Molecular Modeling

Theoretical study on the gas-phase reaction mechanism of ammonia with nitrous oxide Abstract Applications of nitrous oxide (N2O) as an oxidant in green propellants and propulsion systems have attracted a lot of attention. In this study, the reaction pathways for the oxidation of ammonia (NH3) with N2O were studied using the B3LYP/6-31++G** method of density functional theory (DFT). The results reveal that the reaction between N2O and NH3 proceeds through a chain reaction mechanism. N2O reacts with NH3 to form N2 and NH3O first and then NH3O decomposes into NH3 and O. This process corresponds to the apparent reaction N2O+M=N2+O+M (M=NH3), but the energy barrier of the process (183.49 kJ/mol) is much lower than the direct decomposition reaction of N2O=N2+O (279.05 kJ/mol). The O radical produced in this process reacts subsequently with NH3 and N2O to produce more radicals such as NH2, OH, and NO, which will take part in further reactions like NH3+OH=NH2+H2O and NH2+NO=N2+H2O until the reactants are consumed.

Site-directed mutations of anti-amantadine scFv antibody by molecular dynamics simulation: prediction and validation Abstract A recombinant single-chain variable fragment (scFv) antibody was produced from a hybridoma cell strain secreting the monoclonal antibody for amantadine (AMD), and then its recognition mechanisms for AMD were studied using the molecular docking and molecular dynamics. Complex dockings revealed that three regions are involved in antibody recognition; framework 2 of the VL chain (LFR2) GLU40 and TYR42, complementarity-determining region of the VL chain (LCDR3) TYR116, and framework 2 of the VH chain (HFR2) HIS40 and TRP52 were the key amino acid residues. The results of molecular dynamics show that the most important amino acid residues in the interaction between AMD and scFv are HIS40 and TYR116. On the basis of the results of virtual mutation, the scFv antibody was evolved by directional mutagenesis of amino acid residue GLY107 to PHE. Indirect competitive ELISA (icELISA) results indicated that the scFv mutant had highly increased affinity for AMD with up to 3.9-fold improved sensitivity. Thus, the scFv antibody can be applied for mechanistic studies of intermolecular interactions, and our work offered affinity maturated antibodies by site mutations, which were beneficial for valuable anti-AMD antibody design and preparation in future.

Vibrational, thermodynamic, and dielectric properties of ε-CL-20: first-principles calculations Abstract The DFT theory is used to investigate the vibration forms of ε-CL-20 by discussing the phonon DOS and infrared and Raman spectra. By observing them, the detailed vibration forms can be obtained, and the vibrations are different in the different regions. Our calculated vibrational results are consistent with previous data. In order to deeply comprehend CL-20, we also investigate the thermodynamic properties, finding that entropy, enthalpy, Debye temperature, and heat capacity are increased with the rising temperature and the vibrational free energy decreases with the increasing temperature. The εxx, εyy, and εzz are similar, which reflects the small anisotropy among [100], [010], and [001]. Moreover, it can be noticed that the major contribution for static dielectric constants originates from the electronic contribution.

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Effect of sodium gluconate on molecular conformation of polycarboxylate superplasticizer studied by the molecular dynamics simulation Abstract Sodium gluconate (SG) has been accepted as one of the main additional components in polycarboxylate superplasticizer (PCE) system, due to its excellent retarding effect. While the negative effect on dispersion of PCE was reported in the literature, the reason was not completely revealed. In this study, molecular dynamics simulation was used to investigate the mutual influence between SG and PCE in calcium hydroxide (CH) solution. Radial distribution function (RDF) was used to analyze the effects of SG on the complexation of PCE with Ca2+. Radius of gyration (Rg) was adopted to characterize the conformations of the backbone and side chains of PCE in CH solution. Finally, several adsorption and dispersion models were proposed. The results showed that the presence of SG would perturb adsorption of PCE, which was one of the main reasons that affected the dispersion ability of PCE. SG could preferentially combine with Ca2+ so that less amount of Ca2+ is available for combination of PCE, and this could extend the main chain of PCE and show advantage for PCE adsorption. Besides, adding SG could squeeze the side chains of PCE, which would put a negative effect on the dispersion. These findings gave deeper insight into understanding the dispersion mechanism of PCE-SG system.

Effects of boron doping on structural, electronic, elastic, and optical properties of energetic crystal 2,6-diamino-3,5-dinitropyrazine-1-oxide: a theoretical study using the first principles calculation and Hirshfeld surface analysis Abstract Boron-contained compounds are one kind of new energetic materials, and have been synthesized successfully lately. However, the effects of introduced boron atoms into the energetic system are unclear. In this work, using the known insensitive energy crystal 2,6-diamino-3,5-dinitropyrazine-l-oxide (LLM-105) as the model compound, boron doping effects on its crystal structure, band gap and structure, intermolecular contacts, sensitivity, elastic property, optical absorption behavior, and dielectric function were studied by the first principles calculations and Hirshfeld surface analysis. One B atom was doped at four different doping sites in the ring (two kinds of nitrogen N1/N2 and carbon atoms C3/C4), respectively, and formed four new crystals LLM-105-B1/B2/B3/B4. The results showed that the B atom and its doping site both make great influence on the structure and properties. The B doping obviously decreased the band gap and weakened the strength of intermolecular contacts, giving rise to higher sensitivity and worse safety. Especially for LLM-105-B4 which has a 0 eV value of band gap, the doped B atom made great contributions to the density of states around the Fermi level, leading to the suddenly move down of lowest unoccupied molecular orbital and directly link of total density of states at the Fermi level. Doping the B atom at the site C3 improved the ductility and plasticity of LLM-105, while LLM-105-B2 was found to be the most brittle and anisotropic crystal. Doping B atoms at sites N2 and C4 increased the absorption to green, orange, and red lights, while the absorption strength to the infrared light was enhanced in most cases. The dielectric constant and polarity were significantly increased by doping boron atoms at sites C3 and C4.

EMPIRE: a highly parallel semiempirical molecular orbital program: 3: Born-Oppenheimer molecular dynamics Abstract Direct NDDO-based Born-Oppenheimer molecular dynamics (MD) have been implemented in the semiempirical molecular orbital program EMPIRE. Fully quantum mechanical MD simulations on unprecedented time and length scales are possible, since the calculation of self-consistent wavefunctions and gradients is performed in a massively parallel manner. MD simulations can be performed in the NVE and NVT ensembles, using either deterministic (Berendsen) or stochastic (Langevin) thermostats. Furthermore, dynamics for condensed-phase systems can be performed under periodic boundary conditions. We show three exemplary applications: the dynamics of molecular reorganization upon ionization, long timescale dynamics of an endohedral fullerene, and calculation of the vibrational spectrum of a nanoparticle consisting of more than eight hundred atoms. Graphical Abstract A snapshot from an MNDO-H simulation of NH4+@C60 at 4000 K shortly before a proton crosses the fullerene wall to give NH3@C60H+.

Electronic structure of polythiophene gas sensors for chlorinated analytes Abstract Density functional theory studies are performed to investigate the response of polythiophene as a sensor for chlorinated gaseous analytes. Interaction of polythiophene with these analytes is studied from both H-side (dipole-dipole) and Cl-side (halogen bonding) of analyte to get the most stable interaction site. Inferences from interaction energy, natural bond orbital, and Mulliken charge analyses are in line with those from geometric analysis. Interaction energies reveal that polythiophene has specificity and selectivity towards chlorine. Interestingly, the halogen bond in PT-Cl2 complexes is stronger than ion-dipole bond in the complexes of polythiophene with other analytes. The sensing of polythiophene towards these analytes is also measured by perturbing the electronic properties including ionization potential, electron affinity, λmax, and H→L gap. The spectroscopic properties (UV absorption spectra) reveal the interaction behavior of polythiophene with these chlorinated analytes. All these parameters including orbital analysis and H→L energies indicate high sensitivity of polythiophene for chlorine. Graphical abstract Interaction of chlorinated gaseous analytes with polythiophene surface

Theoretical study on the stability of the complexes A···BX 3 [A = CH 3 NH 3 + , NH 2 CHNH 2 + , NH 2 CHOH + ; B = Sn 2+ , Pb 2+ ; X = F − , Cl − , Br − , I − ] Abstract The interaction of corresponding molecular building blocks of the complexes A···BX3 would provide valuable information to quickly estimate the properties of the solar cell. In this work, the H···X hydrogen bond between the organic cations A+ (CH3NH3+, NH2CHNH2+, NH2CHOH+) and the inorganic anions BX3− (B = Sn2+, Pb2+, X = F−, Cl−, Br−, I−) were studied by theoretical calculation at the B3LYP-D3/ma-def2-TZVP level to investigate the stability of the complexes A···BX3. The strength of H···X hydrogen bond is enhanced in the order of NH2CHNH2+ < CH3NH3+ < NH2CHOH+, Sn2+ < Pb2+, and weakened in the order of F− > Cl− > Br− > I−, indicating that the complexes A···BX3 enhances with the increase of electron donating ability of B and the decrease of electron donating ability of X, and application of the substituent A = NH2CHOH+ may be effective to enhance the stability of perovskite and replace the toxic metal Pb by Sn. Graphical abstract

Exploiting σ-hole interaction to design small uncharged ligand molecules to stabilize G-quadruplex-DNA: a computational study Abstract Small neutral seleno molecules were designed to stabilize G-quadruplex-DNA to accelerate the death of cancer cells. A new approach was considered in this study to design new ligands to stabilize G-quadruplex-DNA using the non-covalent σ-hole interaction. The systematic study has been performed with ligands in the absence and presence of σ-hole interaction to stabilize G-tetrad. Fluorine-substituted seleno ligands interact with the bases of G-quadruplex strongly with the σ-holes present in the ligands. The binding of the fluorinated ligands FSeCF2SeCF2 SeF2(4) (~75.0 kcal/mol) is stronger than that of BRACO-19 (~70.0 kcal/mol) calculated at the same level of theory with G-tetrad. It is reported that BRACO-19 is employed to inhibit the enzymatic activity of telomerase. The calculated results also reveal the importance of optimum chain length of ligands to achieve a better binding ability with G-tetrad. The MESP calculations and AIM analysis corroborate the trends of binding of these ligand molecules with G-quadruplexes. The small neutral molecules possess considerable advantage to pass through the lipid bilayer of the cell membrane by passive transport and are of choice in biological research and for clinical trials. Graphical Abtract Small neutral ligands with σ-holes can stabilize G-quadruplex to inhibit enzymatic activity of telomerase.