Theoretical studies on the structures and isomerization of the LiSiF3 system

Various possible isomers of LiSiF₃ system and isomerization between them have been studied at G2(MP2) level usingab initio calculations. The relative energies of four minimum points on the potential energy surface are-128.6,-194.3,-12.7 and-122.8 kJ/mol (taking the sum of the energies of LiF and SiF₂ as zero). The structural energy of the four-membered ring that contains three F-Si-F-Li four-membered rings with C_3v symmetry is the lowest. The highest potential barrier for the isomerization of the remaining three- or four-membered structure is 12.5 kJ/ mol. Project supported by the National Natural Science Foundation of China (Grant No. 29673026).     

Theoretical studies on the structures and isomerization of the LiSiF_3 system

Various possible isomers of LiSiF_3 system and isomerization between them have been studied at G2(MP2) level using ab initio calculations. The relative energies of four minimum points on the potential energy surface are -128.6, -194.3, -12.7 and -122.8 kJ/mol (taking the sum of the energies of LiF and SiF_2 as zero) . The structural energy of the four-membered ring that contains three F-Si-F-Li four-membered rings with C_(3v) symmetry is the lowest. The highest potential barrier for the isomerization of the remaining three-or four-membered structure is 12.5 kJ/mol.     

类氮烯HNLiF构型和异构化反应理论研究

本文在量子化学从头算水平上, 用RHF/3-21G方法和梯度解析技术研究了类氮烯HNLiF势能面的主要特征, 得到三种平衡几何构型和两个异构化反应过渡态构型。平衡构型的能量按三元环构型、σ构型和p构型的顺序递增。三元环构型为类氮烯的主要存在形式。文中分析了各构型特点并给出其电荷分布和前线轨道。为用类氮烯合成含氮化合物提供了理论依据。     

Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore

We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.     

团簇Fe4P异构化反应的理论研究

采用B3LYP泛函以及程序内置的LANL2DZ基组并结合拓扑学原理,运用Gaussian 09程序对团簇Fe4 P的16种初始构型进行优化,得到8种优化构型.依据过渡态理论,从化学热力学和动力学方面对团簇Fe4 P的异构化反应进行研究,结果表明:二重态构型的稳定性最大且自旋多重度会影响团簇Fe4 P异构化转化的反应程度...     

Theoretical and experimental studies of the structure and intermolecular interactions in 2-biphenylmethanole

The crystalline structure of 2-biphenylmethanol has been investigated by the radiographic method at room temperature, and its IR transmission spectra were measured in the 400–4000 cm^?1 range. Structural-dynamic models of free molecules of 2-biphenylmethanol, biphenyl and methanol, hydrogen-bonded complexes of 2-biphenylmethanol with methanol and a tetramer of methanol molecules have been built by the density functional method (B3LYP/6-31G*). The structure, the energy, mechanical and electro-optical parameters, the frequency and intensity of normal vibrations in IR spectra of each of the mentioned molecular systems were calculated. The crystalline structure of 2-biphenylmethanol, its features determined by the hydrogen bond formation in the crystal has been found, its structure-forming role and energy were assessed, and IR spectra interpreted on the basis of single crystal X-ray diffraction data, the analysis of measured IR spectra, and results of molecular modeling.     

Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy, and electrochemistry

Quantum mechanical calculations at the density functional theory (DFT) level have been performed on diruthenium tetracarboxylates of different levels of molecular complexity: from unsolvated monomers to oligomers. The agreement between the calculated and experimental molecular structures and vibrational modes of the simple [Ru2(micro-O2CCH3)4]0/+ and [Ru2(micro-O2CCH3)4(H2O)2]0/+ systems made us confident in our calculation methodology. Therefore, it has been applied to the analysis of two different kinds of properties of these compounds: the trends in the UV/vis spectroscopy and electrochemistry along the [Ru2(micro-O2CCH3)4X2]- (X=Cl-, Br-, I-) series, and the crystalline polymorphism related to the polymeric strand conformation in extended Ru2(micro-O2CR)4Cl compounds. For the [Ru2(micro-O2CCH3)4X2]- series, we report new spectroscopic and electrochemical results and interpret the trends on the basis of time dependent DFT-polarized continuum model calculations, local charge and spin analysis, and X donor properties. As far as the polymeric conformation is concerned, it has been previously suggested that the Ru-Cl-Ru angle results from a compromise between packing, orbital overlap, and microsegregation. Our calculations on [Ru2(micro-O2CCH3)4Cl]2Cl- and [Ru2(micro-O2CCH3)4Cl]3Cl- oligomers provide insights on the influence of the first two factors on the strand conformation and allows a suggestion on what is the equatorial aliphatic chain's influence on this issue.     

Theoretical and experimental investigation of the energetics of cis-trans proline isomerization in peptide models

The energetics of cis-trans proline isomerization in small peptide models have been investigated using the hybrid density functional theory method B3LYP with a 6-31+G* basis set. The molecules studied are models for the phospho-Ser/Thr-Pro substrate for Pin-1, a peptidyl-prolyl isomerase (PPIase) involved in cell division. Pin-1 requires phosphorylation of a Ser or Thr residue adjacent to a Pro residue in the substrate and catalyzes cis-trans isomerization about the proline amide bond. The dihedral angle that would correspond to the reaction coordinate for isomerization of the omega peptide bond was investigated for several small models. Relaxed potential energy scans for this dihedral angle in N-methylacetamide, 1, N,N-dimethylacetamide, 2, acetylpyrrolidine, 3 and acetylproline, 4, were carried out in 20 degrees steps using the B3LYP/6-31+G* level of theory. In addition, similar scans were carried out for 1-4 protonated on the acetylamide carbonyl oxygen. Optimized structures for 1-4 protonated on the amide nitrogen were also obtained at B3LYP/6-31+G*. Relative proton affinities were determined for each site at various angles along the reaction coordinate for isomerization. The relative proton affinities were anchored to experimental gas phase proton affinities, which were taken from the literature for 1 and 2, or determined in an electrospray ionization-quadrupole ion trap instrument using the extended kinetic method for 3 and 4. Proton affinities of 925 +/- 10 and 911 +/- 12 kJ/mol were determined for 3 and 4, respectively. These studies suggest that the nitrogen atom in these amides becomes the most basic site in the molecule at a dihedral angle of ca. 130 degrees . In addition, the nitrogen atoms in 2-4 are predicted to attain basicities in the range 920-950 kJ/mol, making them basic enough to be the preferred site for hydrogen bonding in the Pin-1 active site, in support of the proposed mechanism for PPIases.     

A theoretical study of C4H5N isomers: Comparison of cyano and isocyano as substituents

Ab initio molecular orbital calculations using a 3-21G basis set have been used to optimize geometries for pyrrole, CH₃(X)CCH₂, CH₃(H)CCHX (both cis and trans), c-C₃H₅X, and CH₂CHCH₂X, where X is CN and NC. In all the alkenyl derivatives methyl groups are found to adopt the conformation in which the methyl hydrogen eclipses the double bond. 6-31G*∥3-21G level calculations show the alkenyl cyanides to be of similar energy to pyrrole, but the isocyanides are ～20 kcal mol^?1 higher in energy. For both substituents the cyclopropyl derivatives are higher in energy by ～10 kcal mol^?1. At the 6-31G* level ring strain is 27.7 kcal mol^?1 for the cyanide and 30.6 kcal mol^?1 for the isocyanide. Data on the relative energies of RCN and RNC are compared when R is (i) a saturated hydrocarbon, (ii) an unsaturated hydrocarbon, (iii) an α-carbenium ion, (iv) an allyl cation, and (v) an α-carbanion.     

Theoretical and experimental studies on formation of diethylzinc-triphenylphosphine complex

This work is mainly focused on understanding the complex-forming behavior of diethylzinc with neutral phosphine ligands such as triphenylphosphine (PPh₃) to yield [Zn(PPh₃)₂Et₂]. The complex formation in solution is observed in the presence of a large excess of diethylzinc, but leaving an insoluble solid on aging. The product formed in solution was analyzed by spectroscopic data. ³¹P-NMR was also used as a tool to observe this behavior, i.e., the disappearance of the chemical shift of PPh₃ (δ -5.45) requires 14-fold excess of ZnEt₂ in solution. The alkyl chains reduce the Lewis acidity on Zn and thereby the formation of phosphine adducts is restricted. Results obtained from orbital analyses calculations reveal that the LUMO appears to be asymmetrically distributed, and localized on one of the PPh₃ ligands. The length of alkyl chains also influence the stability of [Zn(PPh₃)₂R₂] and the longer chains on Zn impart less stability.     

Theoretical studies on the structure and spectroscopic properties of pseudohalides

Pseudohalogen-containing compounds have attracted significant interest among nonmetal chemists and theorists, not only owing to their potential use in various fields but also due to difficulties in their experimental preparation and characterization. Since its introduction in 1925, the pseudohalide principle has been used extensively and, therefore, a remarkable progress has been made in the experimental and theoretical research on the compounds of this kind. In this work, we review studies on structural investigations and theoretical characterizations of several pseudohalide-containing compounds in order to contribute to better understanding of the chemistry of many such species.     

无机不饱和类烯H~2NBLiF的构型及异构化反应的理论研究

用HF/D95^*^*解析梯度方法研究了无机不饱和类烯H~2NBLiF的结构,共得到4个平衡构型和3个异构化反应的过渡态构型。动力学分析表明,其中两种平衡构型是它们存在和参加化学反应的基本构型。分析了各平衡构型的结构特点及稳定性,给出了各构型的Mulliken集居数,并简单讨论了两种基本构型的化学活性。     

Theoretical and experimental studies on the Raman spectra of electrosynthesized polynaphthalene

Polynaphthalene (Pnap) was electrosynthesized through the direct oxidation of naphthalene in boron trifluoride diethyl etherate and was characterized with IR and Raman spectroscopy, matrix‐assisted laser desorption/ionization time‐of‐flight mass spectroscopy, and thermogravimetric analysis. Raman spectra of oligonaphthalene were calculated with Gaussian 98 at the B3LYP/6‐31G* level. Combining the computational and experimental results, we assigned the Raman bands of pristine Pnap. The Raman bands related to the chain‐stretching vibrations of Pnap around 1600 cm^?1 shifted to higher wave numbers as the polymerization degree increased. This phenomenon was in contrast to that of other conducting polymers bearing simple aromatic rings, such as polythiophene and polyfuran. The reason was that the condensed ring of Pnap and the steric repulsion of the interring hydrogen atoms prevented the elongation of conjugation sequences with the polymer chain length. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 241–251, 2005     

Theoretical and experimental studies on the adsorption of aromatic compounds onto cellulose

The adsorption of several aromatic compounds over microcrystalline cellulose was studied by molecular modeling and experimentally using gas chromatography. Experimental adsorption enthalpies were obtained from an equation based on Clausius-Clapeyron formalism and the temperature dependence of retention volume at infinite dilution. Four different cellulose surfaces (three crystalline (110, 100, and 010) and one amorphous) were modeled. Overall strong agreement was observed between the experimental and theoretical work with 84% of the adsorbate-cellulose systems having differences between measured and predicted values of less than 20%. Based on both calculated and experimental data, a morphology for the microcrystalline cellulose as a weighted combination of the four surfaces was proposed: 39% (110), 28% (100), 10% (010), and 23% amorphous. By adopting this distribution, differences between experimental and weighted average predicted adsorption energies were 10% or less for 14 out of 17 compounds; a maximum of 15% was observed for guaiacol. Experimental results for monosubstituted aromatic compounds revealed that adsorption enthalpies are related to the hydrophilic/hydrophobic character of the substituent groups: 3.5 kJ mol(-1) for a methyl group, 15.7 kJ mol(-1) for a double bond, 21.0 kJ mol(-1) for a methoxyl group, 22.8 kJ mol(-1) for a carbonyl group, and 27.6 kJ mol(-1) for a hydroxyl group. These tendencies were confirmed by modeling, except for the aldehyde carbonyl group, where an overestimation of 10.8 kJ mol(-1) was observed. Analysis of experimental and predicted adsorption enthalpies of multisubstituted aromatic compounds suggests that the efficiency of their interaction with cellulose depends on a compromise between the roughness of the cellulose surface and their conformational adaptability.     

Theoretical and experimental studies of the all gas-phase iodine laser

All gas-phase iodine laser (AGIL) powered by the decomposition of nitrogen trichloride (NCl₃) is studied. This reaction scheme uses commonly available reagents and reaction paths are milder than the previously studied azide-based AGIL. Theoretical studies revealed the necessary operational conditions for achieving positive gain. An apparatus is made based on the results of the theoretical works. Positive gain at iodine I(² P _1/2)-I(² P _3/2) transition is observed for the first time. The article is published in the original.     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

Theoretical study on the isomerization and tautomerism in barbituric acid

Isomerization and tautomerism of 16 isomers of barbituric acid (BA) were studied at the MP2 and B3LYP levels of theory. Activation energies (E _a), imaginary frequencies (υ), and Gibbs free energies (ΔG ^#) of the amine-imine and keto-enol tautomerisms and O–H internal rotations were calculated. The activation energies of amine-imine tautomerisms were in the range of 110–200 kJ/mol and for keto-enol tautomerisms were larger than 200 kJ/mol. The calculated activation energies of internal O–H rotations were smaller than 60 kJ/mol. Effect of micro-hydration on the transition state structures and activation energies of the tautomerisms were also investigated. Water molecule catalyzed the tautomerisms and decreased the activation energies of both the amine-imine and keto-enol tautomerisms about 100–120 kJ/mol.     

Theoretical and experimental studies on the structure-antioxidant activity relationship of synthetic 4-methylcoumarins

The development of antioxidants as useful drugs for the treatment of neurodegenerative diseases such as Alzheimer??s is extremely challenging in medicinal chemistry. Coumarins have attracted great attention as possible therapeutic tools against oxygen radicals in human degenerative diseases. In order to establish the possible structure-antioxidant activity relationship, a series of twenty four 4-methylcoumarin derivatives were examined by employing reducing power measurements, and comparison with bond dissociation enthalpy and ionization potential calculations. Based on the reducing potency of 4-methylcoumarin derivatives with respect to trolox, these compounds were classified into five groups as ??most active??, ??more active??, ??moderately active??, ??less active?? and ??inactive?? derivatives. The presence of hydroxyl groups is an essential requirement for the activity, and substitution of hydroxyl groups by methoxy groups leads to non-active derivatives. The results revealed that dihydroxyl groups in the ortho position show a better antioxidant activity with respect to dihydroxyl groups in the meta position. This is ascribed to the ability to construct more stable 4-methylcoumarin radical intermediates by rearrangement of intra-molecular hydrogen bonding. Our findings indicate that other important factors to enhance the antioxidant activity of coumarins are the number of hydroxyl groups, the presence of ester substitutions and a thiono functional group on the pyrone ring. However, bond dissociation enthalpy and ionization potential calculations alone are not sufficient to identify the best antioxidant structures. As a result, chemical and functional properties of molecules such as 4-methylcoumarins should be examined as a whole entity, considering all substitutions versus a single substitution to design functional compounds with good antioxidant activity.