Authors:Xun Zhu, Xiuqin Zhou, Dongsheng Xiang, Ping Wu Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. This paper focuses on the thermal elimination of alkenes from methyl alkyl thionacetates and thiolacetates. Three alkyl groups are calculated: ethyl, isopropyl and tert-butyl. Possible elimination mechanisms are considered, including six- and four-membered ring transition states for alkene elimination, four-membered ring isomerization and a possible five-membered ring decomposition. Theoretical calculations are performed with the MP2 method and the 6-31G* basis set. Wiberg bond indices are also summarized to monitor the reaction progress. • The calculation of thermolysis of di(tri) thioncarbonates at MP2/6-31G(d) level was performed. • Four possible mechanisms were proposed to compare the thermolysis process. • Wiberg bond indices were calculated to elucidate the thermolysis process. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:56Z DOI: 10.1142/S0219633618500141

Authors:Dongyun Zhang, Yaning Lin, Shenhua Song, Peixin Zhang, Hongwei Mi Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. In this paper, in order to effectively utilize salt lake magnesium resources, we focused on a functional material containing magnesium, i.e. magnesium oxide, MgO, which is a type of antibacterial material. Through a first-principles study from the atomic level, the microstructure of MgO containing doped point defects of different elements was studied. The relationship between the microscopic structure of the material and its special antibacterial function was explored. The results are as following: the interstitial impurities in MgO are more helpful than substituted impurities for the improvement of the electronic structure. The analysis of the influence of different doping elements on the microstructure confirmed theoretically that Ag and Cu have the same highly active antimicrobial properties with the same change of microstructure, thereby confirming the relationship between microstructure and antimicrobial activity. The results of the simulations match the experimental results, thereby theoretically demonstrating the relationship between defects and antibacterial activities and providing further insight into the nature of the antibacterial mechanism. • The difference in the microelectronic structure affects the antibacterial mechanism. • The micro-electronic properties, including the band gap, partial density of states (PDOS), charges and electron density difference, were found to have the same effect, whether the impurities were interstitial or substitutional doped elements. • The interstitial impurities in MgO are more helpful for improving the antibacterial property. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:55Z DOI: 10.1142/S0219633618500189

Authors:Jiang Yi, Feiwu Chen Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. Applications of the multireference linearized coupled-cluster single-doubles (MRLCCSD) to atomic and molecular systems have been carried out. MRLCCSD is exploited to calculate the ground-state energies of HF, H2O, NH3, CH4, N2, BF, and C2 with basis sets, cc-pVDZ, cc-pVTZ and cc-pVQZ. The equilibrium bond lengths and vibration frequencies of HF, HCl, Li2, LiH, LiF, LiBr, BH, and AlF are computed with MRLCCSD and compared with the experimental data. The electron affinities of F and CH as well as the proton affinities of H2O and NH3 are also calculated with MRLCCSD. These results are compared with the results produced with second-order perturbation theory, linearized coupled-cluster doubles (LCCD), coupled-cluster doubles (CCD), coupled-cluster singles and doubles (CCSD), CCSD with perturbative triples correction (CCSD(T)). It is shown that all results obtained with MRLCCSD are reliable and accurate. • Multireference linearized coupled-cluster single and double methods are implemented to calculate the ground state energies of molecular systems, electronic affinity and proton affinity as well as the spectroscopic constants of diatomic molecules. • The proposed method is cheap and accurate. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:51Z DOI: 10.1142/S0219633618500165

Authors:Xin Tan, Na Liu, Fiona S. Legge, Minghui Yang, Jun Zeng Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. Previously, we developed a method to predict epitopes on a protein recognized by specific antibodies. In this study, we have applied this method to identify the epitopes of the human papillomavirus 16 (HPV16) L1 capsomer that is bound by monoclonal antibodies U4, AE3 and AG7. Initially, the method was validated by the identification of epitopes of HPV16 L1 capsomer that bind to antibody U4. Our predicted epitopes were in agreement with the cryto-electron microscopy (cryto-EM) structure of the complex. The method was then used to predict the epitopes of HPV16 L1 binding of antibodies AE3 and AG7. Our calculations indicated that antibody AE3 binds to the HPV16 L1 capsomer at two different regions. Firstly, the region recognized by antibody U4 and secondly, the region recognized by antibody V5, which have been shown in the cryto-EM structure of the V5 and HPV16 L1 complex. In comparison, the antibody AG7 binds to the capsomer only at the epitopes bound by antibody U4. Therefore, antibody AE3 is predicted to have higher affinity than antibody AG7 and could be used for developing highly efficient anti-HPV monoclonal antibodies in the clinical treatment of HPV infections. • Several epitopes of HPV16 L1 protein have been predicted for the three antibodies U4, AE3 and AG7. • While the calculations have reproduced the recognition region of antibody U4 as shown in cryto-electron microscopy structure of the complex between HPV16 L1 capsomer and U4, several binding peptides from L1 protein have been predicted as possible epitopes for the antibodies AE3 and AG7 with qualitative indications of different antibody-antigen binding affinities. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:45Z DOI: 10.1142/S0219633618500177

Authors:Song Geng, Xiaoli Sang, Xiaoqiang Liu, Yi Ren, Ying Xue Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. The conformation, electron structure, and antioxidant mechanism of chryso-obtusin, extracted from Leguminosae of traditional Chinese herb, have been studied in CH3OH by the density functional theory B3LYP/PCM/6-311[math]G(2df,p)//B3LYP/PCM/6-31G([math]) method. Three mechanisms of antioxidant actions are examined, which contain hydrogen atom transfer (HAT), single-electron transfer-proton transfer (SET-PT), and sequential proton loss transfer (SPLET), by using the computed corresponding indicators (BDE, IP, and PDE). Still, the spin density is employed to measure the delocalization of the antioxidant and its radical form. The finding suggests that hydrogen bond interaction is the main cause for the antioxidant activity of this antioxidant. • The density functional theory method was used to investigate the structural and radical scavenging properties of chryso-obtusin (CHO) in methanol. • The calculated results showed that the hydrogen atom transfer (HAT) mechanism is the thermodynamic preferred radical scavenging mechanism for CHO, due to the fact that the dielectric constant of solvent methanol is relatively small and breaking of O-H bond only accompanies with the breaking of a moderate hydrogen bond. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:37Z DOI: 10.1142/S0219633618500153

Authors:Huixia Guo, Xiaohua Xi, Renxiang Yan, Xiaoquan Lu Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. Derived from diarylamine sensitizer diphenyl-(7-pyridin-4-yl-9H-carbazol-2-yl)-amine (N13), a series of novel D[math]A carbazole-based organic dye sensitizers with different [math]-linkers were designed for searching more effective sensitizers in dye-sensitized solar cells (DSSCs) design. Optimized geometries, electronic structure, and other parameters, which can evaluate the performance of DSSCs effectively and intuitively, were theoretically calculated by density functional theory (DFT) and time-dependent DFT methods at the M06/6-31G(d,p) level. The results indicated that the maximum absorption wavelength of designed dye was red-shifted and the molar absorption coefficient ([math]) became higher. This phenomenon can be explained by the modification of the [math]-bridge. The simulated Ultraviolet–visible spectroscopy (UV-Vis) absorption spectrum showed that the designed N,N-diphenyl-7-(5-(7-(5-(pyridin-4-yl)thiophen-2-yl)benzo[c][1,2,5]thiadiazol-4-yl)thiophen-2-yl)-9H-carbazol-2-amine (N22) dye presents the largest red-shifted absorption band and the designed (E)-N,N-diphenyl-7-(2-(5[math]-(pyridin-4-yl)-[2,2[math]-bithiophene]-5-yl)vinyl)-9H-carbazol-2-amine (N21) dye showed the largest [math], both of them depicted a high short-circuit photocurrent density ([math]. Meanwhile, the charge separation hampered by long [math]-linkers was also observed. These results are helpful for designing new sensitizers and providing effective guiding to experimental synthesis. • Different functions or basis sets were studied to find a proper theoretical method. • The change of π-linker induces perfect electronic and photovoltaic performance. • The efficiency of DSSCs is evaluated theoretically. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:26Z DOI: 10.1142/S0219633618500190

Authors:Ali Shokuhi Rad Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. Density functional theory (DFT) was used for studying the adsorption of dimethyl ether (DME) onto four nanoclusters: [math] ([math], B and [math], P). The interaction energy along with the adsorption energy was investigated, and it was found that DME molecule has higher binding energies upon adsorption on Al-containing clusters, but on the other hand, it results in higher alteration in the electronic structure of B-containing cluster. Outcomes of charge analysis and frontier molecular orbital confirm higher alteration in the electronic structure of the later clusters, suggesting the possible potential of B[math]N[math] and B[math]P[math] as two sensitive sensors for DME. Nevertheless, Al-containing clusters showed much better adsorbent property, judging from their higher adsorption energies. The positive values of charge transfer upon DME adsorption confirm the p-type semiconducting property of all these clusters. • Adsorption of DME onto four fullerene-like nanoclusters (X12Y12) was investigated. • p-Type semiconducting property of all nanoclusters was observed upon DME adsorption. • High DME adsorption was found on Al-clusters while high sensor ability was found for B-clusters. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:16Z DOI: 10.1142/S021963361850013X

Authors:Babak Azarnavid, Elyas Shivanian, Kourosh Parand, Soudabeh Nikmanesh Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. In this paper, a model of simultaneous mass and heat transfer within a porous catalyst in a flat particle is considered. A new modification of the shooting reproducing kernel Hilbert space (SRKHS) method is proposed, which is also capable of handling the system of nonlinear boundary value problems by employing Newtons method. The proposed method is a well-performance technique in both predicting and calculating multiple solutions of the nonlinear boundary value problems. Applying the SRKHS method shows that the mentioned model might admit multiple stationary solutions (unique, dual or triple solutions) depending on the values of the parameters of the model. Furthermore, the convergence of the method is proved and some numerical tests reveal the high efficiency of this new version of SRKHS method. • We have proved by the new version of SRKHS method that the model of simultaneous mass and heat transfer within a porous catalyst in a flat particle may have multiple stationary solutions depending on the values of the parameters of the problem. • An important aim of this work is to show how much information can be obtained using the numerical computations. • The proposed method can produce good globally smooth numerical solutions, and with the ability to solve many differential systems with complex constraints conditions. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:14Z DOI: 10.1142/S0219633618500207

Authors:Giovanni Di Nicola, Gianluca Coccia, Sebastiano Tomassetti Abstract: Journal of Theoretical and Computational Chemistry, Volume 17, Issue 02, March 2018. This work presents a modification of the Kardos equation specifically oriented to refrigerants. The proposed equation was tested for both liquid and vapor thermal conductivities along saturation of the main refrigerants. In the Kardos equation, the thermal conductivity of liquids is a function of the density of the liquid, heat capacity at constant pressure, speed of sound in the liquid and average distance between the centers of the molecules. In the present version, the liquid molar volume and the distance between the surfaces of adjacent molecules were replaced by two constant parameters widely available for all the fluids: the critical density and radius of gyration. In this way, the resulting equation is much simpler, still being a scaled equation. In the proposed equations, an adimensional factor was regressed to minimize the deviations. The final equations were able to predict the thermal conductivity with AAD[math] for liquids and AAD[math] for vapors. • This work presents a modification of the Kardos equation specifically oriented to refrigerants. The proposed equation was tested for both liquid and vapor thermal conductivities along saturation of the main refrigerants. • In the Kardos equation, the thermal conductivity of liquids is a function of the density of the liquid, the heat capacity at constant pressure, speed of sound in the liquid and the average distance between the centers of the molecules. • In the present version, the liquid molar volume and the distance between the surfaces of adjacent molecules were replaced by two constant parameters widely available for all the fluids: the critical density and radius of gyration. • The final equations were able to predict the thermal conductivity with AADL = 3.6% for liquids and AADV = 9.8% for vapors. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-04-11T08:48:04Z DOI: 10.1142/S0219633618500128

Authors:Zhe Jia, Lin Li, Yunhui Peng, Feng Ding, Emil Alexov Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Integrins are cellular adhesion proteins located on cell surface. They are known to have open and closed conformations that correspond to high and low binding affinity to ligands, respectively. Integrin [math]2 binds to the ligands via the ligand binding domain, [math]2-I domain, which also has open and closed conformations. Experimentally, the closed to open conformation change is shown to be triggered by pulling the C-terminal away from the ligand binding site, but how the signal propagates from the distant C-terminal to the binding site is unknown. To explain the mechanisms of the conformation change, we built models of the [math]2-I domain open and closed conformations in ligand free and ligand bound states, respectively. We found that the signaling pathway consists of F313-I280-V252 residues that connect the C-terminal and the ligand binding site. The pathway is highly conserved as revealed by a protein sequence analysis among 55 species. Furthermore, MM/PBSA energy calculations on the stabilities and ligand binding affinities of the closed and open conformations are consistent with experimental measurements. The open conformation is more favorable for ligand binding, and the closed conformation is more stable in unbound state. Energy analysis also revealed the “hot spots” for ligand binding, and most residues that contribute strongly to ligand binding free energy are highly conserved in evolution. In addition, the electrostatic analysis showed that the closed conformation has stronger long-range electrostatic attraction to the ligand compared with the open conformation. The difference is caused by the rearrangement of several charged residues during the binding. These observations make us suggest that the integrin [math]2-I domain binding process involves the two-step “dock-lock” mechanism. The closed conformation first attracts the ligand from a long distance and afterwards, the open conformation locks the ligand at the binding site with high binding affinity. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2018-02-05T03:58:07Z DOI: 10.1142/S0219633618400011