• Bulletin of the Korean Chemical Society
• /
• v.32 no.10
• /
• pp.3641-3643
• /
• 2011

Multiconfigurational wavefunctions were adopted to study structural isomers, their isomerization reactions and excited states of $HN_3$. In addition to the known linear isomer, two new structural isomers were found. The three isomers can be classified as sp, $sp^2$ and $sp^3$ hybridized species, respectively. The sp3 hybridized species turned out to be the second most stable. Large reaction barriers among these species prevent thermal isomerizations. A low-lying $^3A'$ exists with a relative energy of 13.5 kcal/mol. Dramatic re-hybridization and bond elongation was found in the first excited $^1A"$.

• Journal of Ginseng Research
• /
• v.43 no.3
• /
• pp.368-376
• /
• 2019

Background: In the current phytochemical research on ginseng, the differentiation and structural identification of ginsenosides isomers remain challenging. In this paper, a two-dimensional mass spectrometry (2D-MS) method was developed and combined with statistical analysis for the direct differentiation, identification, and relative quantification of protopanaxadiol (PPD)-type ginsenoside isomers. Methods: Collision-induced dissociation was performed at successive collision energy values to produce distinct profiles of the intensity fraction (IF) and ratio of intensity (RI) of the fragment ions. To amplify the differences in tandem mass spectra between isomers, IF and RI were plotted against collision energy. The resulting data distributions were then used to obtain the parameters of the fitted curves, which were used to evaluate the statistical significance of the differences between these distributions via the unpaired t test. Results: A triplet and two pairs of PPD-type ginsenoside isomers were differentiated and identified by their distinct IF and RI distributions. In addition, the fragmentation preference of PPD-type ginsenosides was determined on the basis of the activation energy. The developed 2D-MS method was also extended to quantitatively determine the molar composition of ginsenoside isomers in mixtures of biotransformation products. Conclusion: In comparison with conventional mass spectrometry methods, 2D-MS provides more direct insights into the subtle structural differences between isomers and can be used as an alternative approach for the differentiation of isomeric ginsenosides and natural products.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.4
• /
• pp.555-562
• /
• 2002

Isomers based on the RS and EZ geometrical isomerism of the neutral, deprotonated species of HMPAO and their complexes with zinc(Ⅱ) ion have been investigated by semiempirical AM1 optimization method. The Hartree-Fock energies on AM1 geometries o f HMPAO species were calculated with HF/6-31G* methods. Twenty-two isomers of the neutral and twenty isomers of the deprotonated species of HMPAO have been found. The presence of four EE-series isomers of both zinc(Ⅱ) complexes with the neutral and deprotonated HMPAO have been expected and the SREE typical isomer of both types of complexes is the most stable isomer. Energies of complexation of zinc(Ⅱ)/HMPAO isomers with AM1 geometries were calculated by HF/ 6-31G*method. Due to the complexations with zinc(Ⅱ), the structural reorganizations of some isomers of the neutral HMPAO have been occurred. The optimized geometrical parameters of the related conformations have been discussed in terms of their stabilities and existences.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.8
• /
• pp.897-904
• /
• 1999

We have presented the thermodynamic, structural and dynamic properties of liquid pentane isomers - normal pentane, isopentane, and neopentane - using an expanded collapsed atomic model. The thermodynamic properties show that the intermolecular interactions become weaker as the molecular shape becomes more nearly spherical and the surface area decreases with branching. The structural properties are well predicted from the site-site radial, the average end-to-end distance, and the root-mean-squared radius of gyration distribution func-tions. The dynamic properties are obtained from the time correlation functions - the mean square displacement (MSD), the velocity auto-correlation (VAC), the cosine (CAC), the stress (SAC), the pressure (PAC), and the heat flux auto-correlation (HFAC) functions - of liquid pentane isomers. Two self-diffusion coefficients of liquid pentane isomers calculated from the MSD's via the Einstein equation and the VAC's via the Green-Kubo relation show the same trend but do not coincide with the branching effect on self-diffusion. The rotational re-laxation time of liquid pentane isomers obtained from the CAC's decreases monotonously as branching increases. Two kinds of viscosities of liquid pentane isomers calculated from the SAC and PAC functions via the Green-Kubo relation have the same trend compared with the experimental results. The thermal conductivity calculated from the HFAC increases as branching increases.

• Mass Spectrometry Letters
• /
• v.10 no.3
• /
• pp.93-101
• /
• 2019

Algorithms and software for predicting tandem mass spectra have been developed in recent years. In this work, we explore how distinct in silico $MS^2$ spectra are predicted for isomers, i.e. compounds having the same formula and similar molecular structures, to differentiate between them. We used the CFM-ID 2.0/3.0 predictor with regard to (a) test compounds, whose experimental mass spectra had been randomly sampled from the MassBank of North America (MoNA) collection, and to (b) the most widespread isomers of test compounds searched in the PubChem database. In the first validation test, in silico mass spectra constitute a reference library, and library searches are performed for test experimental spectra of "unknowns". The searches led to the true positive rate (TPR) of ($46-48{\pm}10$)%. In the second test, in silico and experimental spectra were interchanged and this resulted in a TPR of ($58{\pm}10$)%. There were no significant differences between results obtained with different metrics of spectral similarity and predictor versions. In a comparison of test compounds vs. their isomers, a statistically significant correlation between mass spectral data and structural features was observed. The TPR values obtained should be regarded as reasonable results for predicting tandem mass spectra of related chemical structures.

• Mass Spectrometry Letters
• /
• v.9 no.1
• /
• pp.37-40
• /
• 2018

Farinomalein is a maleimide-bearing compound well known for its anti-fungal activity. In the present study, synthesis of farinomalein is achieved via Stobbe condensation followed by Haval-Argade contrathermodynamic rearrangement. Kinetically driven Stobbe condensation followed by condensation with beta-alanine reveals formation of two isomers of farinomalein. This article describes application of LC-MS/MS in structure elucidation of farinomalein 1 and its isomers 2 and 3 encountered in its synthesis. The proposed distinct fragmentation pathway is supported by rational organic reaction mechanism. These fragmentation pathways are significant for analytical method development of farinomalein in near future. The structures of farinomalein 1 and its isomers 2 and 3 have been assigned undisputedly.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.5
• /
• pp.1722-1728
• /
• 2012

During the analyzing processes of the compounds, some researchers are puzzled by the analytical signals for some TSNAs (with or without splitting peaks at various pHs and temperatures). In this work, a detailed theoretical study of structural and thermal properties of the $E/Z$ isomers of TSNAs and the corresponding protonated structures was performed using DFT methods. The calculations showed that the $E$ isomers are almost stable than $Z$ isomers, while the $Z$ isomers would be more stable when in protonation. The calculated results predicted the possibility of separation of their $E$ and $Z$ isomer forms and also showed that protonation affects the dipole moment of molecules significantly (0.1-0.5 to 0.7-2.1 Debye). The calculations agreed well with the experiments that the split-up of the HPLC signal for TSNAs into two peaks are very sensitive to the pH and temperature of the mobile-phase.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.2
• /
• pp.241-244
• /
• 2002

Using ab initio method, we have studied the structural stabilities, the electronic structures and properties between the two isomers with $C_{2h}$ and $C_{2v}$ symmetry of AlN four-membered-ring single precursors $[Me_2AlNHR]_2$ (R = Me, $^iPr$, and $^iBu$). In the viewpoint of bond lengths in optimized structures, the N-C bonds are considerably affected by the change of the R groups bonded to nitrogen, but the bonding characters of the Al-N and Al-C bonds are little affected. Also the structural stabilities between the two isomers with $C_{2h}$ and $C_{2v}$ symmetry by using Hartree-Fock (HF) and the second order Moeller-Pleset (MP2) calculations agree well with the experimental results for the relative stability of bis(dimethyl- m-isopropylamido-aluminum) (BDPA) and bis(dimethyl- m-t-butylamido-aluminum) (BDBA), while the semiempirical AM1 and PM3 calculations for BDPA were reverse. Thus, our results may aid in designing an optimum precursor for a given process by explaining the experimental results through the elimination of the R groups bonded to nitrogen.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.4
• /
• pp.452-459
• /
• 2004

The geometrical structures of various isomers of hexafluoro-1,3-butadiene (HFBD), tetrafluoro-1,3-butadiene (TFBD), and difluoro-1,3-butadiene (DFBD) have been studied theoretically. Natural steric and natural resonance theory (NRT) analyses indicate that the lower energy of skew s-cis conformer of hexafluoro-1,3-butadiene than that of the s-trans conformer is originated from the strong steric repulsions between fluorine atoms particularly in the s-trans conformer. The resonance structures generated by NRT also show that the lone electron pairs of fluorine atoms effectively extend the conjugation, and the large differences in energy among the structural isomers of tetrafluoro-1,3-butadiene and difluoro-1,3-butadiene are in part attributed to the differences in the delocalization energies, in addition to the steric repulsion between fluorine atoms. Other interatomic interactions, such as hydrogen bonding, also play important roles in determination of the structures of isomers of tetrafluoro-1,3-butadiene and difluoro-1,3-butadiene.

• Journal of the Korean Chemical Society
• /
• v.55 no.3
• /
• pp.405-411
• /
• 2011

The ab initio calculations for fluoromethyl fluoroperoxides have been carried out using MP2/6-311G(d,p) and B3LYP/6-311++G(d,p) method. The structural optimizations were performed for several isomers and conformers of methyl fluoroperoxide, $CH_3OOF$ and the vibrational frequencies were calculated. The most stable conformer of $CH_3OOF$ is skew form and has fairly short O-O bond distance. The trans and cis conformers have 8-12 kcal/mol higher energies than skew form and the other isomers are very unstable. The structures of $CH_2FOOF$, $CHF_2OOF$ and $CF_3OOF$ are also optimized and vibrational frequencies were calculated. These molecules also have skew forms as the lowest energy conformers. The O-O bond distances are longer and C-O bond distances are shorter than $CH_3OOF$, but the structural parameters are almost independent of the number of fluorine atoms in methyl group.