Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.     

Reaction of C2HCl2＋O2： Combined TR-FTIR Spectroscopy and Electronic Structure

The product channels and mechanisms of the C2HC12＋O2 reaction are investigated by step-scan time-resolved Fourier transform infrared emission spectroscopy and the G3MP2// B3LYP/6-311G（d,p） level of electronic structure calculations. Vibrationally excited products of HCI, CO, and CO2 are observed in the IR emission spectra and the product vibrational state distribution are determined which shows that HCI and CO are vibrationally excited with the nascent average vibrational energy estimated to be 59.8 and 51.8 kJ/mol respectively. In combination with the G3MP2//B3LYP/6-311G（d,p） calculations, the reaction mechanisms have been characterized and the energetically favorable reaction pathways have been suggested.     

A computational study of the ground and excited state structure and absorption spectra of free-base N-confused porphine and free-base N-confused tetraphenylporphyrin

Computational investigations into the ground and singlet excited-state structures and the experimental ground-state absorption spectra of N-confused tetraphenylporphyrin tautomers 1e and 1i and N-confused porphines (NCP) 2e and 2i have been performed. Structural data for the ground state, performed at the B3LYP/6-31G(d), B3LYP/6-31+G(d)//B3LYP/6-31G(d), and B3LYP/6-311+G(d)//B3LYP/6-31G(d) levels, are consistent with those performed at lower levels of theory. Calculations of the gas-phase, ground-state absorption spectrum are qualitatively consistent with condensed phase experiments for predicting the relative intensities of the Q(0,0) and Soret bands. Inclusion of implicit solvation in the calculations substantially improves the correlation of the energy of the Soret band with experiment for both tautomers (1e, 435 nm predicted, 442 nm observed in DMAc; 1i, 435 nm predicted, 437 nm observed in CH2Cl2). The x- and y-polarized Q-band transitions were qualitatively reproduced for 1e in both the gas phase and with solvation, although the low-energy absorption band in 1i was predicted at substantially higher energy (646 nm in the gas phase and 655 nm with solvation) than observed experimentally (724 nm in CH2Cl2). Franck-Condon state and equilibrated singlet excited-state geometries were calculated for unsubstituted NCP tautomers 2e and 2i at the TD-B3LYP/SVP and TD-B3LYP/TZVP//TD-B3LYP/SVP levels. Electronic difference density plots were calculated from these geometries, thereby indicating the change of electron density in the singlet excited states. Adiabatic S1 and S2 geometries of these compounds were also calculated at the TD-B3LYP/SVP level, and the results indicate that while 2i is a more stable ground-state molecule by approximately 7.0 kcal mol-1, the energy difference for the S1 excited states is only approximately 1.0 kcal mol-1 and is 6.1 kcal mol-1 for the S2 excited states.     

Infrared multiple photon dissociation spectroscopy of cationized histidine: effects of metal cation size on gas-phase conformation

The gas phase structures of cationized histidine (His), including complexes with Li(+), Na(+), K(+), Rb(+), and Cs(+), are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by a free electron laser, in conjunction with quantum chemical calculations. To identify the structures present in the experimental studies, measured IRMPD spectra are compared to spectra calculated at B3LYP/6-311+G(d,p) (Li(+), Na(+), and K(+) complexes) and B3LYP/HW*/6-311+G(d,p) (Rb(+) and Cs(+) complexes) levels of theory, where HW* indicates that the Hay-Wadt effective core potential with additional polarization functions was used on the metals. Single point energy calculations were carried out at the B3LYP, B3P86, and MP2(full) levels using the 6-311+G(2d,2p) basis set. On the basis of these experiments and calculations, the only conformation that reproduces the IRMPD action spectra for the complexes of the smaller alkali metal cations, Li(+)(His) and Na(+)(His), is a charge-solvated, tridentate structure where the metal cation binds to the backbone carbonyl oxygen, backbone amino nitrogen, and nitrogen atom of the imidazole side chain, [CO,N(α),N(1)], in agreement with the predicted ground states of these complexes. Spectra of the larger alkali metal cation complexes, K(+)(His), Rb(+)(His), and Cs(+)(His), have very similar spectral features that are considerably more complex than the IRMPD spectra of Li(+)(His) and Na(+)(His). For these complexes, the bidentate [CO,N(1)] conformer in which the metal cation binds to the backbone carbonyl oxygen and nitrogen atom of the imidazole side chain is a dominant contributor, although features associated with the tridentate [CO,N(α),N(1)] conformer remain, and those for the [COOH] conformer are also clearly present. Theoretical results for Rb(+)(His) and Cs(+)(His) indicate that both [CO,N(1)] and [COOH] conformers are low-energy structures, with different levels of theory predicting different ground conformers.     

Remarks on GIAO-DFT predictions of 13C chemical shifts

Predicting (13)C chemical shifts by GIAO-DFT calculations appears to be more accurate than frequently expected provided that: (a) the comparison between experimental and theoretical data is performed using the linear regression method, (b) a sufficiently high level of theory [e.g. B3LYP/6-311 + + G(2d,p)//B3LYP/6-311 + + G(2d,p) or PBE1PBE/6-311 + G(2df,p)//B3LYP/6-311 + + G(2d,p)] is used, (c) the experimental data originate from the measurements performed in one solvent whose influence is taken into account at the molecular geometry optimization step and, first of all, during the shielding calculation, (d) the experimental data are free of heavy atom effects or such effects are appropriately treated in calculations, and finally (e) the conformational compositions of the investigated objects are known.     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been 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 have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been 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. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

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.     

Au+(1S, 3D)与N2O(1Σ+)反应机理的理论研究

采用密度泛函B3LYP方法, O和N用6-311+G*基组, Au+用赝势基组(8s7p6d)/[6s5p3d], 研究了Au+(1S, 3D)离子和N2O(1Σ+)分子的反应机理. 报道了在基态单重态和激发三重态势能面上各反应物、中间体和过渡态的构型特征及能量. 结果表明, 两个主反应通道Au+(1S)+ N2O(1Σ+)→1NA-Complex-1→1NA-TS1→1NA-Complex-2→1NA-Crossing→[3OAuNN]+和Au+(1S)+ N2O(1Σ+)→1NB-Complex→1NB-Crossing→[AuNN(1Σ+)]++O(3P)都需经过反应交叉势能面, 出现“系间窜越”. 用内禀坐标单点计算垂直激发态的方法确定了势能面交叉点, 并用含时密度泛函TD-B3LYP方法进一步探讨了自旋翻转机理.     

戊烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组，分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化，并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型，与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上，进行了B3LYP和UMP2(full)方法的超精细偶合常数计算，得到了比以往更好的结果.     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

尿嘧啶和5-氯尿嘧啶1S0→1S2跃迁动态结构的共振拉曼光谱

采用含时量子波包理论的简单模型对5-氯尿嘧啶和尿嘧啶的共振拉曼光谱开展了强度分析拟合, 获得了1(π, π*)激发态的几何结构变化动态特征. 结果表明, 尿嘧啶1S0→1S2跃迁的动态结构特征因5-位氯原子取代而改变. 5-氯尿嘧啶的动态结构特征主要沿C5=C6伸缩振动+C6H12 弯曲振动和N3H9/N1H7弯曲振动+N1C6伸缩振动反应坐标展开, 而尿嘧啶的动态结构特征主要沿嘧啶环的伸缩振动+C5H11/C6H12/N1H7弯曲振动和C4=O10伸缩振动反应坐标展开. π和π*轨道中氯原子的pz电子参与嘧啶环的p-π共轭作用导致了在1(π, π*)激发态上5-氯尿嘧啶的振动重组能更多地配分给嘧啶环的弯曲振动模式和C5=C6伸缩振动模式. 尿嘧啶在甲醇中的激发态动态结构特征与在水中的基本一致, 但波包沿C5H11/C6H12/N1H7弯曲振动+N1C6伸缩振动(υ12)和环呼吸振动(υ17)反应坐标的运动明显增强.     

FT-IR and FT-Raman spectroscopic investigation, computed vibrational frequency analysis and IR intensity and Raman activity peak resemblance analysis on 2-nitroanisole using HF and DFT (B3LYP and B3PW91) calculations

Fourier-transform Raman and infrared spectra of 2-nitroanisole are recorded (4000-100 cm(-1)) and interpreted by comparison with respective theoretical spectra calculated using HF and DFT method. The geometrical parameters with C(S) symmetry, harmonic vibrational frequencies, infrared and Raman scattering intensities are determined using HF/6-311++G (d, p), B3LYP/6-311+G (d, p), B3LYP/6-311++G (d, p) and B3PW91/6-311++G (d, p) level of theories. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The SQM method, which implies multiple scaling of the DFT force fields has been shown superior to the uniform scaling approach. The vibrational frequencies and the infrared intensities of the C-H modes involved in back-donation and conjugation are also investigated.     

Theoretical and spectroscopic study of infrared spectra of hydrogen-bonded 1-methyluracil crystal and its deuterated derivative

Theoretical simulation of the band shape and fine structure of the N-H(D) stretching band is presented for 1-methyluracil and its deuterated derivative taking into account anharmonic coupling between the high-frequency N-H(D) stretching and the low-frequency N...O stretching vibrations, resonance interaction between two equivalent hydrogen bonds in the dimer, anharmonicity of the potentials for the low-frequency vibrations in the ground and excited state of the N-H(D) stretching mode, Fermi resonance between the N-H(D) stretching and the first overtone of the N-H(D) bending vibrations, and electrical anharmonicity. The effect of deuteration has been successfully reproduced by our model calculations. Infrared, far-infrared, Raman, and low-frequency Raman spectra of the polycrystalline 1-methyluracil have been recorded. The geometry and experimental frequencies are compared with the results of harmonic and anharmonic B3LYP6-311++G(**) calculations.     

A microwave spectroscopic and quantum chemical study of propa-1,2-dienyl selenocyanate (H(2)==C==CHSeC[triple bond]N) and cyclopropyl selenocyanate (C(3)H(5)SeC[triple bond]N)

The microwave spectra of propa-1,2-dienyl selenocyanate, H(2)C==C==CHSeC[triple bond]N, and cyclopropyl selenocyanate, C(3)H(5)SeC[triple bond]N, are reported. The spectra of the ground and two vibrationally excited states of the (80)Se isotopologue and the spectrum of the ground state of the (78)Se isotopologue were assigned for one rotameric form of H(2)C==C[double bond, length as m-dash]CHSeC[triple bond]N. This conformer is characterized by a C-C-Se-C dihedral angle of 129(5) degrees from synperiplanar (0 degrees ) and is shown to be the global minimum of H(2)C[double bond, length as m-dash]C[double bond, length as m-dash]CHSeC[triple bond]N. The spectra of the ground and of three vibrationally excited states of the (80)Se isotopologue, as well as of the ground state of the (78)Se isotopologue of one rotamer of C(3)H(5)SeC[triple bond]N were assigned. This conformer has a H-C-Se-C dihedral angle of 80(4) degrees from synperiplanar and is at least 3 kJ mol(-1) more stable than any other form of the molecule. The microwave study has been augmented by quantum chemical calculations at the B3LYP/6-311+ +G(3df,3pd) and MP2/6-311+ +G(3df,3pd) levels of theory.     

CH_2CO+CH_2的多通道反应的理论研究

利用密度泛函(DFT)和自然键轨道理论(NBO)及高级电子耦合簇[CCSD(T)]和电子密度拓扑(AIM)方法,对单重态和三重态CH2与CH2CO反应的微观机理进行了研究.在B3LYP/6-311+G(d,p)水平上优化了反应通道各驻点的几何构型.在CCSD(T)/6-311+G(d,p)水平上计算了各物种的单点能量,并对总能量进行了校正.计算表明,单重态CH2与CH2CO的C-H键可发生插入反应,与C=C、C=O可发生加成反应,存在三条反应通道,产物为CO和C2H4,从能量变化和反应速控步骤能垒两方面考虑,反应II更容易发生.对反应通道中的关键点进行了自然键轨道及电子密度拓扑分析.三重态CH2与CH2CO的反应存在三条反应通道,一条是与C-H键的插入反应,另一条是三重态CH2与C=C发生加成反应,产物为CO和三重态C2H4,通道II势垒较低,更容易发生.最后一条涉及双自由基的反应活化能最大,最难发生.     

Mass-analyzed threshold ionization study of vinyl bromide cation in the first excited electronic state using vacuum-ultraviolet radiation generated by four-wave mixing in Hg

The vibrational spectrum of the vinyl bromide cation in the first excited electronic state A 2A' was obtained by one-photon mass-analyzed threshold ionization (MATI) spectroscopy. The use of an improved vacuum-ultraviolet radiation source based on four-wave sum frequency mixing in Hg resulted in excellent sensitivity for MATI signals. From the MATI spectrum, the ionization energy to the A 2A' state of the cation was determined to be 10.9150+/-0.0006 eV. Nearly complete vibrational assignments for the MATI peaks were possible by utilizing the vibrational frequencies and Franck-Condon factors calculated at the density-functional theory (DFT) and time-dependent DFT/B3LYP levels with the 6-311+G(df,p) basis set.     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.     

FT-IR and FT-Raman spectral investigation, computed IR intensity and Raman activity analysis and frequency estimation analysis on 4-chloro-2-bromoacetophenone using HF and DFT calculations

In this work, the experimental and theoretical spectra of 4-chloro-2-bromoacetophenone (4C2BAP) are studied. FT-IR and FT-Raman spectra of title molecule have been recorded in the region 4000-100 cm(-1). The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock and density functional method (B3LYP) with the 6-31G (d, p) and 6-311G (d, p) basis sets. The vibrational frequencies are calculated and scaled values are compared with the experimental FT-IR and FT-Raman spectra. The DFT (B3LYP/6-311G (d, p)) calculations are more reliable than the ab initio HF/6-311G (d, p) calculations for the vibrational study of 4C2BAP. The optimized geometric parameters (bond lengths and bond angles) are compared with experimental values of the molecule. The alteration of vibrational bands of the carbonyl and acetyl groups due to the presence of halogens (Cl and Br) in the base molecule is also investigated from their characteristic region of linked spectrum.     

Environmental photochemistry of nitro-PAHs: direct observation of ultrafast intersystem crossing in 1-nitropyrene

Femtosecond broadband transient absorption experiments of 1-nitropyrene, a nitro-polycyclic aromatic hydrocarbon of environmental concern are presented in cyclohexane and hexane solutions. The transient absorption spectra show the presence of three species that are assigned to the Franck-Condon excited lowest singlet (S1) state, the structurally relaxed S1 state, and the lowest excited triplet state. The spectral changes at early times are interpreted in terms of conformational dynamics; primarily due to an ultrafast rotation of the nitro group in the S1 state. This excited state relaxation is followed by intersystem crossing with a time constant of 7 ps. CIS/6-31G(d,p) calculations predict planarization of the nitro-aromatic torsional angle as the major nuclear relaxation coordinate, from 32.8 degrees at the HF/6-31G(d,p) level of theory in the ground state (27.46 degrees at B3LYP/6-31++G(d,p)) to 0.07 degrees in the S1 state. Vertical excitation energies at the TDDFT/6-31++G(d,p) and TDDFT/IEFPCM/6-31++G(d,p) levels of theory predict a small energy gap (<0.12 eV) between the S1(pipi*) state and the third excited triplet state T3(npi*) in the gas phase and in cyclohexane, respectively. The small energy gap suggests a large spin-orbit coupling between the S1(pipi*) and T3(npi*) states, which explains the ultrafast intersystem crossing of 1-nitropyrene in nonpolar solvents.