Structures of aliphatic amino acid proton-bound dimers by infrared multiple photon dissociation spectroscopy in the 700-2,000 cm(-1) region

Structural aspects of proton-bound dimers composed of amino acids with aliphatic side chains are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations. Features in the IRMPD spectra in the 700-2,000 cm-1 range are due primarily to C=O stretching, NH2 bending, and COH bending. It was possible to distinguish between isomeric structures by comparing the experimental IRMPD spectra and those predicted using B3LYP/6-31+G(d,p). It was possible, based on the calculations and IRMPD spectra, to assign the experimental spectrum of the glycine proton-bound dimer to a structure which was slightly different from that assigned by previous spectroscopic investigations and in agreement with recent thermochemical studies. Since all proton-bound dimers studied here, composed of the different amino acids, have very similar spectra, it is expected that they also have very similar lowest-energy structures including the mixed alanine/glycine proton-bound dimer. In fact, the spectra are so similar that it would be very challenging to distinguish, for example, the glycine proton-bound dimer from the alanine or valine proton-bound dimers in the 700-2,000 cm-1 range. According to the calculated IR spectra it is shown that in the approximately 2,000-3,200 cm-1 range differentiating between different structures as well as different proton-bound dimers may be possible. This is due mainly to differences in the asymmetric stretch of the binding proton which is predicted to occur in this region.     

Molecular structure of 2-(hydroxyimino)propanohydroxamic acid in solid state and DMSO solution

The 1H and 13C NMR spectra of 2-(hydroxyimino)propanohydroxamic acid (hpha) were measured in DMSO-d6 solution. The set of several monomeric structures along with the cluster of H-bonded hpha with three DMSO molecules were proposed to fit the experimental data. The calculated chemical shifts [B3LYP/6-311++G(d,p)] strongly suggested the formation of the cluster in which all the labile protons were H-bonded to the solvent molecules. The comparison between experimental and calculated Raman spectra of hpha in DMSO also suggested that in these conditions the investigated compound forms the proposed cluster rather than dimers. According to our calculations [B3LYP/6-31+G(d)] this cluster was energetically stabilized (84-106 kJ mol-1) compared to postulated dimeric structures. On the other hand, formation of dimers was proposed to be present for hpha in solid state. The comparison of the vibrational data (IR, RS) with the computed harmonic frequencies of three most probable dimers [B3LYP/6-31+G(d)] suggested that the dimer in which molecules adopted the zEe-keto form and were linked by two symmetric, almost linear H-bonds between the carbonyl oxygen atoms and the hydroxamic O-H protons was the predominant species of hpha in the solid state. Thus, the structures of hpha in solid state and DMSO solution appeared to be different.     

C50富勒烯及其二聚物C100、C101的光学性质

运用B3LYP方法在6-31G*基组水平上对C50富勒烯以及它的两个不同二聚物C100、C101的几何构型进行了全优化. 在优化所得构型的基础上, 采用TDB3LYP方法在3-21G*基组水平上对其激发态性质、电子吸收光谱进行了研究, 根据计算得到的态态间跃迁偶极矩和跃迁能等数据, 结合使用态求和公式进一步计算得到了它们不同光学过程中的三阶非线性极化率. 结果表明, 当C50富勒烯二聚以后, 其电子吸收光谱的最大波长吸收峰发生了明显的红移, 三阶非线性极化率有了较大的提高. 其中, [5,5]-[5,5]哑铃型二聚物C101有着比[2+2]闭环型二聚物C100更大的三阶非线性极化率.     

Structure and optical properties of the 4-cyano-4′-n-pentylbiphenyl dimers and trimers

ABSTRACT

The variation of the spectral characteristics of liquid crystal molecules based on 4-cyano-4′-n-pentylbiphenyl (5CB) was analysed depending on its associates structure using the quantum–chemical density functional hybrid potential methods B3LYP/6-31G and B3LYP/6-31G**. The electronic absorption spectra and IR spectra of dimers and trimers 5CB were calculated. It was shown that spectra are sensitive to the associates’ structure. We can observe the appearance of new bands in spectra and splitting characteristic CN stretching vibrations (1–5 cm^?1) in the vibrational spectra.     

Isomer structures of thioketene and its cyclic oligomers. <Emphasis Type="Italic">Ab initio</Emphasis> calculations

The thioketene molecule, as well as its isomer and dimer molecules, were calculated by the HF, MP2, and DFT (B3LYP) ab initio methods. The 6-31G (d) and 6-311G (2d, p) basis sets were used. The sequence of stable isomers is refined, and vibrational spectra are calculated for three most stable structures. The assignment of some absorption bands is changed. The most stable dimers and trimers of thioketene are calculated.     

Mixed Aggregates of 1-Methoxyallenyllithium with Lithium Chloride

A combined computational and ¹³C NMR study was used to investigate the formation of mixed aggregates of 1-methoxyallenyllithium and lithium chloride in tetrahydrofuran (THF) solution. The observed and calculated chemical shifts, as well as the calculated free energies of mixed aggregate formation (MP2/6-31+G(d)), are consistent with the formation of a mixed dimer as the major species in solution. Free energies of mixed dimer, trimer, and tetramer formation were calculated by using the B3LYP and MP2 methods and the 6-31+G(d) basis set. The two methods generated different predictions of which mixed aggregates will be formed, with B3LYP/6-31+G(d) favoring mixed trimers and tetramers in THF solution, and MP2/6-31+G(d) favoring mixed dimers. Formation of the sterically unhindered mixed dimers is also consistent with the enhanced reactivity of these compounds in the presence of lithium chloride. The spectra are also consistent with some residual 1-methoxyallenyllithium tetramer, as well as small amounts of higher mixed aggregates. Although neither computational method is perfect, for this particular system, the calculated free energies derived using the MP2 method are in better agreement with experimental data than those derived using the B3LYP method.     

Structures, stabilities, and electronic and optical properties of C62 fullerene isomers

The 2385 classical isomers and four nonclassical isomers of fullerene C62 have been studied by PM3, HCTH/3-21G//SVWN/STO-3G, B3LYP/6-31G(d)//HCTH/3-21G, and B3LYP/6-31G(d)//B3LYP/6-31G(d). The Cs:7mbr isomer, with a chain of four adjacent pentagons surrounding a heptagon, is predicted to be the most stable isomer, followed by C2v:4mbr which is 3.15 kcal/mol higher in energy. C2:0032 with three pairs of adjacent pentagons is the most stable isomer in the classical framework. To clarify the relative stabilities of C62 isomers at high temperatures, the entropy contributions are taken into account on the basis of the Gibbs energy at the B3LYP/6-31G(d) level. Analyses reveal that Cs:7mbr prevails in a wide temperature range. The vibrational frequencies of the five most stable C62 fullerene isomers are also predicted at the B3LYP/6-31G(d) level, and the simulated IR spectra show important differences in positions and intensities of the vibrational modes for different isomers. The nucleus-independent chemical shift and the density of states of the three most stable isomers show that the square in C2v:4mbr and the adjacent pentagons in Cs:7mbr and C2:0032 possess high chemical reactivity. In addition, the electronic spectra and second-order hyperpolarizabilities are determined by means of ZINDO and the sum-over-states mode. The intensity-dependent refractive index gamma(-omega; omega, omega, -omega) at omega = 2.3305 eV of Cs:7mbr is very large because of resonance with the external field. The second-order hyperpolarizabilities of the five most stable isomers of C62 are predicted to be larger than those of C60.     

Association of Diphenylguanidine and Quantum-Chemical Calculations of the Structure of Its Cyclic Dimers

The frequencies and intensities of the two tautomeric structures of the N, -diphenylguanidine monomer and its hydrogen-bonded cyclic dimers were calculated for structure elucidation of the monomer and dimer forms of this compound and identification of the stretching vibration band NH of this molecule in solution. Ab initio HF/3-21G and B3LYP/6-31G(d,p) calculations of DPG monomers and cyclic associates suggest that the asymmetric tautomer is dominant, proving that the dimer structures with two C=(Ph)N...H–NPh hydrogen bonds prevail in solution. An assignment of IR absorption frequencies of DPG in solution is suggested.     

Theoretical and experimental vibrational spectrum study of 4-hydroxybenzoic acid as monomer and dimer

Theoretical calculations on the molecular geometry and the vibrational spectrum of 4-hydroxybenzoic acid were carried out by the Density Functional Theory (DFT/B3LYP) method. In addition, IR and Raman spectra of the 4-hydroxybenzoic acid in solid phase were newly recorded using them in conjunction the experimental and theoretical data (including SQM calculations), a vibrational analysis of this molecular specie was accomplished and a reassignment of the normal modes corresponding to some spectral bands was proposed. The geometries of monomers and dimers in gas phase were optimized using the DFT B3LYP method with the 6-31G*, D95** and 6-311++G** basis sets. Also, both the vibrational spectra recorded and the results of the theoretical calculations show the presence of one stable conformer for the 4-hydroxybenzoic acid cyclic dimer. The B3LYP/6-31G* method was used to study the structure for cyclic dimer of 4-hydroxybenzoic acid and for a complete assignment our results were compared with results of the cyclic dimer of benzoic acid. A scaled quantum mechanical analysis was carried out to yield the best set of harmonic force constants. The formation of the hydrogen bond was investigated in terms of the charge density by the AIM program and by the NBO calculations.     

Structures, stabilities, electronic, and optical properties of C64 fullerene isomers, anions (C64(2-) and C64(4-)), metallofullerene Sc2@C64, and Sc2C2@C64

The 3465 classical isomers of C(64) fullerene have been investigated by quantum chemical methods PM3, and the most stable isomers have been refined with HCTH/3-21G//SVWN/STO-3G, B3LYP/6-31G(d)//HCTH/3-21G, and B3LYP/6-311G(d)//B3LYP/6-31G(d) level. C(64)(D(2):0003) with the lowest e(55) (e(55) = 2), the number of pentagon-pentagon fusions, is predicted to be the most stable isomer and it is followed by the C(64)(C(s):0077) and C(64)(C(2):0103) isomers within relative energy of 20.0 kcal/mol. C(64)(D(2):0003) prevails in a wide temperature range according to energy analysis with entropy contribution at B3LYP/6-31G(d) level. The simulated IR spectra and electronic spectra help to identify different fullerene isomers. All the hexagons in the isomers with e(55) = 2 display local aromaticity. The relative stabilities of C(64) isomers change with charging in ionic states. Doping also affects the relative stabilities of fullerene isomers as demonstrated by Sc(2)@C(64)(D(2):0003) and Sc(2)@C(64)(C(s):0077). The bonding of Sc atoms with C(64) elongates the C-C bond of two adjacent pentagons and enhances the local aromaticity of the fullerene cages. Charging, doping, and derativization can be utilized to isolate C(64) isomers through differentiating the electronic and steric effects.     

Experimental and quantum chemical study of biosynthetic lignin models — dehydropolymers

Using IR Fourier transform spectroscopy we consider biosynthetic lignin models, namely, dehydropolymers. Quantum chemical calculations of IR spectra of model lignin structures were carried out within the framework of the density functional theory with the B3LYP functional in the 6-31+G(d,p) basis. The IR spectrum of a dimer with the C(8)—O—C(4) fragment describes well the specific features of the spectrum of the dehydropolymer synthesized from coniferyl alcohol. The presence of dimeric structures with double bonds in aliphatic chains and ether bonds between aromatic rings was determined in dehydropolymers from ferulic acid. The results of theoretical and experimental studies were shown to be in agreement with each other.     

不饱和类碳烯H_2C=CLiCl的构型及异构化的理论研究

采用量子化学中的DFT理论方法, 在B3LYP/6-311G*水平上全优化得到了不饱和类碳烯H2C=CLiCl的平衡结构。 结果表明, 不饱和类碳烯H2C=CLiCl只有2种平衡结构。 对这2种平衡结构之间相互转化的过渡态进行计算, 同时, 采用统计热力学及过渡态理论, 研究了2种平衡结构之间相互转化的热力学及动力学性质, 进而讨论了2种平衡结构在不同温度下的稳定性问题, 结果表明在所研究的100～600K温度范围内, 只有一种平衡结构能够存在。 在计算得到振动频率及吸收强度的基础上, 模拟了稳定平衡结构的红外光谱图。     

Studies on the Structures and Spectra of Benzothiophene Oligomers

Theoretical studies on a series of oligobenzothiophenes were carded out with the AM 1 and DFT methods. Based on B3LYP/6-31G（D） optimized geometries, the electronic spectra, IR spectra and NMR spectra of the oligomers were calculated by INDO/CIS, AM1 and B3LYP/6-31G（D） methods, respectively. The energy gaps decrease, and the absorption in elec- tronic spectra exhibits a red-shift as polymerization increases. The IR frequencies are little affected by the polymerization and substituents. The ^13C chemical shifts are changed to be upfield since the electron-donating groups increase the electron density of carbon atoms but remain unchanged with the increase of polymerization.     

乙醛二聚体内蓝移型氢键的理论研究

利用理论方法研究了乙醛二聚体内的氢键. 在MP2/6-31＋G(d), B3LYP/6-31＋G(d), B3LYP/6-311＋＋G(d,p)和B3LYP/6-311＋＋G(3df,2p)水平上, 利用常规方法和均衡校正方法对3种稳定的乙醛二聚体进行了几何优化和振动频率计算. 计算结果表明: 在二聚体A和C中乙醛中C—H键强烈收缩, 存在显著的C—H…O蓝移型氢键. 自然键轨道(NBO)分析表明, 电子供体轨道和电子受体轨道之间相互作用的稳定化能、分子内电子密度重排、轨道再杂化和结构重组是决定氢键红移和蓝移的主要因素. 其中, 轨道间稳定化能属于键伸长效应, 分子内电子密度重排、轨道再杂化和电子受体内部结构重组属于键收缩效应. 在二聚体A和C中, 由于键收缩效应处于优势地位导致C—H…O蓝移氢键存在.     

Prediction of low-energy isomers of large fullerenes from C132 to C160

To predict energetically favored isomers, we used a topological scheme as a prescreening tool to select candidate isomers for each fullerene from C(106) to C(160). Comparison with the PM3 and tight-binding (TB) potential calculated results and few published data for the low-energy isomers of C(106) to C(130) indicates that the prescreening approach is feasible. For each fullerene from C(132) up to C(160), the selected 1000 candidate isomers were further optimized by PM3 and TB potential. The analysis of the semiempirical PM3 and TB results of C(106) to C(160) provides some qualitative features of the large fullerenes. Furthermore, calculations at the B3LYP/6-31G*//B3LYP/3-21G level of theory were carried out on the top ten PM3 and TB low-energy isomers of C(132) to C(160) to accurately predict the stable isomers, and the HOMO-LUMO gap, the ionization energy, and electron affinity of the lowest-energy isomers were also investigated at the same level.     

Molecular structure and vibrational analysis of 3-Ethylpyridine using ab initio HF and density functional theory (B3LYP) calculations

The FT-Raman and FT-IR spectra for 3-Ethylpyridine (3-EP) have been recorded in the region 4000-100 cm(-1) and compared with the harmonic vibrational frequencies calculated using HF/DFT (B3LYP) method by employing 6-31G(d,p) and 6-311++G(d,p) basis set with appropriate scale factors. IR intensities and Raman activities are also calculated by HF and DFT (B3LYP) methods. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values of some substituted benzene. The experimental geometrical parameters show satisfactory agreement with the theoretical prediction from HF and DFT. The scaled vibrational frequencies at B3LYP/6-311++G(d,p) seem to coincide with the experimentally observed values with acceptable deviations. The theoretical spectrograms (IR and Raman) have been constructed and compared with the experimental FT-IR and FT-Raman spectra. Some of the vibrational frequencies of the pyridine are effected upon profusely with the C2H5 substitutions in comparison to pyridine and these differences are interpreted.     

Sequence- and regioselectivity in the montmorillonite-catalyzed synthesis of RNA

The possible role of catalysis in forming a limited number of RNAs from activated monomers is investigated by examining the sequence- and regioselectivity in the montmorillonite-catalyzed formation of RNA dimers and trimers. The reactivity of A was similar to that of G, and C was comparable in reactivity to U. Yet the reactivity of the purine nucleotides differed from that of the pyrimidines. In the reaction of nucleotides (pN) with activated monomers (ImpN), the sequence- and regioselectivity was Pu(3')Py > Pu(3')Pu = Pu(2')Py > Pu(2')Pu. The 5'-pyrimidine initiated dimers formed less efficiently than the 5'-purine initiated dimers. Trimer formation was investigated by the synthesis of 8 dimers (pNpN) and measuring the yields of trimers formed in the reaction of each dimer with a mixture of equal molar amounts of four activated monomers. The reactivity of the dimers depended on the nucleotide attached to the 3'-end of the RNA and the regiochemistry of the phosphodiester bond. Rules based on these studies are proposed to predict the sequence- and regioselectivity of the RNAs formed in montmorillonite-catalyzed reactions. These rules are consistent with the structures of the 2-5-mers formed in the reaction of equimolar amounts of ImpA and ImpC. This research establishes that the montmorillonite catalyst limits the number of RNA oligomer isomers formed. The potential significance of these findings to the origins of life is discussed.     

Density functional theory studies on the structures and vibrational spectra of 3,6-dichlorocarbazole and 3,6-dibromocarbazole

Becke 3-Lee-Yang-Parr density functional theory (DFT) calculations using 6-311G** and 6-311G(2df,p) basis sets were carried out to study molecular structures and vibrational spectra of 3,6-dichlorocarbazole and 3,6-dibromocarbazole. The optimized geometries, vibrational frequencies, IR intensities, and Raman activities have been obtained. On the basis of B3LYP calculations, a normal mode analysis was performed to assign the vibrational fundamental frequencies according to the potential energy distributions. The computational frequencies are in good agreement with the observed results.     

Structures, stabilities, and electronic and optical properties of C52 fullerene, ions, and metallofullerenes

The 437 classical isomers of fullerene C52 have been studied by PM3, HCTH/3-21G, and B3LYP6-31G(d). C(2):029 with the least number of adjacent pentagons is predicted to be the most stable isomer. The investigations show that both the number of adjacent pentagons and the degree of aromaticity play important roles in the relative stabilities of fullerene isomers. To clarify the relative stabilities of the C52 isomers in a wide range of temperatures, the entropy contributions are taken into account on the basis of the Gibbs energy at the B3LYP6-31G(d) level. C(2):029 prevails in a wide temperature range. In addition, the electronic spectra and second-order hyperpolarizabilities are determined by means of ZINDO and sum-over-states model. The static second-order hyperpolarizability of C(2):029 is 51% larger than that of C60. Furthermore, intensity-dependent refractive index gamma (-omega;omega,omega,-omega) (omega=1.1653 eV) of C(2):029 is 13 times larger than that of C60. The encapsulation of Ca atom in C52 fullerene is exothermic and the metallofullerene Ca-C52 is described as Ca2+-C52(2-).     

Vibrational assignment of aluminum(III) tris-acetylacetone

The geometry, frequency and intensity of the vibrational bands of aluminum(III) Tris-acetylacetone Al(AA)3 and its 1,3,5-(13)C derivative were obtained by the Hartree-Fock (HF) and Density Functional Theory (DFT) with the B3LYP, B1LYP, and G96LYP functionals and using the 6-31G* basis set. The calculated frequencies are compared with the solid IR and Raman spectra. All of the measured IR and Raman bands were interpreted in terms of the calculated vibrational modes. Most computed bands are predicted to be at higher wavenumbers than the experimental bands. The calculated bond lengths and bond angles are in good agreement with the experimental results. Analysis of the vibrational spectra indicates a strong coupling between the chelated ring modes. Four bands in the 500-390 cm(-1) frequency range are assigned to the vibrations of metal-ligand bonds.