Cyclobutyl-carbonyl substituted PNA: synthesis and study of a novel PNA derivative

A new, optically active, cyclobutyl-carbonyl substituted PNA monomer has been synthesized stereoselectively from a chiral amino acid prepared from (+)-α-pinene. A conformational search shows a lack of conformational bias for the monomer and incorporation of the monomer into a standard oligomer is tolerated without changing the binding affinity towards sequence complementary RNA, DNA or PNA targets.     

Exploiting rotational and translational invariance of the energy in derivative calculations in quantum chemistry

It is shown how the invariance of the Born—Oppenheimer potential energy to overall translations and rotations of a molecule can be used to reduce the computational labor required for derivative evaluations at various orders.     

Dipeptide structure determination by vibrational circular dichroism combined with quantum chemistry calculations.

The solution structure and the local solvation environments of alanine dipeptide (AD, 1 a) and its isotopomer (AD*, 1 b, 13C on the acetyl end C==O) are studied by using infrared (IR) spectroscopy and vibrational circular dichroism (VCD). From the amide I IR spectra of AD* in various protic solvents, it is found that each of the two carbonyl groups is fully H-bonded to two water molecules. However, the number of alcohol molecules H-bonded to each C==O varies from one to two, and the local solvation environments are asymmetric around the two peptides of AD* in alcohol solutions. The amide I VCD spectra of AD and AD* in D2O are also measured, and a series of density functional theory (DFT, B3LYP/6-311++G**) calculations are performed to obtain the amide I normal-mode rotational strengths of AD and the intrinsic rotational strengths of its two peptide fragments. By combining the VCD-measurement and DFT-calculation results and employing a coupled oscillator theory, we show that the aqueous-solution structure of the dipeptide can be determined. We believe that the present method will be of use in building up a library of dipeptide solution structures in water.     

Synthesis and crystal structure of a pyrazole derivative of artemisia ketone

The oxime of artemisia ketone is smoothly converted to the pyrazole derivative by sodium nitrite and acetic acid in CHCl₃. The structure of the pyrazole was found by x-ray structural analysis. The PMR and¹³C NMR spectra were interpreted using two-dimensional¹H–¹³C NMR (COSY, COLOC).Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 121–123, March–April, 2000.     

Design,synthesis and biological activity of novel substituted pyrazole amide derivatives targeting Ec R/USP receptor

In order to discover highly active ecdysone analogs, a series of new substituted pyrazole amide derivatives were obtained using structure-guided optimization method and further screened for their insecticidal activities, in the basis of the core structures of the two active compounds N-(3-methoxyphenyl)-3-(tert-butyl)-1-phenyl-1H-pyrazole-5-carboxamide(6e) and N-(4-(tert-butyl)phenyl)-3-(tert-butyl)-1-phenyl-1H-pyrazole-5-carboxamide(6i), previously presented by us. The chemical structures of the title compounds were identified by spectral analyses. The preliminary bioassay results indicated that one among the synthesized pyrazole derivatives, compound 34, endowed with good activity against Mythimna Separata at 10 mg/L, which was equal to that displayed by the positive control tebufenozide. In addition, examples of molecular docking and molecular dynamics studies demonstrated that 34 may be the potential inhibitor to Ec R and its docking conformation was similar to that of tebufenozide. In addition, increasing the hydrophobic effect and considering the suitable bulk effect on pyrazole ring are beneficial to the inhibiting activity to Ec R and activity in vivo.     

The structure of chlorophyll a-water complexes: insights from quantum chemistry calculations

Computations show that chlorophyll a is able to coordinate a maximum of two water molecules in hydrophobic media that form a bridge between the Mg atom and the methyl ester carbonyl group.     

Molecular structure, vibrational spectral studies of pyrazole and 3,5-dimethyl pyrazole based on density functional calculations

In this work, the experimental and theoretical vibrational spectra of pyrazole (PZ) and 3,5-dimethyl pyrazole (DMP) have been studied. FTIR and FT-Raman spectra of the title compounds in the solid phase are recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1), respectively. The structural and spectroscopic data of the molecules in the ground state are calculated using density functional methods (B3LYP) with 6-311+G** basis set. The vibrational frequencies are calculated and scaled values are compared with experimental FTIR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete vibrational assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SM) method. 13C and 1H NMR chemical shifts results are compared with the experimental values.     

Synthesis, crystal structure, electrochemistry and in situ FTIR spectroelectrochemistry of a bisferrocene pyrazole derivative

One novel bisferrocene pyrazole derivative, bis [2-(5-trifluoromethyl-3-ferrocenyl) pyrazolyl] methane (abbreviated as (3)), was synthesized and fully characterized. A single crystal of (3) was obtained and solved by X-ray diffraction analysis. The bisferrocene derivative exhibits MLCT (metal to ligand charge transfer) and π→π* transitions in the UV-visible range, which have been verified by density functional theory (DFT) calculations. Its electrochemical properties were studied with the aid of cyclic voltammetry (CV), differential pulse voltammetry (DPV) and rapid scan time-resolved Fourier transform infrared spectroscopy (RS-TRS FT-IR) analysis. Furthermore, the electrochemical mechanism was elucidated based on the results from the cyclic voltabsorptometry (CVA) determination technique. (3) apparently shows a single wave in the cyclic voltammetric experiments which indicates there is no intermediate, however, the intermediate of (3) was observed by employing the RS-TRS FT-IR spectroelectrochemistry technique. The detailed investigation brought us safely to the conclusion that the methylene can also act as a linker, leading to electronic communication in either D-π-D and A-π-A systems.     

Spectroscopic characterization, crystal structure determination and interaction with DNA of novel cyano substituted benzimidazole derivative

Novel cyano-substituted benzimidazole derivatives 3 and 4 were synthesized from 4-N,N-dimethylamino-benzaldehyde and 2-cyanomethyl-benzimidazole. 2-(1H-benzimidazol-2-yl)-3-(4-N,N-dimethylamino-phenyl)-acrylonitrile hydrochloride monohydrate 4 has been studied by ¹H and ¹³C NMR, IR, MS, UV/Vis and fluorescence spectroscopy and confirmed by X-ray crystal structure analysis. The interaction of 4 with ct-DNA has also been investigated by fluorescence spectroscopy and melting temperature determination experiment. According to the emission spectra recorded in the absence and presence of ct-DNA at different ratios r ([compound]/[polynucleotide]), 4 showed marked decrease in the fluorescence intensity and very strong hypochromic effect. Melting temperature experiment showed weak stabilization of double helix. To determine binding mode of 4, other additional experiments are necessary. The molecules of 4 are almost planar with the dihedral angle between benzimidazole and phenyl rings of 6.99(6)°. The protonation of nitrogen atom of benzimidazole ring is followed by π-electrons delocalization in the region resulting in C–N bond distances equality [1.341(2) and 1.337(2) Å]. Both NH groups of benzimidazole ring form intermolecular hydrogen bonds, one with the oxygen atom of water molecule [N···O 2.689(2) Å] and the other with Cl^? ion (N···Cl^? 3.051(1) Å). Except proton acceptor, water molecule acts as double proton donor in the formation of intermolecular hydrogen bonds with Cl^? ion [O···Cl^? 3.126(2) and 3.169(2) Å]. In that way, infinite chains along [110] direction are formed.     

Functionalized 4-hydroxy coumarins: novel synthesis, crystal structure and DFT calculations

A novel short-step methodology for the synthesis in good yields of functionalized coumarins has been developed starting from an activated precursor, the N-hydroxysuccinimide ester of O-acetylsalicylic acid. The procedure is based on a tandem C-acylation-cyclization process under mild reaction conditions. The structure of 3-methoxycarbonyl-4-hydroxy coumarin has been established by X-ray diffraction analysis and its geometry was compared with optimized parameters by means of DFT calculations.     

Microwave-assisted synthesis,characterization and biological activity of novel pyrazole derivatives

A series of 1-(4-substitutedphenyl)-3-phenyl-1H-pyrazole-4-carbaldehydes 4a–l have been synthesized and tested for their biological activities. Formation of the pyrazole derivatives was achieved by treating with Vilsmeier-Haack reagent. The newly synthesized compounds were evaluated for their anti-inflammatory and analgesic activities compared to Diclofenac sodium as standard drug. Compounds 4g, 4i and 4k exhibited the maximum anti-inflammatory and analgesic activities. The detailed synthesis, spectroscopic and toxicity data are reported.     

Synthesis,nematicidal activity and docking study of novel chromone derivatives containing substituted pyrazole

A series of chromone derivatives containing substituted pyrazole were designed and synthesized. Preliminary bioassays showed that most of the synthesized compounds exhibited good nematicidal activity in vivo against Meloidogyne incognita at 10 mg/L.     

A quantum chemistry study on the structure and properties of a novel stable strained cyclophane

Different levels of theoretical methods have been used to study a novel stable cylcophane 1,8-[1,8-naphthalenediylbis(4,4-biphenyldiyl)]naphthalene. It was concluded that HF/3-21g* was the most efficient method for the system, which could well reproduce the experimental structure. In addition, HF/3-21g* / /B3LYP/3-21g* calculations explained the experimental observation that the cyclophane was much easier to be oxidized to the corresponding radical cation than its related compound 1,8-bisphenyl-naphthalene. It was proposed that the more effective - and -cation interactions in the radical cation of the cyclophane caused the above behavior.     

Synthesis, structure, and electronic calculations of group VII substituted pyridazines

A series of 5,6-fused ring cyclopentadienyl tricarbonyl manganese and rhenium complexes, [M(CO)₃{η ⁵-1,2-C₅H₃(1,4-(R)₂N₂C₂}] (2a–3d) were isolated by employing an off-metal ring closure route. Reacting thallium cyclopentadienide (Cp) salts (1a–d) with [MBr(CO)₅] (M = Mn, Re) provided pyridazyl complexes (2a–3d) in high yield (75–99 %). Spectroscopic characterization (NMR, IR, MS) confirmed the identity of the desired organometallic pyridazines. The off-metal synthetic pathway employed did improve upon the isolation of these complexes as compared to previously reported routes. The molecular and electronic structure of complexes 2a–3d and their optimal energy structures have been characterized with quantum chemistry calculations. Vibrational frequencies calculated were compared to their experimental counterparts. The excited state calculations predict that the dominant low-energy transition involves a ligand-to-metal charge transfer.     

Structural defects and the electronic structure of zirconium hydrides: x-ray emission spectra and quantum chemical calculations

X-ray emission spectroscopy and the Green function LMTO band method was used to study the effect of structural defects in the hydrogen sublattice on the electronic structure and chemical bonding in ZrH₂.Institute of Metal Physics, Urals Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 70–74, November–December, 1989.     

The synthesis and fluorescence of a methoxy-phenyl substituted C_60-pyrrolidine derivative

A new 4-methoxyphenyl substituted C60-pyrrolidine derivative, C60(C10H13NO) (1), was prepared and its room-temperature fluorescence was studied. Its fluorescence intensity is three times stronger than that of C60. Its singlet energy was estimated to be 25 kJ/mol lower than that of C60. The fluorescence lifetime was determined to be 2.1+0.3 ns by using the frequency domain method. The fluorescence quenching by concentration and aromatic electron donor: N, N-dimethyl aniline (DMA) was investigated. Data show that its fluorescence could not be quenched by DMA.     

Three conformational polymorphs of di-mu-chlorotetrakis(1-methylboratabenzene)diyttrium: synthesis, x-ray structures, quantum chemical calculations, and lattice energy minimizations

The reaction of yttrium trichloride with lithium 1-methylboratabenzene (1/2) in toluene (110 degrees C, 3 days) afforded the donor-free dinuclear sandwich complex [(C(5)H(5)BMe)(2)Y(mu-Cl)](2) (1) in 85% yield as pale-yellow crystals. By means of single crystal and powder diffraction methods, three conformational polymorphs, alpha-1 [P2(1)/n (No. 14), monoclinic, a = 6.6124(8) A, b = 14.352(9) A, c = 14.120(1) A, beta = 95.57(1) degrees, V = 1333.7(9) A(3), Z = 2], beta-1 [P2(1)/a (No. 14), monoclinic, a = 8.542(2) A, b = 13.712(6) A, c = 11.76(1) A, beta = 102.60(4) degrees, V = 1344.5(13) A(3), Z = 2], and gamma-1 [Pbca (No. 61), orthorhombic, a = 20.091(5) A, b = 13.527(3) A, c = 9.976(2) A, V = 2711.2(11) A(3), Z = 4], were characterized in the solid state of 1. The molecules in the three phases vary remarkably in the rotational position of boratabenzene ligands with differences of 91.1, 133.1, and 24.9 degrees between each pair. DFT calculations at the B3LYP/LanL2DZ level reveal that the three molecular structures observed in the solid state correspond closely to three minima on the gas-phase potential energy surface. The beta conformation is 2.8 and 7.2 kJ/mol more stable than the alpha and gamma conformations, respectively. Lattice energy minimizations predict that the alpha-1 phase is about 5.5 and 18.7 kJ mol(-)(1) more stable than the beta-1 and gamma-1 modifications, in agreement with the packing coefficients and the molecular volumes of the three crystal structures. While the alpha-1 and beta-1 modifications have comparable total energies, the gamma-1 form is less stable. The total energy differences among the polymorphs are greater than generally expected.     

Synthesis,crystal structure and electrochemical properties of carbonylchromium and tungsten complexes containing substituted pyrazole ligands

A series of carbonylchromium and tungsten complexes containing substituted pyrazole ligands, M(CO)₅L, have been synthesized by the photochemical reactions of substituted pyrazoles with M(CO)₆ (M = Cr or W). Their electrochemical behavior, investigated by cyclic voltammetry, indicates that the chromium complexes exhibit one reversible or quasi-reversible couple corresponding to a one-electron oxidation, whereas the tungsten complexes have one irreversible oxidation process. The crystal structure of W(CO)₅L [L = 3(5)-t-butylpyrazole] was determined by X-ray diffraction, indicating that 3(5)-t-butylpyrazole is a monodentate ligand, and that the central metal is six-coordinate with a quasi-octahedral coordination geometry. All new compounds were characterized by elemental analyses, i.r., ¹H-n.m.r. and by ¹³C-n.m.r. in the case of the tungsten complexes.     

FT-IR, FT-Raman spectra and quantum chemical calculations of some chloro substituted phenoxy acetic acids

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of o-chlorophenoxy acetic acid (OCPAA) and p-chlorophenoxy acetic acids (PCPAA). The FT-IR and Fourier transform-Raman spectra of both the compounds was recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods with 6-311++G(d,p) basis set and harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compounds were also performed at B3LYP/6-311++G(d,p) level of theory. A detailed interpretation of the infrared and Raman spectra of o-chloro and p-chlorophenoxy acetic acid is reported. The theoretical FT-IR spectrograms for the title molecules have been constructed.     

Quantum chemistry of quantum size‐effects in semiconductors: Small clusters electronic structure calculations

Ab initio RHF SCF calculations are used for some small clusters M_xX_y, where M=Cd, Ag; X=S, I; and x, y≤7. Variation of electronic structure with size for some clusters with the bulklike tetrahedral coordination and with the lower symmetry allows one to predict their possible geometries which are compared with experimental data on the existence of the clusters. The chemical‐bonding factor (the chemical nature of bounded atoms, coordination number for metal and nonmetal atoms, hybridization, etc.) is of more importance for properties of the clusters than is the familiar quantum confinement effect of semiconductor clusters. The essential difference in regularities of small cluster formation is analyzed for CdS‐ and AgI‐based structures. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 337–341, 1999