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1.
A systematic comparison is made between experimental and computational data gained on vicinal disulfide bridges in proteins and peptides. Structural and stability data of ab initio and density functional theory (DFT) calculations on the model compound 4,5-ditiaheptano-7-lactam and the model peptide HCO-ox-[Cys-Cys]-NH2 at RHF/3-21G*, B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory are presented. The data on Xxx-Cys-Cys-Yyy type amino acid sequence units retrieved from PDB SELECT, along with data on sequence units that have vicinal disulfide bridge, taken from the Brookhaven Protein Data Bank, are conformationally characterized. Amino acid backbone conformations, cis-trans isomerism of the amide bond between the two cysteine residues, and ring puckering are studied. Ring puckers are characterized by their relation to the conformers of the parent 4,5-ditiaheptano-7-lactam. Computational precision and accuracy are proved by frequency calculation and solvent model optimization on selected conformers. It is found that the ox-[Cys-Cys] unit is able to accept types I, II, VIa, VIb, and VIII beta-turn structures.  相似文献   

2.
Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol-1, mainly localized around 37±2 kcal·mol-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [2s + 2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.  相似文献   

3.
In this work, the Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 2-aminobiphenyl (2ABP) were recorded in the solid phase. The optimised geometry, frequency and intensity of the vibrational bands of 2ABP were obtained by the density functional theory (BLYP and B3LYP) methods with complete relaxation in the potential energy surface using 6-31G(d) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed spectrograms.  相似文献   

4.
The anomeric effect of 2-substituted 1,4-dioxane derivatives was calculated and compared with the values for substituted cyclohexane. The bond lengths, bond angles, torsion angles, and relative energies of axial and equatorial conformers of 2-substituted 1,4-dioxanes were calculated by the second-order Møller–Plesset (MP2), density functional theory (DFT/B3LYP), and Hartree–Fock (HF) methods using 6-31G basis set. The energy differences between the axial and equatorial conformers, endo and exo-anomeric effects, repulsive non-bond and H-bonding interactions were investigated. A linear free energy relationship (LFER) between calculated (MP2/6-31G) anomeric effect and inductive substituent constants (σI) was obtained for 2-substituted-1,4-dioxanes (slope = 6.19 and r2 = 0.967). The calculated energy differences indicate lower equatorial orientation for 2-substituted-1,4-dioxanes compared to the 2-substituted-tetrahydropyrans. The contribution of resonance, hyperconjugation, inductive, steric, hydrogen bonding, electrostatic interaction, and level of theory influences the anomeric effect.  相似文献   

5.
[Ir(CO)Cl(PCy3)2] was obtained by the slow attack of 1,2-dichloromethane on (Bu4N)[Ir2(μ-Dcbp)(CO)2(PCy3)2] (Dcbp = 3,5-dicarboxylatepyrazole). The Ir-CO, Ir-Cl and Ir-P bond distances are 1.778(10), 2.374(3) and 2.3486(8) Å, respectively. The Ir-P bond distances for a number of different Vaska complexes indicate the shortest bond distances for phoshines containing electron withdrawing groups. An excellent correlation between DFT (OLYP/ZORA/TZP) and experimental structures is obtained as reflected by the RMSD values (H excluded) of between 0.083 and 0.268 Å for the different complexes studied. The calculated Ir-P bond distances and ν(CO) stretching frequencies closely follow the trends obtained from the experimental results.  相似文献   

6.
The electron affinities of beryllium and magnesium tetramers are calculated at the ROMP2 level employing the Dunning-type aug-cc-pVQZ basis set. The vertical electron detachment energy (VEDE) amounts to 1.685 eV for Be4 and 0.943 eV for Mg4 . The decomposition of the VEDE into physical components and an atomic orbital population analysis are used to elucidate the nature of the outer electron binding in these anions.Figure The lowest unoccupied molecular orbitals in the ground state of Mg4 : a LUMO, symmetry A1, b LUMO + 1, symmetry T2; c the highest occupied molecular orbital (HOMO), symmetry A1 in the ground state of Mg4.   相似文献   

7.
ABSTRACT

FT-IR and FT-Raman spectra of 2,2′-bipyridine-3,3′-dicarboxylic acid (B3DA), 2,2′-bipyridine-4,4′-dicarboxylic acid (B4DA) and 2,2′-bipyridine-5,5′-dicarboxylic acid (B5DA) were recorded and analysed. The quantum chemical calculations of the title compounds begin with barrier potentials at different rotation angles around the C–C′ and C–Cα bonds in order to arrive conformation of lowest energy using DFT employing B3LYP functional with 6-311++G(d,p) basis set. This confirmation was further optimised to get the global minimum geometry. The vibrational frequencies along with IR, Raman intensities were computed, the rms error between observed and calculated frequencies were 11.2 cm?1, 10.2 cm?1 and 12.2 cm?1 for B3DA, B4DA, and B5DA. An 87-element modified valence force field is derived by solving the inverse vibrational problem using Wilson’s GF matrix method. This force field is refined using 163 observed fundamentals employing in overlay least-squares technique. The average error between computed and experimental frequencies was found as 12.85 cm?1 using potential energy distribution (PED) and eigenvectors. By using the gauge-independent atomic orbital (GIAO) method calculate the 1H and 13C NMR chemical shifts of the molecules and compared with experimental results. The first-order hyperpolarisability, HOMO and LUMO energies, molecular electrostatic potential (MESP) and natural orbital analysis (NBO) of titled compounds were evaluated using DFT.  相似文献   

8.
Full geometric optimization of endo-tricyclo[3.2.1.02,4]oct-6-ene (endo-TCO) by ab initio and DFT methods allowed us to investigate the structure of the molecule. The double bond is endo-pyramidalized and its two faces are no longer found to be equivalent. The exo face of the double bond has regions with far more electron density (qi,HOMO) and more negative electrostatic potential. The endo-TCO-Br2 system was investigated at the B3LYP/6-311+G** level and the endo-TCO···Br2(exo) molecular complex was found to be relatively more stable than the endo-TCO···Br2(endo) complex. The cationic intermediates of the reaction were studied by ab initio and DFT methods. The bridged exo-bromonium cation(I) is relatively more stable than the endo-bromonium cation(II). An absolute exo-facial selectivity should be observed in the addition reaction of Br2 to endo-TCO, which is caused by steric and electronic factors. The nonclassical rearranged cation IV was found to be the most stable ion among the cationic intermediates and the ionic addition occurs via the formation of this cation. The mechanism of the addition reaction is also discussed.  相似文献   

9.
10.
The stoichiometries and stability constants of a series of Al3+-N-phosponomethyl glycine (PMG/H3L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative 27Al and 31P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6 M NaCl, 25 °C). Besides the mononuclear AlH2L2+, Al(H2L)(HL), and Al(HL)L2−, dimeric Al2(HL)L+ and trinuclear complexes have been postulated.1H and 31P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the 31P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions.  相似文献   

11.
The complexes {ReOCl2[(py)2C(O)(OR)]}, (R = CH2CH3 (1), CH2CH2CH3 (2)) were obtained from the metal-assisted alcoholysis reaction of di-2-pyridylketone. Their crystal structures were determined by single-crystal X-ray diffraction. The structures of 1 and 2 consist of neutral mononuclear molecules containing the [ReO]3+ core. In both compounds the Re(V) central ion is also bonded to an oxygen and both nitrogens from the organic ligand and two chlorides in a distorted octahedral environment. Cyclic voltammograms in CH3CN solutions showed two main redox responses, both of them involving one electron transfer. Comparative theoretical studies on equilibrium geometries and electronic properties were conducted in the framework of the density functional theory (DFT).  相似文献   

12.
Electrospray (ESI) mass spectra analysis of acetonitrile solutions of a series of neutral chloro dimers, pincer type, and monomeric palladacycles has enabled the detection of several of their derived ionic species. The monometallic cationic complexes Pd[κ1-C1-N1-S-C(CH3S-2-C6H4)C(Cl)CH2N(CH3)2]+ (1a) and [Pd[κ1-C1-N1-S-C(CH3S-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)]+ (1b) and the bimetallic cationic complex [κ1-C1-N1-S-C(CH3S-2-C6H4)C(Cl)CH2N(CH3)2]Pd-Cl-Pd[κ1-C1-N1-S-C(CH3S-2-C6H4)C(Cl)CH2N(CH3)2]+ (1c) were detected from an acetonitrile solution of the pincer palladacycles Pd[κ1-C1-N1-S-C(CH3S-2-C6H4)C(Cl)CH2N(CH3)2](Cl) 1. For the dimeric compounds {Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](μ-Cl)}2 (2, Y=H and 3, CF3), highly electronically unsaturated palladacycles [Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2]+ (2d, 3d) and their mono and di-acetonitrile adducts, namely, [Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)]+ (2e, 3e) and [Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)2]+ (2f and 3f) were detected together with the bimetallic complex [Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2]-Cl-Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N](CH3)2]+ (2a, 3a) and its acetonitrile adducts [κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)Pd-Cl-Pd[ κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2]+ (2b, 3b) and [κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)Pd-Cl-Pd[κ1-C, κ1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2(CH3CN)]+ (2c, 3c). The dimeric palladacycle {Pd[κ1-C1-N-C(CH3O-2-C6H4)C(Cl)CH2N(CH3)2](μ-Cl)}2 (4) is unique as it behaves as a pincer type compound with the OCH3 substituent acting as an intramolecular coordinating group which prevents acetonitrile full coordination, thus forming the cationic complexes [(C6H4(o-CH3O)CC(Cl)CH2N(CH3)2OCN)Pd]+ (4b), [(C6H4(o-CH3O)CC(Cl)CH2N(CH3)2- κOCN)Pd(CH3CN)]+ (4c) and [(C6H4 (o-MeO)CC(Cl)CH2N(CH3)2O, κCN)Pd-Cl-Pd(C6H4(o-CH3O)CC(Cl)CH2N(CH3)2OCN)]+ (4a). ESI-MS spectra analysis of acetonitrile solutions of the monomeric palladacycles Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](Cl)(Py) (5, Y=H and 6, Y=CF3) allows the detection of some of the same species observed in the spectra of the dimeric palladacycles, i.e., monometallic cationic 2d-3d, 2e-3e and {Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](Py)}+ (5a, 6a) and {Pd[κ1-C1-N-C(Y-2-C6H4)C(Cl)CH2N(CH3)2](CH3CN)(Py)}+ (5b, 6b) and the bimetallic 2a, 3a, 2b, 3b, 2c and 3c. In all cationic complexes detected by ESI-MS, the cyclometallated moiety was intact indicating the high stability of the four or six electron anionic chelate ligands. The anionic (chloride) or neutral (pyridine) ligands are, however, easily replaced by the acetonitrile solvent.  相似文献   

13.
The inner mechanism and dynamic stereochemistry of electrophilic addition of bromine to bisbenzotetracyclo[6.2.2.2(3,6).0(2,7)]tetradeca-4,9,11,13-tetraene(BBTT) molecule have been investigated by the methods of quantum chemistry. The structure of the BBTT molecule has been studied by ab initio and DFT/B3LYP methods using the 6-31G(d) and 6-311G(d) basis sets. The double bonds of BBTT molecule are endo-pyramidalized. The structure and stability of the cationic intermediates and products of the addition reaction have been investigated by HF/6-311G(d), HF/6-311G(d,p), B3LYP/6-311G(d) and B3LYP/6-311++G(2d,p)//B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable nonclassical delocalized N- and U-type cations and the difference between the stability of these cations is small. For the determination of the direction of addition reaction and the stereochemistry of the products, the stability of nonclassical delocalized N- and U-type ions and the structure of their cationic centres play a vital role. Since the cationic centre of the N-type ion is in interaction with the benzene ring from the exo face, the nucleofilic attackof the bromide anion to this centre occurs from the endo face and the exo,endo-isomer of the N-type product is obtained. The attack of bromide anion, towards the cationic centre of U-type ion from the endo face is sterically hindered by the hydrogen atom therefore the attack occurs from the exo face, which interacts with the benzene ring and the more stable exo,exo-isomer of U-type product is formed. Although, the U-type cation was 2.232 kcal mol(-1) more stable than the N-type cation, the U-type product was 0.587 kcal mol(-1) less stable than the N-type product.  相似文献   

14.
The structure, energies and spectroscopic properties of a simple [FeO(NH(3))(5)](2+) model with ground states (3)A(2g) and (5)A(1g) (in approximate C(4v) symmetry) have been studied in some detail using density functional (DFT) and simplified correlated multireference ab initio methods. The results reveal similarities as well as some pronounced differences in the properties of the molecule in the two alternative spin states.  相似文献   

15.
A series of beta-cellobiose analogs were studied at the B3LYP/6-311++G** level of theory to isolate and understand how the various electronic components of the beta-(1-->4)-linked disaccharide, cellobiose, contribute to the energetic stability of the molecule in vacuo. Previous studies on beta-cellobiose (see accompanying paper) showed that the most energetically stable conformation was that in which the dihedral angle phi (phi(H)) was 'flipped' by approximately 180 degrees relative to the 'normal' form. From our examination of eight sets of structures in which different combinations of functional hydroxyl and hydroxymethyl groups were removed, it was determined that only beta-cellobiose and one other analog (analog 7, beta-xylobioside), an analog in which both hydroxymethyl groups were removed but the exocyclic hydroxyl groups retained, can form a 'cooperative' hydrogen-bonding network. Only in these two molecules did we find continuous synergistic 'communication' through hydrogen bonding from one sugar moiety to the other. This 'cooperative' hydrogen bonding energetically stabilizes the 'flipped' conformation of beta-cellobiose and beta-xylobioside, while the other analogs studied were unable to form a 'cooperative' grouping of hydrogen bonds and thus were more stable in their 'normal' conformational state.  相似文献   

16.
As a part of our continuing program on the synthesis of steroidal heterocycles, it has been prepared a series of novel steroidal pyrimidine derivatives 46 via TMSCl, steroidal ketones (1c3c), urea and benzaldehyde. The systems presented here, are novel scaffolds and have not been described before at 6th position of steroidal-6-one (1c–3c). Structural assignment of newly synthesized compounds was performed by DFT/B3LYP calculations as well as spectral and analytical data. The interactions of compounds (46) with HSA were studied by fluorescence spectroscopy, DLS, CD and molecular docking, under imitated physiological conditions. The antitumor activity has been tested in vitro against three cancer cell lines MDA-MB231 (breast carcinoma), HeLa (human cervical carcinoma), HepG2 (hepatic carcinoma) and one non-cancer normal cell lines, PBMCs (peripheral blood mononuclear cell) by MTT assay. In addition, in vitro antioxidant activity and apoptosis assay of the synthesized compounds (46) have also been investigated.  相似文献   

17.
The bis-chelate complex of Zn2+ with 2-hydroxy-(4-methylthio)butanoate (MHA-H the anion derived from the so-called methionine hydroxy-analogue, MHA) is an effective, bioavailable mineral supplement for animal feeding. It can be obtained in two solid forms: the anhydrous [Zn(OC(O)CH2CH(OH)CH2CH2SCH3)2] and the corresponding dihydrate species, both well distinguishable by IR spectroscopy and powder X-ray diffraction. The crystal and molecular structure of the dihydrate form has been solved by single-crystal X-ray diffraction. It consists of dinuclear bis-chelate species with a bridging carboxylate group, both zinc atoms displaying hexacoordination involving all the hydroxyl and carboxyl groups from the four MHA-H anions and three oxygens from different water molecules. The fourth water molecule does not participate in coordination. Therefore, the dihydrate complex must be formulated as [Zn2(OC(O)CH2CH(OH)CH2CH2SCH3)4(H2O)3] · H2O (1). A molecular computational analysis has been carried out by density functional theory (DFT) on three possible MHA-H zinc chelates, i.e. the dinuclear bis-chelate observed in the solid state, the mononuclear bis-chelate diaquo-complex, and the monochelate tetraaquo-complex. Calculations have suggested that between the dinuclear and mononuclear bis-chelates, the preferred form in aqueous solution may be the second one. Moreover, both 1H (chemical shifts and relaxation rates) and 13C NMR data provide further evidence for the formation of Zn/MHA-H chelates in solution.  相似文献   

18.
19.
A luminescent palladium(II) complex [Pd(L)Cl], 1a was synthesized with the acyclic tridentate quinoline-2-carboxaldehyde-2-pyridylhydrazone ligand, HL, 1. The ligand, 1 showed a selective chromogenic behavior towards Pd2+ by changing the color of the solution from yellow to blue-violet, which can easily be detected by the naked-eye. DFT and TDDFT calculations were performed to determine the geometry optimized structures of the ligand 1 and the complex 1a as well as to correlate the electronic transitions. The complex 1a exhibits strong interaction towards DNA as revealed from Kb (intrinsic binding constant) and Ksq (Stern Volmer quenching constant) values, which are 1.47 × 105 M−1 and 5.67, respectively. The cytotoxicity of 1a has been examined with human prostate cancer cells (PC-3) and the sub-lethal dose (8 μM) determined by dose-dependence studies. The relative degree of apoptotic and necrotic cell death using a sub-lethal dose were measured by flow cytometry. The cell cycle analysis shows that the complex 1a exhibits effective cell growth inhibition by triggering G2/M phase arrest and apoptosis in cancer cells. Moreover, its treatment triggers the mitochondrial pathway resulting in cytochrome c release and caspase-3 activation.  相似文献   

20.
In the present study Cervatana and Almagra models from decision support system, MicroLEIS DSS, were applied to segregation of arable land surfaces from the marginal ones and suitability evaluation of wheat (Triticum aestivum), maize (Zea mays) and alfalfa (Medicago sativa) in Souma area with approximately 4100 ha extension in West Azarbaijan. Obtained results from both models are presented and discussed in this research work. Soil morphological and analytical data were collected from 35 soil profiles, representative of the study area and stored in SDBm plus database. The control or vertical section of soil for applying and running the models for annual selected crops, was calculated by soil layer generator 0.0–50 cm in depth, or between the surface and the limit of useful depth when the latter is between 0.0 and 50 cm. According to results, 80.49% of the total area was good capable for agricultural uses and 19.51% must be reforested and not dedicated to agriculture. The lands with good capability for agricultural uses is classified as highly suitable area (S2) for wheat, maize and alfalfa, but results in 822 ha for maize and in 126 ha for alfalfa refers to an excellent suitable (S1) and moderately suitable (S3) classes respectively. The most important limitation factors are soil texture and carbonate alone or together and maize — wheat — alfalfa can be selected as the best crop rotation. A simple map subsystem (ArcView GIS) was used for basic data and models result demonstration on a map.  相似文献   

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