Exploration of small hydroxy‐9,10‐anthraquinones as anthracycline analogues: physicochemical characteristics and DNA binding for comparison

Hydroxy‐9,10‐anthraquinones resemble anthracycline‐based anticancer drugs. By varying the pH of the solution, the proton dissociation constants of 1,2,5,8‐tetrahydroxy‐9,10‐anthraquinone (THAQ) were determined. Interaction of THAQ with calf thymus DNA (ct DNA) was studied by UV–Vis spectroscopy to determine the overall binding constant and site size of interaction. The binding constant values (~10⁴) for THAQ interacting with ct DNA at different pH were an order less than that known for anthracyclines. From knowledge of the overall binding constants at different pH values and the first pK of THAQ, the contribution of each form (neutral and monoanionic) towards overall binding with ct DNA could be obtained under physiological conditions. Hence, knowing the contributions of the neutral and monoanionic forms, it now becomes possible to know the overall binding constant for an interaction of THAQ with ct DNA at any pH. The calculated parameters help in understanding the role of the negative charge on the monoanionic form during interaction and suggests suitable chemical modifications that could prevent the development of such negative charges. This could lead to an increase in binding of THAQ to ct DNA. The study also helps to recognize the importance of sugar units in anthracycline anticancer drugs in DNA interaction. Copyright © 2011 John Wiley & Sons, Ltd.     

Micellar effects on aromatic nucleophilic substitution by the ANRORC mechanism. Hydrolysis of 2‐chloro‐3,5‐dinitropyridine

The hydrolysis of 2‐chloro‐3,5‐dinitropyridine by sodium hydroxide in the presence of micelles of cetyltrimethylammonium bromide (CTABr), cetyltrimethylammonium chloride (CTACl) and sodium dodecyl sulfate (SDS) has been studied. The reaction follows a consecutive reaction path involving the formation of a long‐lived intermediate 3 and finally giving the product, 3,5‐dinitro 2‐pyridone 2 . The mechanism follows an addition of the nucleophile, ring opening and ring closure (ANRORC) reaction path. The rate constant was observed to be first‐order dependent on [OH^?]. The rate of reaction increased on increasing [CTABr] and, after reaching to the maxima, it started decreasing. The anionic SDS micelles inhibited the rate of hydrolysis. The results of the kinetic experiments were treated with the help of the pseudophase ion exchange model and the Menger–Portnoy model. The added salts, viz. NaBr, Na‐toluene‐4‐sulphonate, and (CH₃)₄NBr on varying [CTACl] and [SDS] inhibited the rate of reaction. The various kinetic parameters in the presence and absence of salts were determined and are reported herewith. Copyright © 2011 John Wiley & Sons, Ltd.     

4‐Alkyl‐2,2,6,6‐tetramethyl‐1,4,2,6‐oxaazadisilinanes: synthesis,structure, and conformational analysis

4‐Alkyl‐2,2,6,6‐tetramethyl‐1,4,2,6‐oxaazadisilinanes RN[CH₂Si(Me)₂]₂O [R = Me ( 1 ), i‐Pr ( 2 )] were synthesized by two methods which provided good yields up to 84%. Low temperature NMR study of compounds ( 1 ) and ( 2 ) revealed a frozen ring inversion with the energy barriers of 8.5 and 7.7 kcal/mol at 163 and 143 K, respectively, which is substantially lower than that for their carbon analog, N‐methylmorpholine. DFT calculations performed on the example of molecule ( 1 ) showed that N? Me_ax conformer to exist in the sofa conformation with the coplanar fragment C? Si? O? Si? C, and its N? Me_eq conformer in a flattened chair conformation. Copyright © 2009 John Wiley & Sons, Ltd.     

Excited‐state structural dynamics and vibronic coupling of 1,3‐dithiole‐2‐thione—resonance Raman spectroscopy and density functional theory calculation study

1,3‐Dithiole‐2‐thione (DTT) was synthesized and characterized using NMR, FT‐Raman, FT‐IR, UV spectroscopies. Resonance Raman spectra (RRs) were obtained with 341.5, 354.7 and 368.9 nm excitation wavelengths and density functional calculations were done to elucidate the electronic transitions and the RRs of DTT in cyclohexane solution. The RRs indicate that the Franck‐Condon region photodynamics is predominantly along the CS stretch+ H‐CC‐H scissor υ₄, accompanied by the H‐CC‐H scissor υ₃, S‐C‐S symmetric stretch υ₆, CC stretch υ₂, and overtone of the non‐totally symmetric SC‐S2 out‐of‐plane deformation 2υ₁₁. The excited‐state dynamics and the force constant of CS stretch calculated by the RRs were discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Experimental and theoretical FT‐IR and FT‐Raman spectroscopic analysis of N1‐methyl‐2‐chloroaniline

In this work, the experimental and theoretical vibrational spectra of N1‐methyl‐2‐chloroaniline (C₇H₈NCl) were studied. FT‐IR and FT‐Raman spectra of the title molecule in the liquid phase were recorded in the region 4000–400 cm^?1 and 3500–50 cm^?1, respectively. The structural and spectroscopic data of the molecule in the ground state were calculated by using density functional method (B3LYP) with the 6‐311++G(d,p) basis set. The vibrational frequencies were calculated and scaled values were compared with experimental FT‐IR and FT‐Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. ¹³C and ¹H NMR chemical shifts results were compared with the experimental values. The optimized geometric parameters (bond lengths and bond angles) were given and are in agreement with the corresponding experimental values of aniline and p‐methyl aniline. Copyright © 2008 John Wiley & Sons, Ltd.     

Bond cutting in K‐doped tris(8‐hydroxyquinoline) aluminium

A series of Al 2p, K 2p, O 1s and N 1s core‐level spectra have been used to characterize the interaction between potassium (K) and tris(8‐hydroxyquinoline) aluminium (Alq₃) molecules in the K‐doped Alq₃ layer. All core‐level spectra were tuned to be very surface sensitive in selecting various photon energies provided by the wide‐range beamline at the National Synchrotron Radiation Research Center, Taiwan. A critical K concentration (x = 2.4) exists in the K‐doped Alq₃ layer, below which the K‐doped atoms generate a strained environment near the O and N atoms within 8‐quinolinoline ligands. This creates new O 1s and N 1s components on the lower binding‐energy side. Above the critical K coverage, the K‐doped atoms attach the O atoms in the Al—O—C bonds next to the phenoxide ring and replace Al—O—C bonds by forming K—O—C bonds. An Alq₃ molecule is disassembled into Alq₂ and Kq by bond cutting and bond formation. The Alq₂ molecule can be further dissociated into Alq, or even Al, through subsequent formations of Kq.     

Synthesis and Raman spectroscopic investigation of a new self‐assembly monolayer material 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid for organic light‐emitting devices

We have synthesized 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid (4‐[PBA]) and investigated its molecular vibrations by infrared and Raman spectroscopies as well as by calculations based on the density functional theory (DFT) approach. The Fourier transform (FT) Raman, dispersive Raman and FT‐IR spectra of 4‐[PBA] were recorded in the solid phase. We analyzed the optimized geometric structure and energies of 4‐[PBA] in the ground state. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was studied using natural bond orbital analysis. The results show that change in electron density in the σ* and π* antibonding orbitals and E₂ energies confirm the occurrence of intramolecular charge transfer within the molecule. Theoretical calculations were performed at the DFT level using the Gaussian 09 program. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution. The good agreement between the experimental and theoretical spectra allowed positive assignment of the observed vibrational absorption bands. Finally, the calculation results were applied to simulate the Raman and IR spectra of the title compound, which show agreement with the observed spectra. Copyright © 2011 John Wiley & Sons, Ltd.     

IR,Raman and SERS spectra of 5‐sulphosalicylic acid dihydrate

IR, Raman and surface‐enhanced Raman scattering (SERS) spectra of 5‐sulphosalicylic acid were recorded and analysed. The vibrational wavenumbers were computed by density functional theoretical (DFT) method using B3LYP/6–31G* basis. The bands due to the stretching modes CO, C S and SO₂ are intense in the SERS spectrum. The C H stretching mode also appears in the SERS spectrum. The molecule is found to adsorb through both the carboxyl and sulphonyl groups. A possible tilted orientation of the molecule is suggested. Copyright © 2006 John Wiley & Sons, Ltd.     

Binding of regulatory protein omega from Streptococcus pyogenes plasmid pSM19035 to direct and inverted 7‐base pair repeats of operator DNA

pSM19035‐encoded dimeric regulator omega (ω₂) belongs to the MetJ/Arc family of ribbon–helix–helix DNA binding proteins. ω₂ binds to a set of unspaced 7‐base pair repeat units with sequence 5′‐^A/_TATCAC^A/_T‐3′. Protein ω₂ and its variant ω₂ΔN18, lacking the first 18 N‐terminal amino acids, bind poorly to one heptad DNA, but the affinity to DNA markedly increases with two and more heptads organized in direct or inverted orientation. Raman difference spectra indicate that ω₂ and ω₂ΔN18 bind to operator DNA in the major groove and contact thymine, adenine and guanine residues. The mode of ω₂ or ω₂ΔN18 interaction with operator DNA is not affected by the orientation and number of heptads. The Raman data of ω₂T29A, an ω₂ variant with Ala instead of Thr at position 29 of the β‐sheet, show a sequence‐independent binding mode to DNA, which differs from the binding mode of wt ω₂ protein to its cognate site. The Raman data strongly support the notion that the 18 N‐terminal amino acids are not required for ω₂ activity, whereas Thr29 plays an essential role for operator DNA binding. The data suggest the formation of a hydrogen bond between Thr29 of wild‐type ω₂ to one of the bases in the central 5′‐TCA‐3′/5′‐TGA‐3′ stretch of the 7‐bp binding site. Copyright © 2006 John Wiley & Sons, Ltd.     

Adsorption of 4,4′‐thiobisbenzenethiol on silver surfaces: surface‐enhanced Raman scattering study

Adsorption of 4,4′‐thiobisbenzenethiol (4,4′‐TBBT) on a colloidal silver surface and a roughened silver electrode surface was investigated by means of surface‐enhanced Raman scattering (SERS) for the first time, which indicates that 4,4′‐TBBT is chemisorbed on the colloidal silver surface as dithiolates by losing two H‐atoms of the S H bond, while as monothiolates on the roughened silver electrode. The different orientations of the molecules on both silver surfaces indicate the different adsorption behaviors of 4,4′‐TBBT in the two systems. It is inferred from the SERS signal that the two aromatic rings in 4,4′‐TBBT molecule are parallel to the colloidal silver surface as seen from the disappearance of ν_{C H} band (3054 cm⁻¹), which is a vibrational mode to be used to determine the orientation of a molecule on metals according to the surface selection rule, while on the roughened silver electrode surface they are tilted to the surface as seen from the enhanced signal of ν_{C H}. The orientation of the C‐S bond is tilted with respect to the silver surface in both cases as inferred from the strong enhancement of the ν_{C S}. SERS spectra of 4,4′‐TBBT on the roughened silver electrode with different applied potentials reveal that the enhancement of 4,4′‐TBBT on the roughened silver electrode surface may be related to the chemical mechanism (CM). More importantly, the adsorption of 4,4′‐TBBT on the silver electrode is expected to be useful to covalently adsorb metal nanoparticles through the free S H bond to form two‐ or three‐ dimensional nanostructures. Copyright © 2007 John Wiley & Sons, Ltd.     

Molecular structure,vibrational spectroscopic,first‐order hyperpolarizability and HOMO,LUMO studies of 3‐hydroxy‐2‐naphthoic acid hydrazide

The Fourier‐transform infrared spectrum of 3‐hydroxy‐2‐naphthoic acid hydrazide (3H2NAH) was recorded in the region 4000–400 cm⁻¹. The Fourier‐transform Raman spectrum of 3H2NAH was also recorded in the region 3500–10 cm⁻¹. Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of 3H2NAH were carried out by density functional theory (DFT/B3LYP) method with 6‐31G(d,p) as basis set. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The values of the electric dipole moment (µ) and the first‐order hyperpolarizability (β) of the investigated molecule were computed using ab initio quantum mechanical calculations. The UV spectrum was measured in ethanol solution. The calculation results also show that the 3H2NAH molecule might have microscopic nonlinear optical (NLO) behavior with non‐zero values. A detailed interpretation of the infrared and Raman spectra of 3H2NAH is also reported based on total energy distribution (TED). The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT‐IR and FT‐Raman spectra for the title molecule have also been constructed. Copyright © 2009 John Wiley & Sons, Ltd.     

Charge‐transfer contributions in surface‐enhanced Raman scattering from Ag,Ag2S and Ag2Se substrates

The degree of charge‐transfer in Ag–4‐mercaptopyridine (Mpy) and Ag₂S–4‐Mpy systems is investigated by use of surface‐enhanced Raman spectroscopy (SERS). Ag₂S and Ag₂Se nanoparticles are prepared on the basis of the former formation of Ag nanoparticles to make the SERS analytical objects comparable. We utilize the intensity of the non‐totally symmetric modes (either b₁ or b₂) as compared with the totally symmetric a₁ modes to measure the degree of charge‐transfer. We find ~25% of charge‐transfer contribution for Ag–4‐Mpy, whereas 81 ~ 93% for Ag₂S–4‐Mpy. It means that the charge‐transfer resonance contribution dominates the overall enhancement in SERS of Ag₂S–4‐Mpy. Energy level diagram is applied to discuss the likely charge‐transfer transition between Ag, Ag₂S, Ag₂Se and 4‐Mpy. This article may point out the link among the three main resonance sources and could enable some insights into the electronic pathways available to the metal‐molecule and semiconductor‐molecule systems. Copyright © 2012 John Wiley & Sons, Ltd.     

DFT,FT‐Raman,FT‐IR and NMR studies of 2‐fluorophenylboronic acid

The experimental and theoretical vibrational spectra of 2‐fluorophenylboronic acid (2fpba) were studied. The Fourier transform Raman and Fourier transform infrared spectra of the 2fpba molecule were recorded in the solid phase. The structural and spectroscopic analysis of the molecule was carried out by using Hartree‐Fock and density functional harmonic calculations. For the title molecule, only one form was found to be the most stable structure, by using B3LYP level with the 6‐31++G(d,p) basis set. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution (TED). The ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of the 2fpba molecule were calculated using the Gauge‐Invariant‐ atomic orbital (GIAO) method in DMSO solution using IEF‐PCM model and compared with the experimental data. Finally, geometric parameters, vibrational wavenumbers and chemical shifts were compared with available experimental data of the molecule. Copyright © 2009 John Wiley & Sons, Ltd.     

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐ pentane‐2,4‐dione—synthesis,spectroscopic, theoretical and structural elucidation

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐pentane‐2,4‐dione is spectroscopically and structurally elucidated by means of linear‐polarized IR spectroscopy (IR‐LD) of oriented solids as a colloidal suspension in nematic liquid crystal. Structural information and IR‐spectroscopic assignment are supported by quantum chemical calculations at MP2 and B3LYP level of theory and 6‐311++G** basis set. The geometry is characterized with an inramolecular hydrogen bond of NH^…O?C with length of 2.526 Å and a NHO angle of 140.5(1)°. The NH? C(CH₃)C?C? C?O(CH₃) fragment is nearly flat with a maximal deviation of total planarity of 10.4°. Copyright © 2007 John Wiley & Sons, Ltd.     

Structural and vibrational analyses of 2‐(2‐benzofuranyl)‐2‐imidazoline

We have studied 2‐(2‐benzofuranyl)‐2‐imidazoline (BFI) and characterized it by using infrared and Raman spectroscopies. The density functional theory (DFT) method together with Pople's basis set shows that two conformers exist for the title molecule as have been theoretically determined in the gas phase and that, probably, an average of both conformations is present in the solid phase. The harmonic vibrational wavenumbers for the optimized geometry of the latter conformer were calculated at the B3LYP/6‐31G* level in the proximity of the isolated molecule. For a complete assignment of the IR and Raman spectra in the compound in the solid phase, DFT calculations were combined with Pulay's scaled quantum mechanics force field (SQMFF) methodology in order to fit the theoretical wavenumbers to the experimental ones. Copyright © 2010 John Wiley & Sons, Ltd.     

FT‐Raman spectroscopic spectra on 3‐phenylpropylamine inclusion compounds

Some new Hofmann‐3‐phenylpropylamine‐type clathrates with chemical formulae of M(3‐phenylpropylamine)₂ Ni(CN)₄. 2G (MNi or Co, G = 1,2‐dichlorobenzene or 1,3‐dichlorobenzene) have been prepared and their Fourier transform infrared(FT‐IR; 4000–400 cm⁻¹), far‐infrared (600–100 cm⁻¹) and FT‐Raman (4000–60 cm⁻¹) spectra are reported. The ligand molecule, guest molecules, polymeric sheet and metal‐ligand bands of the clathrates are assigned in detail. The compounds are also characterized by thermal gravimetric analysis (TGA), differential thermal analysis (DTA), elemental analysis and magnetic susceptibility measurements. From the results, the monodentate 3‐phenylpropylamine ligand molecule bonds to the metal atom of |M‐Ni(CN)₄ | _∞ polymeric layers in the trans‐gauche‐gauche (TGG) form, and 1,2‐dichlorobenzene or 1,3‐dichlorobenzene molecules are guested by this structure revealing the inclusion ability of the host complexes. Copyright © 2010 John Wiley & Sons, Ltd.     

Structural and vibrational study of 2‐(2′‐ furyl)‐4,5‐1H‐dihydroimidazole

In this study 2‐(2′‐furyl)‐4,5‐1H‐dihydroimidazole (1) was prepared and then characterized by infrared, Raman, and multidimensional nuclear magnetic resonance (NMR) spectroscopies. The crystal and molecular structures of 1 were determined by X‐ray diffraction methods. The density functional theory (DFT) and second‐order Møller–Plesset theory (MP2) with Pople's basis set show that there are two conformers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, conformer I, is present in the solid phase. NMR spectra observed for 1 were successfully compared with the calculated chemical shifts at the B3LYP/6‐311++G** level theorized for this conformer. The harmonic vibrational frequencies for the optimized geometry of the latter conformer were calculated at the B3LYP/6‐311++G** level in the approximation of the isolated molecule. For a complete assignment of the IR and Raman spectra in the solid phase of 1 , DFT calculations were combined with Pulay´s scaled quantum mechanics force field (SQMFF) methodology to fit the theoretical frequency values to the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd.     

Molecular structure,spectroscopic (FTIR,FTIR gas phase,FT‐Raman) first‐order hyperpolarizability and HOMO–LUMO analysis of 4‐methoxy‐2‐methyl benzoic acid

Vibrational spectral analysis was carried out for 4‐methoxy‐2‐methyl benzoic acid (4M2MBA) by using Fourier transform infrared (FT‐IR) (solid, gas phase) and FT‐Raman spectroscopy in the range of 400–4000 and 10–3500 cm⁻¹ respectively. The effects of molecular association through O H···O hydrogen bonding have been described by the single dimer structure. The theoretical computational density functional theory (DFT) and Hatree‐Fock (HF) method were performed at 6–311++G(d,p) levels to derive the equilibrium geometry, vibrational wavenumbers, infrared intensities and Raman scattering activities. The scaled theoretical wavenumbers were also shown to be in good agreement with experimental data. The first‐order hyperpolarizability (β₀) of this novel molecular system and related properties (β, α₀ and Δα) of 4M2MBA are calculated using the B3LYP/cc‐pvdz basis set, based on the finite‐field approach. A detailed interpretation of the infrared and Raman spectra of 4M2MBA is reported. The theoretical spectrograms for FT‐IR and FT‐Raman spectra of the title molecule were also constructed and compared with the experimental one. Copyright © 2010 John Wiley & Sons, Ltd.     

Mechanism of 4‐methyl‐1,2,4‐triazol‐3‐thiole reaction with formaldehyde. A DFT study

Contrary to the typical nucleophilic substitution, occurring on the sulfur atom of 4‐methyl‐1,2,4‐ triazol‐3‐thiole, the reaction with formaldehyde leads to the formation of the N? C bond rather than the S? C bond. The mechanism of this reaction has been characterized theoretically. Calculations indicate that the reaction proceeds via a cyclic transition state involving one solvent molecule with the Gibbs free activation energy of only 2 kcal/mol. The alternative pathway that leads to the S? C bond formation is about 5 kcal/mol more energetically demanding. Copyright © 2007 John Wiley & Sons, Ltd.