Molecular Orbital Simulations Research Articles

Self-Assembled Monolayers of Gemini-Type Amphiphilic Hexabenzocoronenes on Gold: Contribution of Their Triethylene Glycol Side Chains to Self-Assembly Formation.

We report on a two-dimensional self-assembled structure of a supramolecule with hydrophilic oligoethylene glycol (EG) units, which are capable of stronger electrostatic interactions than van der Waals (vdW) interactions between alkyl chains. For this purpose, hexabenzocoronene (HBC) with two hydrophobic dodecyl chains on one side of the HBC core and two hydrophilic triethylene glycol (TEG) chains on the other side of the HBC core (HBCGemini) and HBCGemini with a trinitrofluorenone (TNF) added to the end of one TEG chain (HBCTNFGemini) were employed. Scanning tunneling microscopy (STM) revealed the presence of multiple two-dimensional self-assembled structures in each of HBCGemini and HBCTNFGemini deposited on the gold substrate in vacuum. The role of polar functional groups in these observations is discussed based on semiempirical molecular orbital simulations. Two types of 2D organized structures of HBC-TEG were observed: one with rectangular and relatively dense unit cells and the other with nearly square and relatively sparse unit cells. In both organized structures, the phenyl group TEG units and alkyl chains were considered to be the main molecular interactions with each other. On the other hand, in HBCTNFGemini, three types of organized structures were observed, which could be explained by the mechanism of interdigitation of the TEG-containing side-chain moieties to form a dimeric core. The EG units are more flexible than the alkyl chains and thus can interact flexibly with the hydrophobic HBC core, and the glycol side chains facilitate the intermolecular interactions as well as the alkyl chains.

Study on synthesis of ursodeoxycholic acid by reduction of 7-ketolithocholic acid in double aprotic solvents and molecular simulations

Ursodeoxycholic acid (UDCA) is not only safer than chenodeoxycholic acid in the treatment of hepatobiliary diseases, but also has a wide range of applications in Acute Kidney Injury and Parkinson’s Disease. The purpose of this experiment is to improve the conversion rate of 7-ketocholic acid (7K-LCA) and the yield of ursodeoxycholic acid in aprotic solvents during electrochemical reduction process. Three aprotic solvents were investigated as electrolytes. 1,3-Dimethyl-2-imidazolidinone (DMI) has a stable five-membered ring structure, and 7K-LCA has undergone two nucleophilic reactions and “Walden” inversion, the 7K-LCK was stereoselectively reduced to UDCA. Hexamethylphosphoramide (HMPA) and 1,3-methyl-3,4,5,6-Tetrahydro-2(1H)-pyrimidinone (DMPU) can be attacked by chloride ions to produce by-products. Molecular orbital theory-based simulations were conducted to study the reducibility of three aprotic solvents [hexamethylphosphoramide (HMPA), 1,3-methyl-3,4,5,6-Tetrahydro-2(1H)-pyrimidinone (DMPU), and 1,3-Dimethyl-2-imidazolidinone (DMI)] in combination with experiments. Choose the best solvent based on the simulation results, the electrolysis reaction can be carried out by applying current and voltage when lithium chloride is used as electrolytes. Calculations using Materials Studio showed that Cu, Pb, Hg–Cu, and Ni exhibited the highest binding energies to the substrate in this system. Using Cu as the electrode when the solvent is a 1:1 mix of DMI and HMPA, the conversion rate of 7-ketocholic acid (could reach 98%, the yield of ursodeoxycholic acid was up to 80%. Under the same conditions, linear voltammetry was performed on the electrochemical workstation to study the electrolysis behavior, and the obtained results were consistent with the experiment.Graphical

Benzethonium chloride as a tungsten corrosion inhibitor in neutral and alkaline media for the post-chemical mechanical planarization application

The cleaning solution for the post-chemical mechanical planarization (post-CMP) process of tungsten in neutral-alkaline media requires corrosion inhibitors as an additive, especially for advanced devices where the device node size shrinks below 10 nm. In the present study, the corrosion inhibition performance of benzethonium chloride (BTC) is evaluated in neutral-alkaline conditions. The electrochemical impedance spectroscopy (EIS) analysis showed ∼ 90 % of corrosion inhibition efficiency with an optimum concentration of 0.01 wt% BTC at both pH 7 and 11. Langmuir adsorption isotherm, frontier molecular orbital theory, molecular simulation, contact angle, precipitation study, and X-ray photoelectron spectroscopy analysis were performed to identify the inhibition mechanism of the BTC molecule on the W surface. Based on the proposed mechanism, the electrostatic attraction between the positively charged N atom in the BTC molecule and the negatively charged W surface initiates the adsorption of the molecule. The high dipole moment and large molecular size enhance the physical adsorption of the molecule to the surface. In addition to this, the adsorption isotherm analysis shows that possible chemical interaction with a moderate value of Gibbs free energy change of adsorption exists between the W and BTC molecule. The excellent corrosion inhibition efficiency of BTC on W is confirmed by the frontier molecular orbital theory and molecular dynamic simulation analysis.

Density Functional Theory Study on Antioxidant Activity of Three Polyphenols.

In recent years, research on the antioxidant activity of natural antioxidants has become more and more popular. Polyphenols are a large number of natural antioxidants in plants. This paper selected three common polyphenols to study their antioxidant activity based on quantum chemistry theory. This experiment hopes to provide a theoretical basis for the further development of polyphenol health food with strong antioxidant activity. Three polyphenols resveratrol, liquiritigenin, and isoliquiritigenin were optimized at the level of B3lyp/6-311G (d, p), and the single point energy was calculated with B3lyp/6-311 + + G (2d, 2p). The phenol hydroxyl bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) were calculated in different phase states study the antioxidant mechanism. Draw the frontier molecular orbital and conduct dynamic simulation analysis scavenging · OH and · OOH to explore the most possible active sites in different phenolic hydroxyl sites. The bond length, dihedral angle, BDE, IP, PDE, PA and ETE were compared to speculate the antioxidant activity: Resveratrol > isoliquiritigenin > liquiritigenin. By analyzing the frontier molecular orbital and dynamic simulation results, it is speculated that the phenolic hydroxyl groups at C4', C4', and C4 are the most likely active sites of resveratrol, liquiritigenin, and isoliquiritigenin, respectively. In different phase states, the three compounds showed the same antioxidant activity, and the phenolic hydroxyl activities of the three compounds were different at different sites.

Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study

BackgroundThe chemokine CXCL12 and its two receptors (CXCR4 and CXCR7) are involved in inflammation and hematopoietic cell trafficking. This study was designed to investigate molecular docking interactions of four popular cardiovascular-active natural compounds; curcumin, resveratrol, quercetin, and eucalyptol; with these receptors and to predict their drug-like properties. We hypothesize that these compounds can modify CXCL12/CXCR4/CXCR7 pathway offering benefits for coronary artery disease patients.MethodsDocking analyses were carried and characterized by Molecular Environment (MOE) software.Protein Data Bank (http://www.rcsb.org/) has been retrieved from protein structure generation and crystal structures of CXCR4 and CXCR7 receptors (PDB code = 3ODU and 6K3F). The active sites of these receptors were evaluated and extracted from full protein and molecular docking protocol was done for compounds against them. The presented parameters included docking scores, ligand binding efficiency, and hydrogen bonding. The pharmacokinetic/toxic properties (ADME/T) were calculated using SwissADME, ProTox-II, and Pred-hERG softwares to predict drug-like properties of the compounds. The thermochemical and molecular orbital analysis, and molecular dynamics simulations were also done.ResultsAll compounds showed efficient interactions with the CXCR4 and CXCR7 receptors. The docking scores toward proteins 3ODU of CXCR4 and 6K3F of CXCR7 were − 7.71 and − 7.17 for curcumin, − 5.97 and − 6.03 for quercetin, − 5.68 and − 5.49 for trans-resveratrol, and − 4.88 and − 4.70 for (1 s,4 s)-eucalyptol respectively indicating that all compounds, except quercetin, have more interactions with CXCR4 than with CXCR7. The structurally and functionally important residues in the interactive sites of docked CXCR4-complex and CXCR7-complex were identified. The ADME analysis showed that the compounds have drug-like properties. Only (1 s,4 s)-Eucalyptol has potential weak cardiotoxicity. The results of thermochemical and molecular orbital analysis and molecular dynamics simulation validated outcomes of molecular docking study.ConclusionsCurcumin showed the top binding interaction against active sites of CXCR4 and CXCR7 receptors, with the best safety profile, followed by quercetin, resveratrol, and eucalyptol. All compounds demonstrated drug-like properties. Eucalyptol has promising potential because it can be used by inhalation or skin massage. To our knowledge, this is the first attempt to find binding interactions of these natural agents with CXCR4 and CXCR7 receptors and to predict their druggability.

Density Functional Theory Calculations of Pinus brutia Derivatives and Its Response to Light in a Au/n-Si Device

In this study, the performance of an organic dye obtained from the bark of the red pine (Pinus brutia) tree growing in Muğla/Turkey as an interface layer in the Au/n-Si Schottky diode (SD) structure was evaluated. For this purpose, at first, the optimized molecular structure, the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) simulations of the organic dye were calculated by the Gauss program and it was theoretically proven that the dye exhibits semiconducting properties. Then, the electrical and photodiode variables such as ideality factor, effective barrier height, series resistance, interface states density distribution, photosensitivity, and photo responsivity were evaluated employing current-voltage measurements under dark and different illumination densities. Additionally, C-V measurements were used to demonstrate that the fabricated device has capacitive features and this capability varies as a function of the frequency. Under these measurements, the possible conduction mechanism for the organic dye-based Au/n-Si device was investigated and the results showed that Au/Pinus brutia/n-Si may be a good candidate for optoelectronic applications.

Electrical, photodiode, and DFT studies of newly synthesized π-conjugated BODIPY dye-based Au/BOD-Dim/n-Si device

A π-conjugated 4,4-difluoro-4- bora-3a,4a-diaza-s-indacene (BODIPY) dimer (BOD-Dim) compound has been synthesized and characterized. The optimized molecular structure, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) simulations, and static isotropic polarizability of the isolated compound were computed via the Gaussian program. The simulated static dielectric constant value was calculated. The effect of the BOD-Dim interlayer on the diode characteristics of the Au/n-Si diode was investigated. The electrical and photovoltaic parameters of the Au/BOD-Dim/n-Si/In diode such as ideality factor (n), barrier height (ΦB), open-circuit voltage (Voc), short-circuit current (Jsc), photosensitivity (S), and photoresponsivity (R) have been investigated by current-voltage measurements at dark and under various illumination intensities. The possible current conduction mechanism has been examined through the forward bias ln(IF)-ln(VF) and ln(IR)-VR1/2 characteristics. All obtained results confirmed that Au/BOD-Dim/n-Si/In diode exhibits a photovoltaic behavior and presents great potential as a photosensor for optoelectronic device applications.

Proposal of novel inhibitors for vitamin-D receptor: Molecular docking, molecular mechanics and ab initio molecular orbital simulations

The specific binding of active vitamin-D to the vitamin-D receptor (VDR) is closely related to the onset of immunological diseases. To inhibit the binding, various compounds have been developed as potent inhibitors against VDR. Among them, a compound NS-54c, which was developed based on the first VDR antagonist TEI-9647 (25-dehydro-1α-hydroxyvitamin D3-26,23-lactone), was revealed to posse almost 1000-fold improved antagonistic activity over the original TEI-9647. However, the reason for this significant improvement has not been elucidated. In the present study, we investigated the specific interactions between VDR and these inhibitors, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results simulated, we furthermore proposed novel inhibitors and investigated their binding properties to VDR. The results elucidate that the replacement of propyl group at the 24th site of NS-54c by a phenethyl group can enhance the binding affinity of the inhibitor to VDR. This finding provides useful information for developing novel potent inhibitors against VDR.

Specific interactions between tau protein and curcumin derivatives: Molecular docking and ab initio molecular orbital simulations

Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the world, and there is currently no potent medicine for the treatment of ADs. Curcumin, a primary chemical contained in the ancient Indian herb known as turmeric, has been extensively studied and shown to be effective in inhibiting the aggregations of amyloid-β and tau proteins, both of which are observed in the brains of AD patients. In the present study, we focused on the tau protein and investigated its specific interactions with curcumin derivatives, using molecular simulations based on molecular docking, molecular mechanics and ab initio fragment molecular orbital calculations. Based on the results, we attempted to propose novel potent inhibitors against the tau protein aggregation. Our molecular simulations provide useful information for developing novel medicines for the treatment of ADs.

Structural change of retinoic-acid receptor-related orphan receptor induced by binding of inverse-agonist: Molecular dynamics and ab initio molecular orbital simulations

To elucidate structural changes in the retinoic acid receptor-related orphan receptor gamma (RORγt) induced by the binding of an agonist or an inverse agonist, we conducted molecular dynamics (MD) simulations in explicit water. In addition, ab initio fragment molecular orbital calculations were carried out for certain characteristic structures obtained from the MD simulations to reveal important interactions between the amino acid residues of RORγt, and to distinguish the different effects in the binding of an agonist and an inverse agonist on the structure of RORγt. The results elucidate that the hydrogen bond between His479 of helix11 (H11) and Tyr502 of helix12 (H12) is important to keep the H12 conformation in the agonist-bound RORγt. In contrast, in the inverse-agonist-bound RORγt, the side chain of His479 rotates, significantly weakening the interaction between His479 and Tyr502, leading to a conformational change in H12. Therefore, the present molecular simulations clearly indicate that the conformational change in the side chain of His479 in the inverse-agonist-bound RORγt is the main reason for the H12 destabilization induced by the binding of the inverse agonist. Such a conformational change does not occur on the binding of the agonist in RORγt, owing to the strong hydrogen bond between His479 and Tyr502.

Experimental and theoretical study of thermoelectric properties of rhombohedral GeSb5Te10 thin films

Rhombohedral GeSb5Te10 thin films are synthesized onto Al2O3 substrate by a pulsed-DC magnetron sputtering method using a target prepared by hot-pressing method. Thermoelectric properties of these films are studied as a function of temperature from room temperature to 773 K and correlated to the microstructural and surface properties. It is found that the phase transformation from amorphous to rhombohedral phase of GeSb5Te10, observed in temperature range 473–773 K, involved lattice-swelling and atomic diffusion within the crystalline structure. The completion of phase transformation at annealing temperature 673 K minimized the average crystallite size of thin film and enhanced the Seebeck coefficients (~140 μVK−1) and thermoelectric power factor (~4.5 mWm−1 K−2). Molecular orbital simulations of small cluster model, performed using linearly decreasing scattering variable along with the temperature dependent Fermi energy for onto determining the electrical and thermoelectric properties, were found in agreement to the experimental results.

Systematic Interaction Analysis of Anti-Human Immunodeficiency Virus Type-1 Neutralizing Antibodies with High Mannose Glycans Using Fragment Molecular Orbital and Molecular Dynamics Methods.

A series of broadly neutralizing antibodies called PGT have been shown to be bound directly to human immunodeficiency virus type-1 via high mannose glycans on glycoprotein gp120. Despite the sequence similarities of amino acids of the antibodies, their affinities to the glycan differ. Glycan-antibody interactions among these antibodies are systematically compared with quantum chemical fragment molecular orbital calculations and molecular dynamics simulations. The differences among structural stability of the glycan in the active site of the complexes and total interaction energies as well as binding free energies between the glycan and antibodies agree well with the experimentally shown affinities of the glycan to the antibodies. The terminal saccharide, Man D3, is structurally stable and responsible for the glycan-antibody binding through electrostatic and dispersion interactions. The structural stability of nonterminal saccharides such as Man 4 or Man C plays substantial roles in the interaction via direct hydrogen bonds. © 2019 Wiley Periodicals, Inc.

Kinetics of environmentally assisted cracking in SiNx barrier films

Kinetics of environmentally assisted subcritical cracking in SiNx barrier films is studied by in situ optical microscopy experiments and quantum chemical molecular orbital theory simulations. The activation volume of 0.83–1.11 cm3/mol and the activation energy of 138 kJ/mol (1.43 eV) are experimentally measured for subcritical crack growth in moist air. The quantum chemical simulations reveal the molecular mechanism of stress corrosion in mechanically strained SiNx under water attack, and the predicted activation energy and activation volume are in good agreement with the experimental results. The combined experimental and modeling studies provide a fundamental understanding of subcritical crack growth in SiNx barrier films for flexible electronic device applications.

Solar photocatalytic decomposition of Probenazole in water with TiO2 in the presence of H2O2

ABSTRACTThe photocatalytic decomposition of Probenazole in water using TiO2/H2O2 under sunlight illumination is studied. The addition of H2O2 is effective for the improvement of photocatalytic decomposition of Probenazole with TiO2. Furthermore, the operating conditions, such as photocatalyst dosage, temperature, pH, sunlight intensity and illumination time are also optimized. The kinetics of photocatalytic decomposition follow a pseudo–first–order kinetic law, and the rate constant is 0.129 min−1. The activation energy (Ea) is 11.34 kJ/mol. The photocatalytic decomposition mechanism is discussed on the basis of molecular orbital (MO) simulation for frontier electron density.

Molecular simulation for thermoelectric properties of c-axis oriented hexagonal GeSbTe model clusters

Using a combination of molecular orbital and molecular dynamics simulations, electronic and thermoelectric properties of GeSbTe model clusters are presented. The unit cells of Ge13Sb20Te52, Ge7Sb12Te40 and Ge14Sb6Te26 model clusters are designed corresponding to GeSb2Te4, GeSb4Te7 and Ge2Sb2Te5 compositions in hexagonal phase, oriented in the c-axis direction. The electronic structures of clusters have been simulated by discrete-variational molecular orbital calculation using Hartree-Fock-Slater approximation to determine the electrical conductivity and Seebeck coefficients in Mott expression. For thermal properties, molecular dynamics simulations have been employed on clusters in amorphous, cubic and hexagonal phases using Verlet's algorithm and subsequently using Green–Kubo relation for lattice thermal conductivity. We assumed inter-atomic interaction, defined by the Morse-type potential function added to Busing-Ida potential function, which considers partial electronic charges on the ions, bond length of the cation–anion pair, and depth and shape of the potential. Based on our simulations, detailed variation of electrical conductivity, carrier thermal conductivity, lattice thermal conductivity, Seebeck coefficients, power factor and figure of merit, are presented as a function of temperature in 300–700K range. Thermoelectric parameters obtained in present study were compared and explained with those of experimentally results of Ge2Sb2Te5 composition in hexagonal phase.

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl4, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17O and 1H nuclei monitoring the nuclear magnetic relaxation times of 1H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the solvent, although the correlation is weaker than that for the methanol solution of 1. The lower sensitivity of 2 to the solvent is attributed to the smaller number of oxygen atoms and the less negative electrostatic potential at the proton-accepting sites. The present study indicates that the specific interactions with protic solvents or strong H-bond-accepting solvents affect the geometry and dynamic behavior of short intramolecular H-bonds.

Applications of deuterium-tritium equation of state based on density functional theory in inertial confinement fusion

An accurate equation of state for deuterium-tritium mixture is of crucial importance in inertial confinement fusion. The equation of state can determine the compressibility of the imploding target and the energy deposited into the fusion fuel. In the present work, a new deuterium-tritium equation of state, which is calculated according to quantum molecular dynamic and orbital free molecular dynamic simulations, has been used to study the target implosion hydrodynamics. The results indicate that the peak density predicted by the new equation of state is ∼10% higher than the quotidian equation of state data. During the implosion, the areal density and neutron yield are also discussed.

Change in specific interactions between lactose repressor protein and DNA induced by ligand binding: molecular dynamics and molecular orbital calculations

Lactose repressor protein (LacR) plays an essential role in controlling the transcription mechanism of genomic information from DNA to mRNA. It has been elucidated that a ligand binding to LacR regulates allosterically the specific interactions between LacR and operator DNA. However, the effect of the ligand binding on the specific interactions has not been clarified at an atomic level. In this study, we performed classical molecular dynamics (MD) and ab initio fragment molecular orbital simulations to elucidate the effect of ligand binding at atomic and electronic levels. The MD simulations for the solvated complexes with LacR-dimer, DNA and ligand demonstrate that the binding of an inducer IPTG to LacR-dimer significantly changes the structure of LacR-monomer to cause strong interactions between LacR-monomers, resulting in weakening the interactions between LacR-dimer and DNA. In contrast, the binding of an anti-inducer ONPF to LacR-dimer was found to enhance the interactions between LacR-dimer and DNA. These findings are consistent with the functions of IPTG and ONPF as an inducer and an anti-inducer, respectively. We therefore proposed a simplified model for the effect of the ligand binding on the specific interactions between LacR-dimer and DNA.

Single-stranded DNA adsorption characteristics by hollow spherule allophane nano-particles: pH dependence and computer simulation

Clay mineral surfaces have been important for the prebiotic organization and protection of nucleic acids. The morphological observation to provide insight into the adsorption structure and characteristics of single-stranded DNA (ss-DNA) by natural allophane particles was presented. The molecular orbital (MO) computer simulation has been used to probe the interaction of ss-DNA and/or adenosine 5′-monophosphate and allophane with active sites. Our simulations predicted that the strand undergoes some extent of the elongation, which induces the alteration of the conformation of the phosphate backbone, base–base distance and excluded volume correlation among bases. This work demonstrates the ss-DNA adsorption by the allophane particles with novel insights into the morphological features and detailed molecular level information. The overall results support a general adsorption mechanism for the ss-DNA/allophane complexation.

Allophane–Pt nanocomposite: Synthesis and MO simulation

Allophane nanoparticles were synthesized through a hydrothermal treatment of precursor with Si/Al molar ratio of 0.75 at 100°C for 48h and characterized by using field emission scanning electron microscopy, pore-size distribution based on the Cranston–Inkley method, 29Si and 27Al magic angle spinning nuclear magnetic resonance, X-ray diffractometry, and energy dispersive X-ray spectroscopy. It is demonstrated that the synthetic allophane nanoparticle leads to a novel allophane–Pt nanocomposite with the metal particle size of ~2nm and narrow size distribution. The synthetic allophane particles promote the reduction of K2PtCl4 to Pt0 and act as a support substratum. The molecular orbital computer simulation was performed to provide insight into the structure and stability of Pt nanoparticles during complexation by the functional (OH)Al(OH2) groups on the wall perforations of the synthetic allophane.