MCF-7 cells. Moreover, in silico studies involving molecular docking, Density Functional Theory (DFT) calculations, Molecular Dynamics (MD) simulations, MM-GBSA, Principle Component Analysis of Trajectories (PCAT), in addition to Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) predictions underscored the molecular interactions, energetics, and pharmacokinetic properties of compound 18b and the other derivatives further supporting its potential. Our integrated approach, combining in vitro experimens with in silico predictions provides valuable insights into the therapeutic potential of compound 18b as a robust VEGFR-2 inhibitor and lays the groundwork for future optimization.

GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules.

A detailed understanding of ligand-protein interaction is essential for developing rational drug-design strategies. In recent years, technological advances in cryo-electron microscopy (cryo-EM) brought a new era to the structural determination of biological macromolecules and assemblies at high resolution, marking cryo-EM as a promising tool for studying ligand-protein interactions. However, even in high-resolution cryo-EM results, the densities for the bound small-molecule ligands are often of lower quality due to their relatively dynamic and flexible nature, frustrating their accurate coordinate assignment. To address the challenge of ligand modeling in cryo-EM maps, here we report the development of GOLEM (Genetic Optimization of Ligands in Experimental Maps), an automated and robust ligand docking method that predicts a ligand's pose and conformation in cryo-EM maps. GOLEM employs a Lamarckian genetic algorithm to perform a hybrid global/local search for exploring the ligand's conformational, orientational, and positional space. As an important feature, GOLEM explicitly considers water molecules and places them at optimal positions and orientations. GOLEM takes into account both molecular energetics and the correlation with the cryo-EM maps in its scoring function to optimally place the ligand. We have validated GOLEM against multiple cryo-EM structures with a wide range of map resolutions and ligand types, returning ligand poses in excellent agreement with the densities. As a VMD plugin, GOLEM is free of charge and accessible to the community. With these features, GOLEM will provide a valuable tool for ligand modeling in cryo-EM efforts toward drug discovery.

Octupole moment driven free charge generation in partially chlorinated subphthalocyanine for planar heterojunction organic photodetectors

In this study, high-performance organic photodetectors are presented which utilize a pristine chlorinated subphthalocyanine photoactive layer. Optical and optoelectronic analyses indicate that the device photocurrent is primarily generated through direct charge generation within the chlorinated subphthalocyanine layer, rather than exciton separation at layer interfaces. Molecular modelling suggests that this direct charge generation is facilitated by chlorinated subphthalocyanine high octupole moment (−80 DÅ2), which generates a 200 meV shift in molecular energetics. Increasing the thickness of chlorinated subphthalocyanine leads to faster response time, correlated with a decrease in trap density. Notably, photodetectors with a 50 nm thick chlorinated subphthalocyanine photoactive layer exhibit detectivities approaching 1013 Jones, with a dark current below 10−7 A cm−2 up to −5 V. Based on these findings, we conclude that high octupole moment molecular semiconductors are promising materials for high-performance organic photodetectors employing single-component photoactive layer.

Benzothiazole-derived Compound with Antitumor Activıiy: Molecular Structure Determination Using Density Functional Theory (Dft) Method

The Gaussian computational chemistry software package was employed to investigate the molecular structure and energetics of benzothiazole, a compound known for its anti-tumor properties. Density functional theory (DFT) calculations were conducted using the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) method, coupled with the LanL2DZ basis set. Molecular structure optimization was carried out to determine the most stable configurations of the benzothiazole compound. Furthermore, thorough analyses of molecular orbital energies, molecular properties, and molecular electrostatic potential surface maps were performed on the optimized molecular system. Our current research suggests that the compound 2-(4-aminophenyl) benzothiazole, containing benzothiazole, maybe a potential drug candidate for free radical species on cells due to its anti-cancer properties.

Projective quantum eigensolver via adiabatically decoupled subsystem evolution: A resource efficient approach to molecular energetics in noisy quantum computers.

Quantum computers hold immense potential in the field of chemistry, ushering new frontiers to solve complex many-body problems that are beyond the reach of classical computers. However, noise in the current quantum hardware limits their applicability to large chemical systems. This work encompasses the development of a projective formalism that aims to compute ground-state energies of molecular systems accurately using noisy intermediate scale quantum (NISQ) hardware in a resource-efficient manner. Our approach is reliant upon the formulation of a bipartitely decoupled parameterized ansatz within the disentangled unitary coupled cluster framework based on the principles of nonlinear dynamics and synergetics. Such decoupling emulates total parameter optimization in a lower dimensional manifold, while a mutual synergistic relationship among the parameters is exploited to ensure characteristic accuracy via a non-iterative energy correction. Without any pre-circuit measurements, our method leads to a highly compact fixed-depth ansatz with shallower circuits and fewer expectation value evaluations. Through analytical and numerical demonstrations, we establish the method's superior performance under noise while concurrently ensuring requisite accuracy in future fault-tolerant systems. This approach enables rapid exploration of emerging chemical spaces by the efficient utilization of near-term quantum hardware resources.

Unveiling Tst3, a Multi-Target Gating Modifier Scorpion α Toxin from Tityus stigmurus Venom of Northeast Brazil: Evaluation and Comparison with Well-Studied Ts3 Toxin of Tityus serrulatus.

Studies on the interaction sites of peptide toxins and ion channels typically involve site-directed mutations in toxins. However, natural mutant toxins exist among them, offering insights into how the evolutionary process has conserved crucial sequences for activities and molecular target selection. In this study, we present a comparative investigation using electrophysiological approaches and computational analysis between two alpha toxins from evolutionarily close scorpion species of the genus Tityus, namely, Tst3 and Ts3 from T. stigmurus and T. serrulatus, respectively. These toxins exhibit three natural substitutions near the C-terminal region, which is directly involved in the interaction between alpha toxins and Nav channels. Additionally, we characterized the activity of the Tst3 toxin on Nav1.1-Nav1.7 channels. The three natural changes between the toxins did not alter sensitivity to Nav1.4, maintaining similar intensities regarding their ability to alter opening probabilities, delay fast inactivation, and induce persistent currents. Computational analysis demonstrated a preference for the down conformation of VSD4 and a shift in the conformational equilibrium towards this state. This illustrates that the sequence of these toxins retained the necessary information, even with alterations in the interaction site region. Through electrophysiological and computational analyses, screening of the Tst3 toxin on sodium isoform revealed its classification as a classic α-NaTx with a broad spectrum of activity. It effectively delays fast inactivation across all tested isoforms. Structural analysis of molecular energetics at the interface of the VSD4-Tst3 complex further confirmed this effect.

Effects of calcium and barium chloride salts on the solubility and dissolution thermodynamics of glycine and DL-alanine from 288.15 K to 328.15 K

This investigation primarily examines the solubility at equilibrium and the dissolution thermodynamics of two crucial amino acids, glycine and DL-alanine, in aqueous solutions containing calcium and barium chloride salts. The solubilities were measured from 288.15 K to 328.15 K using the analytical gravimetric method. The resulting solubilities were then used to deduce the thermodynamics of the solutions. Subsequently, the free energies associated with solvation through transfer were examined.Furthermore, the research delved into various thermophysical characteristics within electrolyte solutions in aqueous media, establishing correlations. In addition, this study elucidated various non-covalent processes, including the solubility and stability of amino acids, by considering short-range interactions such as solute–solvent, solvent–solvent, and acid–base interactions. This analysis primarily provides insights into the involved molecular interactions and energetics that govern the solubility and behavior of amino acids in various solution environments.

Molecular Dynamics and Binding Energetics of Fluspirilene With BACE1: Implications for Alzheimer's Disease Intervention

ABSTRACTAlzheimer's disease (AD) is a serious neurodegenerative disorder that results in cognitive deterioration, amnesia, and alterations in behavior, rendering it a significant issue in public health. The pathogenesis involves amyloid plaques highlighting the importance of targeting BACE1. This study explores fluspirilene, a di‐phenyl‐butyl‐piperidine as a potential BACE1 inhibitor for AD treatment. Fluspirilene was analyzed for ADMET. In silico molecular docking assessed fluspirilene's binding affinity with BACE1. Re‐docking a co‐crystallized ligand confirmed the docking process. Molecular dynamics simulations and related multifaceted computational analyses were conducted to assess the stability of docked complexes. Fluspirilene had good physicochemical and pharmacokinetic characteristics according to ADMET profiling. In silico molecular docking showed multiple BACE1 interactions with a binding affinity of −9.2 kcal/mol and fluspirilene–BACE1 complex stability was confirmed by molecular dynamics simulation results. Possible therapeutic applications in lowering Aβ generation and treating AD are indicated by the compound's pharmacokinetics, molecular interactions, and binding energetics. Validation and optimization of experiments are necessary for the clinical development of fluspirilene as a BACE1 inhibitor for AD.

Dispersion Control over Molecule Cohesion: Exploiting and Dissecting the Tipping Power of Aromatic Rings.

ConspectusWe have learned over the past years how London dispersion forces can be effectively used to influence or even qualitatively tip the structure of aggregates and the conformation of single molecules. This happens despite the fact that single dispersion contacts are much weaker than competing polar forces. It is a classical case of strength by numbers, with the importance of London dispersion forces scaling with the system size. Knowledge about the tipping points, however difficult to attain, is necessary for a rational design of intermolecular forces. One requires a careful assessment of the competing interactions, either by sensitive spectroscopic techniques for the study of the isolated molecules and aggregates or by theoretical approaches. Of particular interest are the systems close to the tipping point, when dispersion interactions barely outweigh or approach the strength of the other interactions. Such subtle cases are important milestones for a scale-up to realistic multi-interaction situations encountered in the fields of life and materials science. In searching for examples that provide ideal competing interactions in complexes and small clusters, aromatic systems can offer a diverse set of molecules with a variation of dispersion and electrostatic forces that control the dominant and peripheral interactions. Our combined spectroscopic and theoretical investigations provide valuable insights into the balance of intermolecular forces because they typically allow us to switch the aromatic substituent on and off. High-resolution rotational spectroscopy serves as a benchmark for molecular structures, as correct calculations should be based on correct geometries. When discussing the competition with other noncovalent interactions, obvious competitors are directional hydrogen bonds. As a second counterweight to aryl interactions, we will discuss aurophilic/metallophilic interactions, which also have a strong stabilization with a small number of atoms involved. Vibrational spectroscopy is most sensitive to interactions of light atoms, and the competition of OH hydrogen bonds with dispersion forces in a molecular aggregate can be judged well by the OH stretching frequency. Experiments in the gas phase are ideal for gauging the accuracy of quantum chemical predictions free of solvent forces. A tight collaboration utilizing these three methods allows experiment vs experiment vs theory benchmarking of the overall influence of dispersion in molecular structures and energetics.

Noise-independent route toward the genesis of a COMPACT ansatz for molecular energetics: A dynamic approach.

Recent advances in quantum information and quantum science have inspired the development of various compact, dynamically structured ansätze that are expected to be realizable in Noisy Intermediate-Scale Quantum (NISQ) devices. However, such ansätze construction strategies hitherto developed involve considerable measurements, and thus, they deviate significantly in the NISQ platform from their ideal structures. Therefore, it is imperative that the usage of quantum resources be minimized while retaining the expressivity and dynamical structure of the ansatz that can adapt itself depending on the degree of correlation. We propose a novel ansatz construction strategy based on the abinitio many-body perturbation theory that requires no pre-circuit measurement and, thus, remains structurally unaffected by any hardware noise. The accuracy and quantum complexity associated with the ansatz are solely dictated by a pre-defined perturbative order, as desired, and, hence, are tunable. Furthermore, the underlying perturbative structure of the ansatz construction pipeline enables us to decompose any high-rank excitation that appears in higher perturbative orders into the product of various low-rank operators, and it thus keeps the execution gate-depth to its minimum. With a number of challenging applications on strongly correlated systems, we demonstrate that our ansatz performs significantly better, both in terms of accuracy, parameter count, and circuit depth, in comparison to the allied unitary coupled cluster based ansätze.

Molecular mechanisms and energetics underlying the dynein priming stroke

Molecular mechanisms and energetics underlying the dynein priming stroke

Insight into molecular interactions and energetics of surfactant self-assembly in hydrated glucose-urea deep eutectic solvent

Self-assembled structures in highly biocompatible Natural Deep Eutectic Solvent (NADES) are gaining popularity as new drug delivery systems due to their inherent advantages. Although glucose-urea (GU) based NADES satisfies the criterion of an efficient DES in terms of low toxicity, stability at desirable pH range, low viscosity and biocompatible polarity its potential as a medium for molecular self-assembly is yet unexplored. In this work we present first systematic study of self-assembly of pharmaceutically important excipients like sodium deoxycholate (NaDC), cetylpyridinium chloride (CPC) and Brij 35 (B35) in three hydrated GUNADES using isothermal titration calorimetry. The findings are correlated to the microstructure of these solvents as delineated from molecular dynamics simulations. Micro-environment of the micelles in a typical hydrated GU NADES has been studied using time resolved fluorescence anisotropy measurements. Cyto-toxicity of the proposed NADES has been assessed using MTT assay. CMC values of the surfactants increased with increase in glucose-urea concentration in the NADES indicating increased solvophilicity in GUNADES. Fluorescence studies indicate higher polydispersity of sodium deoxycholate in water than GUNADES. Cyto-toxicity study of GU80 shows good biocompatibility.

Molecular mechanisms and energetics of lipid droplet formation and directional budding.

The formation and budding of lipid droplets (LDs) are known to be governed by the LD size and by membrane tensions in the endoplasmic reticulum (ER) bilayer and LD-monolayers. Using coarse-grained simulations of an LD model, we first show that ER-embedded LDs of different sizes can form through a continuous transition from wide LD lenses to spherical LDs at a fixed LD size. The ER tendency to relax its bilayer modulates the transition via a subtle interplay between the ER and LD lipid densities. By calculating the energetic landscape of the LD transition, we demonstrate that this size-independent transition is regulated by the mechanical force balance of ER and LD-tensions, independent from membrane bending and line tension whose energetic contributions are negligible according to our calculations. Our findings explain experimental observation of stable LDs of various shapes. We then propose a novel mechanism for directional LD budding where the required membrane asymmetry is provided by the exchange of lipids between the LD-monolayers. Remarkably, we demonstrate that this budding process is energetically neutral. Consequently, LD budding can proceed by a modest energy input from proteins or other driving agents. We obtain equal lipid densities and membrane tensions in LD-monolayers throughout budding. Our findings indicate that unlike LD formation, LD budding by inter-monolayer lipid exchange is a tension-independent process.

How ATP suppresses the fibrillation of amyloid peptides: analysis of the free-energy contributions.

Recent experiments have revealed that adenosine triphosphate (ATP) suppresses the fibrillation of amyloid peptides - a process closely linked to neurodegenerative diseases such as Alzheimer's and Parkinson's. Apart from the adsorption of ATP onto amyloid peptides, the molecular understanding is still limited, leaving the underlying mechanism for the fibrillation suppression by ATP largely unclear, especially in regards to the molecular energetics. Here we provide an explanation at the molecular scale by quantifying the free energies using all-atom molecular dynamics simulations. We found that the changes of the free energies due to the addition of ATP lead to a significant equilibrium shift towards monomeric peptides in agreement with experiments. Despite ATP being a highly charged species, the decomposition of the free energies reveals that the van der Waals interactions with the peptide are decisive in determining the relative stabilization of the monomeric state. While the phosphate moiety exhibits strong electrostatic interactions, the compensation by the water solvent results in a minor, overall Coulomb contribution. Our quantitative analysis of the free energies identifies which intermolecular interactions are responsible for the suppression of the amyloid fibril formation by ATP and offers a promising method to analyze the roles of similarly complex cosolvents in aggregation processes.

Performance Evaluation of DFTB1 and DFTB2 Methods in reference to the Crystal Structures and Molecular Energetics of Siloxaalkane Molecular Compass

In the lately developed computational paradigms and state-of-art theoretical analyses, the density-functional based tight-binding (DFTB) scheme and its profound theoretical features extended to address the crystalline molecular systems stand as the most versatile quantum mechanical method. Being its computational parser codes extremely efficient and even assessable directly as a low-cost scheme despite hosting ab initio functionalities comprising mathematical formulations, the “non-self-consistent-charge” (DFTB1) and “self-consistent-charge" (DFTB2) approaches are extensively applied to the wide ranged molecular systems under both crystalline (PBC) and non-crystalline conditions. The "dispersion energy corrections (DECs)" features of it further add an additional value to their rational applications. Herewith, the intensive evaluations on their performances are carried out based on the results they produced for the experimentally synthesized amphidynamic type molecular crystal with macroscopic compass like supramolecular assembly possessing central dipolar difluorophenylene rotator (compass needle), axial Si-C bond spin axis, and peripheral -Si- & -Si-O- made siloxaalkane stator. It is found that the DFTB2 performed far better than the DFTB1 in reference to its datasets: (a) lengths for the bonds associated with rotator, stator, and spin axis, (b) free-volume unit around the rotator, (c) rotational energy barriers, viz. = 5.99 kcal/mol, & 5.52 kcal/mol under PBC with and without DECs, and (d) locations of the 1p-flipped (rotator) degenerate equilibrium structures, viz. at f = 0.505p & 1.493p (Expt. f = 0.56p & 1.56p) radians. Besides this, the dispersion constants for the F atom; cutoff =3.8Å, polarizability =3.4Å3, and effective nuclear charge =3.5au determined by DFTB2, and the precise unit-cell geometries derived by undertaking these numeral values further exemplified its superiority over DFTB1. It is believed that all the justifications and quantitative interpretations conferred throughout this article put considerable demands on the accuracy of DFTB2 for investigating crystal structures and molecular energetics explicitly.

Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network

Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key posttranslational modification involved in physiology and disease. The ability to robustly and rapidly predict protease-substrate specificity would also enable targeted proteolytic cleavage by designed proteases. Current methods for predicting protease specificity are limited to sequence pattern recognition in experimentally derived cleavage data obtained for libraries of potential substrates and generated separately for each protease variant. We reasoned that a more semantically rich and robust model of protease specificity could be developed by incorporating the energetics of molecular interactions between protease and substrates into machine learning workflows. We present Protein Graph Convolutional Network (PGCN), which develops a physically grounded, structure-based molecular interaction graph representation that describes molecular topology and interaction energetics to predict enzyme specificity. We show that PGCN accurately predicts the specificity landscapes of several variants of two model proteases. Node and edge ablation tests identified key graph elements for specificity prediction, some of which are consistent with known biochemical constraints for protease:substrate recognition. We used a pretrained PGCN model to guide the design of protease libraries for cleaving two noncanonical substrates, and found good agreement with experimental cleavage results. Importantly, the model can accurately assess designs featuring diversity at positions not present in the training data. The described methodology should enable the structure-based prediction of specificity landscapes of a wide variety of proteases and the construction of tailor-made protease editors for site-selectively and irreversibly modifying chosen target proteins.

Development of zero-noise extrapolated projective quantum algorithm for accurate evaluation of molecular energetics in noisy quantum devices.

The recently developed Projective Quantum Eigensolver (PQE) offers an elegant procedure to evaluate the ground state energies of molecular systems in quantum computers. However, the noise in available quantum hardware can result in significant errors in computed outcomes, limiting the realization of quantum advantage. Although PQE comes equipped with some degree of inherent noise resilience, any practical implementation with apposite accuracy would require additional routines to eliminate or mitigate the errors further. In this work, we propose a way to enhance the efficiency of PQE by developing an optimal framework for introducing Zero Noise Extrapolation (ZNE) in the nonlinear iterative procedure that outlines the PQE, leading to the formulation of ZNE-PQE. Moreover, we perform a detailed analysis of how various components involved in it affect the accuracy and efficiency of the reciprocated energy convergence trajectory. Additionally, we investigate the underlying mechanism that leads to the improvements observed in ZNE-PQE over conventional PQE by performing a comparative analysis of their residue normlandscape. This approach is expected to facilitate practical applications of quantum computing in fields related to molecular sciences, where it is essential to determine molecular energies accurately.

Hydrogen-Bonding-Assisted Substituent Engineering for Modulating Magnetic Spin Couplings and Switching in m-Phenylene Nitroxide Diradicals.

Rational modification of the coupler for the theoretical design of molecular magnets has attracted extensive interest. Substituent insertion is a widely used strategy for adjusting molecular properties, but its effect and modulation on magnetic spin couplings have been less investigated. In this work, we predict the magnetic properties of the design m-phenylene nitroxide (NO) diradicals regulated by introducing substituents. The calculated results for those two pairs of diradicals indicate that the signs of their magnetic coupling constants J do not change, but the magnitudes remarkably change after substituent regulation in the range from 253 to 730 cm-1. Such noticeable magnetic changes induced by introducing subsituents are mainly attributed to different electronic effects of substituents, assisted by the proximity of two NO groups, good planarity, conjugation, and an intramolecular hydrogen bond. In particular, the insertion of intramolecular H-bonds not only indicates an electronic effect but also has greatly changed the spin density distribution. Further aromaticity of the coupler ring, spin densities, and molecular orbitals and energetics was evaluated to gain a better understanding of magnetic regulation. Interestingly, further protonation of some substituents (e.g., -NO2 and -CO2) can noticeably turn the spin coupling from ferromagnetic to antiferromagnetic, showing manipulable magnetic switching. This work provides a promising strategy based on substituent engineering for magnetic spin coupling modulation, not only turning the coupling magnitude but also enabling the magnetic switching, thus providing insights into molecular magnetic manipulation for spintronics applications.

Theoretical Investigations of the Crystal Structures and Molecular Energetics of High Quality Silicon Carbide (β-SiC) Precursor Compound 1,4-bis(trimethylsilyl)benzene

Over the last decades, the rapidly growing theoretical methods have revolutionized whole scientific paradigm, developed state-of-art analyses, and created substantial computational platforms through the huge support of outstanding mathematical algorithms. The self-consistent-charge density-functional based tight-binding (SCC-DFTB) scheme is one of them that offers versatile and efficient quantum mechanical calculations with some unique features compatible especially to the crystalline solid even at low computational resources. Its effective parametrizations and computational implementations under the Gaussian standardized interface as an "External program" via the users' script (Gaussian- External methodology; GEM) has added an additional value because of which various in-built high-level Gaussian computations are directly accessible. Herewith, the Gaussian offered geometry optimization algorithms and convergence criteria plus the ModRedundant type relaxed potential energy surface (PES) scanning techniques are assessed through the GEM, and characterized the crystal structures with concerned molecular energetics and PES of the experimentally synthesized 1,4-bis (trimethylsilyl) benzene (1,4-BTMSB) compound; a potential precursor for the high quality Silicon Carbide (β-SiC) coating particles, and an ideal "Internal Standard" for the quantitative spectroscopic analyses. The general results reveal that the 1,4- BTMSB molecules in its unit-cell and crystal lattice experience significant non-bonding interactions that induces them to attain the definite molecular geometry with recognizable ring, angle, torsional, and steric strains. The quantitative analyses of its PES depict that the phenylene ring has to overcome multiple yet unidentical energy barriers with the tallest Ea1= 5.3 kcal/mol in order to undergo internal 2π angular rotation around the 1,4-(C-Si) axes. And, exhibiting such type internal rotation of its phenylene ring is energetically highly probable as this compound is widely employed in coating high temperature reactors, and in quantizing analyte in high energy run spectroscopic facilities. The same quantification is referred here in order to underscore the significance of adopting perfectly closed topological molecular architectures while designing/synthesizing amphidynamic type crystalline free molecular gyrotops and their prototypes.

Gaussian-External Methodology Predicted Crystal Structures, Molecular Energetics, and Potential Energy Surface of the Crystalline Molecular Compass

Nanoscience, Nanotechnology, and Molecular machines have triggered the scientists of wide-ranging disciplines alike for decades now, offered the most innovative technologies to maneuver the nanoscale devices molecule by molecule. In this arena of the nano-metric world, the strategical laboratorial syntheses & computational designations of the prototype molecules/nanomaterials and the most probable techniques for their effective functionalization always stand as mandatory credentials. Among various types of functionalizing nanomaterials, the topologically closed Si and -(Si-O)x- based dipolar crystalline macrocyclic molecular compounds exhibiting macroscopic compass/gyroscope like functions at ambient temperatures have attracted the greatest admirations. In this outlook, the research works presented herewith by employing a Gaussian-external methodology for the quantum mechanical characterizations of the crystal structures, computations of the molecular energetics, and derivations of the rotational potential energy surface (PES) of the experimentally synthesized difluoro- /dichloro- phenylene encapsulated amphidynamic/non-amphidynamic crystalline ROT-2F/ROT-2Cl siloxaalkane macrocages can be taken as a stepping stone. Under the standardized interface of Gaussian, we ran SCC-DFTB scheme via the user's script as an external program, and accessed the PES scanning techniques of the former plus the "Dispersion Energy correction" features of the latter computationally. The results reported herein are mainly found to (a) validate the X-ray produced degenerate and non-degenerate crystal structures, (b) justify the experimentally observed structural deformations of the static siloxaalkane spokes, (c) quantize the free-volume units available around the rotator, (d) disclose the energy barrier Ea to be overcome by the rotator while exhibiting 1p-flipping motion, (e) foresee the structural requisites to be adopted for designing functional crystalline free-rotors, etc. It is believed that present theoretical study enlightens us about the most essential structural and dynamical features of the gyroscopic nanostructures & molecular compasses quantitatively.