Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.     

Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed

Understanding the chromophore maturation process in fluorescent proteins is important for the design of proteins with improved properties. Here, we present the results of electronic structure calculations identifying the nature of a blue intermediate, a key species in the process of the red chromophore formation in DsRed, TagRFP, fluorescent timers, and PAmCherry. The chromophore of the blue intermediate has a structure in which the π-system of the imidazole ring is extended by the acylimine bond, which can be represented by the model N-[(5-hydroxy-1H-imidazole-2yl)methylidene]acetamide (HIMA) compound. Ab initio and QM/MM calculations of the isolated model and protein-bound (mTagBFP) chromophores identify the anionic form of HIMA as the only structure that has absorption that is consistent with the experiment and is stable in the protein binding pocket. The anion and zwitterion are the only protonation forms of HIMA whose absorption (421 and 414 nm, or 2.95 and 3.00 eV) matches the experimental spectrum of the blue form in DsRed (the absorption maximum is 408 nm or 3.04 eV) and mTagBFP (400 nm or 3.10 eV). The QM/MM optimization of the protein-bound anionic form results in a structure that is close to the X-ray one, whereas the zwitterionic chromophore is unstable in the protein binding pocket and undergoes prompt proton transfer. The computed excitation energy of the protein-bound anionic form of the mTagBFP-like chromophore (3.04 eV) agrees with the experimental absorption spectrum of the protein. The DsRed-like chromophore formation in red fluorescent proteins is revisited on the basis of ab initio results and verified by directed mutagenesis revealing a key role of the amino acid residue 70, which is the second after the chromophore tripeptide, in the formation process.     

Nitrogen 1s near-edge X-ray absorption fine structure spectroscopy of amino acids: Resolving zwitterionic effects

Considerable variation is observed in the near-edge X-ray absorption fine structure (NEXAFS) spectra of amino acids. To unambiguously characterize the chemical origin of this variation, we have acquired the nitrogen 1s NEXAFS spectra of several amino acids and other model compounds and complemented these experimental measurements with ab initio calculations of isolated molecules and molecular clusters. The systematic differences observed between the zwitterionic and un-ionized forms of amino acids arise directly from the structural difference (-NH2 vs -NH3+), which leads to a change in the degree of Rydberg-valence mixing. Further change arises from quenching of this Rydberg character in the spectra of condensed amino acids. Ab initio calculations are used to explore the degree of Rydberg-valence mixing in the solid state.     

Protonation of the chromophore in the photoactive yellow protein

The photoactive yellow protein (PYP) acts as a light sensor to its bacterial host: it responds to light by changing shape. After excitation by blue light, PYP undergoes several transformations, to partially unfold into its signaling state. One of the crucial steps in this photocycle is the protonation of p-coumaric acid after excitation and isomerization of this chromophore. Experimentalists still debate on the nature of the proton donor and on whether it donates the hydrogen directly or indirectly. To obtain better knowledge of the mechanism, we studied this proton transfer using Car-Parrinello molecular dynamics, classical molecular dynamics, and computer simulations combining these two methods (quantum mechanics/molecular mechanics, QMMM). The simulations reproduce the chromophore structure and hydrogen-bond network of the protein measured by X-ray crystallography and NMR. When the chromophore is protonated, it leaves the assumed proton donor, glutamic acid 46, with a negative charge in a hydrophobic environment. We show that the stabilization of this charge is a very important factor in the mechanism of protonation. Protonation frequently occurs in simplified ab initio simulations of the chromophore binding pocket in vacuum, where amino acids can easily hydrogen bond to Glu46. When the complete protein environment is incorporated in a QMMM simulation on the complete protein, no proton transfer is observed within 14 ps. The hydrogen-bond rearrangements in this time span are not sufficient to stabilize the new protonation state. Force field molecular dynamics simulations on a much longer time scale have shown which internal rearrangements of the protein are needed. Combining these simulations with more QMMM calculations enabled us to check the stability of protonation states and clarify the initial requirements for the proton transfer in PYP.     

Chromophores in spectroscopy: Ab initio studies of localized descriptions of molecular electronic excitations

We review a computationally efficient approach, based jointly on the Random Phase Approximation (RPA) and on localized molecular orbitals, for calculating and analyzing electronic excitations in terms of the nature of the chromophore and its interaction with its molecular surroundings. The method is applied to two typical chromophoric systems using ab initio extended-basis calculations: the non-conjugated but electronically coupled ethylenic double bonds in norbornadiene (NBD, bicyclo[2.2.1]hepta-2,5-diene) and the chirally perturbed carbonyl chromophore inequatorial 4-methyladamantanone (EMAO). The analyses are a posteriori in nature but provide insights into the spectroscopic properties of medium-sized molecules.     

Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study

13C NMR spectroscopy, ab initio quantum mechanics, and molecular mechanics have been used to investigate the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane chair/twist-boat equilibrium. The molecular mechanics calculations were based upon the MM3 and AMBER force fields. A 6-31G basis set was used for the ab initio calculations, and MP2 correlation corrections were applied. Both the ab initio and AMBER molecular mechanics calculations are consistent with the (13)C NMR chemical shift differences for the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane conformers. The predicted chair to twist-boat equilibrium suggested by the MM3 calculations is not consistent with the experimental data. These results support the suggestion by Howard et al. (Howard, A. E.; Cieplak, P.; Kollman, P. A. J. Comput.Chem. 1995, 16, 243-261) on the critical role of electrostatic interactions in determining the chair/twist-boat equilibrium.     

CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field

High-level ab initio calculations have been carried out to study weak CH/pi interactions and as a check of the CHARMM force field for aromatic amino acids. Comparisons with published data indicate that the MP2/cc-pVTZ level of theory is suitable for calculations of CH/pi interaction, including the T-shape benzene dimer. This level of theory was, therefore, applied to investigate CH/pi interactions between ethene or cis-2-butene and benzene in a variety of orientations. In addition, complexes between ethene and a series of model compounds (toluene, methylindole and p-cresol) representing the aromatic amino acids were studied motivated by the presence of CH/pi interactions in biological systems. Ab initio binding energies were compared to the binding energies obtained with the CHARMM22 force field. In the majority of orientations, CHARMM22 reproduces the preferred binding modes, with excellent agreement for the benzene dimer. Small discrepancies found in the calculations involving methylindole along with a survey of published thermodynamic data for the aromatic amino acids prompted additional optimization of the tryptophan force field. Partial atomic charges, Lennard-Jones parameters, and force constants were improved to obtain better intra- and intermolecular properties, with significant improvements obtained in the reproduction of experimental heats of sublimation for indole and free energies of aqueous solvation for methylindole.     

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase

Collisions between O³⁺ ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum–chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non‐negligible amount of the radical cation monomer is observed. New fragment‐ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.     

Photodissociation dynamics of hydroxybenzoic acids

Aromatic amino acids have large UV absorption cross-sections and low fluorescence quantum yields. Ultrafast internal conversion, which transforms electronic excitation energy to vibrational energy, was assumed to account for the photostability of amino acids. Recent theoretical and experimental investigations suggested that low fluorescence quantum yields of phenol (chromophore of tyrosine) are due to the dissociation from a repulsive excited state. Radicals generated from dissociation may undergo undesired reactions. It contradicts the observed photostability of amino acids. In this work, we explored the photodissociation dynamics of the tyrosine chromophores, 2-, 3- and 4-hydroxybenzoic acid in a molecular beam at 193 nm using multimass ion imaging techniques. We demonstrated that dissociation from the excited state is effectively quenched for the conformers of hydroxybenzoic acids with intramolecular hydrogen bonding. Ab initio calculations show that the excited state and the ground state potential energy surfaces change significantly for the conformers with intramolecular hydrogen bonding. It shows the importance of intramolecular hydrogen bond in the excited state dynamics and provides an alternative molecular mechanism for the photostability of aromatic amino acids upon irradiation of ultraviolet photons.     

Ab initio study of the electronic structure of the crystalline high-mobility organic semiconductor 1,4-diiodobenzene

We use ab initio crystalline calculations to explore the role of iodine in determining the properties of 1,4-diiodobenzene. The results strongly suggest that the large halogen is an important or perhaps the dominant determinant of the ability of diiodobenzene to transport holes. We conjecture that the high mobility of diiodobenzene is due to a combination of electronic and phononic effects, both influenced by the presence of the iodine.     

Photoinduced isomerization of the photoactive yellow protein (PYP) chromophore: interplay of two torsions, a HOOP mode and hydrogen bonding

We report on a detailed theoretical analysis, based on extensive ab initio calculations at the CC2 level, of the S(1) potential energy surface (PES) of the photoactive yellow protein (PYP) chromophore. The chromophore's photoisomerization pathway is shown to be fairly complex, involving an intimate coupling between single-bond and double-bond torsions. Furthermore, these torsional modes are shown to couple to a third coordinate of hydrogen out-of-plane (HOOP) type whose role in the isomerization is here identified for the first time. In addition, it is demonstrated that hydrogen bonding at the phenolate moiety of the chromophore can hinder the single-bond torsion and thus facilitates double-bond isomerization. These results suggest that the interplay between intramolecular factors and H-bonding determines the isomerization in native PYP.     

General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions

We developed a methodology to optimize exponential damping functions to account for charge penetration effects when computing molecular electrostatic properties using the multicentered multipolar expansion method (MME). This methodology is based in the optimization of a damping parameter set using a two-step fast local fitting procedure and the ab initio (Hartree-Fock/6-31G** and 6-31G**+) electrostatic potential calculated in a set of concentric grid of points as reference. The principal aspect of the methodology is a first local fitting step which generates a focused initial guess to improve the performance of a simplex method avoiding the use of multiple runs and the choice of initial guesses. Three different strategies for the determination of optimized damping parameters were tested in the following studies: (1) investigation of the error in the calculation of the electrostatic interaction energy for five hydrogen-bonded dimers at standard and nonstandard hydrogen-bonded geometries and at nonequilibrium geometries; (2) calculation of the electrostatic molecular properties (potential and electric field) for eight small molecular systems (methanol, ammonia, water, formamide, dichloromethane, acetone, dimethyl sulfoxide, and acetonitrile) and for the 20 amino acids. Our results show that the methodology performs well not only for small molecules but also for relatively larger molecular systems. The analysis of the distinct parameter sets associated with different optimization strategies show that (i) a specific parameter set is more suitable and more general for electrostatic interaction energy calculations, with an average absolute error of 0.46 kcal/mol at hydrogen-bond geometries; (ii) a second parameter set is more suitable for electrostatic potential and electric field calculations at and outside the van der Waals (vdW) envelope, with an average error decrease >72% at the vdW surface. A more general amino acid damping parameter set was constructed from the original damping parameters derived for the small fragments and for the amino acids. This damping set is more insensitive to protein backbone and residue side-chain conformational changes and can be very useful for future docking and molecular dynamics protein simulations using ab initio based polarizable classical methods.     

Anharmonic vibrational calculations modeling the raman spectra of intermediates in the photoactive yellow protein (PYP) photocycle

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.     

某些含氧酸中原子净电荷与pK_a的关系

在量子化学从头算 (分别采用HF/STO 3G ,HF/STO 3G ,HF/ 3 2 1G和MP2 /STO 3G)水平下 ,对 11种含氧酸分子 (H2 O ,H2 O2 ,HNO2 ,HNO3 ,HClO ,HClO2 ,HClO3 ,HCO2 H ,CH3 CO2 H ,HBrO和HIO)进行几何构型全优化和电子结构计算 ,将获得的电子结构数据与 pKa 实验值进行逐步回归分析 ,结果发现含氧酸中羟基氢原子净电荷、含氧酸中与羟基氧相连非氢原子净电荷两项与 pKa 呈良好的二元线性关系 ,表明含氧酸中羟基氧所连原子的净电荷在决定含氧酸的酸性上起重要作用     

Semiempirical MO methods: the middle ground in molecular modeling

Semiempirical methods occupy an important middle ground between molecular mechanics and ab initio MO calculations in the repertoire of methods available for studying the structures, properties and reactions of molecules. They have a unique combination of speed and generality which makes it possible to study many chemical systems which are beyond the reach of classical force fields and too large for ab initio MO methods. Indeed, semiempirical calculations are often the first computational technique to be applied to a chemical problem. Three examples where semiempirical MO calculations have provided significant mechanistic insight are the cylcopropylcarbinyl cation, porphyrin structure and dynamics, and the role of C---H hydrogen bonds in polymer miscibility. In each case Semiempirical calculations have been at the fore, and their results have been generally confirmed by subsequent ab initio calculations and experiment.     

氨基酸分子的光学活性和频效应

用带限制场Hartree-Fock (RHF/6-311++G^**)从头算的方法进行分子构型优化, 单激发态组态相互作用(CIS/6-311++G^**)计算各种需要的相关数据; 应用态求和理论, 以长度偶极矩和速度偶极矩两种形式模拟了一系列氨基酸离子的光学活性和频效应(OA-SFG)光谱. 结果表明速度偶极矩计算得到的一系列氨基酸离子的和频效应光谱强度顺序能很好地与实验相吻合, 而长度偶极矩形式计算得到的结果与实验不吻合. 引起这两种形式和频效应光谱理论计算结果差别的原因是由于长度偶极矩形式具有原点敏感性, 而速度偶极矩没有. 速度偶极矩方法更适用于分子光学活性和频效应的模拟.     

Intra- and intermolecular topological properties of amino acids: a comparative study of experimental and theoretical results

The charge densities rho(r) of the six amino acids L-Asn.H(2)O, DL-Glu.H(2)O, DL-Lys.HCl, DL-Pro.H(2)O, DL-Ser, and DL-Val were determined from high-resolution X-ray diffraction experiments at 100 K using synchrotron radiation and area detection (CCD) techniques. Bond topological parameters derived from these densities and from those of six additional amino acids published earlier are compared to each other and to the results of ab initio calculations. Experimental and theoretical properties for each chemically equivalent bond are in a fair agreement, and their variances are of similar magnitude. A noticeable outlier is the positive curvature of the density at the bond critical point, for which no correlation between the experimental and theoretical values can be established. The location of nonbonded valence shell charge concentrations derived from the crystalline densities scatter in a wider range than those obtained for the isolated molecules.     

Understanding hydrogen bonding of hydroxamic acids with some amino acid side chain model molecules

The hydrogen-bonding abilities of a few amino acid side chains have been studied through aggregation of methylamine, methanol, and acetic acid (as model molecules) with formo- and thioformo- hydroxamic acids using ab initio calculations. Forty six aggregates representing all possible H-bond interactions between these amino acid side chain groups and two most stable keto and enol tautomeric forms of both hydroxamic acids have been optimized. Although participation of conventional H-bond donors and acceptors leads to significant stabilization energies, yet C–H···O, C–H···N, S–H···O, and S–H···N etc. unconventional H-bonds also contribute to stabilize interactions in many aggregates. Strength of H-bonds of the molecules with formo- and thioformo- hydroxamic acid studied follows the order acetic acid > methylamine > methanol. A comparative study of atomic charges and orbital interactions employing NBO analysis has been carried out to explore the role of bond polarizations, charge transfer, and electron delocalizations as contributors to stabilization energy.