Molecular Mechanics Method Research Articles

Mechanical Properties of Two-Dimensional Metal Nitrides: Numerical Simulation Study.

It is expected that two-dimensional (2D) metal nitrides (MNs) consisting of the 13th group elements of the periodic table and nitrogen, namely aluminium nitride (AlN), gallium nitride (GaN), indium nitride (InN) and thallium nitride (TlN), have enhanced physical and mechanical properties due to the honeycomb, graphene-like atomic arrangement characteristic of these compounds. The basis for the correct design and improved performance of nanodevices and complex structures based on 2D MNs from the 13th group is an understanding of the mechanical response of their components. In this context, a comparative study to determine the elastic properties of metal nitride nanosheets was carried out making use of the nanoscale continuum modelling (or molecular structural mechanics) method. The differences in the elastic properties (surface shear and Young's moduli and Poisson's ratio) found for the 2D 13th group MNs are attributed to the bond length of the respective hexagonal lattice of their diatomic nanostructure. The outcomes obtained contribute to a benchmark in the evaluation of the mechanical properties of AlN, GaN, InN and TlN monolayers using analytical and numerical approaches.

Quantum mechanics/molecular mechanics (QM/MM) methods in drug design: a comprehensive review of development and applications

The integration of quantum mechanics (QM) and molecular mechanics (MM) methods, known as QM/MM, has emerged as a powerful computational approach in drug design. This hybrid technique combines the accuracy of QM calculations for the reactive region with the computational efficiency of MM methods for the surrounding environment. QM/MM methods have proven invaluable in studying chemical reactions, exploring enzyme mechanisms, and investigating ligand-protein interactions, all of which are crucial for rational drug design. This review provides a comprehensive overview of the QM/MM methodology, its theoretical foundations, and its applications in various aspects of drug design. We discussed the key components, such as QM and MM region partitioning, link atom schemes, and boundary treatments. Additionally, we highlight recent advancements and challenges in QM/MM methods, including polarizable force fields, implicit solvation models, and enhanced sampling techniques. Furthermore, we present illustrative examples showcasing the successful application of QM/MM methods in lead optimization, virtual screening, and the elucidation of biochemical mechanisms relevant to drug targets. Finally, we provide perspectives on future developments and the potential impact of QM/MM methods on the drug discovery pipeline.

Prediction Model for Coformer Screening of Energetic Eutectics Based on Flory‐Huggins Interaction Parameter

AbstractBased on intermolecular interactions, Flory‐Huggins interaction parameter χAB>0 was presented as a prediction model to screen the coformer of energetic eutectics. To evaluate the predictive accuracy of this model, 80 energetic eutectics were collected from literatures. The molecular structures were optimized by computationally cheap molecular mechanics and high precision dispersion‐corrected density functional, respectively. Then the weighted Monte Carlo method was used to calculate the mixing energy ΔEmix of the binary system and thus derive the dimensionless χAB. The results show that the prediction accuracy is up to 85% based on M06‐2X‐D3/6‐311+G (d, p) optimization geometry and RESP charge, much greater than 45% of molecular mechanics method. Furthermore, size/shape mismatch between eutectic molecules was considered by shape index and molecular volume to enrich the prediction model. Based on this prediction model, a new energetic eutectic MTNP‐TNT was discovered, whose χAB value is 3.376 obtained by M06‐2X‐D3/6‐311+G (d, p) method. Experimentally, the classical “V” phase diagram drawn from the differential scanning calorimetry (DSC) data also suggests the MTNP‐TNT eutectic with eutectic temperature of 54.41°C at the molar ratio of 51.50: 48.50. Theoretical and experimental results successfully validate the χAB>0 prediction model for screening the coformers of energetic eutectics. This work opens a way for the crystal engineering of energetic eutectic solid forms with attractive physicochemical properties using a computational approach.

Molecular Mechanics Simulation and Ftir Spectrocopy Optimization of Secondary Structure of Aβ (25-35) Peptide

Abstract In this study, we probed the secondary structure of a soluble Aβ (25-35) peptide in water solution by applying a molecular mechanics method as well as infrared spectroscopy. We have used Fourier Transformed Infrared Spectroscopy (FTIR) to examine the secondary structure of this peptide. The amide I bands of Ab (25-35) obtained from transmission-FTIR spectra consists of one main band at 1658 cm-1, at both concentrations used (200 mM and 1 mM). This band shows us that Ab (25-35) in aqueous solution was mostly organized into a a-helical structure (48 %). The contribution of the unordered structure was found to be about 12 %. The proportion of b-sheet and b-turn structures are slightly lower, 12-15 % and 13-14 %, respectively for both concentrations. FTIR spectra of the peptide in water solution (100 µM) after incubation for 12h showed Aβ peptide conformation is critically dependent on the environmental conditions used. The simulation approach reveals that the C-terminal octapeptide of this molecule preferably adopts an α-helical structure, while the N-terminal tripeptide may exist as a β-turn and unordered structures.

Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach.

Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South-type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North-type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South-type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC)2 and (GCAC*GAC)2], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.

Theoretical Investigation on the Initial Reaction Mechanism of Hexaethynylbenzene on Au(111) Surface.

Graphyne has attracted considerable interest and attention since its successful synthesis, due to its enormous potential for applications in the fields of electronics, energy, catalysis, information technology, etc. Although various methods for synthesizing graphyne have been explored, single-layer graphynes have not been successfully developed. Hexaethynylbenzene (HEB) is considered an ideal precursor molecule because it can undergo Glaser coupling reactions between molecules to synthesize single layer graphdiyne on single crystal metal surfaces via on-surface reactions. Unfortunately, this method fails to achieve the expected results, and the underlying mechanism is not clear. In this work, we employed a combination of ab initio molecular dynamics (AIMD) and quantum mechanics (QM) methods to investigate the initial reaction mechanism of HEB molecules on a Au(111) surface. We revealed that HEB molecules undergo both intermolecular coupling and intramolecular cyclization on the Au(111) surface. The favorable pathways of these two types of reactions were then distinguished, confirming that the distance between the terminal carbon atoms of the ethynyl groups plays an important role in C-C coupling. The insights revealed from this work could facilitate the rational design of precursor molecules and deepen the understanding of the reaction processes.

Bridging the Gap in the Structure-Function Paradigm of Enzymatic PET Degradation-Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite.

Understanding all parameters contributing to enzyme activity is crucial in enzyme catalysis. For enzymatic PET degradation, this involves examining the formation of the enzyme-PET complex. In IsPETase (WT), a PET-degrading enzyme from Ideonella sakaiensis, mutating two non-catalytic residues (DM) significantly enhances activity. Such mutations, depending on their position in the tertiary structure, fine-tune enzyme function. However, detailed molecular insights into these mutations' structure-function relationship for PET degradation are lacking. This study characterizes IsPETase's catalytic ability compared to WT TfCut2 using molecular dynamics simulations and quantum mechanical methods. We explore the conformational landscape of the enzyme-PET complex and quantify residue-wise interaction energy. Notably, aromatic and hydrophobic residues Tyr, Trp, and Ile in the catalytic subsite S1, and aromatic Phe and polar Asn in the anchoring subsite S3, crucially optimize PET binding. These residues enhance PET specificity over non-aromatic plastics. Our findings suggest that the balance between binding at subsite S1 and subsite S3, which is influenced by cooperative mutations, underlies catalytic activity. This balance shows a positive correlation with experimentally obtained kcat/Km values: WT TfCut2<WT IsPETase≪DM IsPETase.

Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SN2 reactions and Claisen rearrangement

This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of SN2 reactions involving methyl iodide with NH2OH and NH2O−, as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the SN2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA.

A rate-dependent cohesive zone model for dynamic crack growth in carbon nanotube reinforced polymers

Carbon nanotubes (CNTs) enhance the fracture toughness of polymer-based matrix composites by dissipating the fracture energy through the pull-out deformation damage mechanism. The rate-dependent behavior of the matrix phase and the CNT/matrix interface affects the contribution of CNTs in enhancing the fracture toughness under dynamic loading and rapid crack growth. A continuum-based finite element (FE) model is utilized in this research to analyze the CNT pull-out damage mechanism. The influence of CNTs on the dynamic fracture behavior of polymer-based composites is studied taking into account the crack opening speed and loading rate effects. The matrix phase is treated as a viscoelastic-viscoplastic material and a new rate-dependent cohesive zone model (CZM) is proposed for modeling the behavior of interface between the CNTs and matrix. The rate-dependent traction-separation laws for the cohesive zone elements are established at different pull-out or crack opening speeds. The proposed rate-dependent FE model of pull-out mechanism facilitates the investigation of the effective factors of CNTs, including length, orientation, and waviness, on fracture energy dissipation at different pull-out speeds. Developed model is very suitable for very long CNTs where atomistic-based molecular dynamics and molecular mechanics methods are associated with difficulties and are more costly and time-consuming.

Computational design of novel highly connected COFs for CH4/H2 adsorption and separation

Ten new highly connected cubic boronitrate (-B4N4O12-) base covalent organic frameworks (BN-COFs) were designed in the lta and aco topologies. These structures were optimized and characterized computationally using density functional theory (DFT) and molecular mechanics methods. The structural characterization reflects that these BN-COFs possess the appropriate structural parameters for CH4/H2 adsorption and separation, such as low density (0.52–1.28 g·cm−3), high pore porosity (22 %-72 %), appropriate pore limiting diameter (PLD, 2.45–6.71 Å) and the largest cavity diameter (LCD, 3.21–19.96 Å), large pore volume (0.15–1.37 cm3·g−1) and accessible surface area (332–3974 cm2·g−1). Grand canonical Monte Carlo (GCMC) simulations were conducted to investigated the adsorption and separation properties of CH4 and H2 in ten BN-COFs. The results indicate that the uptake capacity of methane and hydrogen in BN-COF-5, −9 and −10 has exceeded the targets set by the U.S. Department of Energy (DOE). Furthermore, the CH4/H2 selectivity of ten BN-COFs is comparable to that of typical porous materials. The outstanding CH4/H2 adsorption and separation properties of these BN-COFs can provide some references and inspirations for researchers to develop high-performance porous adsorbents in experimental studies.

PM3 QUANTUM CHEMICAL CALCULATIONS OF THE BIOACTIVE ALA-TYR DIPEPTIDE

Ala-Tyr (Alanine-Tyrosine) dipeptide is a compound with hypertensive and high antioxidant effect. Here, the structural features of this molecule were studied using the PM3 semi-empirical quantum-chemical method. In order to investigate the research, the initial coordinates of the molecule were obtained by the molecular mechanics method. Geometric and electronic parameters, HOMO and LUMO energies, energy gap, dipole moment and partial charges of atoms were calculated for the stable conformations, belonging to both folded and extended shapes of the dipeptide backbone. The obtained results can be used in the research of the structure-function relationships of the investigated bioactive dipeptide and in the design of new peptidomimetics.

A Thorough Examination of the Variables Affecting the Quantum Efficiency of Radiative Decay of Trichlorotriphenylmethyl Radicals.

Fluorescence quantum efficiency is determined by the competition between radiation and nonradiation processes of the excited states. Understanding the factors affecting the radiation and nonradiative decay rates is of great significance for the design of luminescent materials. The excitation state deactivation mechanisms of singlet and triplet states have been extensively studied, providing a comprehensive understanding of the processes involved in the relaxation of these states. However, research on free radical systems involving doublet states is relatively scarce. Therefore, in this study, radiation and nonradiative decay rates and the mechanism of a series of trichlorotriphenylmethyl-based radicals were investigated theoretically. The results indicate that the relative rotations of electron donor and acceptor, as well as the internal rotations of trichlorotriphenylmethyl moiety, play important roles in energy dissipation through nonradiative channels. The effect of a solid-state environment on the radiation and nonradiative decay rates of radicals was investigated using a combination of quantum mechanics and molecular mechanics methods. The results indicate that the solid-state environment restricts the expansion of the conjugated system in the excited state of radicals, leading to a slight decrease in radiative decay rate. In addition, the solid-state environment reduces the reorganization energy and also affects the adiabatic excitation energy of radicals. The reduction in reorganization energy results in a decrease in nonradiative rate, while the opposite effect is observed for adiabatic excitation energy. The nonradiative rate of radicals in a solid-state environment is thus inflected by a combination of molecular geometric structure relaxation and ground-excited state energy gap.

Studying quantum effects of fine scaling on the buckling behavior of CNTs under torsional loading using the density functional theory and molecular mechanics approach

In this study, we introduce a comprehensive investigation into the buckling behavior of carbon nanotubes (CNTs) using a combined approach of quantum mechanics and molecular mechanics methods. A novel aspect of our research lies in the exploration of the quantum effects of fine scaling on the buckling behavior of finite‐length nanotubes across various dimensions and chiralities. Specifically, we analyze the critical buckling strain variations in CNTs with distinct lengths, diameters, and chiralities, revealing pronounced differences influenced by atomic arrangement and the type of structure used in nanotube construction. Our findings elucidate that at smaller dimensions, nanotubes exhibit a higher critical buckling strain than other chiralities, while zigzag atomic arrangements demonstrate greater resistance to torsional loading at larger diameters. Additionally, we compare the buckling behavior of nanotubes obtained by wrapping armchair and zigzag nanosheets, highlighting differential resistance trends. This research not only underscores the critical role of quantum effects in determining nanotube buckling but also provides valuable insights into the nuanced influences of atomic arrangement and nanosheet type on the mechanical properties of CNTs. Thus, our work contributes a novel perspective to the field, bridging the gap between quantum mechanics and the mechanical behavior of nanostructures, which has significant implications for the design and application of nanoscale materials

Study of the stability of the biologically active compound N-[2-[4-oxo-3(4H)-quinazolinyl]propionyl]-guanidine using electrophoresis and mass spectrometry

At the Scientific Centre of Innovative Medicines of Volgograd State Medical University, a number of pyrimidine derivatives of guanidine were designed and synthesised to study them as promising inhibitors of sodium-hydrogen exchanger isoform 1 (NHE-1), which can reduce tissue damage during ischemia. N-[2-[4-oxo-3(4H)-quinazolinyl]propionyl]-guanidine (VMA-13-15) proved to be the most pharmacologically valuable compound. When preparing regulatory documentation for a new medicine, one of the quality criteria is the amount of related impurities. They can be technological impurities and degradation products of the active substance. The aim of the research was to study the stability of the biologically active compound N-[2-[4-[4-oxo-3(4H)-quinazolinyl]propionyl]-guanidine. Anticipated degradation products were determined by stress testing, using capillary electrophoresis and mass spectroscopy. The study of the molecule of VMA-13-15 and the use of computer technologies allowed us to predict possible degradation processes. Among them, the most likely to occur is the hydrolysis reaction during thermostating of the solution of the studied compound in an alkaline medium. In silico optimisation of the geometry of the studied structures was carried out by the MM+ molecular mechanics method using HyperChem 8.0.9. The final spatial optimisation of the geometry of the modelled molecules was carried out by the density functional theory method ub3lyp with 6-311G** basis sets. The resulting vibrational analysis of thermodynamic characteristics was carried out in Orca, which allowed us to obtain enthalpy and entropy values for the studied compounds. By capillary electrophoresis, the degradation products of an aqueous solution of the studied substance were analysed by stress tests. They were used to study the effect of thermal treatment on VMA-13-15 in the presence of 0.1 M hydrochloric acid solution and 0.1 M sodium hydroxide solution. We found that the alkaline environment had the greatest effect on the stability of N-[2-[4-oxo-3(4H)-quinazolinyl]propionyl]-guanidine. It was consistent with the results of the computational experiment. We studied the mass spectrum of the degradation product detected during thermostatic treatment in alkaline medium. Based on its molar mass and release time, it was confirmed that the impurity on the chromatograms of VMA-13-15 is unsubstituted quinazolin-4(3H)-one, the initial product of the synthesis

СТРУКТУРНАЯ ОРГАНИЗАЦИЯ ГЛИПРОЛИНОВОЙ ГЕКСАПЕПТИДНОЙ МОЛЕКУЛЫ

Computer modeling based on the use of the method of theoretical conformational analysis and programs that allow obtaining a graphic image of the spatial structures of biomolecules was performed for a hexapeptide molecule – glyproline H-Phe-Gly-Gly-Phe-Gly-Pro-OH. Glyprolines are short peptides whose amino acid sequences contain glycine and proline residues. Their mechanisms of action are currently poorly understood. Using the method of molecular mechanics, the spatial structure and conformational possibilities of this hexapeptide molecule were determined. Its potential energy was estimated as the sum of non-valente, electrostatic, torsion interactions and the energy of hydrogen bonds. 9 low-energy structures were found for the glyproline hexapeptide, the values of the dihedral angles of the main and side chains of the amino acids included in the molecule. The energy of intra- and interresidual interactions was estimated. The calculation showed that the folded forms of the main chain are low-energy for the hexapeptide. In them, the side chains of amino acids phenylalanine and proline, which are conformationally rigid, carry out effective interactions with all parts of the hexapeptide molecule.

КОНФОРМАЦИОННЫЕ СВОЙСТВА И ЭЛЕКТРОННАЯ СТРУКТУРА ПРОТИВООПУХОЛЕВОГО АГЕНТА TYR-SER-LEU

Molecular modeling methods were used to study the features of the spatial and electronic structure of the antitumor tripeptide YSL (Tyr-Ser-Leu), developed by Chinese scientists. The conformational analysis of the molecule revealed a limited set of its energetically preferable conformational states in a certain range of relative energy. The nature of the forces stabilizing the low-energy conformations of the tripeptide molecule was determined. As a result of the study, the energetically preferable ranges of dihedral angles, the energy contributions of interresidual interactions and hydrogen bonds, as well as the mutual arrangement of residues and their side chains in low-energy conformations of the tripeptide were also determined. Using the methods of molecular mechanics, the energy contributions of intramolecular interactions in low-energy conformational states of the molecule were obtained. Based on quantum-chemical calculations, the distribution of electron density and the values of dipole moments of the most optimal spatial structures of the YSL tripeptide molecule were determined. The reactivity of the tripeptide was also studied by quantum chemical calculations based on the obtained electronic characteristics of each low-energy conformation of the molecule. Using the calculated coordinates of the atoms of the energetically preferable structures of the molecule, their molecular models were built, the comparison of which makes it possible to identify the structural criteria necessary to create a drug suitable for clinical use.

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

ELECTRONIC PARAMETERS OF CONFORMATIONAL STATES OF ABETA-AMYLOID PEPTIDE (25-35)

Confinement effects of mandrel degradation in ICF target fabrication.

Understanding and further regulating the degradation of mandrel materials is a key aspect of target fabrication in inertial confinement fusion (ICF). Here, a quasi-one-dimensional confinement model is developed using a series of single-walled carbon nanotubes with varying diameters (Dm), and the degradation of poly-α-methylstyrene (PAMS) as a typical mandrel material is investigated under such confined conditions by using the combined method of quantum mechanics and molecular mechanics. In comparison to the isolated system, the calculations show that confinement can decrease or increase the energy barriers of PAMS degradation, which directly depends on Dm. Following which a clear exponential relationship between the degradation rate of PAMS and its own density is derived, indicating that the density of PAMS can be used to regulate mandrel degradation. This work highlights the important effects of confinement on degradation and provides a valuable reference for further development of polymer degradation technologies in ICF target fabrication and other fields.

Analyzing fine scaling quantum effects on the buckling of axially-loaded carbon nanotubes based on the density functional theory and molecular mechanics method

In this paper, the quantum effects of fine scaling on the buckling behavior of carbon nanotubes (CNTs) under axial loading are investigated. Molecular mechanics and quantum mechanics are respectively utilized to study the buckling behavior and to obtain the molecular mechanics coefficients of fine-scale nanotubes. The results of buckling behavior of CNTs with different chiralities with finite and infinite dimensions are given, and a comparison study is presented on them. The differences between finite and infinite nanotubes reflect the quantum effects of fine scaling on the buckling behavior. In addition, the results show that the dimensional changes highly affect the mechanical properties and the buckling behavior of CNTs to certain dimensions. Moreover, dimensional changes have a significant effect on the critical buckling strain. Beside, in addition to the structure dimensions, the arrangement of structural and boundary atoms have a major influence on the buckling behavior.

Physicochemical and structural evaluation of natural products as a potential source for viral disease treatment

This research article aims to investigate six selected medicinal plants of Achillea millefolium (Yarrow), Alkanet, Rumex patientia (Patience dock), Dill, Tarragon, and Sweet fennel including some principal chemical compounds of achillin, alkannin, cuminaldehyde, dillapiole, estragole and fenchone. The definitive roles of these medicinal plants in Omicron treatment have been investigated through quantum mechanics and molecular mechanic methods. However, given the unprecedented challenges faced should be given a fair amount of consideration for contribution during this pandemic. In this work, it has been investigated the compounds of achillin, alkannin, cuminaldehyde, dillapiole, estragole and fenchone as a probable anti pandemic Omicron receptor derived from medicinal plants. Anti-Omicron drugs through the hydrogen bonding through physico-chemical properties of medicinal ingredients bound to the database amino acids fragment of Tyr-Met-His as the selective zone of the Omicron have been estimated with infrared (IR) and nuclear magnetic resonance (NMR) methods. A comparison of these structures has provided new insights for the design of substrate-based anti-targeting Omicron. Finally, five medicinal ingredients of achillin, alkannin, cuminaldehyde, dillapiole, and estragole bound to TMH have conducted to a Monte Carlo (MC) simulation for evaluating the absorbance of these inhibitor-active site complexes. Here, we used the network pharmacology, metabolite analysis, and molecular simulation to figure out the biochemical basis of the health-raising influence of medicinal plants. This research article peruses the drug ability, metabolites and potential interaction of some medicinal plants with Coronavirus-induced pathogenesis.