Calculated vertical ionization energies of the common α-amino acids in the gas phase and in solution

The vertical ionization energies of the low-lying conformers of the α-amino acids found in proteins have been calculated. Geometry optimizations were first performed at the B3LYP/6-311G(d,p) level of theory, and then reoptimized at the MP2/6-311G(d,p) level of theory. Vertical ionization energies were then computed by three methods, electron propagator in the partial third-order (P3) approximation, Outer-Valence-Green's Functions, and by evaluating the difference in the total energy between the cation radical and the neutral amino acid in the geometry of the neutral species. When available, the results are compared to the experimental vertical ionization energies. The vertical ionization energies calculated using the MP2/P3 method gave the best overall agreement with the experimental results. Next, the ionization energies in solution are calculated for the zwitterionic forms of the α-amino acids by using IEFPCM methods. To obtain the vertical ionization energy in solution, it is necessary to use the nonequilibrium polarizable continuum model (NEPCM), the results of which are reported here for the α-amino acids.     

DFT Calculations of the Ionization Potential and Electron Affinity of Alaninamide

Adiabatic and vertical ionization potentials (IPs) and valence electron affinities (EAs) of alaninamide in gas phase have been determined using density functional theory (BLYP,B3LYP,B3P86) methods with 6-311++G(d,p) basis set,respectively. IPs and EAs of alaninamide in solutions have been calculated at the B3LYP/6-311++G(d,p) level. Five possible conformers of alaninamide and their charged states have been optimized employing density functional theory B3LYP method with 6-311++(d,p) basis set,respectively.     

The triplet state of cytosine and its derivatives: electron impact and quantum chemical study

The excitation of the lowest electronic states and vibrational excitation of cytosine (C) have been studied using electron energy loss spectroscopy (EELS, 0-100 eV) with angular analysis. The singlet states have been found to be in good agreement with UV-VIS absorption results on sublimed films, slightly blueshifted by about 0.1 eV. The EEL spectra recorded at residual energy below 2 eV show clear shoulders at energy losses of 3.50 and 4.25 eV (+/-0.1 eV). They are assigned to the lowest triplet electronic states of cytosine. Energies and molecular structures of the lowest-lying triplet state of C and its methylated and halogenated 5-X-C, 6-X-C, and 5-X, 6-X-C substituted derivatives (X=CH3, F, Cl, and Br) have been studied using quantum chemical calculations with both molecular orbital and density functional methods, in conjunction with the 6-311++G(d,p), 6-311++G(3df,2p), and aug-cc-pVTZ basis sets. The triplet-singlet energy gap obtained using coupled-cluster theory [CCSD(T)] and density functional theory (DFT) methods agrees well with those derived from EELS study. The first C's vertical triplet state is located at 3.6 eV, in good agreement with experiment. The weak band observed at 4.25 eV is tentatively assigned to the second C's vertical triplet excitation. For the substituted cytosines considered, the vertical triplet state is consistently centered at 3.0-3.2 eV above the corresponding singlet ground state but about 1.0 eV below the first excited singlet state. Geometrical relaxation involving out-of-plane distortions of hydrogen atoms leads to a stabilization of 0.6-1.0 eV in favor of the equilibrium triplet. The lowest-lying adiabatic triplet states are located at 2.3-3.0 eV. Halogen substitution at both C(5) and C(6) positions tends to reduce the triplet-singlet separations whereas methylation tends to enlarge it. The vibrational modes of triplet cytosine and the ionization energies of substituted derivatives were also evaluated.     

Thermochemical properties of molecules and cations of MgNnHm (n=1,2 and m=1–6): enthalpies of formation, proton affinities and ionization energies

Ab initio molecular orbital calculations are reported for small neutral molecules and cations containing magnesium, nitrogen and hydrogen. Structures have been optimized using gradient techniques at B3LYP/6-31+G(d) and at MP2(full)/6-311++G(d,p). Single-point calculations are reported at QCISD(T)(full)/6-311++G(2df,p) and at CCSD(T)(full)/6-311++G(2df,p) levels using geometries optimized at MP2(full)/6-311++G(d,p). Standard enthalpies of formation at 298 K have been calculated at these two higher levels of theory. Other thermochemical properties calculated include ionization energies and proton affinities. The binding enthalpies of ammonia to Mg⁺, MgNH₂⁺ and MgNH₃⁺ are also reported.     

Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids

Energies of different conformers of 22 amino acid molecules and their protonated and deprotonated species were calculated by some density functional theory (DFT; SVWN, B3LYP, B3PW91, MPWB1K, BHandHLYP) and wave function theory (WFT; HF, MP2) methods with the 6-311++G(d,p) basis set to obtain the relative conformer energies, vertical electron detachment energies, deprotonation energies, and proton affinities. Taking the CCSD/6-311++G(d,p) results as the references, the performances of the tested DFT and WFT methods for amino acids with various intramolecular hydrogen bonds were determined. The BHandHLYP method was the best overall performer among the tested DFT methods, and its accuracy was even better than that of the more expensive MP2 method. The computational dependencies of the five DFT methods and the HF and MP2 methods on the basis sets were further examined with the 6-31G(d,p), 6-311++G(d,p), aug-cc-pVDZ, 6-311++G(2df,p), and aug-cc-pVTZ basis sets. The differences between the small and large basis set results have decreased quickly for the hybrid generalized gradient approximation (GGA) methods. The basis set convergence of the MP2 results has been, however, very slow. Considering both the cost and the accuracy, the BHandHLYP functional with the 6-311++G(d,p) basis set is the best choice for the amino acid systems that are rich in hydrogen bonds.     

Ab initio studies of the conformers and conformational distribution of the gaseous hydroxyamino acid threonine

Systematic and extensive conformational search has been performed to characterize the gas-phase threonine structures. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP/6-311G* level of the theory and then subjected to further optimization at the B3LYP/6-311++G** level. A total of 71 conformers were found and their rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies and vertical ionization energies of all the conformers were determined. Single-point energies were also calculated at the MP2/6-311G(2df,p) and B3LYP/6-311G(2df,p) levels. Characteristic H-bonding types were classified and listed for all the conformers. The conformational distributions of gaseous threonine at various temperatures were calculated.     

NH0-1+2-3离解能等的高级ab initio计算与评价

A recent experimental determination[1] of the dissociation energies (D0) for H2N-H, H2N+-H and H2N-H+, the ionization energies for NH3 and NH2 resulted in large deviations when compared with those of the earlier values and the QCISD(T)/6-311+G(3df,2p) ab initio calculations. We have performed some higher level ab initio calculations on these data by utilizing the Gaussian 92/DFT and Gaussian 94 pakages of programs and have assessed the available experimental values. Our calculations were carried out at the QCISD (TQ)/aug-cc-pVDZ, G2(QCI), QCISD(T)/6-311 ++G(3df,3pd) and QCISD(T)/aug-cc-pVTZ levels of theory. Geometries were optimized at both of the MP2(full)/6-31G(d) and the MP2(full)/6-31(d,p) levels, and were compared with those of the experiments if available. The MP2(full)/6-31G(d,p) tight-optimized geometries for the neutrals are closer to those of the experiments than those of the MP2 (full)/6-31G(d), and are in excellent agreement with the experimental results as shown in Table 1. In this case, we assumed that the optimized geometries for the cations would be better if p polarization functions are added to the hydrogen atoms. We firstly noted that the symmetry of the NH3+ cation was D3h, other than Cs. as reported in ref.[1]. All of the zero-point energies and the final geometries are calculated at the MP2(full)/6-31G(d,p) level of theory. We have also repeated the QCISD(T )/6-311 + G(3df,2p) calculations of ref. [1], because we could not identify their level of goemetry optimization. It is found that the total energy, -55.244 19 Hartrees, for NH2+(1A1 ) in ref.[1] might be in error. Our result is -55.336 29 Hartrees at the same level of theory. At our highest level [QCISD(T)/aug-cc-pVTZ] of calculations as shown in Table 3, the D0 (temperature at zero Kelvin) values of H2N-H, H2N+-H(3B1for NH2+ ) and H2N- H+ are 4.51, 5.49 and 8.00 eV, respectively. These data reported in re f.[1] were 4.97, 5.59 and 8.41 eV, respectively. Our result on D0(H2N-H) supports the work of ref.[2,3,5,6]. The ionization energies (IE) for NH3 and NH2 (3B1 for NH2+) at our highest level are 10.11 and 11.09 eV while in ref.[1] were 10.16 and 10.78 eV, respectively. For the latter, our result supports the experiment of ref.[3]. Our predicted D0 for HN2+-H and IE for NH2 (1A1 for each NH2+) are 6.80 and 12.39 eV, respectively. These values differ greatly from the predicted values (9.29 and 14.88 eV) of ref.[1] where the total energy of NH2+(1A1) might be in error. The D0 value for HN-H has not been found in ref.[1]. Our result supports the work of ref.[3]. We have also derived all of these values at the temperature of 298K and under the pressure of 101kPa at several levels of thoery as shown in Table 3. On examining the experiment of ref.[1] in detail, it is easy to find that all of the larger deviations might be from a too high value of the appearance potential of proton AP(H+). Indeed, ref.[1] has mentioned that the determintion of AP(H+), due to kinetic shift, would lead to a hihger value for the dissociation energy as has been pointed out by Berkowitz and Ruscic. In this work, we concluded that, besides some mistakes in the theoretical calculations of ref.[1], the dissociation energies for H2N-H and H2N-H+,the IE for NH2 (3B1 for NH2+) might also be unreliable and need to be re-examined.
     

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.     

NH_(2-3)~(0-1 )离解能等的高级ab initio计算与评价

FeiQi等人[1]最近对H2N－H、H2N －H的离解能以及NH3、NH2的电离能，用真空紫外光电离实验进行了重新测定，并同时得到了H2N－H 的离解能．他们还在QCISD（T）／6－311＋G（3df，ZP）／／MPZ（full）／6刁IG（d）水平（GZ理论的参考水平）上对这些数据及其它相关分子的某些性质     

TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach

A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of pisigma* type Rydberg transition was found near the lowest singlet pipi* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases.     

Nitrogen-rich oligoacenes: candidates for n-channel organic semiconductors

The successive replacement of CH moieties by nitrogen atoms in oligoacenes (benzene to hexacene) has been studied computationally at the B3LYP/6-311+G(d,p)//6-31G(d) level of theory, and the effects of different heteroatomic substitution patterns on structures, electron affinities, excitation, ionization, and reorganization energies are discussed. The calculated tendencies are rationalized on the basis of molecular orbital arguments. To achieve electron affinities of 3 eV, a value required to allow for efficient electron injection from common metal electrodes, at least seven nitrogen atoms have to be incorporated into tetracenes or pentacenes. The latter require rather small reorganization energies for electron transfer (<0.20 eV) making these compounds promising candidates for n-channel semiconducting materials. Particularly interesting are heptaazapentacenes 5 and 6 in which the nitrogen atoms are arranged to form self-complementary systems with a maximum number of intermolecular CH-N contacts in planar oligomers. These interactions are expected to facilitate the formation of graphite-like sheet structures with cofacial arrangements of the pi systems and short interlayer distances due to attractive N-C(H) interlayer interactions. This should not only be ideal for charge transfer but also might contribute to improved air stability of these semiconductors. Self-complementarity is maintained in azaacenes containing two cyano groups in the terminal rings. These compounds require lower reorganization energies than the unsubstituted heterocycles (0.13-0.14 eV), show high electron affinities (3.3 eV), and are thus promising candidates for materials applications.     

C6F5X＋（X=Cl,Br,I,CH3）离子的理论研究

用DFT B3LYP方法及6-311G（d,p）,6-311＋G（d,p）和LanL2dz基组,对C6F5X＋（X=Cl,Br,I,CH3）阳离子做了理论研究,优化了它们的电子基态的构型,计算了对应分子的垂直电离势（VIP）和绝热电离势（AIP）.结果表明四种离子的构型的对称点群和对应分子相同,但构型参数有明显差别.B...     

Adiabatic ionization potential and electron affinity of formaldehyde

The adiabatic ionization potential and electron affinity for CH₂O have been calculated using high levels of ab initio molecular orbital theory. Harmonic vibrational frequencies and zero-point energies also have been predicted. At the CCSD(T)/6-311++G(3df,3pd) level of theory, the adiabatic ionization potential is calculated as 10.82 eV as compared to the experimental literature value of 10.8887±0.0030 eV. The electron affinity is calculated to be −0.96 eV, compared to the experimental literature value of −0.65±0.05 eV.     

An evaluation of various computational methods for the treatment of organoselenium compounds

A reliable computational method for the prediction of organoselenium geometries and bond dissociation energies (BDEs) has been determined on the basis of the performance of density functional theory (DFT: B3LYP and B3PW91) and ab initio molecular orbital procedures (Hartree-Fock (HF)) in conjunction with various Pople basis sets including (but not limited to) the 6-31G(d), 6-31G(d,p), 6-311G(d), 6-311G(d,p), 6-311G(2df,p), and 6-311G(3df,3pd) sets. Predicted geometries and BDEs are compared with available experimental data and quadratic configuration interaction including single and double substitutions (QCISD) results. The B3PW91/6-311G(2df,p) level of theory is recommended for the prediction of the geometries and energetics of organoselenium compounds.     

Theoretical determinations of ionization potentials of dopamine

Adiabatic and vertical ionization potentials (IPs) of nine conformers of dopamine in the gas phase are determined using density functional theory (DFT) B3LYP, B3P86, B3PW91 methods and high level ab initio HF method with 6-311++G** basis set, respectively. And the nine stable cationic states have been found in the ionization process of dopamine. Vertical ionization potentials of nine conformers of dopamine are calculated using the older outer-valence Green’s function (OVGF) calculations at 6-311++G** basis set. Vibrational frequencies and infrared spectrum intensities of G1b and G1b⁺ at B3LYP/6-311++G** level are discussed.     

Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH-->CH2CN + H2O

The reaction of acetonitrile with hydroxyl has been studied using the direct ab initio dynamics methods. The geometries, vibrational frequencies of the stationary points, as well as the minimum energy paths were computed at the BHandHLYP and MP2 levels of theory with the 6-311G(d, p) basis set. The energies were further refined at the PMP4/6-311+G(2df, 2pd) and QCISD(T)/6-311+G(2df, 2pd) levels of theory based on the structures optimized at BHandHLYP/6-311G(d, p) and MP2/6-311G(d, p) levels of theory. The Polyrate 8.2 program was employed to predict the thermal rate constants using the canonical variational transition state theory incorporating a small-curvature tunneling correction. The computed rate constants are in good agreement with the available experimental data.     

HO3、HO+3、HO-3光谱和结构的MP2和DFT理论研究

用B3LYP和MP2量子化学理论,详细地计算了HO3、HO+3、HO-3可能的平衡构型、能量和光谱参数,分析了它们可能的解离通道和稳定性.还分析了HO3的电离势(IE)及电子亲和势(Ea),讨论了HO3、HO3-自由基的光电子能谱的特征,及用光电子能谱去探测HO3的可能性.     

线性簇合物SC2nS2－(n =1～12)电子吸收光谱

应用密度泛函理论,在B3LYP/6-31G*水平上优化了线性簇合物SC2nS2－(n =1～12)的基态平衡几何结构,并计算了它们的谐振动频率.在基态平衡构型下,通过TD-B3LYP/cc-pvTZ和TD-B3LYP/cc-pvDZ计算,确定了簇合物SC2nS2－(n =1～10) 电子跃迁的垂直激发能和对应的振子强度.基于计算结果,导出了电子跃迁吸收波长与体系大小n的解析关系式,以及SC2nS2－体系第一电离能与体系大小n的解析表达式,并讨论了不同端位原子对碳链体系激发态性质的影响.     

Li+粘贴CHnCl3-nO2和CFnCl3-nO2( n = 1~3 )自由基：Li+–CHnCl3-nO2和 Li+–CFnCl3-nO2的结构与性质的研究

The structures and stabilities of these still experimentally unknown CH_nCl_(3-n)O_(2-)Li~ and CF_nCl_(3-n)O_(2-)Li~ ionshave been theoretically investigated by ab initio molecular orbital theory and density functional theory(DFT)inconjunction with the 6-311G(d,p),6-311 G(d,p),6-311 G(2d,p)and 6-311 G(2df,2p)basis sets.The optimizedgeometries,chemical bonding and NBO analysis indicate that these complexes of CH_nCl_(3-n)O_(2-)Li~ and CF_nCl_(3-n)O_(2-)Li~ exist as ion-dipole molecules.The calculated affinity energies of these species exceed 41.9 kJ/mol,which arelarge enough to suggest the possibility that these title complexes could be detected as stable species in gas phase byLi~ ion attachment mass spectrometry.