Time Dependent Density Functional Theory Modeling of Chiroptical Properties of Small Amino Acids in Solution

A general method to predict optical rotations of chiral molecules from their structures

The relationship of the chiroptical response of a molecule to its absolution configuration does not exist now. In this letter, I intend to report a general rule with exceptions to predict the sign of optical rotation of chiral molecules with a RCHXY structure from their absolute configurations using the Hammett constant, σ _p, which is based on the electron withdrawing/donating power of functional groups. In this rule, a priority list of functional groups based on the electron withdrawing powers of the groups are used. When the lowest priority group is in the back of the molecule, a clockwise arrangement of the other three priorities from the most electron withdrawing to the least withdrawing (1-2-3) is predicted to be dextrorotatory, the counterclockwise arrangement is predicted to be levorotatory.

A Density Functional Theory Study of Optical Rotation in Some Aziridine and Oxirane Derivatives

We present time-dependent density functional theory (TDDFT) calculations of the electronic optical rotation (ORP) for seven oxirane and two aziridine derivatives in the gas phase and in solution and compare the results with the available experimental values. For seven of the studied molecules it is the first time that their optical rotation was studied theoretically and we have therefore investigated the influence of several settings in the TDDFT calculations on the results. This includes the choice of the one-electron basis set, the exchange-correlation functional or the particular polarizable continuum model (PCM). We can confirm that polarized quadruple zeta basis sets augmented with diffuse functions are necessary for converged results and find that the aug-pc-3 basis set is a viable alternative to the frequently employed aug-cc-pVQZ basis set. Based on our study, we cannot recommend the generalized gradient functional KT3 for calculations of the ORP in these compounds, whereas the hybrid functional PBE0 gives results quite similar to the long-range correct CAM-B3LYP functional. Finally, we observe large differences in the solvent effects predicted by the integral equation formalism of PCM and the SMD variant of PCM. For the majority of solute/solvent combinations in this study, we find that the SMD model in combination with the PBE0 functional and the aug-pc-3 basis set gives the best agreement with the experimental values.

Concise Syntheses of Hyrtioreticulins C and D via a C-4 Pictet-Spengler Reaction: Revised Signs of Specific Rotations

The first syntheses of hyrtioreticulins C and D via a Pictet-Spengler reaction at the C-4 position of the indole rings are described. The synthesis proceeds in only two steps from commercially available starting materials. In this Communication, the structures of the natural products were confirmed. Furthermore, we revise the signs of the specific rotations of hyrtioreticulins C and D.

Molecular mechanisms for the reaction between (˙)OH radicals and proline: insights on the role as reactive oxygen species scavenger in plant stress

The accumulation of proline (Pro) and overproduction of reactive oxygen species (ROS) by plants exposed to stress is well-documented. In vitro assays show that enzyme inactivation by hydroxyl radicals ((•)OH) can be avoided in the presence of Pro, suggesting this amino acid might act as a (•)OH scavenger. Although production of hydroxyproline (Hyp) has been hypothesized in connection with such antioxidant activity, no evidence on the detailed mechanism of scavenging has been reported. To elucidate whether and how Hyp might be produced, we used density functional theory calculations coupled to a polarizable continuum model to explore 27 reaction channels including H-abstraction by (•)OH and (•)OH/H2O addition. The structure and energetics of stable species and transition states for each reaction channel were characterized at the PCM-(U)M06/6-31G(d,p) level in aqueous solution. Evidence is found for a main pathway in which Pro scavenges (•)OH by successive H-abstractions (ΔG(‡,298) = 4.1 and 7.5 kcal mol(-1)) to yield 3,4-Δ-Pro. A companion pathway with low barriers yielding Δ(1)-pyrroline-5-carboxylate (P5C) is also supported, linking with 5-Hyp through hydration. However, this connection remains unlikely in stressed plants because P5C would be efficiently recycled to Pro (contributing to its accumulation) by P5C reductase, hypothesis coined here as the "Pro-Pro cycle".

Determination of the absolute configurations of bicyclo[3.1.0]hexane derivatives via electronic circular dichroism, optical rotation dispersion and vibrational circular dichroism spectroscopy and density functional theory calculations

The electronic circular dichroism (ECD), optical rotation dispersion (ORD), and vibrational circular dichroism (VCD) spectra of a pair of enantiomers, i.e. 3 and 4, of a bicyclo[3.1.0]hexane derivative have been measured in acetonitrile and acetonitrile-d(3), respectively. Extensive conformational searches at the B3LYP/6-311++G** level have been carried out for 3, which has four OH and one N(3) functional groups. For the bicyclo[3.1.0]hexane ring of 3, the boat-like conformers have been found to be much more stable than the chair-like conformers, while the number and the strength of the intramolecular hydrogen bonds have been identified as the dominant factors in the relative stability among the boat-like and among the chair-like conformers. DFT simulations of the ECD, ORD and VCD spectra have been performed for all low energy conformers at the B3LYP/6-311++G** and B3LYP/aug-cc-pVDZ level. Implicit continuum polarization model has been used to account for solvent effects in all these chiroptical measurements. Comparison of the DFT simulations with the experimental data shows that all three chiroptical properties yield the same absolute configuration assignment for . This work demonstrates that using multiple chiroptical spectroscopic methods in combination with DFT calculations allows one to determine absolute configurations with high confidence for chiral carbohydrates and their analogues, which possess a large number of rotatable bonds.

Time-dependent density functional response theory for electronic chiroptical properties of chiral molecules

Methodology to calculate electronic chiroptical properties from time-dependent density functional theory (TDDFT) is outlined. Applications of TDDFT to computations of electronic circular dichroism, optical rotation, and optical rotatory dispersion are reviewed. Emphasis is put on publications from 2005 to 2010, but much of the older literature is also cited and discussed. The determination of the absolute configuration of chiral molecules by combined measurements and computations is an important application of TDDFT chiroptical methods and discussed in some detail. Raman optical activity (ROA) spectra are obtained from normal-mode derivatives of the optical rotation tensor and other linear response tensors. A few selected (ROA) benchmarks are reviewed.

Computational modeling of the optical rotation of amino acids: a new look at an old rule for pH dependence of optical rotation

The molar rotation of a solution of a natural alpha amino acid is changed in the positive direction by addition of a strong acid. Three decades ago, an attempt to rationalize this old rule, named for Clough, Lutz, and Jirgensons (CLJ), was made by assigning circular dichroism octants for overlapping carbonyl n to pi* transitions. Modern quantum chemical methods allow us to take a new look at this phenomenon. Time-dependent density functional theory was used to model the electronic structure and transitions responsible for CLJ. We show that sector rules originally developed for circular dichroism (CD) can be applied to the optical rotation in this case, but with some restrictions, and with great caution, due to the change of the overall charge of the acids upon protonation and the distortion of the COO- chromophore in the zwitterions. We have prepared sector maps based on first-principles computations to study the correspondence between CD and optical rotation for zwitterionic and protonated l-amino acid chromophores. The CLJ effect is correctly obtained from the computations for all 12 amino acids studied in this work.

Temperature Dependence of the Optical Rotation in Six Bicyclic Organic Molecules Calculated by Vibrational Averaging

The vibrational corrections and the temperature dependence of the specific rotation of six rigid organic molecules (alpha-pinene, beta-pinene, cis-pinane, camphene, camphor, and fenchone) were calculated at three wavelengths using hybrid time-dependent density functional theory (TDDFT). A technique for calculating the temperature dependence of the vibrational average of a molecular property has been applied to obtain the specific rotation of the molecules as a function of temperature. For cases in which accurate equilibrium optical rotations can be obtained as a "base value," and for which there is little effect from solvation, accurate predictions of the trends in the temperature-dependence of the specific rotations can be calculated. For other cases, the method can be used to extract purely vibrational contributions to the overall temperature dependence of optical rotation.

Ab Initio Study of the Two-Photon Circular Dichroism in Chiral Natural Amino Acids

Two-photon circular dichroism spectra calculated within an origin-invariant density functional theory approximation in the absorption region where the lowest electronic excited states appear are presented for all 19 essential amino acids in the gas phase. A comparison of intensities and characteristic features is made with the corresponding two-photon absorption and one-photon circular dichroism spectra for each species. Also, the contributions of the electric dipole, magnetic dipole, and electric quadrupole transitions to the rotational strengths are analyzed in some detail. The remarkable fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.

Calculation of circular dichroism spectra from optical rotatory dispersion, and vice versa, as complementary tools for theoretical studies of optical activity using time-dependent density functional theory

A comparison of two theoretical methods based on time-dependent density functional theory for the calculation of the linear dispersive and absorptive properties of chiral molecules has been made. For this purpose, a recently proposed computational method for the calculation of circular dichroism (CD) spectra from the imaginary part of the optical rotation parameter has been applied to six rigid organic molecules. The results have been compared to the CD spectra obtained from the rotatory strengths and from the Kramers-Kronig transformation of optical rotatory dispersion (ORD) curves. We have also investigated a criterion based on the Kramers-Kronig integration formula to determine a number of excitations in truncated CD spectra which may yield a reasonable low frequency resonant ORD. It has been tested by calculating the ORD from the sum-over-states formula both in the nonresonant and resonant regions. Finally, we have applied these methods to model the resonant optical activity of proline at low pH.

Time Dependent Density Functional Theory Modeling of Specific Rotation and Optical Rotatory Dispersion of the Aromatic Amino Acids in Solution

Time Dependent Density Functional Theory (TDDFT) along with the COnductor-like Screening MOdel (COSMO) has been applied to model the specific rotation at 589.3 nm and the optical rotatory dispersion (ORD) of the aromatic amino acids phenylalanine, tyrosine, histidine, and tryptophan. Solution structures at low, neutral, and high pH were determined. Both the anomalous dispersion absorbing (resonance) region and the lower energy (transparent) region of the ORD of the compounds were modeled. Linear response calculation of the specific rotation and ORD as well as Kramers-Kronig transformations of calculated circular dichroism spectra to model resonant ORD were compared with experimental data from the literature.