Vibrational spectra and assignments of 2-amino-5-iodopyridine by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 2-amino-5-iodopyridine were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) methods with the 6-31G(d,p) basis set for C, N, H and LANL2DZ pseudopotential for I. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of 2-amino-5-iodopyridine is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Vibrational spectra and assignments of 5-amino-2-chlorobenzoic acid by ab initio Hartree-Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra of 5-amino-2-chlorobenzoic acid (5A2CBA) were recorded in the solid phase. Geometry opitimizations were done without any constraint and harmonic-vibrational wavenumber and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-311G(d,p) basis set and the results are compared with the experimental values with the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrograms for the FTIR spectra of the title molecule were also constructed.     

Vibrational spectra and assignments of 3-aminobenzyl alcohol by ab initio Hartree-Fock and density functional method

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 3-aminobenzyl alcohol. The FT-Raman and FT-IR spectra of 3-aminobenzyl alcohol were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities, Raman scattering activities, depolarization ratios and reduced masses were calculated by ab initio HF and density functional B3LYP method with 6-311+G(d,p) basis sets. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. A detailed interpretation of the infrared and Raman spectra of 3-aminobenzyl alcohol is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

基于2-(2′-吡啶基)苯并咪唑的Zn2+比例计量型荧光识别

本文以荧光分子2-(2'-吡啶基)苯并咪唑(2-PBI)作为1,1'-联(2-芳杂环)类化合物模型.研究利用其2,2'-N原子螯合Zn2 导芳环共面化和荧光发射红移实现Zn2 比例计量检测的可行性.2-PBI在不同体系中的Zn2 荧光响应行为表明Zn2 结合将导致最大发射波长明显红移(乙腈36 nm;HEPES缓冲液39 nm).具有比例计量型Zn2 荧光探针的基本特点.2-PBI还具有显著的Zn2 荧光响应选择性,可以同时作为构建比例计量型探针的信号团和受体的基本骨架.通过对2-BPI的荧光机制和Zn2 识别行为的分析,提出了以2-PBI为基本骨架构建实用化比例计量型探针的途径.     

Multicomponent one-pot synthesis of (dihydro-1H-benzo[d]imidazole) phosphonate

Abstract

We present a multicomponent reaction strategy to synthesize a (dihydro-1H-benzo[d]imidazole)phosphonate family of compounds, using benzimidazoles, diethyl chlorophosphate and aliphatic amines as starting reactants. Giving its simplicity, our procedure involves reaction times of only few hours and avoid the usage of any catalyst agent. All the newly synthesized compounds were characterized by Nuclear Magnetic Resonance spectroscopy (¹H, ¹³C and ³¹P) and mass spectrometry by the DART method.     

Vibrational spectra and molecular structure of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one by density functional theory and ab initio Hartree-Fock calculations

The vibrational frequencies and molecular geometry of (R)- and (rac)-4-phenly-1,3-oxazolidin-2-one (4-POO) in the ground state have been calculated using the Hartree-Fock and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths are described better by HF while bond angles are reproduced more accurately by DFT (B3LYP). Comparison of the observed fundamental vibrational frequencies of (R)-POO and (rac)-4-POO and calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems.     

Parallel Solid-Phase Synthesis of disubstituted 3-(1H-benzo[d]imidazol-2-yl)imidazolidine-2,4-diones and 3-(1H-benzo[d]imidazol-2-yl)-2-thioxoimidazolidin-4-ones

A multistep approach to construct novel 3-(1H-benzo[d]imidazol-2-yl)imidazolidine-2,4-diones and 3-(1H-benzo[d]imidazol-2-yl)-2-thioxoimidazolidin-4-ones from commercially available amino acids, amines, and carboxylic acids is described. Coupling of Fmoc-amino acid to resin-bound aminobenzimidazole provided following Fmoc elimination free amine. Treatment of the free amine with 1,1′-carbonyldiimidazole or 1,1′-thiocarbonyldiimidazole furnished the corresponding hydantoins and thiohydantoins via intramolecular cyclization. The desired aminobenzimidazole tethered hydantoins or thiohydantoins were isolated in good yields.     

Molecular structure and vibrational assignment of 2-,4-,6-methylquinoline by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments of 2-,4-,6-methylquinoline (2-,4-,6-mq) in the ground state were performed by HF and DFT/B3LYP levels of theory using the 6-31++G(d,p) basis set. Harmonic and anharmonic vibrational frequencies were calculated. 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 by using parallel quantum mechanic solutions program. The general agreements between the observed and calculated frequencies are shown.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-mercaptopropanoic acid

2-(4-Fluorobenzylideneamino)-3-mercaptopropanoic acid (4-FC) was synthesized through the reaction of 4-fluorobenzaldehyde and l-cysteine in refluxing EtOH. Its structure was verified by (1)H NMR, FT-IR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains, respectively. The vibrational wavenumbers of 4-FC were calculated at same level. The scaled theoretical spectra using B3LYP methods, which are in a good agreement with the experimental ones, are superior to those using HF methods.     

Experimental and density functional theory and ab initio Hartree-Fock study on the vibrational spectra of 2-(4-fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid

2-(4-Fluorobenzylideneamino)-3-(4-hydroxyphenyl) propanoic acid (4-FT) was synthesized through the reaction of 4-fluorobenzaldehyde and l-tyrosine in refluxing EtOH. The structure of 4-FT was verified by measuring 1H NMR, FTIR and Raman. The ground-state geometries were optimized at B3LYP/6-31G**, B3LYP/6-31G*, HF/6-31G** and HF/6-31G* levels without symmetry constrains. The vibrational wavenumbers of 4-FT were calculated at same levels. The scaled spectra using B3LYP methods, which are in a good agreement with the measured spectra, are superior to those calculated using HF methods.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 3-(6-benzoyl-2-oxobenzo[d]oxazol-3(2H)-yl)propanoic acid

The molecular structure, vibrational frequencies and infrared intensities of the 3-(6-benzoyl-2-oxobenzo[d]oxazol-3(2H)-yl)propanoic acid were calculated by the HF and DFT methods using 6-31G(d) basis set. The FT-infrared spectra have been measured for the title compound in the solid state. We obtained 11 stable conformers for the title compound, however the Conformer 1 is approximately 3.88 kcal/mol more stable than the Conformer 11. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of the Conformer 1. The harmonic vibrations computed of this compound by the B3LYP/6-31G(d) method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using VEDA 4 program.     

Different synthetic routes to 4-(1H-benzo[d]imidazol-2-yl)aniline

The benzimidazole nucleus is an important pharmacophore in drug discovery, being a good bioisostere of naturally occurring nucleotides. This heterocycle may represent a type of privileged substructure which can interact with proteins and enzymes; it has, hence, been extensively utilized as a drug scaffold in medicinal chemistry. The connection between wide ranging biological activity and compounds containing the benzimidazole nucleus is known, and well documented in the literature. Benzimidazole derivatives have a multitude of interesting pharmacological activity, including antiviral, antitumor, antihypertensive, proton pump inhibitory, anthelmintic, antimicrobial, and anti-inflammatory activity. Accordingly, a brief survey is given below covering the synthesis of 2-phenybenzimidazole derivatives and their biological importance.     

Vibrational spectra and assignments using ab initio and density functional theory analysis on the structure of biotin

Density functional theory (DFT) and Hartree-Fock calculations were performed using the following models: HF/6-311G(d), B3LYP/6-311G(d), B3LYP/6-311+G(d) and B3PW91/6-311G(d) calculations were performed for biotin. It has been characterized by IR and X-ray. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they supported each other. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m degrees, Sm degrees, Hm degrees and temperatures.     

Synthesis,Crystal Structure and Luminescent Property of a Dinuclear Cadmium Complex Based on 2-(2-(1H-Benzo[d]imidazol-2-yl)-phenyl)-1-phenyl-1H-benzo[d]imidazole

A dinuclear cadmium complex [Cd_2(bppb)Cl_4×2DMF](1), where bppb is 2-(2-(1 Hbenzo[d]imidazol-2-yl)phenyl)-1-phenyl-~1 H-benzo[d]imidazole, was synthesized and characterized by X-ray single-crystal structure analyses. For 1: C_(58) H_(50) Cd_2 Cl_4 N_(10) O_2, M_r = 1285.68, monoclinic system, space group P2_1/n, a = 16.136(3), b = 10.612(2), c = 16.270(3) ?, β = 96.209(2)°, V = 2769.7(9) ?~3, Z = 2, D_c = 1.542 g/cm~3, λ = 0.71073 ?, μ(Mo Kα) = 1.013 mm~(–1), F(000) = 1296, S = 1.055, R = 0.0393 and wR = 0.1185 for 4876 observed reflections with I 2σ(I). One 9 mium ion which is five-coordinated by three chloride ions and two nitrogen atoms from bppb. Two cadmium ions are bridged by two chloride ions. The Cd_2(bppb)_2 Cl_2(μ-Cl_2) decomposes at 350 ℃ which is much lower by 70 ℃ than [Cd_2(bpbb)_2 Cl_2(μ-Cl_2)](420 ℃). The complex emits blue luminescence in both DMF solution and solid powder. Phenyl ring substituting NH hydrogen atom of benzimidazole group in ligand can not obviously change the UV-vis and luminescence spectra peaks location of the benzimidazole cadmium complex.     

Molecular structures and vibrational frequencies of 2-, 3- and 4-pyridine carboxaldehydes by ab initio Hartree-Fock and density functional theory calculations

The optimised molecular structures, vibrational frequencies and corresponding vibrational assignments of the cis and trans conformers of 2-, 3- and 4-pyridine carboxaldehydes have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-311++G(d, p) basis set. The calculations were adapted to the C(S) symmetries of all the molecules. The mean vibrational deviations between the vibrational frequency values of the two conformers of all the compounds have been seen to increase while the relative energies increase and it was concluded the more different the molecular structure of the two conformers is the higher the relative energy is between them, and thus a bigger mean vibrational deviation.     

Molecular structure, vibrational and chemical shift assignments of 8-hydroxy-1-methylquinolinium iodide hydrate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, (1)H and (13)C NMR chemical shift values of 8-hydroxy-1-methylquinolinium iodide monohydrate [(C(10)H(10)NO)(+)I(-)H(2)O] in the ground state were performed by HF and B3LYP levels of theory using the LanL2DZ basis set. The optimized bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by HF and DFT methods, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The title compound [(C(10)H(10)NO)(+)I(-)H(2)O] have been studied theoretically in the 4, 000-200 cm(-1) region and the assignment of all the observed bands were made. The analysis of the infrared spectra indicates that there are some structure-spectra correlations. These methods are proposed as a tool to be applied in the structural characterization of 8-hydroxy-1-methylquinolinium iodide monohydrate [(C(10)H(10)NO)(+)I(-)H(2)O], and thus providing useful support in the interpretation of experimental NMR data.     

Vibrational frequencies and structure of 2-thiouracil by Hartree-Fock,post-Hartree-Fock and density functional methods

Vibrational study of the biomolecule 2-thiouracil was carried out. Ab initio and density functional calculations were performed to assign the experimental spectra. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted frequencies of 2-thiouracil. Several scaling procedures were used. The geometry structure of the molecule was determined. The effect of sulfur substitution at C2 position in the uracil molecule, on the N1-H and N3-H frequencies and intensities reflects changes in proton donor abilities of these groups. Calculations with the 6-31 G** basis set with HF and DFT methods appear in general to be useful for interpretation of the general features of the IR and Raman spectra of the molecule. Using specific scale factors a very small error was obtained. The use of these specific scale factors resolve and correct some of the controversial assignments in the literature.     

CuCl3]- and [CuCl4]2- hydrates in concentrated aqueous solution: a density functional theory and ab initio study

In this work, structures and thermodynamic properties of [CuCl(3)](-) and [CuCl(4)](2-) hydrates in aqueous solution were investigated using density functional theory and ab initio methods. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) structures were both taken into account. Our calculations suggest that [CuCl(3)(H(2)O)(n)](-) clusters might favor a four-coordinated CIP structure with a water molecule coordinating with the copper atom in the equatorial position for n = 3 and 4 in aqueous solution, whereas the four-coordinated SSIP structure with one chloride atom dissociated becomes more stable as n increases to 5. For the [CuCl(4)](2-) cluster, the four-coordinated tetrahedron structure is more stable than the square-planar one, whereas for [CuCl(4)(H(2)O)(n)](2-) (n ≥ 1) clusters, it seems that four-coordinated SSIP structures are slightly more favorable than CIP structures. Our calculations suggest that Cu(2+) perhaps prefers a coordination number of 4 in CuCl(2) aqueous solution with high Cl(-) concentrations. In addition, natural bond orbital (NBO) calculations suggest that there is obvious charge transfer (CT) between copper and chloride atoms in [CuCl(x)](2-x) (x = 1-4) clusters. However, compared with that in the [CuCl(2)](0) cluster, the CT between the copper and chloride atoms in [CuCl(3)](-) and [CuCl(4)](2-) clusters becomes negligible as the number of attached redundant Cl(-) ions increases. This implies that the coordination ability of Cl(-) is greatly weakened for [CuCl(3)](-) and [CuCl(4)](2-) clusters. Electronic absorption spectra of these different hydrates were obtained using long-range-corrected time-dependent density functional theory. The calculated electronic transition bands of the four-coordinated CIP conformer of [CuCl(3)(H(2)O)(n)](-) for n = 3 and 4 are coincident with the absorption of [CuCl(3)](-)(aq) species (～284 and 384 nm) resolved from UV spectra obtained in CuCl(2) (ca. 10(-4) mol·kg(-1)) + LiCl (>10 mol·kg(-1)) solutions, whereas the calculated bands of [CuCl(3)(H(2)O)(n)](-) in their most stable configurations are not when n = 0 - 2 or n > 4, which means that the species [CuCl(3)](-)(aq) exists in those CuCl(2) aqueous solutions in which the water activity is neither too low nor too high. The calculated bands of [CuCl(4)(H(2)O)(n)](2-) clusters correspond to the absorption spectra (～270 and 370 nm) derived from UV measurements only when n = 0, which suggests that [CuCl(4)](2-)(aq) species probably exist in environments in which the water activity is quite low.