Molecular Mechanics Method Research Articles

Exploration on dual emission mechanism of CPzP and CPzPO with thermally activated delayed fluorescence

ABSTRACT Thermally activated delayed fluorescence (TADF) molecules with dual emission have attracted extensive attention recently. However, the dual emission mechanism is complex and difficult to be studied especially in solid state. In this paper, asymmetrical diphenylketone derivatives CPzP and CPzPO are investigated in both benzene and in aggregation state with polarisable continuum model (PCM) and combined quantum mechanics and molecular mechanics (QM/MM) method respectively. It is found that there are both quasi-axial (ax) and quasi-equatorial (eq) conformations for CPzP and CPzPO in benzene. The ax conformation is responsible for the high energy band emission, while the low energy band emission is contributed by eq conformations. The dimers with intermolecular hydrogen bond have similar emission wavelengths with monomers. The small energy gap between the first singlet excited state and the first triplet excited state as well as large reverse intersystem crossing rate in eq conformations confirms the generation of TADF in eq conformation, which agree with experimental results that the low energy band emission is TADF. Our calculation results revealed the dual emission mechanism of two TADF molecules, which would favor the understanding of light emitting properties and the design of new type dual emission TADF emitters.

Трехмерная структура пентапептидной молекулы Arg-Glu-Arg-Gly-Pro

It seems relevant to carry out structural and functional studies of glyprolines and their synthetic analogues on model systems using theoretical research methods. Glyprolines are a family of short peptides whose amino acid sequences contain residues of proline and glycine. Currently their mechanisms of action are poorly understood. Great interest in their structure is caused by the possibility of creating new drugs that are the human body’s own reserve. Glyproline molecules are stable and eddicient. Using the method of molecular mechanics, the spatial structure and conformational properties of the glyproline pentapeptide molecule Arg-Glu-Arg-Gly-Pro were determined. The potential energy of the molecule was estimated as the sum of non-valent, electrostatic, torsion interactions and the energy of hydrogen bonds. 9 low-energy conformations were found for glyproline pentapeptide, the values of structure the dihedral angles of the main and side chains, and the energy of intra-and inter-residue interactions was estimated. It is revealed that low energy conformations of this molecule have the half-folded type of backbone. The side chains of the Arg and Glu amino acids in low-energy conformations carry out effective interactions and are conformationally labile amino acids, they bring together the regions of the main chain and the side chains of the amino acids included in the pentapeptide.

Distinguishing the Quantum Yield and Lifetime of Carbazole‐Based Room‐Temperature Phosphorescence Materials: QM/MM Study

AbstractCommercial carbazole derivatives are widely used as typical electron donors in room‐temperature phosphorescence materials. The high phosphorescence quantum yield (Φp) and short lifetime (τp) of the carbazole‐based (9H‐carbazol‐9‐yl)isonicotinonitrile (P‐34N) crystal are distinguished by quantum mechanics and molecular mechanics method. Two inducements are accounted for the high Φp of P‐34N: i) large spin–orbit coupling (0.63 cm−1) induces fast intersystem crossing (ISC) of the lowest singlet excited state (S1) to the lowest triplet excited state (T1), ii) the intermolecular π–π interactions stabilize triplet excitons. Meanwhile, the 3(n, π*) →1(π, π*) of P‐34N favors the nonradiative decay of T1to the ground state (S0), and thus, causes short τp. In contrast to P‐34N, the low Φp of 6‐(9H‐carbazol‐9‐yl)nicotinonitrile (P‐24N) crystal results from the effective reverse ISC process induced by small ΔEST (0.3 eV) between S1 state and the higher triplet state (T2), and the long τp is due to the unfavorable orbital reversals of T1 (π, π*)→S0 (π, π*) transition and the internal conversion process of T2 → T1. This work presents a reasonable interpretation of the Φp and τp of two carbazole‐based crystals.

Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants.

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits - an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins.

First Hyperpolarizabilities of Intramolecular Charge-Transfer Architectures Based on Acenaphthene Derivatives in Gas, Solution, and Solid States.

Constructing charge transfer (CT) systems and packing arrangement are common and effective methods to control the efficiency of nonlinear optical (NLO) materials. Apart from the traditional through-bond CT (TBCT) systems, through-space CT (TSCT) also leads to distinctive optical and electronic properties. Meanwhile, corresponding theoretical investigations of the aggregation effect are highly desired. In this work, some TSCT and model compounds incorporating acenaphthene as a scaffold and triphenylamine (TPA) as the donor are theoretically performed to systematically reveal the effect of both solvent and solid environments on their static first hyperpolarizabilities (βtot) by using the polarizable continuum model (PCM) and the combined quantum mechanics and molecular mechanics (QM/MM) method. Results indicate that the dichloromethane solvent effect within the PCM approach causes an almost 2 times increase of the βtot values. Besides, the different packing modes and intermolecular interactions have remarkable influence on the second-order NLO properties. For the case of TPA-ace-CN in the crystal state, the parallel arrangement will lead to large NLO responses (4.9 × 10-30 esu) compared to the correspondingly isolated molecule (3.4 × 10-30 esu). However, for the TPA-ace-TRZ compound with the TSCT architecture, selection of the molecular arrangement may make the aggregate ineffective due to the offset of the through-space dipole and charge transfer between D-A groups, which lead to the βtot values decreasing from 15.2 × 10-30 to 7.7 × 10-30 esu. We believe that our calculation will serve as a guide for the exploration of more efficient NLO materials wherein the molecules are oriented in their most favorable arrangements.

Predicting and Designing Thermally Activated Delayed Fluorescence Molecules with Balanced ΔEST and Transition Dipole Moment

AbstractThe investigations on the relationship between geometrical structures, excited state properties, and photophysical performance can accelerate the design of thermally activated delayed fluorescence (TADF) molecules. Herein, the photophysical properties of newly proposed organic TADF molecule: [4‐(9,9‐dimethyl‐9,10‐dihydroacridine) phenyl] (pyridin‐4‐yl)‐methanone (PyB‐DMAC), are theoretically investigated by using the quantum mechanics and molecular mechanics method. The photophysical performance dependency of PyB‐DMAC molecule on its geometrical and electronic structures, and aggregation effects are systematically analyzed. The calculated fluorescence quantum efficiencies are in good agreement with the experimental results, for instance, the calculated fluorescence efficiency of 61.2% (exp. 49%) for PyB‐DMAC molecule in the crystal phase. Based on these investigations, novel organic TADF molecules can be designed by balancing the singlet–triplet energy gap (ΔEST) and transition dipole moment. Sixteen unexplored candidates are screened with similar structures to PyB‐DMAC molecule, while two new TADF organic molecules (PyBF‐DMAC and OSOF‐DMAC) are selected with enhanced luminescence performance. The newly designed TADF molecules reveal lower reorganization energies and reduced nonradiative decay rates. The simulation results exhibit that their luminescence quantum efficiencies in toluene solvent and amorphous state are as high as 63.7%, 53.2% and 90%, 97.4%, respectively.

A Quantum-Guided Molecular Mechanics Force Field for the Ferrocene Scaffold.

Ferrocene derivatives have a wide range of applications, including as ligands in asymmetric catalysis, due to their chemical stability, rigid backbone, steric bulk, and ability to encode stereochemical information via planar chirality. Unfortunately, few of the available molecular mechanics force fields incorporate parameters for the accurate study of this important building block. Here, we present a MM3* force field for ferrocenyl ligands, which was generated using the quantum-guided molecular mechanics (Q2MM) method. Detailed validation by comparison to DFT calculations and crystal structures demonstrates the accuracy of the parameters and uncovers the physical origin of deviations through excess energy analysis. Combining the ferrocene force field with a force field for Pd-allyl complexes and comparing the crystal structures shows the compatibility with previously developed MM3* force fields. Finally, the ferrocene force field was combined with a previously published transition-state force field to predict the stereochemical outcomes of the aminations of Pd-allyl complexes with different amines and different chiral ferrocenyl ligands, with an R2 of ∼0.91 over 10 examples.

Conformational Analysis of Tyrosyl-Lysyl-Threonine Tripeptide Using MM, MD and QM Methods and Its Hyperpolarizability Study

Peptides are important structures that offer important opportunities for therapeutic interventions in various diseases. Tyrosyl-Lysyl-Threonine is an important peptide structure that contains the antiviral, antioxidant and anticancer properties of the amino acids in its structure. Examination of the conformational structure, which has great importance on both the ability of the molecule to fulfill its biological functions and electronic properties, is important for molecular studies. In this study, determination of the stable conformations and optimization of the most stable structure of Tyrosyl-Lysyl-Threonine molecule was carried out using molecular mechanical and quantum mechanical methods. With molecular dynamics simulation studies, the changes in conformational structure, RMSD and Rg values in different environments were monitored for 10 ns. Additionally, the hyperpolarizability study of Tyrosyl-Lysyl-Threonine were carried out. As a result of this study, it was aimed to determine the optimized geometry of the tripeptide, its conformational changes and nonlinear optical properties.

Vibrational Properties of (8,8) and (10,10) SWCNTs before and after Albumin Fragment Adsorption: A Molecular Dynamics Study

AbstractSingle‐walled carbon nanotubes (SWNTs) have received great attention for their mechanical, electronic properties, and possible interesting technological applications. Raman spectroscopy has proven to be a sensitive tool for studying the vibrational properties of carbon nanotubes. The frequency of the radial breathing mode (RBM) in the region of 100–350 cm–1 is found to be inversely proportional to the diameter of the nanotube. Using Molecular Mechanics (MM) and Molecular Dynamics (MD) methods conformational and vibrational properties of pure armchair SWCNTs having different diameters and the (10,10) NT after adsorption of an albumin fragment are studied. The distances between carbon atoms in the central part of the nanotube cavity change during MD run at constant temperature (T = 300 K), and the frequencies of this periodic motion are calculated. The conformational and vibrational properties of armchair (10,10) and (8,8) SWCNT, having the diameter equal to 13.56 and 10.85 Å respectively, are here reported. The distances between carbon atoms from opposite sites in the central cavity of the nanotube are calculated during MD runs. Interestingly, for the (10,10) SWCNT the frequency of Raman vibrational mode E2g around 17 cm–1 is correctly calculated. The frequency of motion due to this motion increases with a decreasing curvature of the armchair CNT. After the adsorption process of an albumin fragment on the (10,10) NT, lower frequencies of motion and lower intensities are calculated. This theoretical work can useful to study possible periodic motion in pure nanomaterials or when they interact with protein fragments, water, or molecules.

Inclusion Complexes Between β‐cyclodextrin and the Anticancer Drug 5‐Fluorouracil for its Solubilization: a Molecular Dynamics Study at Different Stoichiometries

AbstractCyclodextrins (CDs) are natural macrocyclic oligosaccharides able to solubilize hydrophobic drugs in water improving their bioavailability, thanks to favorable noncovalent interactions particularly in their hydrophobic cavity. Using a simulation protocol proposed in previous work, in this theoretical study based on Molecular Mechanics (MM) and Molecular Dynamics (MD) methods, inclusion complexes between β‐cyclodextrin and 5‐Fluorouracil (5‐FU) are investigated. 5‐FU is an anticancer drug hardly soluble in water used for more than 50 years. This drug is mainly administered by intravenous injection for the treatment of inner cancers or as a cream in the case of skin‐related cancers. For drug delivery applications, it is important to characterize stable inclusion complexes at different drug concentrations in order to enhance the anticancer activity by maintaining lower dose, thus reducing cytotoxic effects on the normal cells, causing several negative impacts in the course of treatment. In this work, the structure and stability of the host–guest complexes β‐CD:5‐FU in a 1:1 and 1:2 stoichiometries are investigated because this drug is relatively small compared to the size of the hydrophobic β‐CD cavity. The 5‐FU complexes with CDs allow its solubilization, thanks to favorable van der Waals interactions. Interestingly, these intermolecular interactions in inclusion complexes may also affect the release profile. MD simulations are a powerful tool to evaluate interactions between hydrophobic anticancer drugs and hydrophilic carriers with an inner hydrophobic cavity such as CDs and oligosaccharides in general.

Theoretical insights into room temperature phosphorescence emission with anti-Kasha behavior in aggregate

Organic room temperature phosphorescence (RTP) materials with long lifetimes have shown promising applications in organic light emitting diodes and bioimaging fields. However, the inner luminescent mechanisms for RTP especially for high lying triplet state emission, have not been unveiled. Herein, based on density functional theory (DFT) and time-dependent density functional theory (TD-DFT), the photophysical properties of four RTP systems with triphenylethylene derivatives as skeletons are studied. Excited state dynamic process in aggregate is systematically studied by combining quantum mechanics with molecular mechanics (QM/MM) method coupled with thermal vibration correlation function (TVCF) method. Moreover, the intermolecular interactions are measured by the independent gradient model based on Hirshfeld partition (IGMH) method, the Huang-Rhys factor, reorganization energy and spin-orbit coupling (SOC) constant are calculated, radiative and non-radiative decay as well as intersystem crossing (ISC) and reverse intersystem crossing (RISC) processes are all investigated. Results indicate that the radiative decay process from the lowest triplet excited state (T1) to ground state (S0) is low and the non-radiative decay process is high, various calculations are also performed to exclude the emission process from T1 to S0, thus non-luminescence is determined for T1. Furthermore, a large energy gap between T2 and T1 is observed, and high radiative decay and low non-radiative decay processes from T2 to S0 are confirmed. Thus, the mechanisms of RTP from high lying triplet state T2 are revealed. Furthermore, through wise molecular design and detailed calculations, the mechanical insights are detected that the RTP emissions with anti-Kasha behavior are largely related to the unique molecular configurations with triphenylethylene derivatives as skeletons. Our studies give reasonable explanations for the previous experimental measurements and provide underlying perspectives for RTP mechanisms from high lying triplet state T2, which could promote the development of new efficient RTP emitters.

QSAR, molecular docking and ADMET studies of quinoline, isoquinoline and quinazoline derivatives against Plasmodium falciparum malaria

With the aim of researching new antimalarial drugs, a series of quinoline, isoquinoline, and quinazoline derivatives were studied against the Plasmodium falciparum CQ-sensitive and MQ-resistant strain 3D7 protozoan parasite. DFT with B3LYP functional and 6-311G basis set was used to calculate quantum chemical descriptors for QSAR models. The molecular mechanics (MM2) method was used to calculate constitutional, physicochemical, and topological descriptors. By randomly dividing the dataset into training and test sets, we were able to construct reliable models using linear regression (MLR), nonlinear regression (MNLR), and artificial neural networks (ANN). The determination coefficient values indicate the predictive quality of the established models. The robustness and predictive power of the generated models were also confirmed via internal validation, external validation, the Y-randomization test, and the applicability domain. Furthermore, molecular docking studies were conducted to identify the key interactions between the studied molecules and the PfPMT receptor’s active site. The findings of this contribution study indicate that the antimalarial activity of these compounds against Plasmodium falciparum appears to be largely determined by four descriptors, i.e., total connectivity (Tcon), percentage of carbon (C (%)), density (D), and bond length between the two nitrogen atoms (Bond N–N). On the basis of the reliable QSAR model and molecular docking results, several new antimalarial compounds have been designed. The selection of drug candidates was performed according to drug-likeness and ADMET parameters.

Justification of applying collectors from the class of unsaturated tertiary alcohols in flotation of gold-bearing sulphide ores

Given in the paper are the results of calculations of the simplest quantum-chemical parameters of the structures under consideration formed in the mineral–flotation reagent system by the method of molecular mechanics (MM2). Theoretical computations on the interaction mechanism between unsaturated alcohols and gold atoms in various energy states are formulated. There were determined the causes and ascertained the regularities of selective fixation of reagents with triple bonds, which are tertiary alcohols, on the surface of liberated grains of gold and gold-containing minerals. Presented are the results of practical flotation studies, which have showed that the use of acetylene reagents allows one to selectively obtain additional gold recovery from gold-bearing ores from 2.4 to 5.0% relative to the basic flotation indicators.

Insights on isomeric emitters with thermally activated delayed fluorescence: Comparison between solvent and crystal state

Thermally activated delayed fluorescence (TADF) molecules with aggregation-induced emission (AIE) properties have attracted great attention in recent studies. In this study, three isomeric emitters DPAC-4PYPM, DPAC-TRZ and DPAC-6PYPM with TADF are studied in toluene and crystal with the combination of polarizable continuum model (PCM) and quantum mechanics and molecular mechanics (QM/MM) method. Results show that tiny difference of intramolecular interaction is induced due to the variation in the acceptor group, thus similar geometries and stacking patterns in crystal are obtained for three molecules. Our calculation also indicates that the energy diagram is quite different for three molecules in both toluene and crystal state, while the participation of higher triplet excited states provide additional decay channels for the reverse intersystem crossing (RISC) process, which favors the generation of TADF. In addition, the bending vibrations of the phenyl in the donor and the stretching vibrations of the C=C and C-H bonds are suppressed due to the intermolecular interactions in crystal state, thus block the excited-state energy consumption pathway. It indicates that all three molecules are typical AIE systems. Our calculation results agree with experimental measurements and provide more useful information for TADF emitters with AIE properties.

Accelerating molecular dynamics simulations by a hybrid molecular dynamics-continuum mechanical approach

ABSTRACT In this contribution, molecular dynamics (MD) simulations in combination with continuum mechanical (CM) approaches are performed to investigate particle movements under uniaxial deformations of an amorphous polymer at particle resolution. A coarse-grained (CG) model of atactic polystyrene is used as an exemplary model system. We propose a hybrid molecular dynamics-continuum mechanical (MD-CM) approach to simulate the deformation behavior of the polymer. As a reference, purely molecular dynamics systems are used. The methods are compared with regard to the local displacement of the particles and the global stress-strain behavior of the overall system. The good reproducibility of the system’s mechanical behavior with the hybrid molecular dynamics-continuum mechanical method is shown. Furthermore, it is demonstrated that CPU time can be significantly reduced with the hybrid calculation model.

Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins.

Redox potentials have been calculated for 12 different iron–sulfur sites of 6 different types with 1–4 iron ions. Structures were optimized with combined quantum mechanical and molecular mechanical (QM/MM) methods, and the redox potentials were calculated using the QM/MM energies, single-point QM methods in a continuum solvent or by QM/MM thermodynamic cycle perturbations. We show that the best results are obtained with a large QM system (∼300 atoms, but a smaller QM system, ∼150 atoms, can be used for the QM/MM geometry optimization) and a large value of the dielectric constant (80). For absolute redox potentials, the B3LYP density functional method gives better results than TPSS, and the results are improved with a larger basis set. However, for relative redox potentials, the opposite is true. The results are insensitive to the force field (charges of the surroundings) used for the QM/MM calculations or whether the protein and solvent outside the QM system are relaxed or kept fixed at the crystal structure. With the best approach for relative potentials, mean absolute and maximum deviations of 0.17 and 0.44 V, respectively, are obtained after removing a systematic error of −0.55 V. Such an approach can be used to identify the correct oxidation states involved in a certain redox reaction.

Surface Interactions between Ketoprofen and Silica-Based Biomaterials as Drug Delivery System Synthesized via Sol-Gel: A Molecular Dynamics Study.

Biomaterial-based drug delivery systems for a controlled drug release are drawing increasing attention thanks to their possible pharmaceutical and biomedical applications. It is important to control the local administration of drugs, especially when the drug exhibits problems diffusing across biological barriers. Thus, in an appropriate concentration, it would be released in situ, reducing side effects due to interactions with the biological environment after implantation. A theoretical study based on Molecular Mechanics and Molecular Dynamics methods is performed to investigate possible surface interactions between the amorphous SiO2 surface and the ketoprofen molecules, an anti-inflammatory drug, considering the role of drug concentration. These theoretical results are compared with experimental data obtained by analyzing, through Fourier transform infrared spectroscopy (FT-IR), the interaction between the SiO2 amorphous surface and two percentages of the ketoprofen drug entrapped in a silica matrix obtained via the sol–gel method and dried materials. The loaded drug in these amorphous bioactive material forms hydrogen bonds with the silica surface, as found in this theoretical study. The surface interactions are essential to have a new generation of biomaterials not only important for biocompatibility, with specific structural and functional properties, but also able to incorporate anti-inflammatory agents for release into the human body.

Computational Analysis of the Inhibition Mechanism of NOTUM by the ONIOM Method.

Notum is a member of serine hydrolyses that cleaves the palmitoleate moiety from Wingless-related integration site (Wnt) ligands. This enzyme plays crucial functions through modulating the Wnt signaling pathway. Inhibition of Notum carries therapeutic effects against a number of maladies including osteoporosis, cancer, and Alzheimer’s disease. Recently, a class of irreversible inhibitors based on esters of 4-(indolin-1-yl)-4-oxobutanoic acid have been reported. Using the crystal structures of enzyme-4-(indolin-1-yl)-4-oxobutanoate adduct and 4-(indolin-1-yl)-4-oxobutanoic acid-enzyme complex, we studied computationally the proposed inhibition mechanism using model systems based on the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method. In the first place, model systems were formulated to investigate the transesterification between the catalytic serine residue, Ser-232, and the methyl ester of 4-(indolin-1-yl)-4-oxobutanoate. In the second place, the hydrolysis mechanism of the resultant enzyme–inhibitor adduct was studied. The energetics of these steps were analyzed using a density functional theory functional in the ONIOM method. In addition, the roles of active-site residues during these steps were highlighted. It was found that the hydrolysis of the covalent adduct is highly endergonic corroborating the irreversible inhibition mechanism. These results will shed light not only on the inhibition mechanism but also on the catalytic mechanism.

Molecular structure based study on the elastic properties of carbon nanotubes in a thermal environment

In this investigation, a modified mechanical model considering the environmental temperature is established based on a method of molecular structural mechanics. It is assumed that the covalent bonds are traded as a truss, and the boundary condition range is taken into account. The relations of Young's modulus and shear modulus with different diameters of carbon nanotubes are also predicted. Moreover, according to the principle of elastic theory, the Young's modulus, Poisson's ratio and strain energy of both zigzag and armchair carbon nanotubes are also investigated. The influences of temperature and nanotube diameter on elastic properties are significant, and the elastic modulus of multi-walled carbon nanotubes is not only sensitive to the number of layers, but also sensitive to the tube wall thickness.

Automated fitting of transition state force fields for biomolecular simulations.

The generation of surrogate potential energy functions (PEF) that are orders of magnitude faster to compute but as accurate as the underlying training data from high-level electronic structure methods is one of the most promising applications of fitting procedures in chemistry. In previous work, we have shown that transition state force fields (TSFFs), fitted to the functional form of MM3* force fields using the quantum guided molecular mechanics (Q2MM) method, provide an accurate description of transition states that can be used for stereoselectivity predictions of small molecule reactions. Here, we demonstrate the applicability of the method for fit TSFFs to the well-established Amber force field, which could be used for molecular dynamics studies of enzyme reaction. As a case study, the fitting of a TSFF to the second hydride transfer in Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase (PmHMGR) is used. The differences and similarities to fitting of small molecule TSFFs are discussed.