Spectroscopic characterization of aminoacetonitrile,its ions and protonated aminoacetonitrile using quantum chemical methods

We present theoretical vibrational and absorption spectra of aminoacetonitrile, its cation, anion, cyanoprotonated, and aminoprotonated aminoacetonitrile. We used second‐order Moller–Plesset perturbation method (MP2) with TZVP basis set to obtain ground state geometries and vibrational spectra. Time dependent density functional theory method was used to obtain absorption spectra. Shifts in vibrational modes for aminoacetonitrile upon ionization and protonation are determined. The C≡N stretching mode which is the most important mode in detection of nitriles in space is more intense in aminoacetonitrile ions and its two protonated form and is less IR active for neutral aminoacetonitrile. The nature of electronic transition for these molecules is identified. All the electronic transitions for neutral aminoacetonitrile and its cation are the σ → σ* electronic transitions, whereas its anion and protonated aminoacetonitrile display the σ → σ* as well as π → π* transitions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structure and vibrational spectra of mononitroalkanes

Structures and force fields for several mononitroalkane molecules were determined by ab initio quantum-chemical methods. The data obtained were used for calculation of the frequencies and modes of normal vibrations. Potentialities of different methods (RHF, MP2, and B3LYP) and basis sets for estimation of the structures and spectra were studied.     

Modeling the solvation shell of complexes in solution for quantum chemical calculations of electronic spectra

A procedure that allows for solvation effects is suggested; it is designed for quantum chemical calculations of the electronic spectra of complex compounds. Based on Monte Carlo (MC) simulation of the solvation shell one can calculate the electrostatic potential created by the solvation shell at the sites of all atoms of the complex; appropriate corrections are added to the diagonal elements of the Fock matrix and to the matrix elements of the Hamiltonian in the configuration interaction method. The method suggested has been implemented based on the semiempirical (CINDO) version of the CI (configuration interaction) technique and tested on the following compounds: [Ru(NH₃)₅(py)]²⁺, [Ru(NH₃)₅(pyz)]²⁺, [Ru(bpy)(CN)₄]^2?, [Ru(NO)(py)₄-NC-Ru(py)₄(CN)]³⁺.     

Gas-phase electron diffraction,vibrational spectroscopy,and quantum chemical studies of the molecular structure of 3,3-dimethyl-3-silathiane

The 3,3-dimethyl-3-silathiane molecule was studied by gas-phase electron diffraction and vibrational spectroscopy. The initial geometrical parameters and the force field were calculated by the B3LYP/6-311+G** method; the vibrational amplitudes of atomic pairs and vibrational corrections were calculated using the scaled B3LYP/6-311+G** force field. The molecular conformation was found to be a distorted chair with structural parameters close to the expected ones.     

Synthesis,Crystal Structure,Characterizationand Quantum Chemical Studies on 1N-Acetyl-3-（2,4-dichloro-5-fluorophenyl）-5-（p-methyl-phenyl）-2-pyrazoline

1N-Acetyl-3-（2,4-dichloro-5-fluoro-phenyl）-5-（p-methyl-phenyl）-2-pyrazoline has been synthesized and characterized by elemental analysis, IR, UV-Vis and X-ray single-crystal diffraction. Ab intio calculations have been carded out for the compound by using both B3LYP and HF methods at the 6-31G^＊ basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. The electronic absorption spectra calculated by B3LYP/6-31G^＊ method are approximate to the experiments and the Natural Bond Orbital （NBO） analyses suggest that the above electronic transitions are mainly assigned to n→π^＊ and π→π^＊ transitions. CIS-HF/6-31G^＊ method is not suitable to predict the electronic spectra for the title compound. The calculation of the second order optical nonlinearity was carded out, giving the value of molecular hyperpolarizability equal to 2.194^＋ 10^-30 esu. On the basis of vibrational analyses, the thermodynamic properties of the compound at different temperature have been calculated, revealing the correlation between C p, m^0, S m^0, H m^0 and temperature.     

Investigation of oxofluorotitanates (NH4)3TiOF5 and Rb2KTiOF5 by vibrational spectroscopy and quantum-chemical methods

The phase transition effects in (NH₄)₃TiOF₅ and Rb₂KTiOF₅ were studied by vibrational spectroscopy over a wide range of temperatures. Changes in the spectra of these crystals were found for a PT in the region of the internal vibrations of the [TiOF₅]^3? ion. Quantum-chemical simulation of the vibrational spectra of (NH₄)₃TiOF₅ was performed, and band assignments were carried out. The structure of the compound and the mechanism of the structural phase transition were examined. It is shown that the vibrational spectra of the compounds at room temperature depend on the dynamic disordering of the complex anion.     

DFT and experimental studies of the structure and vibrational spectra of curcumin

The potential energy surface of curcumin [1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione] was explored with the DFT correlation functional B3LYP method using 6‐311G* basis. The single‐point calculations were performed at levels up to B3LYP/6‐311++G**//B3LYP/6‐311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X‐ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Infrared vibrational spectra,electronic structures,and formation reactions of polypyrrolic mono‐ and bis‐actinyl complexes: A relativistic DFT study

The development of synthetic techniques has enabled synthesis and characterization of a series of mono and bis‐uranyl complexes of octadentate polypyrrolic macrocycles such as aryl‐lined H₄L^Ar and anthracenyl‐linked H₄L, which is complemented by theoretical investigation via extending to more toxic and radioactive transuranics. The relativistic density functional theory (DFT) study has been dedicated to twelve actinyl complexes supported by the H₄L ligand. The actinides include U, Np, and Pu elements, and either one or two is rendered in complexes with oxidation states of V or VI. Calculated symmetric/asymmetric An = O stretching vibrational frequencies show the decreasing trend along U, Np, and Pu, which is consistent with calculated bond orders. The hydrogen bonds between –yl endo‐oxo and remaining hydrogen atoms of pyrrolides in mononuclear complexes cause pronounced redshift of An = O vibrational frequencies compared to those in binuclear complexes, so does the reduction from hexa‐ to penta valent complexes. The electronic structures of actinyl complexes were calculated. For example, B‐ pyU^VI possesses low‐lying U(5f )‐character virtual orbitals, where f (δ) and f (?) orbitals occur in low‐energy region and π‐type ones are residing further high; the σ*(U = O) and σ(U = O) orbitals are significantly split over 7 eV. The previous experimental observation that the 1:1 reactions between uranyl salts and the macrocycle tend to give a mixture of bis‐ and mono‐uranyl complexes, with bis‐ the major product, has been corroborated by computational studies of the thermodynamics of the reactions.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Crystal structure and quantum chemical investigation of 4-(3,4-dichlorphenyl)-1,2,4-triazole

1,2,4-Triazole derivative substituted in the 4th position — 4-(3,4-dichlorphenyl)-1,2,4-tirazole — has been synthesized. Crystal and molecular structure of the compound were determined by single crystal X-ray diffraction. Molecular geometry optimization and effective charge calculations were performed by DFT methods.     

Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

The IR (4000–50 cm⁻¹) and Raman (3500–170 cm⁻¹) spectra of solid 1,1,3,3-tetramethyl-2-nitroguanidine (TMNG) were obtained. The spectra were interpreted using the scaling of the TMNG quantum-chemical force field in the B3LYP/6-311G(d,p) approximation. Transferable scale factors necessary for the interpretation of spectra of more complex related compounds were determined. The scaled harmonic force field is supposed to be used in the analysis of the available gas-phase electron diffraction data for TMNG. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 495–498, March, 2008.     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.     

Predicted vibrational frequencies and assignment of the spectra of uracil and its n,n-dideutero derivative by quantum chemical methods

A recent theoretical study on the vibrational spectrum and force field of maleimide (ref.1) lead to scale factors transferable to molecules of similar structure (ref.2). The theoretical vibrational spectrum of uracil (refs.2–3) calculated from scaled CNDO/2 force constants using the scale factors of ref.1 agrees better with the experimental results (ref.4) than former calculations by $\text{ab initio}$ STO-3G (ref.5) or MINDO/3 (ref.6) methods. The scaled CNDO/2 force field of uracil has also been used to predict the normal frequencies of a set of its deuterated derivatives.     

N-2-亚甲基-噻酚-二茂铁基芳胺衍生物的合成、晶体结构及电化学性质

以邻、间、对-二茂铁苯胺为原料, 合成了含噻酚的二茂铁苯基席夫碱衍生物并还原得到N-2-亚甲基-噻酚-二茂铁基芳胺衍生物，通过元素分析，IR，UV，¹H NMR和X-射线单晶衍射等分析手段，确证了标题化合物的组成和结构，单晶结构解析表明，化合物2c属于单斜晶系，P2/n空间群。量化计算结果证明，化合物2c在晶体中的结构并不是它的最稳定结构；其HOMO轨道主要由Fe原子及茂环上C的原子轨道组成的；电化学实验证明所得邻、间、对化合物的电化学性质相似，氧化还原峰对应于二茂铁的氧化还原过程，Fc⁺ + e^-←→Fc；说明化合物中的二茂铁基所处的化学环境相同，苯环上取代基位置的不同，对化合物在电极表面的扩散系数影响不大, 但对反应速率常数则有较大的影响。     

Ab initio quantum chemical study on the mechanism of exceptional behavior of lysine for ion yields in MALDI--role of vibrational entropic contribution in thermally averaged proton affinities

To elucidate the mechanism of the exceptional behavior of lysine for the ionization (protonation) yields in matrix-assisted laser desorption/ionization (MALDI) observed by Nishikaze and Takayama [Rapid Commun. Mass Spectrom. 2006, 20, 376], the temperature dependences of proton affinity (PA) and gas phase basicity for 20 amino acids are theoretically analyzed with correlated ab initio molecular orbital method under ideal gas condition. We have found that two different conformations, the linear structure with elongation of the side chain and the folded one having intramolecular hydrogen bonding, play important roles for the exceptional behavior of lysine. At low temperatures of around 298 K, the most stable conformation of the protonated lysine is the folded structure due to the formation of intramolecular hydrogen bonding. Meanwhile, at high temperatures, the Gibbs free energy of linear structure of protonated lysine becomes lower than that of the folded one because of the increment of vibrational entropic contribution. To explicitly take account of the contribution of the free energies, we have proposed the effective PA values thermally averaged using the ratio of Boltzmann distributions for two conformations. Since the effective PA value for lysine drastically decreases as the temperature increases above 1000 K, the linear correlation is clearly obtained between our effective PA values at high temperature and the ion yields in MALDI.     

Investigation of the structural units of germanium sulfide and selenide by quantum chemical methods

This article deals with the modeling of the structural units (clusters) of germanium sulfide and germanium selenide glasses by quantum chemical (ab initio Hartree–Fock) methods. Clusters of different sizes were investigated. Geometric parameters and vibrational frequencies of these structural units were calculated. The quantum chemical calculations were followed by normal coordinate analysis. Based on the yielded results, the vibrational spectra of the clusters were simulated. The results for germanium sulfide and germanium selenide were compared. It was concluded that in the spectral regions where germanium sulfide is not applicable for fiber optics, germanium selenide or different germanium sulfide–selenides are suitable to replace it. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

三环己基锡吡啶酸甲酯的合成、结构、热稳定性及其量子化学计算研究

利用吡啶-3-甲酸与Cy3SnOH反应合成了[(C5H4N)COOSnCy3]n,经元素分析、1H NMR、IR和X-射线衍射表征分子结构。在该配合物的结构中,中心Sn原子呈现五配位畸变三角双锥构型,并通过分子间的N→Sn配位形成一维链状线型聚合物,分子链间的C-H…O氢键作用将配合物分子组装成三维超分子网络结构。利用量子化学G03W软件,在LANL2DZ基组对配合物的稳定性、前沿分子轨道组成及能量进行研究。热重分析表明该化合物在273℃开始发生分解。     

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen,oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.     

Vibrational spectra and structure of methyl-derivatives of imidazo[4,5-c]pyridine based on DFT quantum chemical calculations and XRD studies

The molecular structures, vibrational energy levels and potential energy distribution of 4-methyl-imidazo[4,5-c]pyridine (4MIPc) and 7-methyl-imidazo[4,5-c]pyridine (7MIPc) are derived from the quantum chemical calculations and compared to the experimental results obtained from the X-ray diffraction (XRD), IR and Raman studies. The B3LYP/6-311G(2d,2p) quantum model and PED contributions have been applied for the assignment of the vibrational modes. 4MIPc crystallizes in an orthorhombic structure, space group Pna2₁ and Z = 4 and 7MIPc crystallizes in a triclinic structure, space group P−1 and Z = 4. The almost planar conformation of the molecules and presence of the N–H?N hydrogen bonds formed with the pyridine and imidazole nitrogen atoms was found to be characteristic for the studied systems. The presence of hydrogen bonds is also confirmed by the results of IR studies.