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The UV-vis and ECD spectroelectrochemistry (SEC) of a chiral binaphthalenylamine derivative of the N-butyl naphthalenediimide (NDIB-NH

In this study, we found that a recently discovered ECD-Raman effect dominated over the natural Raman optical activity in a series of atropisomeric naphthalenediimides, and we investigated the kind of information about the molecular structure that could be obtained from the spectra. The ECD-Raman effect is polarised Raman scattering modulated by electronic circular dichroism. We showed that the spectra significantly depended on the substitution of the solute and/or the change of the solvent. Moreover, the spectra could be well-predicted by the theory, thus providing an interesting tool to monitor the chirality of the binaphthyl compounds.

Chirality transfer (also called induced chirality) is a phenomenon present in chiroptical spectra that manifests itself as a new band or bands of an achiral molecule interacting with a chiral one. In the Raman optical activity (ROA) spectroscopy, the bands of achiral solvents have been recently observed, but the latest papers have shown that they corresponded to the new ECD-Raman (eCP-Raman) effect. Here, we show an unambiguous example of chirality transfer observed in the ROA spectra. The spectra registered for the (1:1) mixtures of achiral benzonitrile with the enantiomers of 2,2,2-trifluoro-1-phenylethanol, 1-phenylethanol, and 1-phenylethylamine exhibited the v(CN) vibration band at about 2230 cm

A novel N-acylhydrazone with pharmaceutical importance was subject of structural and IR/VCD investigations in the solid state. In the crystal structure, dimers of anion-cation pairs are stabilized by H-bonding and ionic interactions. Some less common interaction types, like C=N···C-NH

Raman optical activity (ROA) spectra recorded for a chiral naphthalene diimide derivative (nBu-NDI–BINAM) dissolved in a series of solvents exhibit strong solute to solvent induced chirality with: (1) dominating bands of solvents, (2) nBu-NDI–BINAM resonance ROA (RROA) bands which are barely visible, (3) monosignate RROA Solvent spectra with an unexpected sign concordant with that of the ECD band of the resonant electronic state, (4) bisignate RROA bands for a few solvents, and (5) superposition of non-resonant and resonant ROA bands of the chiral solvents. The unusual ROA enhancement was explained in terms of resonance energy transfer with resonant Raman emission. The surprising RROA sign-switching was found to be due to specific conformational equilibria where one solute conformer dominates in the ground and the other in the first excited singlet state, and, the signs of the related ECD bands of these two conformers are opposite., Unusual solute to solvent induced chirality in ROA comes from specific conformer equilibria in the ground and the excited states.

The new terthiophene sulfonamide derivative, TTS, was synthesized and its IR, VCD, UV and ECD spectra were measured and interpreted by means of the DFT calculations. The TTS conformational space analyzed at the molecular mechanics, B3LYP/TZVP/PCM, and B3LYP/def2TZVP/PCM levels, was reduced to 72 conformers none of which appeared to be definitely dominant. A detailed examination of the slight deviations in mutual positions of the three thiophene rings revealed that for each conformer an additional 16 minima are apparently important but only six of them appear to be meaningful in 300 K. Apart from the permanent stereogenic center at the C6 carbon atom, the N-atom constitutes another (labile) stereogenic center connected to the presence of a lone electron pair at this very atom. This is significant because we found that the most stable conformers exhibit almost exclusively the (S)-configuration at the N-atom. The experimental IR and VCD spectra of TTS were fairly well reproduced if its monomers and dimers were taken into account. On the other hand, the experimental ECD spectra were difficult to reproduce because the spectra with slightly deviated thiophene rings produce practically mirror image ECD spectra. Calculated and recorded VCD spectra confirm configuration at the C6 of TTS, which was earlier predicted using stereochemical model for 1,2-addition to N-sulfinylimines proposed by Ellman.

Undecathiophenes substituted by chiral and achiral groups were studied using DFT method. The substituent shift from one end to the other was monitored for: relative energy, the SRCM chirality measure, the chiral Wiener index, the HOMO-LUMO gap, HOMA and NICS aromaticity indices, and theoretical VCD spectrum. For both, all-trans and one-cis conformations, structures substituted at the end were ca. 10 kJ/mol more stable than the other isomers. The SRCMs fluctuations with the conformation made this parameter not useful, but, the topological chiral Wiener index displayed regular yet non-linear changes with the substituent position enabling differentiation of the chiral systems. The HOMO-LUMO gap increased with the substituent shift towards the central ring. It varies regularly with the Wiener index for all-trans but irregularly for one-cis conformers, indicating strong response of the gap on slight conformational changes. The aromaticity indices adopted to linear systems indicated the all-trans to be a bit less delocalized than the one-cis isomers. Finally, the calculated VCD spectra were indicated possibility to monitor the position of the chiral substituent along the all-trans and one-cis structures.

The primary purpose of this work was to demonstrate the suitability of circular dichroism (CD) spectroscopy in stereochemical studies of α,β-unsaturated oximes, with particular emphasis on determination of E and Z geometry of the oxime double bond. As models for this study, O-phenyl and O-triphenylmethyl (trityl) oximes of 4-hydroxy-2-methylcyclopent-2-en-1-one were selected. These model compounds differ in both absolute configuration at C4 carbon atom and E-Z configuration of the oxime double bond. The basic dichroic technique applied was electronic circular dichroism (ECD) assisted by quantum-chemical calculations and vibrational circular dichroism (VCD) for selected cases. Such an approach enabled effective implementation of both goals. Thus, we were able to associate the signs of Cotton effects in the range of 190-240 nm with the absolute configuration at C4 and within 240-300 nm with the E- or Z-geometry of the oxime double bond. Within this work, optical activity of the protecting trityl group was also studied towards formation of the propeller-shaped conformations by using the same combined CD/DFT methodology. As shown, the helical structure of the trityl group has a considerable influence on the ECD spectra. However, the MPM and PMP conformers of the trityl group are in fact almost equally populated in the conformational equilibrium, making it impossible to distinguish them. On the other hand, rotamers of the hydroxyl group at C4 show a decisive impact on the VCD spectra in both phenoxy and trityl oximes.

We studied the conformation and hydration of the SO 3 -Ph-BTP ligand used as hydrophilic actinide and lanthanide separating agent using DFT methods. To avoid a large conformational space, changes in conformation and hydration were considered step-by-step. The central BTP system of the SO 3 -Ph-BTP ligand can be slightly non-planar in the gas phase, but in an aqueous solution it adopts the planar BTP- cc -aq conformation, known from metal complexes with BTP-like ligands. Out of a dozen conformations of protonated BTP, the most stable appeared to be the one protonated at the pyridine N-atom. The analysis of the conformation and hydration of the larger Ph-BTP system indicates that in water the proton dissociates from the protonated BTP core to form a hydronium ion, which additionally interacts with two water molecules H-bonded to triazine's N2-atoms. Considering 24 different protonated Ph-BTP conformers surrounded by five water molecules led us to the conclusion that the core of the most stable form is practically identical to the most stable hydrated and protonated BTP form. Modelling the hydration of both every part of the SO 3 -Ph-BTP ligand independently and the whole SO 3 -Ph-BTP ligand indicated that the hydronium ion formed near the SO 3 H groups can migrate and be stabilized near the center of the SO 3 -Ph-BTP ligand. Thus, in the process of actinide and lanthanide extraction from acidic solutions, the metal ions compete with the hydronium ion for the position at the ligand center.

Fast, simple in use and highly effective voltammetric enantiosensor dedicated for determination of thalidomide (TD) enantiomers (especially towards the toxic (S)-enantiomer) in blood plasma is still desirable. Here we have proven that newly synthesized chiral naphthalene diimide (NDI) derivatives are excellent electroactive materials for TD enantiosensors. The recognition process relies on the specific interaction between the chiral NDI receptor and the thalidomide enantiomer of the opposite configuration. This unique specific interaction between (S)-thalidomide and (R)-NDI derivative counterparts, evident in the DPV voltammograms, was confirmed by molecular modeling. The demonstrated voltammetric enantiosensors are characterized by the low detection limit at the level of μg·L−1, wide analytical range from 5·10−4 – 10 mg·L−1, high selectivity and long lifetime. The results of the recovery rates showed a very good degree of accuracy towards the determination of (S)-thalidomide in the blood samples, so it can be successfully used in the analysis of clinical samples.

The steroidal alkaloid solasodine (1) undergoes inversion of configuration at the C-22 spiro atom when treated with acetic anhydride-pyridine at ambient temperature. The basic solvolysis of the N, O-diacetyl derivative (2) reverses the reaction, yielding the starting solasodine (1). The mechanisms of both processes (acetylation and deacetylation) were studied in terms of possible reaction pathways.

The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.

The IR and vibrational circular dichroism (VCD) spectra of both enantiomers of Me-, iPr-, nBu-, Ph-, and CH2 Ph-substituted isoindolinones in solution and KBr pellets were measured and interpreted by DFT calculations. The spectra in solution revealed no important differences in the C=O stretching vibration region while the interpretation of very distinct spectra taken in pellets required determining the crystal structures. The studied compounds crystallized in the P21 21 21 (Me, iPr, CH2 Ph), P31 (nBu), and P21 (Ph) space groups. We found that the quality of simulated spectra strongly depends on the substituent, the structure of the molecular cluster assumed, basis set, and use of the dispersion correction. The IR spectra can be reproduced well based on the simplest linear arrangement of hydrogen-bonded chains mimicking the molecular arrangement in the crystals. We found no common approach to reproduce all the registered VCD spectra in the crystal phase. For the Me and nBu isoindolinones, the VCD pattern was the best reproduced by full optimization of the selected large molecular clusters. For iPr, Ph and CH2 Ph derivatives optimizing only the position of H-atoms in a fragment frozen as in the crystal provides the best results. Such an approach can reduce the computation time from months to one week.

Two enantiomers of 2-methyl-N-(1-thien-2-ylethyl)propane-2-sulfonamide (TSA) were synthesized, and their VCD, ROA, IR, and Raman spectra were registered. The solved (S)-TSA X-ray structure shows a disorder connected to the presence of two TSA conformers differing by a slight rotation of the thiophene ring. Two molecules in the unit cell of the monoclinic P21 crystal form a net of NH···OS and C*H···OS hydrogen bonds. Out of a series of computational levels tested to interpret the spectra, the B3LYP functional combined with the def2TZVP basis set satisfactorily reproduces the experimental VCD and ROA spectra. To simulate the VCD spectra of TSA enantiomers in KBr pellets, dimers and tetramers, with two different positions of the thiophene ring, were considered. The VCD spectra measured in CDCl3 are completely different from those taken in KBr due to the conformational freedom of TSA in chloroform. Seven TSA conformers fall into two groups of opposite configurations at the pyramidal N atom forming the additio...

Recent work by Wu et al. in connection with the first synthesis of the marine natural product plakinidone revealed that the most salient feature of its purported structure, a six-membered perlactone moiety, was in fact a five-membered lactone, i.e. a 3-methyl-4-hydroxy-2(5H)-furanone or tetronic acid ring. With the planar structure of plakinidone confidently revised, we undertook a new investigation to unambiguously establish its absolute configuration. Upon preparing two stable derivatives 1 and 5 from a sample of naturally occurring plakinidone extracted from the sponge association Plakortis halichondriodes–Xetospongia deweerdtae, the absolute configuration was assigned by synthesis and vibrational and electronic circular dichroism (VCD and ECD) measurements in combination with density functional theory calculations at the B3LYP/aug-cc-pVDZ/PCM(CH3CN) level of theory. Our combined efforts and the agreement between the experimental and calculated VCD/ECD spectra of 1 revealed that the absolute configuration of plakinidone was in fact (11S,17R) and not the formerly reported (11S,17S) diastereomer assigned by Wu et al.. Therefore, we propose that natural plakinidone is accurately represented by structure 12.

The aim of the present work was to verify the usefulness of dimolybdenum tetrakis(μ-pivalate) and tetrakis(μ-isovalerate) as auxiliary chromophores for determining the absolute configuration of optically active vic-diamines, vic-amino alcohols, α-amino and α-hydroxy acids by means of electronic circular dichroism (ECD). To this end, a series of measurements designed to check the dependence of ECD and UV-Vis spectra on time and concentration was carried out. The experimental results were supported by a separate set of detailed DFT calculations. The results obtained allowed us to determine the most probable structure of dominating chiral complexes formed in situ in solution for all ligands studied.

In this paper we provide a computational study of the l-methionine conformational landscape and VCD spectra in the gas phase and a water environment simulated by implicit PCM and the hybrid model, i.e., a combination of explicit "microsolvation" and implicit models. In the gas phase, two groups of conformers differing in H-bonding, i.e., OH···NH2 and NH···O═C, could be distinguished based solely on the IR ν(OH) and ν(NH) stretching vibrations range. On the other hand, VCD better reflected chain differences. The most stable OH···NH2 conformer was predicted to be easily detected, and the presence of two out of four NH···O═C conformers could be confirmed. Three zwitterionic methionine conformers were shown to dominate in water. Their VCD spectra, simulated within the hybrid model at the B3LYP-IEF-PCM/aug-cc-pVDZ level of theory, indicated that they could be recognized in the mixture. Use of the hybrid model is crucial for good reproduction of the hydrogen bonding pattern in the VCD spectra of methionine in water solution. However, the 1300-800 cm(-1) region of the skeleton vibrations of methionine appeared to be relatively insensitive to the model of the solvent.

The absolute configuration of plakinidone (I) is re-assigned as (11S,17R) from the formerly reported (11S,17S) diastereomer.

To measure molecular chirality, the molecule is treated as a finite set of points in the Euclidean R(3) space supplemented by k properties, p(1)((i)), p(2)((i)), ..., p(k)((i)) assigned to the ith atom, which constitute a point in the Property P(k) space. Chirality measures are described as the distance between a molecule and its mirror image minimized over all its arbitrary orientation-preserving isometries in the R(3) × P(k) Cartesian product space. Following this formalism, different chirality measures can be estimated by taking into consideration different sets of atomic properties. Here, for α-amino acid zwitterionic structures taken from the Cambridge Structural Database and for all 1684 neutral conformers of 19 biogenic α-amino acid molecules, except glycine and cystine, found at the B3LYP/6-31G** level, chirality measures have been calculated by a CHIMEA program written in this project. It is demonstrated that there is a significant correlation between the measures determined for the α-amino acid zwitterions in crystals and the neutral forms in the gas phase. Performance of the studied chirality measures with changes of the basis set and computation method was also checked. An exemplary quantitative structure–activity relationship (QSAR) application of the chirality measures was presented by an introductory model for the benchmark Cramer data set of steroidal ligands of the sex-hormone binding globulin.

The stability of all 23 C(58)N(2) and C(58)B(2) heterofullerenes in the singlet and triplet states was determined at the B3LYP/6-31G** level. In equilibrium mixture the achiral (1,4) C(58)N(2) isomer would be populated in ca. 95.8%, the chiral (1,16) one in ca. 3.3%, and the achiral (1,4) C(58)B(2) in 100%, whereas all triplet state isomers are less stable. Fourteen out of 23 C(58)X(2) are chiral. Four different chirality measures were calculated by our own CHIMEA program: pure geometrical, labeled, mass, and charge. Intercorrelations between the measures for all chiral compounds indicate that the pure geometrical chirality measure is unstable and should not be used in QSAR predictions of the other molecular properties, while the labeled and mass-weighted ones are promising QSAR descriptors. For each chiral C(58)N(2) molecule, some very strong VCD bands, of intensity comparable with that in the IR spectra, can serve in identification and characterization of the isomers.

The NMR shielding and indirect spin–spin coupling constants are calculated for 10 most stable conformers of β-alanine, using the B3LYP/aug-cc-pVTZ-su-1 level. In this study the focus is on determination of conformational effects and the intramolecular hydrogen bond on the NMR parameters for β-alanine conformers. Numerous correlations were detected between geometrical, topological and NMR parameters. The 13 C chemical shifts show dependence on intramolecular hydrogen bonds. The 15 N chemical shifts seem to be sufficient in supporting the conformational analysis. Some 1 J-coupling constant correlate with both the bond critical point electron density and the Laplacian. The vicinal proton–proton 3 J-coupling constants show clearly the local arrangements around the respective axes. Therefore, NMR parameters along with the quantum chemical calculations may be able to discriminate between conformers.

Chiral quaternary ammonium salts, catalysts for chiral Darzens reaction of α-chloroacetic acid esters with benzaldehyde to yield glycidates in phase-transfer catalysis conditions, were studied by using the DFT/B3LYP/6-31G∗∗ calculations. Structure and energetics of several complexes between the chiral Darzens reaction catalysts and α-haloacetic ester carboanion were examined. Based on comparison of the complex stabilization energies and experimental ee values it was shown that the complex interaction energy alone is not a crucial parameter for catalyst to be efficient in asymmetric synthesis. A catalyst design was also tried, however, despite the interaction energy for the designed catalyst increased the geometrical arrangement of the reactant and the catalyst favoured a racemic rather than an asymmetric reaction.

The mid-IR, far-IR, and Raman spectra of allyl acrylate were measured and interpreted with support of the B3LYP/aug-cc-pVDZ calculated anharmonic vibrational spectra followed by the potential energy distribution analysis. The experimental 1 H and 13 C NMR spectra of allyl acrylate dissolved in CDCl 3 or C 6 D 6 were interpreted by means of the B3LYP/aug-cc-pVDZ-su2 calculated NMR chemical shifts and J( 1 H, 1 H) and J( 1 H, 13 C) coupling constants. Exactly ten stable allyl acrylate conformers (five s- cis and five s- trans ) were found after careful B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ scan of the conformational space. The experimental IR and Raman spectra are in good agreement with the theoretical spectra of the most stable conformers 1 with a presence of the second stable conformer 2 , both exhibiting cis arrangement of the acrylic moiety. There are however two bands in the IR spectra, at ca. 1270 and 1260 cm −1 , that definitely indicate the conformers with trans arrangement of the acrylic moiety to be present in liquid allyl acrylate. The bands at ca. 2990 and 1650 cm −1 are suggested to be due to Fermi resonances engaging CH and C C stretching vibrations, respectively. The careful inspection of the room temperature 1 H and 13 C NMR spectra of allyl acrylate suggest that a dominating form of the allyl acrylate molecule in an inert solvent exhibits the cis conformation of the acrylic moiety and an extended allyl group.

For the first time the argon-matrix low-temperature FTIR spectra of beta-alanine are recorded. They reveal a quite complicated spectral pattern which suggests the presence of several beta-alanine conformers in the matrix. To interpret the spectra, the eighteen beta-alanine conformers, stable in the gas phase, are estimated at the B3LYP and MP2 levels combined with the aug-cc-pVDZ. Ten low-energy structures are reoptimized at the QCISD/aug-cc-pVDZ and B3LYP and MP2 levels by using the aug-cc-pVTZ basis sets. Assignment of the experimental spectra is undertaken on the basis of the calculated B3LYP/aug-cc-pVDZ anharmonic IR frequencies as well as careful estimation of the conformer population. The presence of at least three beta-alanine conformers is demonstrated. The detailed analysis of IR spectra points to the possible presence of five additional beta-alanine conformers.

The Darzens reaction leading to α,β-epoxy esters was modelled at the B3LYP/aug-cc-pVDZ level. Experimentally, the reaction proceeds at boundary between two phases, water and a non-polar, therefore, the two environments were considered in the simulations. The calculations show the Darzens reaction to be a stepwise process both in the gas phase and in solvents (toluene, acetonitrile, and water). In all considered environments, the first barrier, TS1, associated with formation of an intermediate, is much higher than TS2 associated with the closing of the epoxy ring with the simultaneous Cl− ion release. Therefore, the first process is the rate limiting step of the reaction. TS1 is the lowest for the gas phase, next in toluene, whereas the highest in acetonitrile and water. The same holds true for the small TS2 barrier which is especially low in toluene (0.45 kcal/mol = 157 cm−1). However, the barrier is genuine, because the collective Cl–C4 elongating along with epoxy closing/opening mode in the intermediate and in the product have energies definitely below the barrier.

Ellipticity changes of the electron density at the bond critical points along the [2 + 2] cycloaddition reaction paths were investigated by the AIM method applied to the MP2/aug-cc-pVDZ calculated structures. Elipticities of the σ-bonds being formed and π-bonds being broken in the ketene-vinylimine and allene-isocyanic acid cycloadditions were examined. On this basis we proposed four criteria for differentiation between pericyclic and pseudopericyclic reactions and classified the ketene-vinylimine reaction as pseudopericyclic whereas the allene-isocyanic acid one as pericyclic process. Additionally, we found the π(C=X) ellipticity profiles, X=N, O, suggesting more or less isotropicity of the C=X bond electron density over the whole reaction.

Based on the B3LYP and MP2/aug-cc-pVDZ calculations, 51 cysteine conformers were found to be stable in the gas phase. The calculations were repeated for the most stable eight structures by using the aug-cc-pVTZ basis set. To estimate the influence of water on the cysteine conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 44 neutral and 12 zwitterion conformers to be stable in the water solution. The most stable cysteine structure in water appeared to be the zwitterionic conformer quite similar to the molecule observed in the crystal state.

A new oxidizing system for olefins, consisting of benzeneseleninic anhydride and trimethylsilyl triflate, was studied. The highly reactive benzeneseleninyl cation is presumably formed under these conditions. It has been shown that different products are formed with this species depending on the specific structure of olefin. The 1,1-disubstituted olefins afforded mostly α,β-unsaturated carbonyl compounds. The sterically encumbered tri- or tetrasubstituted olefins yielded 1,2- or 1,4-dihydroxylated products, presumably via four-membered cyclic intermediates.

A new oxidizing system for olefins, consisting of benzeneseleninic anhydride and trimethylsilyl triflate, was studied. The highly reactive benzeneseleninyl cation is presumably formed under these conditions. It has been shown that different products are formed with this species depending on the specific structure of olefin. The 1,1-disubstituted olefins afforded mostly α,β-unsaturated carbonyl compounds. The sterically encumbered tri- or tetrasubstituted olefins yielded 1,2- or 1,4-dihydroxylated products, presumably via four-membered cyclic intermediates.

This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.

The DFT calculations using B3PW91 hybrid functional and 6-311++G** basis set were performed for the two most stable isomers of cytisine ( 1a and 1b ). The conformation 1a differs from 1b by the orientation ( equatorial and axial , respectively) of the hydrogen atom at the piperidine nitrogen atom. In terms of the Gibbs free energy, the conformation 1a is less stable than 1b by 0.25 kcal mol −1 , only. The isomers are separated by 3.6 kcal mol −1 —an activation energy barrier, which is higher in energy than the vibrational modes inverting one isomer into another. Presence of such a barrier explains the existence of the two isomers ( equatorial and axial ) observed previously in apolar solvents.

The infrared low-temperature Ar-matrix spectra of 5-halouracils and unsubstituted uracil were measured and interpreted in terms of the spectra calculated at the DFT/B3PW91/6-311G level followed by a potential energy distribution (PED) analysis. For the PED analysis, the sets of halouracil mode definitions were constructed so that dissimilarities in the interpretations of the different spectra were minimized. Anharmonic frequency calculations enabled more light to be shed on the Fermi resonance (FR) phenomena occurring in the nu(C=O) stretching vibrations region. For each halouracil vibrational spectrum, several FRs manifest themselves in the nu(C=O) stretching vibrations region. We show that the most frequent components participating in these resonances are the nu(C(4)=O(10)) frequency, a beta(N-H) mode frequency, and a beta(C=O) mode frequency. The experimental nu(N-H) frequencies are reproduced by the calculated anharmonic frequencies better than by the scaled harmonic ones, and the nu(C=O) frequencies respond in the opposite manner. The experimental frequencies located below 1500 cm(-1) are reproduced equally well by the two kinds of calculations.

The adiabatic interaction potentials were obtained for the paradigm transition metal-rare gas interactions: Sc(2D)-He and Ti(3F)-He and their di-cations. The ab initio approach included the coupled cluster and multireference configuration interaction methods. He atoms form very weak van der Waals complexes with Sc and Ti with well-depths of ca. 4-5 cm-1. The interactions are characterized by the nearly-degenerate manifolds of adiabatic states with splittings of the order of 0.1 cm-1 or less. The anisotropy of the Ti-He interaction is smaller than that for the Sc-He interaction. The origin of the weak anisotropy of these interactions was analyzed. The exchange repulsion was found to be nearly the same in the ${\rm\Sigma}$ , ${\rm\Pi}$ and ${\rm\Delta}$ states due to the valence d-electrons being submerged under the doubly filled 4s electron sub-shell. The anisotropy of the total potential is controlled by the weakly-anisotropic dispersion interaction.

Infrared and Raman spectra were recorded for solid cytisine—an agonist of nicotinic acetylcholine receptors (nAChRs), and analysed with help of the semiempirical (AM1) and ab initio {DFT(B3PW91)/6-311++G∗∗} calculations performed for monomeric and associated structures (dimer, trimer and tetramer). Among two stable conformers of cytisine (1a and 1b) identified in solution, only one (1a) is present in the solid state, where it is stabilized by intermolecular H-bonds (  C  O ⋯ HN  ). Two different environments for the associated molecules give two different spectral properties. Two component bands can be distinguished for the piperidine ν(NH) and γ(NH) as well as for the pyridine ν(CH), ν(CO) and ν(CC) contours.

Model chiral β -lactam molecules, (3 S )-and (4 R )-fluoro-2-azetidinone, were calculated at the B3PW91/aug-cc-pVTZ level, to be hydrogen bonded with the achiral HX molecule (X=F, Cl, Br). Two stable structures of the complex are possible: a cyclic or a bent H-bond, in which the HX molecule interacts with the CO group and is either close to NH or CH 2 (CHF) moiety, respectively. The VCD effect of these two forms differs in several respects, however, the main difference is the sign of the VCD rotational strength of the ν (HX) stretching vibrations revealing the geometry of the hydrogen bond complex.

The theoretical geometries, rotational constants, VCD, and IR spectra for the chiral ( S )-HXCCCFH (X=F, Cl, Br) allene molecules were calculated at the B3PW91/aug-cc-pVTZ level. We have shown that there is plausible adequacy between IR spectrum of ( S )-1,3-difluoroallene molecule calculated at B3PW91/aug-cc-pVTZ level and experimental spectra of the racemate system. For the other molecules studied, the experimental spectra were not published, yet, although, some results reported earlier for alkilohalogenoallenes are in line with our findings. The halogen influence on the VCD and IR spectra of the studied molecules is discussed.

Halogenoazetidinones are important as synthetic intermediates for preparation of halogen β-lactam (2-azetidinone) antibiotics and as building blocks for carbohydrates and amino acids. In this paper, we consider the influence of the halogen atom, substituted at the C4 position of the 2-azetidinone ring, on the geometry, IR, Raman, and vibrational circular dichroism spectra. The vibrational spectra were calculated for the chiral 4-(R)-X-2-azetidinone (X=F, Cl or Br) molecules at the B3PW91/aug-cc-pVTZ level. It was shown that the geometry of the molecules studied do not change much upon the change of the halogen atom. In case of the vibrational spectra, the position but even more the intensities depend strongly on the kind of halogen substituent.

DFT (B3PW91/6-31G** and B3PW91/6-311G**) calculations were performed for dibenzylcarbamic acid, either monomer or dimer (DBCAD). Six possible structures of the dimer were considered. Calculated geometrical parameters of the most stable dimer were compared with those published for the dibenzylcarbamic acid dimer crystalline solid. The calculated IR spectrum was used for the assignment of the frequencies observed in the experimental IR spectrum of dimer dibenzylcarbamic acid.

The oxetane⋯HCl and thietane⋯HCl complexes have recently been studied by rotational spectroscopy in a supersonic jet. In this Letter we report on stability, axial, and equatorial HCl arrangement in the complexes studied by means of MP2 calculations. The shape of the potential functions was studied for the ring-puckering and HCl inversion motions. For the oxetane complex, the barrier of the ring-puckering is small enough to be overcome by the ring-puckering vibration. For the thietane complex, the analogous barrier is higher than the vibration energy. Therefore, one oxetane and two thietane complex conformations were observed in the experiment.

The theoretical thermodynamic stability was calculated for products of cycloaddition of vinylimine to ketene and isocyanic acid to allene by using the MP2, DFT(B3PW91), and HF methods involving the 6-311++G** basis set. These cycloaddition reactions could yield fourteen different molecules; practically however, free Gibbs energies calculated for the considered molecules suggest that only 4- and 3-methylene-β-lactams can be formed in observable amounts. For these particular isomers the heats of formation, geometry, rotational constants, harmonic vibrational frequencies, infrared intensities, Raman activities, depolarisation ratios, and 1H, 13C, 17O and 15N NMR spectra were evaluated and discussed. The PED analysis carried out for theoretical IR spectra allowed us to assign vibrations of the two isomers. The IR and NMR assignments form a basis for the elucidation of future experimental data.

Benchmark calculations with a goal to find dispersion-corrected DFT-D3 methods suitable for a reliable estimation of matrix shifts on the vibrational frequency were carried out on the ThO molecule in three rare gas (Rg = Ne, Ar, and Kr) matrices. The matrices were modelled by the explicit approach, in which a single and a double shell of Rg atoms around ThO was considered. The selection of exchange-correlation functionals was based on test calculations on triatomic ThO⋯Rg models. The B3LYP, PBE0, CAM-B3LYP, and LC-ωPBE functionals were found to be the best suited for the estimation of matrix shifts. The single shell of Rg's around ThO accounted for a major part of the shifts; the addition of a second Rg shell resulted only in a minor improvement. Continuum solvation models considerably overestimated the effect of Rg matrices both when the whole matrix was treated by the model and when the first shell was treated explicitly and the rest with a continuum solvation model.

Eleven exchange-correlational functionals of different types corrected for dispersion by Grimme's D3 correction in conjunction with the aug-cc-pVTZ basis set were tested on the following noble gas (Ng) dimers: Ne2, Ar2, Kr2, Xe2, and Rn2. For comparison, the D2 and D3BJ corrections were probed with the B3LYP functional. From post-HF wavefunction methods, CCSD(T) theory was also included. The investigated properties involved potential energy curves, equilibrium bond distances, and interaction energies. The B3LYP-D3, B3LYP-D3BJ, and PBE0-D3 functionals performed overall best for bond distances, while B3LYP-D3 and B97-D3 performed best for interaction energies. The importance of fortunate error cancellations was seen in the often reduced agreement with reference data upon correction for BSSE. As several functionals performed well selectively for some noble gases (and poorly for others), we also analysed the performance on the Ng2 dimers individually and recommended DFT-D3 functionals for the calculation of large clusters of each Ng.

Theoretical Gibbs free energies have been determined for a set of cycloaddition products of allene with CO 2 , CS 2 or OCS molecules, and of CH 2 C X with CH 2 C Y molecule (X, Y=O, S). Each of the cycloaddition reactions leads to one or two isomeric products with four-membered heterocyclic ring. Theoretical thermochemical data suggest that the isomers in which sulphur atom is build into the four-membered ring can be easily formed in different reactions whereas formation of those with oxygen atom in the ring strongly depends on the considered reaction. Analysis of the theoretical 1 H and 13 C chemical shifts forms a basis for the detection of the isomer traces in reaction mixtures as well as for the elucidation of future experimental spectra.

Theoretical infrared spectra of diketene (4-methylene-2-oxetanone), its 3- and 2-methylene isomers and their mono- and disulphur analogues were calculated at the MP2/6-311++G∗∗ level. The effect of methylene and sulphur substitution on the IR spectra is discussed in terms of potential energy distribution (PED) analysis.

Equilibrium geometries, rotational constants, harmonic vibrational frequencies, infrared intensities, Raman activities, and 1 H and 13 C NMR spectra were calculated for 1,2-dimethylenecyclobutane and its less stable isomer 1,3-dimethylenecyclobutane by using MP2, DFT (B3PW91), and RHF theoretical methods involving the 6-311++G ∗∗ basis set. The properties calculated theoretically have been compared with the experimental values. The internal coordinates defined for both isomers were used in the potential energy distribution (PED) analysis. The theoretical vibrational and NMR spectra form the basis to differentiate particular compounds in reaction mixture.

An up-to-date perspective on the capability of Vibrational Circular Dichroism (VCD) and Raman Optical Activity (ROA) spectroscopy of the 20 encoded α-amino acids to solve the structural problems appearing in water is provided in this review. VCD and ROA spectroscopy of the α-amino acid molecules reviewed in this chapter refer only to free and single amino acids in water at various pH levels. To well understand the implications of such studies for biology and medicine, we devote one subchapter to the role of free amino acids in an organism’s metabolism and physiology. A variety of side chains that modify the α-amino acids character from acidic to basic and from hydrophilic to hydrophobic makes the possible dissociation equilibria in water very complex and dependent on several factors. Therefore, information on dissociation constants, isoelectric points, and hydrophobicity parameters of α-amino acids is summarised in the next subchapter. The conformational variety, complexity of interactions, and entanglement of equilibria makes considering the influence of these factors on VCD and ROA spectra with quantum chemical analysis absolutely necessary. The elements of the theory of chiroptical vibrational spectra and methods enabling solvent simulations are provided in the subsequent subchapter. We report on experimental methods, techniques and tricks for measuring and simulating the VCD and ROA spectra in water at different pH levels. The review is concluded by listing the not-yet-measured amino acids, a presentation of the main challenges for computational methods, and suggestions for the most promising experimental techniques that may be used in future studies.

Vibrational circular dichroism (VCD) chirality transfer occurs when an achiral molecule interacts with a chiral one and becomes VCD-active. Unlike for H-bonds, for organic electron donor-acceptor (EDA) complexes this phenomenon remains almost unknown. Here, the VCD chirality transfer from chiral quinine to achiral BF3 is studied at the B3LYP/aug-cc-pVDZ level. Accessibility of four quinine electron donor sites changes with conformation. Therefore, the quinine conformational landscape was explored and a considerable agreement between X-ray and the most stable conformer geometries was achieved. The BF3 complex through the aliphatic quinuclidine N atom is definitely dominating and is predicted to be easily recognizable in the VCD spectrum. Out of several VCD chirality transfer modes, the ν(s)(BF3) mode, the most intense in the entire VCD spectrum, satisfies the VCD mode robustness criterion and can be used for monitoring the chirality transfer phenomenon in quinine···BF3 system.

Stabilization energies of the electron donor–acceptor sulfinimine···BF3 complexes calculated at either the B3LYP/aug-cc-pVTZ or the MP2/aug-cc-pVTZ level do not allow to judge, whether the N- or O-atom in sulfinimine is stronger electron-donor to BF3. The problem seems to be solvable because chirality transfer phenomenon between chiral sulfinimine and achiral BF3 is expected to be vibrational circular dichroism (VCD) active. Moreover, the bands associated with the achiral BF3 molecule are predicted to be the most intense in the entire spectrum. However, the VCD band robustness analyses show that most of the chirality transfer modes of BF3 are unreliable. Conversely, variation of VCD intensity with change of intermolecular distance, angle, and selected dihedrals between the complex partners shows that to establish the robustness of chirality transfer mode. It is also necessary to determine the influence of the potential energy surface (PES) shape on the VCD intensity. At the moment, there is still no universal criterion for the chirality transfer mode robustness and the conclusions formulated based on one system cannot be directly transferred even to a quite similar one. However, it is certain that more attention should be focused on relation of PES shape and the VCD mode robustness problem. Chirality. © 2011 Wiley Periodicals, Inc.