Theoretical determination of standard oxidation and reduction potentials of chlorophyll-a in acetonitrile

QM/MM calculations were performed on ethyl chlorophyllide-a and its radical cation and anion, by using the density functional (DF) B3LYP method to determine the molecular characteristics, and a molecular mechanics (MM) method to simulate the solvating medium. The presence of the solvent was accounted for during the optimization of the geometry of the 85-atom chlorophyll-a system by using an ONIOM methodology. A total of 24 solvent molecules were explicitly considered during the optimization process, and these were treated by the universal force field (UFF) method. Initially, the split-valence 3-21G basis set was used for optimizing the geometry of the 85-atom species, neutral, cation and anion. Electronic energies were then determined for the optimized species by making use of the polarized 6-31G(d) basis set. The ionization energy calculated (6.0 eV) is in very good agreement with the observed one (6.1 eV). The MM+ force field was used to investigate the dynamics of the acetonitrile molecules around the neutral species as well as the radical ions of chlorophyll. The required atomic charges on all the atoms were obtained from calculations on all involved molecules at the DFT/6-31G(d) level. Randomly sampled configurations were used to determine the first solvation layer contribution to the free energy of solvation of various species. A truncated 46-atom model of ethyl chlorophyllide-a was used to evaluate the thermal energies of neutral chlorophyll molecule relative to its two radical ions in the gas phase. Born energy, Onsager energy, and the Debye-Huckel energy of the chlorophyll-solvent aggregate were added as perturbative corrections to the free energy of solvation that was initially obtained through molecular dynamics method for the same complex. These calculations yield the oxidation potential as 0.75 +/- 0.32 V and the reduction potential -1.18 +/- 0.31 V at 298.15 K. The calculated values are in good agreement with the experimental midpoint potentials of +0.76 and -1.04 V, respectively.     

A highly cis-selective synthesis of 2-ethynylaziridines by intramolecular amination of chiral bromoallenes: improvement of stereoselectivity based on the computational investigation

The base-mediated intramolecular amination of bromoallenes having an axial chirality is described. The treatment of (4S,aR)-4-alkyl-4-[N-(arylsulfonyl)amino]-1-bromobuta-1,2-dienes with NaH in DMF affords 2,3-cis-2-ethynylaziridines in good to excellent selectivity (2,3-cis:trans = 92:8-99:1). The reaction of (4S,aS)-bromoallenes with NaH/DMF also gives 2,3-cis-2-ethynylaziridines selectively (79:21-91:9). These experimental results have been rationalized by B3LYP density functional calculations together with the 6-31+G(d) basis set and the Onsager solvation model. The transition structures for cis-aziridine formation of both (4S,aR)- and (4S,aS)-bromoallenes in DMF are favored over the corresponding trans transition structures by 4.35 and 1.41 kcal/mol, respectively. Furthermore, the calculations predicted that a less polar solvent gives higher cis selectivity for (4S,aS)-bromoallenes. In fact, improvement of the cis selectivity to 99:1 has been realized by using a less polar solvent such as THF. The cyclization of bromoallenes bearing a beta- or gamma-amino group also affords four- and five-membered azacycles in a highly cis-selective manner.     

可乐定分子构象异构和互变异构的理论研究

采用HF/6-31G*方法, 对氨基型和亚胺型可乐定中性分子以及质子化的可乐定分子进行了构象分析. 之后采用B3LYP/6-31G**方法对处于势能面上的能量极小构象异构体进行全自由度几何优化和频率分析. Onsager反应场溶剂模型用于水相的计算. 结果表明, 在气相和水相中可乐定中性分子主要以亚胺型存在, 这同已有实验结果一致. 进一步, 寻找构象异构化过渡态和氨基型亚胺型互变异构化过渡态, 探讨质子化和水溶剂化效应对异构化过程的几何结构和能量的影响. 为了考察氯苯的共轭效应对可乐定互变异构体稳定性的影响, 在B3LYP/6-31G**水平上, 研究了2-氨基-2-咪唑啉的互变异构化反应机理.     

5-氟尿嘧啶和5-氯尿嘧啶及其互变异构体的理论计算研究

采用HF/3-21G方法, 对6种气相和水相中可能存在的5-氟尿嘧啶(和5-氯尿嘧啶)互变异构体进行了构象分析.采用B3LYP/6-311＋G**方法对处于优势构象时的各互变异构体进行了几何全优化, 并计算出它们的总能量、焓、熵、吉布斯自由能. Onsager反应场溶剂模型用于水相的计算. 计算结果表明, 5-氟尿嘧啶和5-氯尿嘧啶在气相中和水相中主要以双酮形式存在. 5-氟尿嘧啶和5-氯尿嘧啶的熵效应小, 对互变异构平衡没有显著的影响, 而焓变对互变异构产生了主要的影响. 讨论了水溶剂化作用对异构体的能量、电荷分布和偶极矩的影响. 溶剂化自由能与异构体的气相偶极矩存在相关性. 另外, 详细地将5-氟尿嘧啶和5-氯尿嘧啶与尿嘧啶进行了对比, 获得三者最稳定异构体间电子结构异同的有用信息.     

Calculation of electron affinities of polycyclic aromatic hydrocarbons and solvation energies of their radical anion

Electron affinities (EAs) and free energies for electron attachment (DeltaGo(a,298K)) have been directly calculated for 45 polynuclear aromatic hydrocarbons (PAHs) and related molecules by a variety of theoretical methods, with standard regression errors of about 0.07 eV (mean unsigned error = 0.05 eV) at the B3LYP/6-31 + G(d,p) level and larger errors with HF or MP2 methods or using Koopmans' Theorem. Comparison of gas-phase free energies with solution-phase reduction potentials provides a measure of solvation energy differences between the radical anion and neutral PAH. A simple Born-charging model approximates the solvation effects on the radical anions, leading to a good correlation with experimental solvation energy differences. This is used to estimate unknown or questionable EAs from reduction potentials. Two independent methods are used to predict DeltaGo(a,298K) values: (1) based upon DFT methods, or (2) based upon reduction potentials and the Born model. They suggest reassignments or a resolution of conflicting experimental EAs for nearly one-half (17 of 38) of the PAH molecules for which experimental EAs have been reported. For the antiaromatic molecules, 1,3,5-tri-tert-butylpentalene and the dithia-substituted cyclobutadiene 1, the reduction potentials lead to estimated EAs close to those expected from DFT calculations and provide a basis for the prediction of the EAs and reduction potentials of pentalene and cyclobutadiene. The Born model has been used to relate the electrostatic solvation energies of PAH and hydrocarbon radical anions, and spherical halide anions, alkali metal cations, and ammonium ions to effective ionic radii from DFT electron-density envelopes. The Born model used for PAHs has been successfully extended here to quantitatively explain the solvation energy of the C60 radical anion.     

2-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平上,对14种气相和水相中可能存在的2-硫代黄嘌呤互变异构体进行了几何构型全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能.Onsager反应场溶剂模型用于水相的计算.计算结果表明,2-硫代黄嘌呤在气相和水相中主要以酮式结构形式存在,与已有实验结果一致.在气相和水相中,酮式结构—N(7)(H)均比酮式结构—N(9)(H)更稳定.2-硫代黄嘌呤互变异构的熵效应小,对互变异构平衡没有显著的影响,而焓变对互变异构却产生了主要的影响.水溶剂化自由能与异构体的气相偶极矩存在相关性.另外,较详细地考察了2-硫代黄嘌呤与6-硫代黄嘌呤的相对稳定性.     

Probing supercritical water with the n-pi* transition of acetone: a Monte Carlo/quantum mechanics study

The n-pi(*) electronic transition of acetone is a convenient and important probe to study supercritical water. The solvatochromic shift of this transition in supercritical water (adopting the experimental condition of P=340.2 atm and T=673 K) has been studied theoretically using Metropolis NPT Monte Carlo (MC) simulation and quantum mechanics (QM) calculations based on INDO/CIS and TDDFT-B3LYP6-31+G(d) methods. MC simulations are used to analyze hydration shells, solute-solvent interaction, and for generating statistically relevant configurations for subsequent QM calculations of the n-pi(*) transition of acetone. The results show that the average number of hydrogen bonds between acetone and water is essentially 13 of that in normal water condition of temperature and pressure. But these hydrogen bonds have an important contribution in the solute stabilization and in the solute-solvent interaction. In addition, they respond for nearly half of the solvatochromic shift. The INDO/CIS calculations explicitly considering all valence electrons of the water molecules, using different solvation shells, up to the third shell (170 water molecules), give a solvatochromic shift of 670+/-36 cm(-1) in very good agreement with the experimentally inferred result of 500-700 cm(-1). It is found that the solvatochromic effect on n-pi(*) transition of acetone in the supercritical condition is essentially given by the first solvation shell. The time-dependent density-functional theory (TDDFT) calculations are also performed including all solvent molecules up to the third shell, now represented by point charges. This TDDFT-B3LYP6-31+G(d) also gives a good but slightly overestimated result of 825+/-65 cm(-1). For comparison the same study is also made for acetone in water at normal condition. Finally, all average results reported here are statistically converged.     

Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods

We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.     

Asequential Monte Carlo quantum mechanics study of the hydrogen-bond interaction and the solvatochromic shift of the n-pi* transition of acrolein in water

The sequential Monte Carlo (MC) quantum mechanics (QM) methodology, using time-dependent density-functional theory (TD-DFT), is used to study the solvatochromic shift of the n-pi* transition of trans-acrolein in water. Using structures obtained from the isothermal-isobaric Metropolis MC simulation TD-DFT calculations, within the B3LYP functional, are performed for the absorption spectrum of acrolein in water. In the average acrolein makes one hydrogen bond with water and the hydrogen-bond shell is responsible for 30% of the total solvatochromic shift, considerably less than the shift obtained for the minimum-energy configurations. MC configurations are sampled after analysis of the statistical correlation and 100 configurations are extracted for subsequent QM calculations. All-electron TD-DFT B3LYP calculations of the absorption transition including acrolein and all explicit solvent molecules within the first hydration shell, 26 water molecules, give a solvatochromic shift of 0.18 +/- 0.11 eV. Using simple point charges to represent the solvent the shifts are calculated for the first, second, and third solvation shells. The results converge for the calculated shift of 0.20 +/- 0.10 eV in very good agreement with the experimentally inferred result of 0.20 +/- 0.05 eV. All average results presented are statistically converged.     

黄嘌呤及其互变异构体的密度泛函理论研究

嘌呤碱及其衍生物在生物系统中起重要作用。对人具有兴奋和利尿作用的茶碱和咖啡碱就是黄嘌呤的甲基衍生物。黄嘌呤存在多种互变异构体,从理论计算的角度研究这些互变异构体的几何结构、电子结构及相对稳定性,进一步研究溶剂对其结构和性质的影响是有意义旧。密度泛函理论方法既考虑了电子相关,又较其它CI（组态相互作用）或MPn（n级微扰）方法节省机时。其计算结果较好,被广泛应用于研究各种化合物。本文采用密度泛函B3LYP／6—311G方法对14种黄嘌呤可能的互变异构体（见图1）,分别在气相和水相中进行几何构型全自由度优化和能量计算,讨论了异构体的相对稳定性,水的溶剂化作用对异构体的能量、几何构型、电荷分布和偶极矩的影响,探讨了溶剂极性对异构体的能量和偶极矩的影响。     

The sulfonation of pyrrole: Choice of relevant computational procedure for quantum chemical analysis of positional orientation

The influence of the solvent effect, zero-point energy correction, and electron correlation on conclusions about positional orientation of pyrrole sulfonation was studied by the B3LYP, HF, and MP2 methods with the 6-31G(d) and 6-31+G(d) basis sets. The most important role is played by the solvation effects. Basis set extension effects and the inclusion of zero-point energy correction contribute insignificantly. According to calculations using all the methods listed above, the formation of β-pyrrolesulfonic acid in polar solvent is thermodynamically more favorable and less kinetically hindered. B3LYP calculations seem to be more appropriate, because the method allows experimental data on positional orientation of the sulfonation of pyrroles to be interpreted in a simpler and more reliable fashion. Dedicated to Academician V. A. Tartakovsky on the occasion of his 75th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1425–1430, August, 2007.     

Quantum chemical calculations of reduction potentials of AnO2(2+)/AnO2+ (An = U, Np, Pu, Am) and Fe3+/Fe2+ couples

The reduction potentials of the AnO(2)(H(2)O)(5)(2+)/AnO(2)(H(2)O)(5)(+) couple (An = U, Np, Pu, and Am) and Fe(H(2)O)(6)(3+) to Fe(H(2)O)(6)(2+) in aqueous solution were calculated at MP2, CASPT2, and CCSD(T) levels of theory. Spin-orbit effects for all species were estimated at the CASSCF level. Solvation of the hydrated metal cations was modeled both by polarizable conductor model (PCM) calculation and by solvating the solutes with over one thousand TIP3P water molecules in the QM/MM framework. The redox reaction energy calculated by QM/MM method agreed well with the PCM method after corrections using the classical Born formula for the contribution from the rest of the solvation sphere and correction for dynamic response of solvent polarization in the MM region. Calculated reduction potentials inclusive of spin-orbit effect, zero-point energy, thermal corrections, entropy effect, and PCM solvation energy were found to be comparable with experimental data. The difference between CASPT2 calculated and experimental reduction energies were less than 35 kJ/mol in all cases, which ensures that CASPT2 (and CCSD(T)) calculations provide reasonable estimates of the thermochemistry of these reactions.     

5-氟胞嘧啶互变异构的密度泛函理论计算

采用BH-HLYP/6-311＋G**方法对10种气相和水相中可能存在的5-氟胞嘧啶互变异构体进行了几何全优化, 并计算出它们的总能量和吉布斯自由能. Onsager反应场溶剂模型用于水相的计算. 计算结果表明, 5-氟胞嘧啶在气相中主要以烯醇式-氨基式形式存在, 在水相中主要以酮式-氨基式形式存在. 溶剂化自由能与异构体的气相偶极矩存在相关性．进一步求得互变异构化以及构象异构化和顺反异构化的过渡态, 探讨异构化过程中的几何结构和能量的变化.     

On the keto-enol tautomerization of malonaldehyde: an effective fragment potential study

Recent studies have mapped the keto-enol tautomerization of malonaldehyde through a general transition structure that leads exclusively to the Z isomer of the enol. However, it will be shown that a competing general transition structure exists that leads to both the E and Z isomers of the enol at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels of theory. Both the RHF- and DFT-based effective fragment potential methods have been used to model solvation effects, and the results are compared with full ab initio calculations. It is found that two bridging water molecules with two discrete DFT-based effective fragment potential solvent waters at the MP2/6-31G(d,p) level of ab initio theory provides the most computationally effective model for solvent effects in this system. It is shown that the relative energies for this QM/MM model differ from the full MP2/6-31G(d,p) energies by an average absolute relative difference of 2.2 kcal mol-1 across the reaction path when the zero-point vibrational energy correction is included.     

Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study

The performance of semiempirical molecular-orbital methods--MNDO, MNDO-d, AM1, RM1, PM3 and PM6--in describing halogen bonding was evaluated, and the results were compared with molecular mechanical (MM) and quantum mechanical (QM) data. Three types of performance were assessed: (1) geometrical optimizations and binding energy calculations for 27 halogen-containing molecules complexed with various Lewis bases (Two of the tested methods, AM1 and RM1, gave results that agree with the QM data.); (2) charge distribution calculations for halobenzene molecules, determined by calculating the solvation free energies of the molecules relative to benzene in explicit and implicit generalized Born (GB) solvents (None of the methods gave results that agree with the experimental data.); and (3) appropriateness of the semiempirical methods in the hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme, investigated by studying the molecular inhibition of CK2 protein by eight halobenzimidazole and -benzotriazole derivatives using hybrid QM/MM molecular-dynamics (MD) simulations with the inhibitor described at the QM level by the AM1 method and the rest of the system described at the MM level. The pure MM approach with inclusion of an extra point of positive charge on the halogen atom approach gave better results than the hybrid QM/MM approach involving the AM1 method. Also, in comparison with the pure MM-GBSA (generalized Born surface area) binding energies and experimental data, the calculated QM/MM-GBSA binding energies of the inhibitors were improved by replacing the G(GB,QM/MM) solvation term with the corresponding G(GB,MM) term.     

Infrared photodissociation spectroscopy of Na(NH3)n clusters: probing the solvent coordination

The first mass-selective vibrational spectra have been recorded for Na(NH3)n clusters. Infrared spectra have been obtained for n = 3-8 in the N-H stretching region. The spectroscopic work has been supported by ab initio calculations carried out at both the DFT(B3LYP) and MP2 levels, using a 6-311++G(d,p) basis set. The calculations reveal that the lowest energy isomer for n or= 7 is indicative of molecules entering a second solvation shell, i.e., the inner solvation shell around the sodium atom can accommodate a maximum of six NH3 molecules.     

Continuum solvation models in the linear interaction energy method

The linear interaction energy (LIE) method in combination with two different continuum solvent models has been applied to calculate protein-ligand binding free energies for a set of inhibitors against the malarial aspartic protease plasmepsin II. Ligand-water interaction energies are calculated from both Poisson-Boltzmann (PB) and Generalized Born (GB) continuum models using snapshots from explicit solvent simulations of the ligand and protein-ligand complex. These are compared to explicit solvent calculations, and we find close agreement between the explicit water and PB solvation models. The GB model overestimates the change in solvation energy, and this is caused by consistent underestimation of the effective Born radii in the protein-ligand complex. The explicit solvent LIE calculations and LIE-PB, with our standard parametrization, reproduce absolute experimental binding free energies with an average unsigned error of 0.5 and 0.7 kcal/mol, respectively. The LIE-GB method, however, requires a constant offset to approach the same level of accuracy.     

Infrared spectroscopy of hydrated sulfate dianions

We report the first infrared spectra of multiply-charged anions in the gas phase. The spectra of SO(4) (2-)(H(2)O)(n), with n=3-24, show four main bands assigned to two vibrations of the dianionic core, the water bending mode, and solvent libration. The triply degenerate SO(4) (2-) antisymmetric stretch vibration probes the local solvent symmetry, while the solvent librational band is sensitive to the hydrogen bonding network. The spectra and accompanying electronic structure calculations indicate a highly symmetric structure for the n=6 cluster and closure of the first solvation shell at n=12.