Determination of absolute configuration using optical rotation calculated using density functional theory

[structure: see text] We report the first determinations of the absolute configurations (ACs) of chiral molecules using discrete frequency, transparent spectral region optical rotations calculated using density functional theory (DFT). The ACs of 2H-naphtho[1,8-bc]thiophene 1-oxide (3), naphtho[1,8-cd]-1,2-dithiole 1-oxide (4), and 9-phenanthryl methyl sulfoxide (5) are determined by comparison of their specific rotations to values calculated via the time-dependent DFT/gauge-invariant atomic orbital (TDDFT/GIAO) methodology using the B3LYP functional and the aug-cc-pVDZ basis set.     

Determination of the absolute configuration of [3(2)](1,4)barrelenophanedicarbonitrile using concerted time-dependent density functional theory calculations of optical rotation and electronic circular dichroism

The technique of time-dependent density functional theory (TDDFT) has very recently been applied to the calculation of both transparent spectral region optical rotations and electronic circular dichroism (CD). Here, we report the concerted application of the new methodologies to the determination of the absolute configuration (AC) of [3(2)](1,4)barrelenophanedicarbonitrile, 1, the first optically active barrelenophane. 1 is conformationally flexible: the two three-carbon bridges of 1 can each exhibit two conformations, leading to three inequivalent conformations of 1: a, b, and c. Conformational structures and energies are predicted using DFT at the B3LYP/6-31G level. Comparison of the calculated structures to structures obtained via X-ray crystallography of (+)-1 shows that (remarkably) all three conformations a-c are simultaneously present in crystalline (+)-1. The sodium D line specific rotations, [alpha](D), and CD spectra of a-c are calculated using TDDFT at the B3LYP/aug-cc-pVDZ level. Comparison of the conformationally averaged specific rotation and CD spectrum to the experimental data of Matsuda-Sentou and Shinmyozu leads to the AC 9S,12S(+)/9R,12R(-). The same AC is obtained both from [alpha](D) and from the CD, strongly supporting its reliability.     

Comparison of time-dependent density-functional theory and coupled cluster theory for the calculation of the optical rotations of chiral molecules

A comparison of the abilities of time-dependent density-functional theory (TDDFT) and coupled cluster (CC) theory to reproduce experimental sodium D-line specific rotations for 13 conformationally rigid organic molecules is reported. The test set includes alkanes, alkenes, and ketones with known absolute configurations. TDDFT calculations make use of gauge-including atomic orbitals and give origin-independent specific rotations. CC rotations are computed using both the origin-independent dipole-velocity and origin-dependent dipole-length representations. The mean absolute deviations of calculated and experimental rotations are of comparable magnitudes for all three methods. The origin-independent DFT and CC methods give the same sign of [alpha]D for every molecule except norbornanone. For every large-rotation ketone and alkene for which DFT and CC yield the incorrect sign as compared to liquid-phase experimental data, the corresponding optical rotatory dispersion (ORD) curve is bisignate, suggesting that the two models cannot reliably reproduce the relative excitation energies and antagonistic rotational strengths of multiple competing electronic states that contribute to the total long-wavelength rotation. Several potential sources of error in the theoretical treatments are considered, including basis set incompleteness, vibrational and temperature effects, electron correlation, and solvent effects.     

Determination of absolute configuration using concerted ab Initio DFT calculations of electronic circular dichroism and optical rotation: bicyclo[3.3.1]nonane diones

The concerted use of ab initio time-dependent density functional theory (TDDFT) calculations of transparent spectral region optical rotation and of circular dichroism has recently become practicable, permitting the concerted use of transparent spectral region optical rotation and circular dichroism in determining the absolute configurations of chiral molecules. Here, we report concerted TDDFT calculations of the transparent spectral region specific rotations and of the circular dichroism spectra originating in n --> pi C=O group excitations of four bicyclo[3.3.1]nonane diones, 1-4. Comparison to experiment yields absolute configurations for 1-4. For each dione, specific rotations and circular dichroism spectra give identical absolute configurations. Our results are consistent with previous work, with the exception of the Octant Rule-derived absolute configuration of the 2,9-dione.     

Determination of absolute configuration using density functional theory calculations of optical rotation and electronic circular dichroism: chiral alkenes

In principle, the absolute configuration (AC) of a chiral molecule can be deduced from its optical rotation (OR) and/or its electronic circular dichroism (ECD). In practice, this requires reliable methodologies for predicting OR and ECD. The recent application of ab initio time-dependent density functional theory (TDDFT) to the calculation of transparent spectral region OR and ECD has greatly enhanced the reliability with which these phenomena can be predicted. TDDFT calculations of OR and ECD are being increasingly utilized in determining ACs. Nevertheless, such calculations are not perfect, and as a result, ACs determined are not 100% reliable. In this paper, we examine the reliability of the TDDFT methods in the case of chiral alkenes. Sodium d line specific rotations, [alpha]D, are predicted for 26 conformationally rigid alkenes of known AC, ranging in size from 5 to 20 C atoms, and with [alpha]D values in the range of 0-500. The mean absolute deviation of predicted [alpha]D values from experimental values is 28.7. With one exception, beta-pinene, the signs of [alpha]D are correctly predicted. Errors in calculated [alpha]D values are approximately random. Our results define a "zone of indeterminacy" within which calculated [alpha]D values cannot be used to determine ACs with >95% confidence. TDDFT ECD spectra are predicted for eight of the alkenes and compared to experimental spectra. Agreement ranges from modestly good to poor, leading to the conclusion that TDDFT calculations of ECD spectra are not yet of sufficient accuracy to routinely provide highly reliable ACs. TDDFT OR calculations for two conformationally flexible alkenes, 3-tert-butylcyclohexene and trans-4-carene, are also reported. For the former, predicted rotations are incorrect in sign over the range 589-365 nm. It is possible that the AC of this molecule has been incorrectly assigned.     

Optical rotation calculated with time-dependent density functional theory: the OR45 benchmark

Time-dependent density functional theory (TDDFT) computations are performed for 42 organic molecules and three transition metal complexes, with experimental molar optical rotations ranging from 2 to 2 × 10(4) deg cm(2) dmol(-1). The performances of the global hybrid functionals B3LYP, PBE0, and BHLYP, and of the range-separated functionals CAM-B3LYP and LC-PBE0 (the latter being fully long-range corrected), are investigated. The performance of different basis sets is studied. When compared to liquid-phase experimental data, the range-separated functionals do, on average, not perform better than B3LYP and PBE0. Median relative deviations between calculations and experiment range from 25 to 29%. A basis set recently proposed for optical rotation calculations (LPol-ds) on average does not give improved results compared to aug-cc-pVDZ in TDDFT calculations with B3LYP. Individual cases are discussed in some detail, among them norbornenone for which the LC-PBE0 functional produced an optical rotation that is close to available data from coupled-cluster calculations, but significantly smaller in magnitude than the liquid-phase experimental value. Range-separated functionals and BHLYP perform well for helicenes and helicene derivatives. Metal complexes pose a challenge to first-principles calculations of optical rotation.     

Bullvalene trisepoxide and its stereospecific rearrangement to 2,8,12-trioxahexacyclo[8.3.0.0(3,9)0(4,6)0(5,13)0(7,11)]tridecane: two new C3-symmetrical oligocycles with propeller chirality

Epoxidation of bullvalene (1) with a neutralized solution of Oxone gave racemic trisepoxide rac-6 in 93 % isolated yield. Its structure was examined by X-ray crystallography. The two enantiomers of 6 were separated by preparative HPLC and exhibited specific rotations of [alpha](25)(D)= +160, [alpha](25)(365)= +567 (c=0.946, CHCl(3)) for the firstly eluted and [alpha](25)(D)= -157, [alpha](25)(365)= -554 (c=0.986, CHCl3) for the secondly eluted enantiomer of 6. The geometry of (+)-6 and the absolute configuration of (-)-6 were determined by X-ray crystal structure analysis and anomalous diffraction, respectively. According to this, (-)-6 possesses (3R,5S,7S,9R,11R,13S)- and (+)-6 has (3S,5R,7R,9S,11S,13R)-configuration. Upon treatment with BF(3)Et(2)O at -78 degrees C, trisepoxide rac-6 rearranges with retention of the skeletal three-membered carbocycle to give the cage trisether rac-8, as proved by X-ray crystal structure analysis, in virtually quantitative yield. Enantiomers of rac-8 were separated by preparative HPLC and exhibited specific rotations of [alpha](25)(D)= +49, [alpha](25)(365)= +170 (c=1.01, CHCl3) (firstly eluting) and [alpha](25)(D)= -46, [alpha](25)(365)= -160 (c=1.02, CHCl(3)) (secondly eluting enantiomer). The absolute configuration of (-)-8 was determined by anomalous diffraction to be (1R,3R,7R,9R,11R,13R). DFT computations at the TD-B3 LYP/6-31+G(d,p)//B3 LYP/6-31+G(d) level of theory for (3R,5S,7S,9R,11R,13S)-6 and (1R,3R,7R,9R,11R,13R)-8 predicted specific rotations of -206.7 and -83.4, respectively. Acid-catalyzed isomerization of the enantiomerically pure (+)-6 proceeded without racemization to give exclusively (-)-8, and (-)-6 provided only (+)-8. Thus, this isomerization occurs with ring opening of the three C--O bonds in the epoxide moieties in the alpha-position relative to the three-membered carbocycle rather than in the beta-position.     

Determination of molecular structure using vibrational circular dichroism spectroscopy: the keto-lactone product of Baeyer-Villiger oxidation of (+)-(1R,5S)-bicyclo[3.3.1]nonane-2,7-dione

[reaction: see text] The Baeyer-Villiger oxidation of (+)-(1R,5S)-bicyclo[3.3.1]nonane-2,7-dione, 1, can lead to four keto-lactone products, 2a-d. A single isomer is obtained experimentally. We have used IR and VCD spectroscopies to identify the structure of this product. DFT calculations of the IR and VCD spectra of 2a-d show unambiguously that the experimental product is (+)-(1R,6R)-2a, and not the expected product 2b. NMR studies, including comparison of DFT and experimental 1H and 13C spectra, support this conclusion. This work provides the first example of the use of VCD spectroscopy to discriminate between structural isomers of a chiral molecule. The specific rotation of (+)-(1R,6R)-2a, predicted using TDDFT methods, is negative demonstrating that absolute configurations determined from TDDFT calculations of specific rotations are not 100% reliable.     

Matrix model to predict specific optical rotations of acyclic chiral molecules

This paper constructs a new matrix model to analyze the relationship of the stereogenic center and its substituents to the specific optical rotation. The variables used as matrix elements include (1) the substituents' comprehensive masses (m), (2) radii (r), (3) symmetries (s), and (4) the electronegativities (χ) of the atoms or groups which are bound to the stereogenic center. Solution of the matrix determinants was postulated to give scalar numbers proportional to the magnitudes of the specific rotations of the molecules being considered. A total of 94 example calculations were performed to predict the relative magnitude and direction of rotation at the sodium D line. Only two calculations failed to predict the correct direction of rotation and this occurred only when their optical rotation values were less than 0.01°. The B3LYP functional at the aug-cc-pVDZ basis set level was also used to compute the optical rotations of the 66 example chiral molecules whose geometries were previously obtained at the B3LYP/6-31G(d) level. The expected successful predictions for these acyclic molecules' optical rotation values did not appear. Overall, the matrix model is one approach to understand the optical rotation.     

Absolute configuration of natural cyclohexene oxides by time dependent density functional theory calculation of the optical rotation: the absolute configuration of (-)-sphaeropsidone and (-)-episphaeropsidone revised

The optical rotatory power of some natural cyclohexene oxides, such as (+)-chaloxone, 1, (+)-epiepoformine, 2, (+)-epoformine, 3, (+)-epoxidone, 5, (-)-sphaeropsidone, 6, (-)-episphaeropsidone, 7, and the synthetic compound (+)-epitheobroxide, 4, has been calculated by means of the TDDFT/B3LYP method using the 6-31G(d) and aug-cc-pVDZ basis sets, both in the gas phase and in solution by means of the polarizable continuum model. For compounds 1 and 2, which possess high (about 300 units) optical rotations, gas-phase calculations with the smaller basis set are able to reproduce the experimental values both in sign and order of magnitude. By contrast, a larger basis set is required to satisfactorily simulate the OR values of 3 and 4, which show smaller (about 100 units or less) rotations. The inclusion of the solvent effects is different for different compounds; for 1 and 2, it leads to a better agreement between experiment and prediction, while for 3 and 4, the presence of hydrogen bonding groups makes the application of continuum solvation models less satisfactory. For the flexible system 5, the absolute configuration could not be determined using gas-phase calculations and the smaller basis set, but both inclusion of solvent and larger basis set effects are compulsory. It is noteworthy that calculations both in the gas phase and in the solvent lead to a positive rotatory power for the laevorotatory natural compounds 6 and 7 if the ACs reported in the literature are employed to do the theoretical prediction. This strongly indicates that the ACs previously assigned to these compounds in the literature are not correct and that the TDDFT prediction of OR values has become by now a practicable tool for AC assignments.     

Circular dichroism, optical rotation and absolute configuration of 2-cyclohexenone-cis-diol type phenol metabolites: redefining the role of substituents and 2-cyclohexenone conformation in electronic circular dichroism spectra

The absolute configurations of 2-cyclohexenone cis-diol metabolites resulting from the biotransformation of the corresponding phenols have been determined by comparison of their experimental and calculated circular dichroism spectra (TDDFT at the PCM/B2LYP/Aug-cc-pVTZ level), optical rotations (calculated at the PCM/B3LYP/Aug-cc-pVTZ level) and by stereochemical correlation. It is found that circular dichroism spectra and optical rotations of 2-cyclohexenone derivatives are strongly dependent on the ring conformation (M or P sofa S(5) or half-chair), enone non-planarity and the nature and positions of the hydroxy and alkyl substituents. The effect of non-planarity of the enone chromophore, including the distortion of the C=C bond, is determined for the model structures by TDDFT calculations at the PCM/B2LYP/6-311++G(2d,2p) level. Non-planarity of the C=C bond in the enone chromophore is commonly encountered in 2-cyclohexenone derivatives and it is a source of significant rotatory strength contribution to the electronic circular dichroism spectra. It is shown that the two lowest-energy transitions in acrolein and 2-cyclohexenone and its derivatives are n(C=O)-π(C=O)* and π(C=C)-π(C=O)*, as expected, while the shorter-wavelength (below 200 nm) transitions are of more complex nature. In 2-cyclohexenone and its alkyl derivatives it is predominantly a mixture of π(C=C)-π(C=C)* and π(C=C)-σ* transitions, whereas the presence of hydroxy substituent results in a dominant contribution due to the n(OH)-π(C=O)* transition. A generalized model for correlation of the CD spectra of 2-cyclohexenones with their structures is presented.     

Time-dependent density functional calculations of optical rotatory dispersion including resonance wavelengths as a potentially useful tool for determining absolute configurations of chiral molecules

The optical rotations for six organic molecules (verbenone, fenchone, camphor, nopinone, Tr?ger's base, dimethyl-cyclopropane) and the transition metal complex [Co(en)(3)](3+) were calculated as a function of wavelength using time-dependent density functional theory (TDDFT). In the calculations, a realistic behavior of the optical rotation in the vicinity of an electronic transition was obtained by using a phenomenological damping parameter of the order of 0.2 eV (0.007 au). In comparison with experiment, for the molecules studied here the sign and order of magnitude of the optical rotation as well as the excitation energies were reasonably well reproduced in most computations. These findings apply to the investigated wavelength ranges typically between about 200 and 650 nm even when using comparatively small basis sets. Such calculations might therefore routinely be applied to help assigning the absolute configurations of chiral molecules. Supplementary calculations of the circular dichroism (CD) and comparison with experimental CD were used for further assessment of the optical rotation calculations. In particular, a combined study of optical rotation and CD turned out to be useful in cases where the optical rotatory dispersion in a specific energy range exhibits a considerable blue or red shift or where it is difficult to reproduce because of an interplay of several competing Cotton effects. The influence of basis set, density functional, and the damping parameter was also investigated.     

Theoretical studies of perimidine and its derivatives: structures,energies, and spectra

Structural Chemistry - Theoretical calculations at the B3LYP/6-311++G(d,p) level plus GIAO calculations for NMR absolute shieldings have been carried out for the parent perimidine and several of...     

Vertical excitation energies for ribose and deoxyribose nucleosides

Vertical excitation energies for DNA and RNA nucleosides are determined with electron structure calculations using the time-dependent density functional theory (TDDFT) method at the B3LYP/6-311++G(d,p) level for nucleoside structures optimized at the same level of theory. The excitation energies and state assignments are verified using B3LYP/aug-cc-pVDZ level calculations. The nature of the first four excited states of the nucleosides are studied and compared with those of isolated bases. The lowest npi* and pipi* transitions in the nucleoside remain localized on the aromatic rings of the base moiety. New low-energy npi* and pisigma* transitions are introduced in the nucleosides as a result of bonding to the ribose and deoxyribose molecules. The effect on the low-lying excited state transitions of the binding to phosphate groups at the 5'- and 3',5'-hydroxyl sites of the uracil ribose nucleoside are also studied. Some implications of these calculations on the de-excitation dynamics of nucleic acids are discussed.     

Fentanyl and its analogue N-(1-phenylpyrazol-3-yl)-N-[1-(2-phenylethyl)-4-piperidyl]propanamide: 1H- and 13C-NMR spectroscopy,X-ray crystallography,and theoretical calculations

The oxalate salts and free bases of fentanyl and N-[1-(2-phenylethyl)-4-piperidyl]-N-(1-phenyl-4-pyrazolyl)propanamide, a new lead compound for long-acting analgesia, have been characterized by (1)H- and (13)C-NMR spectroscopy. The crystal structure of the hydrochloride of N-[1-(2-phenylethyl)-4-piperidyl]-N-(1-phenyl-4-pyrazolyl)propanamide monohydrate has been determined. Two centrosymmetrically related cations, joined through C(phenyl)-H em leader pi contacts, encapsulate a large void that contains pairs of anions and bridged water molecules into a zero-dimensional (0D) supramolecular motif. The cations are linked to this framework via N(+)H em leader Cl(-) contacts. GIAO/B3LYP calculations have been carried out to compare the experimental (13)C chemical shifts with the absolute shieldings thus calculated. The protonation of both molecules takes place on the piperidine ring (axial protonation), as has been verified both in the solid state (X-ray) and in solution (NMR).     

Axially Chiral BODIPY DYEmers: An Apparent Exception to the Exciton Chirality Rule

The exciton chirality method (ECM) is commonly recognized as one of the best approaches to assign the absolute configuration of biaryls. This paper reports the first exception to this method for a simple biaryl system. ECD and VCD measurements in combination with DFT (B3LYP/6‐311G*), TDDFT (CAM‐B3LYP/6‐311G*), and Coupled‐Cluster (RI‐SCS‐CC2) calculations were used to determine the absolute configurations of axially chiral BODIPY DYEmers. The ECM fails to predict the sign of the intense CD couplet at 500 nm of the 1,1′‐coupled dimer. The odd behavior was rationalized by considering the strong transition magnetic dipole associated with the 500 nm transition, which leads to an unexpected dominance of the μm coupling at the expense of the μμ one in these compounds. This is the first case in which a strong μm coupling hampers the use of the ECM, but this behavior should not be restricted to the BODIPY chromophore.     

Conformational effects on optical rotation. 2-Substituted butanes

The specific rotations of 2-substituted butanes (X = F, Cl, CN, and HCC) were calculated at the B3LYP/aug-cc-pVDZ level as a function of the C-C-C-C torsion angle. The results for the four compounds are remarkably similar, despite large differences in the electronic transition energies. The temperature dependence of the specific rotations for 2-methylbutyronitrile and for 2-chlorobutane was studied to give experimental information about the effect of the torsion angle on the specific rotation. The results were in good accord with B3LYP/aug-cc-pVDZ calculations. The specific rotations derived from the study of 2-chlorobutane are similar to those previously obtained for 3-chloro-1-butene, indicating that the double bond does not have a large effect on the optical rotations, but it did lead to a large difference between calculated and observed specific rotations.     

The formation of RCCCO and CCC(O)R (R = Me, Ph) neutral radicals from ionic precursors in the gas phase: the rearrangement of CCC(O)Ph

Neutrals MeCCCO, CCC(O)Me, PhCCCO and CCC(O)Ph have been made by neutralisation of [MeCCCO](+), [CCC(O)Me](-), [PhCCCO](+) and [CC(CO)Ph](-). Neutrals MeCCCO, CCC(O)Me and PhCCCO are stable for the microsecond duration of the neutralisation experiment. A joint experimental and theoretical study (energies calculated at the B3LYP/aug-cc-pVDZ//B3LYP/6-31G(d) level of theory) suggests that the neutral radical CCC(O)Ph rearranges via a four-centred ipso radical cyclisation/ring opening to form the isomer PhCCCO in an exothermic reaction. (13)C labelling confirms that the rearrangement does not involve O migration. Some of the PhCCCO radicals formed in this reaction are sufficiently energised to effect decomposition to give PhCC and CO.     

Effect of substituents and conformations on the optical rotations of cyclic oxides and related compounds. relationship between the anomeric effect and optical rotation

The effect of substituents on the specific rotation of substituted cyclic oxides (X = F, Cl, CN, and HCC) and related compounds was studied via geometry optimization at the B3LYP/6-311+G** level followed by calculations of the specific rotation with B3LYP/aug-cc-pVDZ and, when practical, also with B3LYP/aug-cc-pVTZ. In some cases chiral samples were prepared so that the calculated specific rotations could be compared with experimental data. With most compounds there was only a minor effect of the basis set on the specific rotations. With the oxiranes and oxetanes, the chloro derivative gave a different behavior than the other substituents, but all substituents behaved in the same fashion with trans-2-methyl-1-X-cyclopropanes. Therefore the unusual behavior of chlorooxirane probably results from an interaction between oxygen and chlorine rather than being due to the presence of a three-membered ring. Chlorine is also an unusual substituent for the tetrahydrofurans. The effect of conformation on the calculated specific rotations was examined with the axial and equatorial 2-substituted tetrahydropyrans, where the anomeric effect is operative with the axial substituent, and also the 3-substituted tetrahydropyrans that would not be subject to the anomeric effect. The unusual effect of chlorine was seen only when it is antiperiplanar with respect to the oxygen.     

Theoretical analysis of [5.7](n)cyclacenes: closed-shell cyclacene isomers

The [5.7](n)cyclacenes represent a novel class of all sp(2)-hybridized carbon structures. In contrast to the isomeric [n]cyclacenes, [5.7](n)cyclacenes are predicted at the B3LYP/6-31G* level of theory to have stable, closed-shell singlet ground state configurations. Predicted geometries, electronic structures, band gaps, nucleus-independent chemical shift (NICS) values, and strain energies for this new family of cyclic conjugated molecules are presented.