Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O · HO)

The hydrogen bonding complexes formed between the H₂O and OH radical have been completely investigated for the first time in this study using density functional theory (DFT). A larger basis set 6‐311++G(2d,2p) has been employed in conjunction with a hybrid density functional method, namely, UB3LYP/6‐311++G(2d,2p). The two degenerate components of the OH radical ²Π ground electronic state give rise to independent states upon interaction with the water molecule, with hydrogen bonding occurring between the oxygen atom of H₂O and the hydrogen atom of the OH radical. Another hydrogen bond occurs between one of the H atoms of H₂O and the O atom of the OH radical. The extensive calculation reveals that there is still more hydrogen bonding form found first in this investigation, in which two or three hydrogen bonds occur at the same time. The optimized geometry parameter and interaction energy for various isomers at the present level of theory was estimated. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. The estimates of the H₂O · OH complex's vibrational modes and predicted IR spectra for these structures are also made. It should be noted that a total of 10 stationary points have been confirmed to be genuine minima and transition states on the potential energy hypersurface of the H₂O · HO system. Among them, four genuine minima were located. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

X-ray analysis at 150?K, synthesis and theoretical calculations of 1-naphthaleneacrylic acid

The X-ray structure, synthesis, theoretical calculation and IR spectra of 1-naphthaleneacrylic acid are reported. The titled compound crystallizes in the monoclinic C 2/c space group with unit cell parameters: a = 14.556(3), b = 5.1332(10), c = 26.832(5) ?, β = 97.02(3)°, V = 1989.8(7) ?³, Z = 8 and form typical centrosymmetric hydrogen-bonded dimers. Theoretical calculations of 1-naphthylacrylic acid isolated molecule and hydrogen-bonded dimer have been carried out using density functional theory at the B3LYP level. For optimized structures the vibrational spectra have been then calculated and compared with experimental IR spectrum. The assignment and characterization of theoretical vibrational spectra were based on the potential energy distribution analysis. This comparison has shown that the theoretical spectrum for the dimer structure is in good agreement with the experimental one. Structural comparisons with naphthalene, and with some substituted 2-propenoic acids have shown influence of the substituent on conformation of the naphthalene ring or 2-propenoic moiety.     

Vibrational assignment and structure of dibenzoylmethane. A density functional theoretical study

Molecular structure and vibrational frequencies of 1,3-diphenyl-1,3-propanedione, known as dibenzoylmethane (DBM), have been investigated by means of density functional theory (DFT) calculations. The results were compared with those of benzoylacetone (BA) and acetylacetone (AA), the parent molecule. IR and Raman spectra of DBM and its deuterated analogue were clearly assigned.The calculated hydrogen bond energy of DBM is 16.15 kcal/mol, calculated at B3LYP/6-311++G** level of theory, which is 0.28 kcal/mol more than that of AA. This result is in agreement with the vibrational and NMR spectroscopy results. The molecular stability and the hydrogen bond strength were investigated by applying the Natural Bond Orbital analysis (NBO) and geometry calculations. The theoretical calculations indicate that the hydrogen bond in DBM is relatively stronger than that in BA and AA.     

气相水杨酸激发态分子内质子转移特性分析

采用密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)研究了气相水杨酸(SA)分子的激发态氢键动力学过程。通过对水杨酸分子基态和激发态结构的优化,以及对其稳态吸收和发射光谱特性、前线分子轨道、红外振动光谱和势能曲线的计算分析,阐明水杨酸分子内质子转移可在激发态下自发地发生,导致其激发态可存在烯醇式和酮式两种异构体结构,并揭示了这种质子转移源于分子内电荷转移的激发态氢键的加强机制。     

IR spectrum and normal mode analysis of the antiAlzheimer’s disease natural product Huperzine A: A quantum chemistry density-functional theory (DFT) investigation

Quantum chemistry density-functional theory (DFT)B3LYP method with 6-31G basis set has been empolyed to study the electronic structure and IR spectrum of Huperzine A. The calculation result showed that the characteristic of the predicted IR bands was in general consistent with the experimental spectrum. 45 vibration modes were assigned clearly from the total of 102 vibration bands. The strongest IR-intensive band corresponds to the stretching vibration of the C=O bond of the pyridone ring, and the highest frequency band belongs to the pyridone N-H stretch. The investigation showed that the obvious differences between the calculated bands and the experimental spectrum existed at the bands involving the hydrogen atoms of amino and pyridone amide groups, which could form intermolecular hydrogen bond with other Huperzine A in the crystal structure. The hydrogen bonds can not only affect the orientation of these hydrogen atoms, but also can affect the force property of the chemical bond, which can change the vibrational frequencies. Project supported by the “863” High Technology Program of China (No. 863-103-04-01) and the National Natural Science Foundation of China (Grant No. 29403027).     

Theoretical and experimental study of the vibrational spectrum of N-acetyl-L-alanine

The energies, vibrational frequencies and IR intensities of cis- and trans-N-acetyl-L-alanine (NAAL) are computed using the density functional theory (B3LYP) combined with the 6-311G(d, p) basis set. The trans conformer is characterized by an intramolecular NH ... O hydrogen bond leading to the formation of a five-membered ring and is by 23 kJ mol(-1) more stable than the cis conformer. The difference between the vibrational frequencies and IR intensities computed for the two conformers is discussed. The IR spectra at different temperatures and the Raman spectra of solid NAAL and its deuterated counterpart are investigated and discussed. The frequencies of the v(OH) vibration and the isotopic ratio suggest the formation of short OH ... O hydrogen bonds in the solid state. The NH group seems also to be involved in a weak hydrogen bond.     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

An ab initio Study of the Rotamers and Rotations of Propane-1,3-dial by DFT and SCF Calculations

Summary.  Eight planar rotamers of the enol form of malonaldehyde were considered at the HF (Hartree-Fock) and DFT (density functional theory) levels with 6-311G^** and D95^** (Dunning/Huzinaga full double-ζ) basis sets with the aim to establish the most stable of them and to find the energy barriers of their conversions. The results show that the rotamer with an intramolecular hydrogen bond is the most stable one. High energy barriers were ascertained for the conversions including rotations around a CC double bond. Most of the reactions connected with breaking of the hydrogen bond display strongly asymmetric energy barriers. Their transition states were determined as first-order saddle points because of one imaginary frequency in the IR spectrum related with a negative energy gradient. Received July 6, 2000. Accepted (revised) September 7, 2000     

Chemistry of naphthazarin derivatives 13. Conformational analysis of 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones by quantum chemistry methods

The molecular structures of various conformers of 2-hydroxy-1,4-naphthoquinone; 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones; 2,5,8-trihydroxy-1,4-naphthoquinone; and 3-(alk-1-enyl)-2,5,8-trihydroxy-1,4-naphthoquinones were studied by density functional theory (B3LYP/6-31(d), B3LYP/6-31(d, p)) and ab initio (MP2/6-31G, MP2/6-31(d)) methods. The strengths of the intramolecular hydrogen bonds formed by the β-hydroxy group with the O atom at C(1) and with the double bond π-electrons of the alkenyl substituents in the quinonoid rings were estimated. The compounds studied mainly exist as rotamers with the former-type hydrogen bonds. The splitting of the quinonoid bands of the stretching vibrations of the β-hydroxy group in the IR spectra of 3-(alk-1-enyl)-2-hydroxy-1,4-naphthoquinones and 3-(alk-1-enyl)-2,5,8-trihydroxy-1,4-naphthoquinones in hexane solutions is due to the existence of rotamers formed upon internal rotation of the alkenyl substituent. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1667–1673, October, 2006.     

Vibrational dynamics of hydrogen‐bonded HCN complexes with OH and NH acids: Computational DFT systematic study

Vibrational properties (band position, infrared [IR], and Raman intensities) of C?N stretching mode were studied in 65 gas phase hydrogen‐bonded 1:1 complexes of HCN with OH acids and NH acids using density functional theory (DFT) calculations at the B3LYP‐6‐311++G(d,p) level. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in acids OH/NH stretching bands were also considered. Experimentally observed blue shift of the C?N stretching band promoted by hydrogen bonding, which shortens the triple bond length, is very well reproduced and quantitatively depends on the hydrogen bond length. Both IR and Raman ν(C?N) band intensities are enhanced, also in good agreement with the experimental results. IR intensity increase is a direct function of the hydrogen bond energy. However, the predicted Raman intensity raise is a more complex function, depending simultaneously on characteristics of both the hydrogen bond (C?N bond length) and the H‐donating acid (polarizability). With these two parameters, ν (C?N) Raman intensities of the complexes are explained with a mean error of ±2.4%. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Pairing of Isolated Nucleobases: Double Resonance Laser Spectroscopy of Adenine–Thymine

The vibronic spectrum of the adenine–thymine (A–T) base pair was obtained by one‐color resonant two‐photon ionization (R2PI) spectroscopy in a free jet of thermally evaporated A and T under conditions favorable for formation of small clusters. The onset of the spectrum at 35 064 cm^?1 exhibits a large red shift relative to the π–π* origin of 9H‐adenine at 36 105 cm^?1. The IR–UV spectrum was assigned to cluster structures with HNH???O?C/N???HN hydrogen bonding by comparison with the IR spectra of A and T monomers and with ab initio calculated vibrational spectra of the most stable A–T isomers. The Watson–Crick A–T base pair is not the most stable base‐pair structure at different levels of ab initio theory, and its vibrational spectrum is not in agreement with the observed experimental spectrum. Experiments with methylated A and T were performed to further support the structural assignment.     

Identification of a new flavone glycoside from <Emphasis Type="Italic">Codonopsis nervosa</Emphasis>

A new flavone glycoside, luteolin 7-O-[(6″′-caffeoyl)-β-D-glucopyranosyl-(1 → 6)]-β-D-glucopyranoside (1), was isolated from Codonopsis nervosa, along with three other known compounds, luteolin 7-O-β-D-glucopyranoside (2), luteolin 7-O-gentiobioside (3), and tangshenoside VI (4). Their structures were determined on the basis of 1D and 2D NMR, IR, and HR-ESI-MS.     

发光共价有机骨架LCOF-NDT1荧光识别甲醛的理论研究

基于密度泛函理论(DFT)和含时密度泛函理论(TD-DFT),探究了发光共价有机骨架LCOF-NDT1与甲醛之间的分叉氢键作用.发现LCOF-NDT1与甲醛氢键作用后发光机理发生改变.氢键复合物的电子激发能减小,激发态下的氢键键长变短,氢键质子供体的~1H-NMR移向高场,氢键质子供体和受体的振动频率发生红移,均表明电子激发态下的氢键增强.氢键复合物的荧光速率系数减小,内转换速率系数增大,阐明电子激发态下氢键的增强有利于非辐射跃迁,不利于辐射跃迁,从而导致LCOF-NDT1荧光减弱或猝灭.计算结果表明LCOF-NDT1在荧光识别甲醛方面有潜在的应用前景.     

IR spectrum and normal mode analysis of the antiAlzheimer''''s disease natural product Huperzine A: A quantum chemistry density-functional theory (DFT) investigation

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Molecular structure, vibrational spectra and NBO analysis of phenylisothiocyanate by density functional method

The molecular geometry, vibrational frequencies and NBO analysis of phenylisothiocyanate (PITC) in the ground state have been calculated by using density functional theory calculation (B3LYP) with 6-311++G(d,p) basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with experimental values. Comparison of the observed fundamental vibrational frequencies of the PITC and calculated result by density functional theory (B3LYP) indicates B3LYP is superior for molecular vibrational problems. The entropy of the title compound was also performed at HF/B3LYP/6-311++G(d,p) levels of theory. Natural bond orbital (NBO) analysis of title molecule is also carried out. A detailed interpretation of the IR and Raman spectra of PITC is reported on the basis of the calculated potential energy distribution (PED). The theoretical spectrogram for IR spectrum of the title molecule has been constructed.     

Time-Dependent Density Functional Theory Study on the Electronic Excited State of Hydrogen-Bonded Clusters Formed by 2-Hydroxybenzonitrile (<Emphasis Type="Italic">o</Emphasis>-Cyanophenol) and Carbon Monoxide

Time-dependent density functional theory (TDDFT) method has been carried out to investigate excited-state hydrogen-bonding dynamics between 2-hydroxybenzonitrile (o-cyanophenol) and carbon monoxide. We have demonstrated that intermolecular hydrogen bond between 2-hydroxybenzonitrile (o-cyanophenol) and C=O group are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen-bonding groups in different electronic states. In this study, we firstly analyze frontier molecular orbitals (MOs). Our results are consistent with the intermolecular hydrogen bond strengthening in the electronically excited state of Coumarin 102 in alcoholic solvents, which has been demonstrated for the first time by Zhao and Han. Moreover, the calculated electronic excitation energies of the hydrogen bonding C=O and O–H groups are markedly red-shifted upon photoexcitation, which illustrates the hydrogen bonds strengthen in the electronically excited state again. And the geometric structures in both ground state and the S₁ state of this hydrogen-bonded complex are calculated using the density functional theory (DFT) and TDDFT methods, respectively.     

Structure and vibrational spectra of the enol form of hexafluoro-acetylacetone. A density functional theoretical study

Molecular and vibrational structure of 1,1,1,6,6,6-hexafluoropentane-2,4-dione (hexafluoro-acetylacetone) have been investigated by means of density functional theory (DFT) calculations and have been compared with those of acetylacetone, the parent molecule. According to the theoretical calculations HFAA has an asymmetric structure with hydrogen bond strength of about 12 kcal mol(-1), about 6 kcal mol(-1) less than that of acetylacetone. This weakening of hydrogen bond is consistent with frequency shifts for OH/OD stretching, OH/OD out of plane bending and O...O stretching modes upon substitution of methyl hydrogen atoms with fluorine atoms. The symmetric structure based on electron diffraction data is interpreted as superposition of two asymmetric structures.     

Spectral analysis of acetylcholine halides by density functional theory calculations

The optimized molecular structures, vibrational frequencies and ¹H and ¹³C NMR chemical shifts of acetylcholine halides (F, Cl, and Br) have been investigated using density functional theory (B3LYP) method with 6-311G(d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.