Applications of natural orbitals for chemical valence in a description of bonding in conjugated molecules

Natural orbitals for chemical valence (NOCV) were used to describe bonding in conjugated pi-electron molecules. The 'single' C-C bond in trans-1,3-butadiene, 1,3-butadiene-1,1,4,4-tetra-carboxilic acid, 1,3,5,7-octatetraene, and 11-cis-retinal was characterized. In the NOCV framework, the formation of the sigma-bond appears as the sum of two complementary charge transfer processes from each vinyl fragment to the bond region, and partially to the other fragment. The formation of the pi-component of the bond is described by two pairs of NOCV representing the transfer of charge density from the neighboring 'double' C-C bonds. The NOCV eigenvalues and the related fragment-fragment bond multiplicities were used as quantitative measures of the sigma- and pi- contributions. The sigma-component of the 'single' C-C bonds appears to be practically constant in the systems analyzed, whereas the pi-contributions increase from butadiene (ca. 7.5%) to retinal (ca. 14%).     

Electronic structure and bonding of the dinuclear metal M<Subscript>2</Subscript>(CO)<Subscript>10</Subscript> decacarbonyls: applications of natural orbitals for chemical valence

The nature of the chemical metal–metal bond in M₂(CO)₁₀ (M?=?Mn, Re, Tc) dinuclear decacarbonyls complexes was investigated for the first time using the natural orbital chemical valence (NOCV) approach combined with the extended transition state (ETS) for energy decomposition analysis (EDA). The optimized geometries carried out at different levels of theory BP86, BLYP, BLYPD and BP86D, showed that the latter method, i.e., BP86D, led to the best agreement with X-ray experimental measurements. The BP86D/TZP results revealed that the computed covalent contribution to the metal–metal bond are 60.5%, 54.1% and 52.0% for Mn–Mn, Re–Re and Tc–Tc, respectively. The computed total interaction energies resulting from attractive terms (ΔE _orb and ΔE _eles), correspond well to experimental predictions, based on bond lengths and energy interaction analysis for the studied complexes.     

Theoretical study on the proton chemical shifts of hydrogen bonded nucleic acid bases.

The variation of the proton chemical shifts due to the formation intermolecular hydrogen bonds is computed for a number of complexes which can be formed between the bases of the nucleic acids. The shifts expected for the isolated base pairs, in particular for the G-N1 H, T(or U)-N3H protons and the protons of the amino groups of A, G c, when combined with previous computations on the shifts to be expected upon base stacking, may enable a refined analysis of the high resolution NMR spectra of self complementary polynucleotides or tRNAs. Two examples are presented of a direct computation of proton shits associated with helix-coil transitions, helpful for deducing the helical structure in solution.     

U-1分解草酸的检测及其降低草酸毒性的研究

草酸是油菜菌核病病菌(Sclerotinia sclerotiorum)致病的重要因子。以实验室分离得到的草酸分解菌U-1为材料,研究U-1分解草酸的能力及其降低草酸对油菜毒性的作用机理。检测U-1分解草酸的能力,即以草酸、U-1 草酸分别培养24 h后,利用高效液相色谱仪检测草酸的含量;研究U-1抑制草酸对油菜毒害的作用机理,即分别以清水、U-1、草酸、U-1 草酸处理油菜叶片,检测不同处理对油菜叶片中防卫反应0相关酶(PAL酶、PPO酶和PO酶)变化的影响。研究结果表明,与草酸单独处理组相比,U-1 草酸处理组草酸含量显著降低;U-1可以显著抑制草酸对油菜中PAL酶、PPO酶和PO酶活性的作用。     

Theoretical mechanistic study of the formic acid decomposition assisted by a Ru(II)-phosphine catalyst

There is considerable evidence, which we discuss, indicating that compressibility and available free space in the crystal lattice are among the factors that govern the sensitivity of an explosive compound. Expanding and extending earlier work, we demonstrate, for 25 explosives, that there is an overall general tendency for greater impact sensitivity as the estimated free space per molecule increases. More specific relationships can be discerned by looking at subgroups of the compounds. The nitramine sensitivities, most of which are quite high, increase nearly linearly but only very gradually with free space. The nitroaromatics cover a wide range of sensitivities but all have an approximately similar intermediate level of free space. The remaining types of compounds show a reasonable sensitivity–free space relationship with one outlier: FOX-7 (1,1-diamino-2,2-dinitroethylene).     

Theoretical study on the thermal decomposition of model compounds for Poly (dialkyl fumarate)

The thermal decomposition of model compounds for poly (dialkyl fumarate) was studied by using ab initio and density functional theory (DFT) calculations. To determine the most favorable reaction pathway of thermal decomposition, geometries, structures, and energies were evaluated for reactants, products, and transition states of the proposed pathways at the HF/6-31G(d) and B3LYP/6-31G(d) levels. Three possible paths (I, II and III) and subsequent reaction paths (IV and V) for the model compounds of poly (dialkyl fumarate) decomposition had been postulated. It has been found that the path (I) has the lowest activation energy 193.8 kJ mol⁻¹ at B3LYP/6-31G(d) level and the path (I) is considered as the main path for the thermal decomposition of model compounds for poly (dialkyl fumarate).      

10个马齿苋类型的脂肪酸和草酸含量分析

该研究采用气相色谱和比色法测定了10种不同来源马齿苋茎、叶中的脂肪酸和草酸含量。结果表明:(1)脂肪酸和草酸在10个不同类型马齿苋茎、叶中的含量均表现出一定的差异显著性。(2)与叶片相比,茎中的脂肪酸含量相对较低;马齿苋茎、叶中以多元不饱和脂肪酸为主;共测出两种多元不饱和脂肪酸,分别是亚麻酸(ω-3脂肪酸)和亚油酸(ω-6脂肪酸);不同类型马齿苋叶片和茎中ω-3和ω-6脂肪酸分别占脂肪酸总量的62.71%~70.91%和9.30%~13.31%,以及26.04%~36.02%和31.61%~43.19%,‘金湖’‘南阳’马齿苋叶片和‘金湖’马齿苋茎中!-3脂肪酸含量显著高于其他类型;国产马齿苋类型,尤其是茎中的!-6/!-3比例明显小于国外马齿苋类型。(3)马齿苋茎中的草酸含量明显高于叶;除‘山东’‘Iran’和‘Pakistan’马齿苋茎中的草酸显著积累外,其他类型马齿苋茎中的草酸含量差异不显著。因此,马齿苋适宜早采收;‘金湖’和‘南阳’,尤其是‘金湖’类型的马齿苋是一种值得研究和推荐的马齿苋类型。     

The effect of ring size on vibrational spectroscopy and hydrogen bonding properties for the complexes between small ring carbonyl compounds with HF and HCl: Theoretical analysis

The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom.     

Benchmark,DFT assessments,cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes

Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields.

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Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexes?

     

Effects of amine ligand bulk and hydrogen bonding on the rate of reaction of platinum(II) diamine complexes with key nucleotide and amino acid residues

NMR spectroscopy has been used to observe the effects of the amine ligand on the rate of reaction of platinum diamine and triamine complexes with DNA and protein residues. Whereas [Pt(dien)Cl]Cl and [Pt(dien)(D(2)O)](2+) have been known to react faster with thioether residues such as N-AcMet than with 5'-GMP, we found that [Pt(Me(4)en)(D(2)O)(2)](2+) appeared to react faster with 5'-GMP. To quantitatively assess the factors influencing the rates of reaction, rate constants at pH 4 were determined for the reactions of [Pt(en)(D(2)O)(2)](2+) [en = ethylenediamine] and [Pt(Me(4)en)(D(2)O)(2)](2+) with N-AcMet, N-AcHis, 5'-GMP, and Guo (guanosine). In each case the less bulky complex ([Pt(en)(D(2)O)(2)](2+)) reacts more quickly than does the bulkier [Pt(Me(4)en)(D(2)O)(2)](2+), as expected. Both complexes reacted faster with 5'-GMP; however, analysis of the rate constants suggests that the [Pt(en)(D(2)O)(2)](2+) complex favors reaction with 5'-GMP due to hydrogen bonding with the 5'-phosphate, whereas [Pt(Me(4)en)(D(2)O)(2)](2+) disfavors reaction with N-AcMet due to steric clashes. Bulk had relatively little effect on the rate constant with N-AcHis, suggesting that peptides or proteins that coordinate via His residues would not have their reactivity affected by bulky diamine ligands.     

Quantitative and chemical fingerprint analysis for quality control of Rhizoma Coptidischinensis based on UPLC-PAD combined with chemometrics methods

To control the quality of Rhizoma Coptidis, a method based on ultra performance liquid chromatography with photodiode array detector (UPLC-PAD) was developed for quantitative analysis of five active alkaloids and chemical fingerprint analysis. In quantitative analysis, the five alkaloids showed good regression (R > 0.999 2) within test ranges and the recovery of the method was in the range of 98.4- 100.8%. The limit of detections and quantifications for five alkaloids in PAD were less than 0.07 and 0.22 μg/ml, respectively. In order to compare the UPLC fingerprints between Rhizoma Coptidis from different origins, the chemometrics procedures, including similarity analysis (SA), hierarchical clustering analysis (HCA), principal component analysis (PCA) were applied to classify the Rhizoma Coptidis samples according to their cultivated origins. Consistent results were obtained to show that Rhizoma Coptidis samples could be successfully grouped in accordance with the province of origin. Furthermore, five marker constituents were screened out to be the main chemical marker, which could be applied to accurate discrimination and quality control for Rhizoma Coptidis by quantitative analysis. This study revealed that UPLC-PAD method was simple, sensitive and reliable for quantitative and chemical fingerprint analysis, moreover, for the quality evaluation and control of Rhizoma Coptidis.     

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.     

Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the acetic acid dimer in the gas phase

In the paper are described studies of the double proton transfer (DPT) processes in the cyclic dimer of acetic acid in the gas phase using Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD). Structures, energies and proton trajectories have been determined. The results show the double proton transfer in 450 K. In the classical dynamics (CPMD) a clear process mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. The DPT mechanism is also asynchronic when quantum tunneling has been allowed in the simulation. It has been found that the calculated values of barrier height for the proton transfer depends very strongly on the used approaches. Barrier received from the free-energy profile at the CPMD level is around 4.5 kcal mol^-1 whereas at the PIMD level is reduced to 1 kcal mol^-1. The nature of bonding in acetic acid dimer and rearrangement of electron density due to the proton movement has been also studied by the topological analysis of Electron Localization Function and Electron Localizability Indicator function.     

Phylogeny of Syllidae (Polychaeta) based on combined molecular analysis of nuclear and mitochondrial genes

The phylogeny of Syllidae is assessed in a combined analysis of molecular data from nuclear 18S rDNA and mitochondrial 16S rDNA and cytochrome c oxidase subunit I. In total, 103 terminal taxa are examined: 88 syllids in the four classical subfamilies Eusyllinae, Exogoninae, Syllinae and Autolytinae, as well as 15 outgroup taxa from Phyllodocida and Eunicida. Maximum parsimony analysis of the combined data set indicates that Syllidae, as currently delineated, is monophyletic, though not with very high support values. Astreptosyllis Kudenov & Dorsey, 1982, Streptosyllis Webster & Benedict, 1884 and SyllidesÖrsted, 1845 comprise a monophyletic group well differentiated from the rest of the Syllidae. The subfamilies Autolytinae and Syllinae are monophyletic. Exogoninae is monophyletic, although not well supported, and Eusyllinae is clearly paraphyletic. Results corroborate previous studies about the evolution of reproductive modes in that epigamy is the plesiomorphic condition and schizogamy appeared independently in Autolytinae and Syllinae. © The Willi Hennig Society 2007.     

NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths

Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the amide protons involved in hydrogen bonds in solution show no measurable protection from exchange in water, cautioning against a direct correspondence between hydrogen bonding and hydrogen exchange protection. The N to O atom distance across a hydrogen bond, R(NO), is related to the size of the (3h)J(NC') trans hydrogen bond coupling constant and the amide proton chemical shift. Both NMR parameters show poorer agreement with the 2.0-A resolution X-ray structure of the cold-shock protein studied by NMR than with a 1.2-A resolution X-ray structure of a homologous cold-shock protein from the thermophile B. caldolyticus. The influence of crystallographic resolution on comparisons of hydrogen bond lengths was further investigated using a database of 33 X-ray structures of ribonuclease A. For highly similar structures, both hydrogen bond R(NO) distance and Calpha coordinate root mean square deviations (RMSD) show systematic increases as the resolution of the X-ray structure used for comparison decreases. As structures diverge, the effects of coordinate errors on R(NO) distance and Calpha coordinate root mean square deviations become progressively smaller. The results of this study are discussed with regard to the influence of data precision on establishing structure similarity relationships between proteins.