Pt(Ⅱ), Pd(Ⅱ) and Ni(Ⅱ) Complexes Binding to the N(7) Position of Guanine: Influence on the Guanine and Watson-crick GC Base Pair

Comprehensive ab initio calculations were performed on the coordination of Pt(Ⅱ),Pd(Ⅱ) and Ni(Ⅱ) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31^* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.     

Theoretical Study on the Mechanisms of Action of Sulfurand Nitrogen-containing Amino Acid Residues with Monofunctional Guanine Adduct Formed by Antitumor Drugs trans-[PtCl2（Am）（isopropylamine）] （Am = Isopropylamine,Dimethylamine and Propylamine） and Their cis Isomers

The mechanisms of action on monofunctional guanine adducts of analogues of transplatin with aliphatic amine ligands,such as trans-[Pt（Am）（isopropylamine）（G）（H2O）] where Am represents dimethylamine,propylamine or isopropylamine and their cis isomers reacting with sulfur- and nitrogen-containing amino acid residues,were explored. Histidine and lysine residues are chosen as the model ligands of nitrogen-containing amino acid residues of proteins; meanwhile,methionine and cysteine residues are chosen as the model ligands of sulfur-containing amino acid residues of proteins. A dominating preference for sulfur-containing ligand over nitrogen-containing ligand is established. The calculated smallest activation barrier for sulfur-containing ligand is 9.9,and 21.1 kcal/mol for nitrogen-containing ligand in aqueous solution,and both of them have trans configurations. The difference in activation energy is 11.2 kcal/mol,indicating the platination of sulfur-containing amino acid residues is faster by seven to eight orders of magnitude than that of nitrogen-containing amino acid residues.     

A Quantum Chemistry Study of Inhibition Properties of Imidazole and Its Derivatives on Iron Surface Corrosion

The geometries of imidazole and its derivatives were respectively optimized by using ab initio method, and the molecular orbital energy levels and the charge densities were obtained for their optimum geometries. The frontier orbital energy levels, and the net charges of N (1) atom and the imidazole ring of those molecules were obtained with ab initio and SCC-DV-Xα methods. It was found that the inhibition properties of those compounds change with the highest occupied molecular orbital energy levels, and the net charges of N (1) atom. We took four iron atoms on the crystal plane (100) of α-iron as the surface which was used to study the adsorption towards the inhibitors. The adsorption models of the inhibitor to be adsorbed on the Fe-cluster surface were optimized with SCC-DV-Xα method. It turns out that the most favorable model is that the inhibitor molecule is adsorbed on the Fe-cluster surface in an inclined state. The calculation shows that the stabilization energies of the systems are well correlated with the inhibition efficiencies.     

A DFT Investigation on Hydrogen Adsorption Based on Alkali-metal Organic Complexes

Using density functional theory calculation based on the B3LYP method,we have studied the interactions of H2 molecules with alkali-metal organic complexes C6H6-nLin(n = 1～3),C6H5Na and C6H5K.A significant part of the electronic charge of M s orbital(Li 2s,Na 3s,K 4s) is donated to phenyl and is accommodated by H2 bonding orbital.For all the complexes considered,each bonded alkali-metal atom can adsorb up to five H2 in molecular form with the mean binding energy of 0.59,0.55 and 0.56 eV/H2 molecule for C6H6-nLin(n = 1～3),C6H5Na and C6H5K,respectively.The kinetic stability of these hydrogen-covered organometallic complexes is discussed in terms of energy gap between HOMO and LUMO.It is remarkable that these alkali-metal organic complexes can store up to 23.80 wt% hydrogen.Therefore,the complexes studied may be used as hydrogen storage materials.     

Theoretical Studies on the Hydrogen Bond Transfer and Proton Transfer between Anamorphoses of the Dihydrated Glycine Complex

The conversion between anamorphoses of the dihydrated glycine complex was studied by means of B3LYP/6-31++G**. It was found that proton transfer was accompanied by hydrogen bond transfer in the process of conversion between different kinds of anamorphoses. With proton transfer, the electrostatic action was notably increased and the hydrogen-bonding action was evidently strengthened when the dihydrated neutral glycine complex converts into dihydrated zwitterionic glycine complex. The activation energy required for hydrogen bond transfer between dihydrated neutral glycine complexes is very low (6.32 kJ·mol-1); however, the hydrogen bond transfer between dihydrated zwitterionic glycine complexes is rather difficult with the required activation energy of 13.52 kJ·mol-1 due to the relatively strong electrostatic action. The activation energy required by proton transfer is at least 27.33 kJ·mol-1, higher than that needed for hydrogen bond transfer. The activation energy for either hydrogen bond transfer or proton transfer is in the bond-energy scope of medium-strong hydrogen bond, so the four kinds of anamorphoses of the dihydrated glycine complex could convert mutually.     

Theoretical studies on structures and UV-Vis spectra of C_(70)O

Systematic studies on eight isomers of C70O were performed by means of INDO methods It has been indicated that the O atom is mainly added to the C1-C2 or C3-C3 bond and an epoxide feature with C1 symmetry is formed.Based on the optimized geometries,the UV-Vis spectra were calculated.It has been found that the main peaks of C70O resemble those of C70 and the characteristic absorptions beyond 460 nm are produced,which is m agree ment with the experimental results.Theoretical assignments about the absorptions were carried out and the reason for the red-shift of the absorptions was discussed.C70O is probably composed of four isomers according to the calculated results.     

Theory Studies on the Intermolecular Interactions of Urea Nitrate with RDX

Six fully optimized geometries of urea nitrate cation and RDX complexes have been obtained with DFT-B3LYP and MP2 methods at the 6-311++G** level. The intermolecular interaction energies have been calculated with basis set superposition error (BSSE) and zero point energy (ZPE) correction. The nature of intermolecular interaction has been revealed by the analysis of AIM and NBO. The results indicate that the greatest binding energy of urea nitrate with RDX is –82.47kJ/mol. The O–H…O and N–H…O hydrogen bonds are important intermolecular interactions of urea nitrate cation with RDX, and the origin of hydrogen bonds is the oxygen atom offering its lone-pair electrons to the σ(O-H)* or σ(O-H)* antibonding orbital. The intermolecular interactions strengthen the N–NO2 bond, leading to the reduced sensitivity of urea nitrate and RDX mixture explosive.     

Bonding and Reactivity in RB-As R Systems(R=H,F,OH,CH_3,CMe_3,CF_3,SiF_3,BO): Substituent Effects

Density functional theory-based calculations have been carried out to study the bonding and reactivity in RB-As R(R=H,F,OH,CH3,CMe_3,CF_3,SiF_3,BO)systems.Our calculations demonstrated that all the studied systems adopted bent geometry(DR-B-As≈180°andDB-As-R≈90°or less).The reason for this bending was explained with the help of a valence-orbital model.The potential energy surfaces for three possible isomers of RB-As R systems were also generated,indicating that the RB-As R isomer was more stable than R_2B-As R when R=SiF_3,CMe_3,and H.The B-As bond character was analyzed using natural bond orbital(NBO)and Wiberg bond index(WBI)calculations.The WBI values for B-As bonds in F3Si B-As SiF_3 and HB-As H were 2.254 and 2.209,respectively,indicating that this bond has some triple-bond character in these systems.While the B centers prefer nucleophilic attack,the As centers prefer electrophilic attack.     

Orbital Interaction of Epoxidation on the Same Curvature Bonds of Single-walled Carbon Nanotubes

The epoxidation of different bonds with the same bond curvature in one nano-tube including armchair,zigzag and chiral tubes was studied. The calculated results showed that for the adducts with opened C–O–C configuration,the magnitude of the binding energies was related with their corresponding bonding characteristics in HOMO,and the larger binding energies were attributed to stronger orbital interaction between one O atom and the nanotube; whereas for the adducts with 3MR structures,the binding energies were related with the changes of C–C bond length and independent of the frontier orbital interaction before and after epoxidation.     

LaCl3提高菠菜光系统Ⅱ活性的作用机制

The effect of LaCl3 on the K3Fe(CN)6 (FeCy) reduction rate and the oxygen-evolving rate of PSU particles of spinach, and the spectral characterization of the D1/D2/Cytb559 of a PSII reaction center complex consisting of three polypeptides from spinach were studied. The experimental results showed that LaCl3 could significantly accelerate the transformation from light energy to electric energy, the electron transport, water photolysis and oxygen evolution of PSII of spinach, which was related to the spectral characterization of the D1/D2/Cytb559 complex.Soret band and Q band of Chl-a of UV-vis spectrum of D1/D2/Cytb559 complex were blue shifted, and the fluorescence emission peak was blue shifted in LaCl3 treated spinach compared with that in the control. The EXAFS (extended X-ray absorption fine structure spectroscopy) revealed that La^3 was coordinated with 8 nitrogen or oxygen atoms in the first coordination shell with La-N or La-O bond length of 0.254 nm, and with 6 nitrogen or oxygen atoms in the second coordination shell with La-N or La-O bond length of 0.321 nm in the D1/D2/Cytb559 complex. The CD suggested that the secondary structure of D1/D2/Cytb559 complex have been litfie affected by the treatment of LaCl3.     

Quantum-chemical Study on the Structures and Properties of Uracil-BX3 （X = F, Cl） Complexes

1 INTRODUCTION The intermolecular interaction of bases in DNA or RNA is of immense interest and significance to che- mists and biologists alike. The interactions of these bases with metal cations, solvent molecules and other small molecules or ions would affect the struc- ture and biological properties or recognition process,which has been investigated widely[1～8]. Boron contained compounds are electron deficient com- pounds and have been extensively used as catalysts in chemical react…     

Theoretical investigation of adenine–BX3 (X=F,Cl) complex

Geometries and binding energies are predicted at B3LYP/6-311+G* level for the adenine–BX₃ (X=F,Cl) systems and four conformers with no imaginary frequencies have been obtained for both adenine–BF₃ and adenine–BCl₃, respectively, and single energy calculations using much larger basis sets (6-311+G(2df,p)) and aug-cc-pVDZ were carried out as well. The most stable conformer is BF₃ or BCl₃ connected to N₃ of adenine and with the stabilization energy of 22.55 or 20.59 kcal/mol at B3LYP/6-311+G* level (BSSE corrected). The analyses for the combining interaction between BX₃ and adenine with natural bond orbital method (NBO) and the atom-in-molecules theory (AIM) have been performed. The results indicate that all the conformers were formed with σ–p type interactions between adenine and BX₃, in which pyridine-type nitrogen or nitrogen atom of amino group offers its lone pair electron to the empty p orbital of boron atom and the concomitances of charge transference from adenine to BX₃ were occurred. Frequency analysis suggested that the stretching vibration of BX₃ underwent a red shift in complexes. Adenine–BF₃ complex was more stable than adenine–BCl₃ although the distance of B–N is shorter in the later.     

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.04, and 8.19 kcal mol(-1), respectively, at BP86/6-311++G(3df,3pd)//B3LYP /6-311++G(3df,3pd) level). Their origin of the cis-preferred difference in energy was investigated with natural bond orbital (NBO) analysis to show that the "cis effect" came mainly from antiperiplanar interactions (AP effect) between the nitrogen lone pair and the neighboring antibonding orbital of the N-X bond (n(N) --> sigma(N'X'*)). The delocalization of halogen lone-pair into the antibonding orbital of the N=N bonds (the LP effects) was also found to enhance the cis preference by 1.20 to 6.58 kcal mol(-1), depending on the substituted halogen atom. The total amount of the AP effect increased as the halogen atom became larger, and the increased AP effect promoted the triple-bond-like nature of the N=N bond (shorter N=N bond length and wider NNX angle). The greater AP effect also made the N'-X' bond easier to cleave (longer N-X bond length), and a higher energy level than that of the nitrogen lone pair was found in the N-Br bonding orbital in 1,2-dibromodiazenes, thus indicating the significant instability of this molecule. The degradability of the N-Cl bond in 1,2-dichlorodiazenes and the fair stability of the N-F bond in 1,2-fluorodiazenes were also confirmed theoretically, and were found to be consistent with the previous experimental and theoretical reports. These results clearly indicate the dominance of lone-pair-related hyperconjugations on the basic electronic structure and energetic natures of 1,2-dihalodiazene systems.     

Structure and Stability of Isomers of the Promising Interstellar Molecule PC3O

DFT/B3LYP/6-311G(d) and CCSD(T)/6-311G(2d) single-point calculations are carried out for exploring the doublet potential energy surface (PES) of PC₃O, a molecule of potential interest in interstellar chemistry. A total of 29 minima connected by 65 interconversion transition states are located. The structures of the most relevant isomers and transition states are further optimized at the QCISD level followed by CCSD(T) single-point energy calculations. At the CCSD(T)/6-311G(2df)//QCISD/6-311G(d)+ZPVE level, the global minimum is the quasi-linear structure PCCCO 1 (0.0 kcal/mol) with a great kinetic stability of 47.9 kcal/mol, and the cumulenic form features largely in its resonance structures. Moreover, the chainlike isomer OPCCC 3 (64.5) and five-membered-ring species cPCCCO 19 (77.8) possess considerable kinetic stability of about 18.0 kcal/mol. All these three isomers are very promising candidates for future experimental and astrophysical detection. Additionally, a three-membered-ring isomer CC-cCOP 10 (69.6) has slightly lower kinetic stability of around 15 kcal/mol and may also be experimentally observable. Possible formation mechanisms of the four stable isomers in interstellar space are discussed. The present research is the first attempt to study the isomerization and dissociation mechanisms of PC _n O series. The predicted spectroscopic properties, including harmonic vibrational frequencies, dipole moments and rotational constants for the relevant isomers, are expected to be informative for the identification of PC₃O in laboratory and interstellar medium.     

Global investigation on the potential energy surface of CH3CN: application of the scaled hypersphere search method

An extensive quantum chemical study of the potential energy surface (PES) for all possible isomerization and dissociation reactions of CH3CN is reported at the DFT (B3LYP/6-311++G(d,p)) and CCSD(T)/ cc-pVTZ//B3LYP/6-311++G(d,p) levels of theory. The pathways around the equilibrium structures can be discovered by the scaled hypersphere search (SHS) method, which enables us to make a global analysis of the potential energy surface for a given chemical composition in combination with a downhill-walk algorithm. Seventeen equilibrium structures and 59 interconversion transition states have been found on the singlet PES. The four lowest lying isomers with thermodynamic stability are also kinetically stable with the lowest conversion barriers of 49.69-101.53 kcal/mol at the CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) level, whereas three-membered-ring isomers c-CH2NCH, c-CH2CNH, and c-CHNHCH can be considered as metastable intermediates which can further convert into the low-lying chain-like isomers and higher lying acyclic isomers with the lowest conversion energies of 21.70-59.99 kcal/mol. Thirteen available dissociation channels depending on the different initial isomers have been identified. A prediction can be made for the possible mechanism explaining the migration of a hydrogen atom in competition with the CC bond dissociation. Several new energetically accessible pathways are found to be responsible for the migration of the hydrogen atom. The present results demonstrate that the SHS method is an efficient and powerful technique for global mapping of reaction pathways on PESs.     

An Ab Initio Molecular Orbital Study of Isophosphinines

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single-point total energy calculation are reported for phosphinine and 13 isophosphinines 7-19 . Isomers 7-11 with an allenic system are calculated to be 8-18 kcal mol m 1 more stable than structures 12-17 with an acetylenic moiety. The calculated energy difference (66.19 kcal mol m 1 ) between phosphinine and the most stable isophosphinine (1-phospha-1,2,4-cyclohexatriene, 10 ) is smaller than the difference (78.96 kcal mol m 1 ) between benzene and the most stable isobenzene (cyclohexa-1,2,4-triene, 2 ). The isophosphinines 18 and 19 , with a butatriene moiety, are calculated to be the least stable isomers.     

胸腺嘧啶-BH3构型与性质的DFT和MP2研究

Geometries and combination energies are predicated at B3LYP / 6-31G（d）and MP2 / 6-31G（d）level for thymine-BH3 complexes and 5 geometries have been obtained. Then single point energy calculations using larger basis sets（6-311 + G（2df）and aug-cc-pVDZ）and vibrational analysis and natural bond orbital analysis are carried out on the 5 optimized conformers. The outcome indicates that the conformers with the boron atom combined with O directly are relatively stable ones,（a）and（b）,with the combination energies of 90. 4 and 88. 0 kJ / mol （B3LYP / 6-31G（d）,BSSE corrected）. The fact is that the nitrogen atom offers electron to the empty atomic orbital of boron which produces the conformers（c）and（d）. Only one conformer is found which is formed because two carbon atoms offer π electron to the empty orbital of boron. The charge transference exists in all the conformers. The combination energies have a good line relation with their charge transference. The calculated results show that when the complex forms their IR spectrum moved to the red side and the frequency shifts are relative to the stabilities of the complexes.     

CH3SH…HOO开壳型氢键复合物的结构及其电子密度拓扑性质

在DFT-B3LYP/6-311++G**水平下求得CH3SH…HOO复合物势能面上的稳定构型. 计算结果表明, 在HOO以其O8—H7作为质子供体与CH3SH分子中的S5原子为质子受体形成的氢键复合物1和2中, O8—H7明显被“拉长”, 且其伸缩振动频率发生显著的红移, 红移值分别为330.1和320.4 cm-1; 在CH3SH分子以其S5—H6作为质子供体与HOO的端基O9原子为质子受体形成的氢键复合物3和4中, 也存在类似的情况, 但S5—H6伸缩振动频率红移不大. 经MP2/6-311++G**水平计算的4种复合物含BSSE校正的相互作用能分别为-20.81, -20.10, -4.46和-4.52 kJ/mol. 自然键轨道理论(NBO)分析表明, 在CH3SH…HOO复合物1和2中, 引起H7—O8键长增加的因素包括两种电荷转移, 即孤对电子n1(S5)→σ*(H7—O8)和孤对电子n2(S5)→σ*(H7—O8), 其中后者为主要作用. 在复合物3和4中也有相似的电荷转移情况, 但轨道间的相互作用要弱一些. AIM理论分析结果表明, 4个复合物中的S5…H7间和O9…H6间都存在键鞍点, 且其Laplacian量▽2ρ(r)都是很小的正值, 说明这种相互作用介于共价键和离子键之间, 偏静电作用为主.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

An Ab Initio Molecular Orbital Study of Valence Bond Isomers of Silabenzene and Phosphabenzene

Ab initio molecular orbital calculation at HF/6-31G*, HF/6-31G**, HF/6-311G**, HF/6-311++G**, RMP2-FC/6-31G*, and B3LYP/6-31G* levels of theory for geometry optimization and MP4(SDQ)/6-31G* for a single point total energy calculation are reported for silabenzene ( 7 ), phosphabenzene ( 8 ) and 16 valence bond isomers of silabenzene and phosphabenzene ( 9-24 ). The calculated energy difference (19.78 kcal mol m 1 ) between silabenzene and the most stable valence bond isomer of silabenzene (1-silabenzvalene, 9 ) is much smaller than the difference (73.60 kcal mol m 1 ) between benzene and benzvalene ( 2 ). The energy difference between phosphabenzene and the most stable valence bond isomer of phosphabenzene (1-phosphabenzvalene, 17 ) is calculated to be 43.29 kcal mol m 1 .