ALBERT

Description:    The reactions of acetone, 2,2,2-trifluoroacetone and hexafluoroacetone in methanesulfonic (MSA) and triflic acids (TFSA) with benzene have been studied at M06-2X/6-311+G(d,p) level using cluster-continuum model, where the carbonyl group is explicitly solvated by acid molecules. The introduction of a trifluoromethyl group into the ketone structure reduces the activation energy of the tetrahedral intermediates formation due to an increase of the electrophilicity of the carbonyl group and raises the activation and the reaction energies of the C-O bond cleavage in formed carbinol due to the destabilization of the corresponding carbocation. The introduction of the second trifluoromethyl group inhibits the hydroxyalkylation reaction due to a very strong increase of the reaction and activation energies of the C-O bond cleavage which becomes the rate determining step. The most important catalytic effect of TFSA compared to MSA is not the protonation of the ketone carbonyl, but the reduction of the activation and reaction energies of the carbinol C-O bond cleavage due to better protosolvation properties. Even for TFSA no complete proton transfer to carbonyl oxygen has been observed for free ketones. Therefore, the protonation energies of free ketones cannot be considered as a measure of ketone reactivity in the hydroxyalkylation reaction. Figure  Reactions of ketones with aromatics in acid media  Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1610-1 Authors Ulises Jiménez Castillo, Instituto de Investigaciones en Materiales Universidad Nacional Autonoma de Mexico, Apartado Postal 70-360, CU, Coyoacan, Mexico DF, 04510 Mexico Mikhail G. Zolotukhin, Instituto de Investigaciones en Materiales Universidad Nacional Autonoma de Mexico, Apartado Postal 70-360, CU, Coyoacan, Mexico DF, 04510 Mexico Lioudmila Fomina, Instituto de Investigaciones en Materiales Universidad Nacional Autonoma de Mexico, Apartado Postal 70-360, CU, Coyoacan, Mexico DF, 04510 Mexico Daniel Romero Nieto, University of Trieste, Via Valerio 10, 34127 Trieste, Italy Lilian Olivera Garza, Instituto de Investigaciones en Materiales Universidad Nacional Autonoma de Mexico, Apartado Postal 70-360, CU, Coyoacan, Mexico DF, 04510 Mexico Serguei Fomine, Instituto de Investigaciones en Materiales Universidad Nacional Autonoma de Mexico, Apartado Postal 70-360, CU, Coyoacan, Mexico DF, 04510 Mexico Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3- O -a-L-rhamnopyranosyl-(1–3)-a-L-rhamnopyranosyl-(1–6)-b-D-galacto- pyranoside (drug 1),kaempfol-7- O -rhamnosyl-3- O -rutinoside (drug 2)andkaempferide-7-O-(4”- O -acetylrhamnosyl)-3- O -ruti- noside (drug 3) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. The free energies are consistent with available experimental results and suggest that the binding site of BSA-drug1 is more stable than those of BSA-drug2 and BSA-drug3. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of BSA-drug1 while the van der Waals interactions contribute largely to stabilization of the binding site of BSA-drug2 and BSA-drug3. The key residues stabilizing the binding sites of BSA-drug1, BSA-drug2 and BSA-drug3 are identified based on the residue decomposition analysis. Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1649-z Authors Xiaodi Niu, Department of Food quality and Safety, Jilin University, Changchun, 130062 People’s Republic of China Xiaohan Gao, Department of Food quality and Safety, Jilin University, Changchun, 130062 People’s Republic of China Hongsu Wang, Department of Food quality and Safety, Jilin University, Changchun, 130062 People’s Republic of China Xin Wang, Department of Food quality and Safety, Jilin University, Changchun, 130062 People’s Republic of China Song Wang, Department of Food quality and Safety, Jilin University, Changchun, 130062 People’s Republic of China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3′-O, 5′-S) thymidine phosphodiester (Tp-ST) (1) , 3′-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH 2 CF 3 ) (2) , 3′-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3′-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO 2 )) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A N D N ) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol −1 ) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group. Figure  Phosphodiester bond in Tp‐ST (1) , Tp‐OCH 2 CF 3 (2) Tp‐OPh(o‐Cl) (3) and Tp‐OPh(p‐NO 2 ) (4) Content Type Journal Article Category Original Paper Pages 1-11 DOI 10.1007/s00894-012-1630-x Authors Mahboobeh Rahimian, Department of Chemistry, University of Pune, Pune, 411007 India Shridhar P. Gejji, Department of Chemistry, University of Pune, Pune, 411007 India Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller−Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials ( V S,min ) and the most positive electrostatic potentials ( V S,max ) on the electron density contours of the individual species. The greater the V S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species. Figure  The character of the cooperativity between the X···O/S halogen bond (XB) and the Y―H···O hydrogen bond (HB) in OH/SH···HOX···HY (X=Cl, Br; Y=F, Cl, Br) complexes has been investigated by means of second-order Møller—Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1657-z Authors Wenjie Wu, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Yanli Zeng, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Xiaoyan Li, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Xueying Zhang, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Shijun Zheng, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Lingpeng Meng, College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp 2 -like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The −0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems. Figure  First-principles van der Waals density functional (vdW-DF) calculations show that aromatics are physisorbed on the side wall of perfect single-walled carbon nanotubes (SWCNTs) as well as at the edge site of defective nanotubes  Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1652-4 Authors Masoud Darvish Ganji, Center of Nano-Science, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran Maryam Mohseni, Center of Nano-Science, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran Anahita Bakhshandeh, Center of Nano-Science, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    Based on DFT-B3LYP/6-311G** method, the molecular geometric structures of polynitramineprismanes are fully optimized. The detonation performances, energy gaps, strain energies, as well as their stability were investigated to look for high energy density compounds (HEDCs). Our results show that all polynitramineprismanes have high and positive heat of formation. To construct the relationship between stabilities and structures, energy gaps and bond dissociation energies are calculated, and these results show that the energy gaps of prismane derivatives are much higher than that of TATB (0.1630). In addition, the C-C bonds on cage are confirmed as trigger bond in explosive reaction. All polynitramineprismanes have large strain energies, and the strain energies of all compounds are slightly smaller than prismane, which indicated that the strain energies were somewhat released compared to prismane. Considering the quantitative criteria of HEDCs, hexanitramineprismane is a good candidate of high energy compounds. Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1648-0 Authors Wei-Jie Chi, School of Chemistry and Material Science, Shanxi Normal University, 041004 Linfen, China Lu-Lin Li, School of Chemistry and Material Science, Shanxi Normal University, 041004 Linfen, China Bu-Tong Li, School of Chemistry and Material Science, Shanxi Normal University, 041004 Linfen, China Hai-Shun Wu, School of Chemistry and Material Science, Shanxi Normal University, 041004 Linfen, China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    A novel polynitro cage compound 4,8,11,14,15-pentanitro-2,6,9,13-tetraoxa-4,8,11,14,15–pentaazaheptacyclo [5.5.1.1 3,11 .1 5,9 ]pentadecane(PNTOPAHP) has been designed and investigated at the DFT-B3LYP/6-31(d) level. Properties, such as electronic structure, IR spectrum, heat of formation, thermodynamic properties and crystal structure have been predicted. This compound is most likely to crystallize in C2/c space group, and the corresponding cell parameters are Z  = 8, a  = 29.78 Å, b  = 6.42 Å, c  = 32.69 Å, α  = 90.00°, β  = 151.05°, γ  = 90.00°and ρ  = 1.94 g/cm 3 . In addition, the detonation velocity and pressure have also been calculated by the empirical Kamlet-Jacobs equation. As a result, the detonation velocity and pressure of this compound are 9.82 km/s, 44.67 GPa, respectively, a little higher than those of 4,10-dinitro-2,6,8,12–tetraoxa−4,10-diazaisowurtzitane(TEX, 9.28 km/s, 40.72 GPa). This compound has a comparable chemical stability to TEX, based on the N-NO 2 trigger bond length analysis. The bond dissociation energy ranges from 153.09 kJ mol –1 to 186.04 kJ mol –1 , which indicates that this compound meets the thermal stability requirement as an exploitable HEDM. Content Type Journal Article Category Original Paper Pages 1-8 DOI 10.1007/s00894-012-1629-3 Authors He Lin, School of chemical engineering, Nan Jing University of Science and Technology, Jiangsu, Nanjng 210094, China Shun-guan Zhu, School of chemical engineering, Nan Jing University of Science and Technology, Jiangsu, Nanjng 210094, China Lin Zhang, School of chemical engineering, Nan Jing University of Science and Technology, Jiangsu, Nanjng 210094, China Xin-hua Peng, School of chemical engineering, Nan Jing University of Science and Technology, Jiangsu, Nanjng 210094, China Peng-yuan Chen, School of chemical engineering, Nan Jing University of Science and Technology, Jiangsu, Nanjng 210094, China Hong-zhen Li, Insititute of Chemical Materials, Chinese Academy of Engineering Physic, Sichuan, Mianyang 621900, China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    The mechanism and kinetics of the radical 3 C 2  + C 3 H 8 reaction have been investigated theoretically by direct ab initio kinetics over a wide temperature range. The potential energy surfaces have been constructed at the CCSD(T)/B3//UMP2/B1 levels of theory. The electron transfer was also analyzed by quasi–restricted orbital (QRO) in detail. It was shown that all these channels proceed exclusively via hydrogen abstraction. The overall ICVT/SCT rate constants are in agreement with the available experimental results. The prediction shows that the secondary hydrogen of C 3 H 8 abstraction by 3 C 2 radical is the major pathway at low temperatures (below 700 K), while as the temperature increases, the primary hydrogen of C 3 H 8 abstraction becomes more important and more favorable. A negative temperature dependence of the rate constants for the reaction of 3 C 2  + C 3 H 8 was observed. The three–( k 3 ) and four–parameter ( k 4 ) rate-temperature expressions were also provided within 243–2000 K to facilitate future experimental studies. Figure  Three types of hydrogen abstraction from C 3 H 8 by 3 C 2 radical have been considered. The prediction shows that the secondary hydrogen of C3H8 abstraction by 3C2 radical is the major pathway. Content Type Journal Article Category Original Paper Pages 1-10 DOI 10.1007/s00894-012-1616-8 Authors Rui-Ping Huo, State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023 People’s Republic of China Xiang Zhang, School of Chemistry and Materials Science, Shanxi Normal University, Linfen, 041004 People’s Republic of China Xu-Ri Huang, State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023 People’s Republic of China Ji-Lai Li, State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023 People’s Republic of China Chia-Chung Sun, State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023 People’s Republic of China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    We report the molecular characterization of β-1,3-glucanase-producing Bacillus amyloliquefaciens —an endophyte of Hevea brasiliensis antagonistic to Phytophthora meadii . After cloning and sequencing, the β-1,3-glucanase gene was found to be 747 bp in length. A homology model of the β-1,3-glucanase protein was built from the amino acid sequence obtained upon translation of the gene. The target β-1,3-glucanase protein and the template protein, endo β-1,3-1,4-glucanase protein (PDB ID: 3o5s), were found to share 94 % sequence identity and to have similar secondary and tertiary structures. In the modeled structure, three residues in the active site region of the template—Asn52, Ile157 and Val158—were substituted with Asp, Leu and Ala, respectively. Computer-aided docking studies of the substrate disaccharide (β-1, 3-glucan) with the target as well as with the template proteins showed that the two protein-substrate complexes were stabilized by three hydrogen bonds and by many van der Waals interactions. Although the binding energies and the number of hydrogen bonds were the same in both complexes, the orientations of the substrate in the active sites of the two proteins were different. These variations might be due to the change in the three amino acids in the active site region of the two proteins. The difference in substrate orientation in the active site could also affect the catalytic potential of the β-1,3 glucanase enzyme. Content Type Journal Article Category Original Paper Pages 1-9 DOI 10.1007/s00894-012-1645-3 Authors Amith Abraham, School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India Sunilkumar Puthenpurackal Narayanan, High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, Kinokawa, Japan Shaji Philip, Rubber Research Institute of India, Kottayam, Kerala, India Divya Gopalakrishnan Nair, Department of Biotechnology and microbiology, School of Lifesciences, Kannur University, Thalassery Campus, Kannur, Kerala, India Aparna Chandrasekharan, School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India Jayachandran Kochupurackal, School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940

Description:    Drug permeability determines the oral availability of drugs via cellular membranes. Poor permeability makes a drug unsuitable for further development. The permeability may be estimated as the free energy change that the drug should overcome through crossing membrane. In this paper the drug permeability was simulated using molecular dynamics method and the potential energy profile was calculated with potential of mean force (PMF) method. The membrane was simulated using DPPC bilayer and three drugs with different permeability were tested. PMF studies on these three drugs show that doxorubicin (low permeability) should pass higher free energy barrier from water to DPPC bilayer center while ibuprofen (high permeability) has a lower energy barrier. Our calculation indicates that the simulation model we built is suitable to predict drug permeability. Content Type Journal Article Category Original Paper Pages 1-7 DOI 10.1007/s00894-012-1655-1 Authors Fancui Meng, State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193 People’s Republic of China Weiren Xu, Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193 People’s Republic of China Journal Journal of Molecular Modeling Online ISSN 0948-5023 Print ISSN 1610-2940