DFT Calculated Structures and IR Spectra of the Conformers of para-Bromocalix[4]aryl Derivatives

Ahn, Sangdoo,Lee, Dong-Kuk,Choe, Jong-In Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.12

Molecular structures of the various conformers of para-bromocalix[4]aryl derivatives 1-4 were optimized using the DFT B3LYP calculation method. The total electronic and Gibbs free energies and normal vibrational frequencies of the different structures (CONE, partial cone (PACO), 1,2-Alternate(1,2-A) and 1,3-Alternate(1,3-A)) were calculated from the four kinds of para-bromocalix[4]aryl derivatives. The B3LYP/6-31G(d,p) calculations suggested the following: 1(PACO) is the most stable among four conformers of 1; 2(CONE) is the most stable among five conformers of 2; 3(PACO) is the most stable among four conformers of 3; 4(1,3-A) is the most stable among four conformers of 4. All the most stable structures optimized by the B3LYP calculation method were in accordance with the experimental crystal structures of 1-4. The calculated IR spectra of the various conformers (CONE, PACO, 1,2-A and 1,3-A) of 1-4 were compared.

Novel Fluorescent Schiff Base Derivatives of 4-Aminoantipyrine with Large Stokes Shifts and Dual Emission Properties: Crystal Structure, Molecular Interactions, Molecular Surfaces, Conformational and DFT Analyses

Mohammad Sayed Alam,이동웅 대한화학회 2015 Bulletin of the Korean Chemical Society Vol.36 No.10

Two novel Schiff base analogs derived from 4-aminoantipyrine, namely, (E)-4-(2-nitrobenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (3a) and (E)-4-(4-nitrobenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (3b), were synthesized using a mild and efficient method and characterized by FT-IR,1H NMR, mass spectrometry, and single-crystal X-ray diffraction studies. X-ray analysis of a single crystal of 3a revealed an orthorhombic space group P2(1)2(1)2(1) structure, with an E-configuration around the azomethine (C12N3) double bond. One unit cell was found to contain four molecules showing π−π and π−σ van der Waals stacking interactions. Plausible intermolecular interactions were analyzed using 3D Hirshfeld surfaces and the related 2D fingerprint plots. The optimized molecular structure, potential energy surface (PES) scan, vibrational frequencies, Mulliken charge distribution, molecular electrostatic potential (MEP) maps, frontier molecular orbitals (FMOs), and associated energies of 3a and 3b were calculated using density functional theory (DFT) calculations using the B3LYP method and the 6-311G(d,p) basis set. PES scans showed that the conformational energy profiles of 3a and 3b were dissimilar around the torsion angles N3–C12–C13–C14/C18 and C12–N3–C3–C2/C1 due to substituent position effects on the benzylidene phenyl ring. Mulliken charge distribution analysis revealed that O1, N1, and N3 atoms of 3a and 3b could act as electron donors and coordinate with metals, while MEP analysis showed that O1, N3, and O2–O3 are the most suitable sites for electrophilic attack. Regarding drug–receptor interactions, molecular lipophilic potential (MLP) maps demonstrated that the benzylidene phenyl ring favors lipophilic contact and the pyrazolone ring hydrophilic contact. In addition, UV–vis and fluorescence spectroscopic experiments showed that both compounds have good absorbance and fluorescent properties and large Stokes shifts. Interestingly, both compounds showed dual emission in ethanol, acetone, and diethyl ether, possibly due to conformational isomerization induced by photoexcitation.

DFT Calculated Structures and IR Spectra of the Conformers of para-Bromocalix[4]aryl Derivatives

안상두,이동국,최종인 대한화학회 2014 Bulletin of the Korean Chemical Society Vol.35 No.12

Molecular structures of the various conformers of para-bromocalix[4]aryl derivatives 1–4 were optimized using the DFT B3LYP calculation method. The total electronic and Gibbs free energies and normal vibrational frequencies of the different structures (CONE, partial cone (PACO), 1,2-Alternate(1,2-A) and 1,3- Alternate(1,3-A)) were calculated from the four kinds of para-bromocalix[4]aryl derivatives. The B3LYP/6- 31G(d,p) calculations suggested the following: 1(PACO) is the most stable among four conformers of 1; 2(CONE) is the most stable among five conformers of 2; 3(PACO) is the most stable among four conformers of 3; 4(1,3-A) is the most stable among four conformers of 4. All the most stable structures optimized by the B3LYP calculation method were in accordance with the experimental crystal structures of 1–4. The calculated IR spectra of the various conformers (CONE, PACO, 1,2-A and 1,3-A) of 1–4 were compared.

Theoretical Studies on the Progonation Equilibria of Benzoyl Derivatives

김왕기,김용빈,김창곤,이본수,Kim, Wang Gi,Kim, Yong Bin,Kim, Chang Gon,Lee, Bon Su Korean Chemical Society 2001 Bulletin of the Korean Chemical Society Vol.22 No.4

The effects of ortho- (R = H and CH3) and Y-substituents (Y = OCH3, CH3H and CN), which are directly attached to the carbonyl carbon, on the protonation equilibria of the para-X-substituted benzoyl derivatives, 4-X -2, 6-di-R-C6H2-C(=O)-Y, are investigated theoretically using the B3LYP method with 6-31+G* basis set. Structurally, both of the (B) and (BH+ ) forms in the species with R = H are nearly coplanar regardless of the Y-substituents implying that the steric repulsion between Y-substituent and R = H is relatively small. In the species with R = CH3 , the tortional angle (Θ) between the carbonyl moiety and aryl ring varies from zero to near right angle depending on the degree of steric repulsion between Y and R = CH3 and the resonance demand. However the reaction energies, ΔG°, for the protonation processes are more favorable for R = CH3 than for R = H due to stronger electron donating effect of R = CH3 , although the species with R = CH3 are unfavorable sterically. On the other hand, the Hammett type plots are progressively better correlated with б+ than with б values on going from Y = OCH3 to Y = CN for both species with R = H and CH3 indicating that the degree of resonance delocalization between carbonyl moiety and X-substituent is increased for a more electron accepting Y-substituent. Nevertheless the effects of R = CH3 on the magnitude of Hammett type reaction constants ( б or б+ ) are not much different from those of R = H.

DFT Study for p-tert-Butylcalix[4]arene Crown Ether Bridged at the Lower Rimwith Pyridyl Unit Complexed with Potassium Ion

최종인 대한화학회 2007 Bulletin of the Korean Chemical Society Vol.28 No.12

Stable molecular conformations were calculated for the p-tert-butylcalix[4]arene crown ether bridged at the lower rim with pyridyl unit (1) in the various conformers and their potassium-ion complexes. The structures of three distinct conformations have been optimized using DFT B3LYP/6-31G(d,p) method. Relative stability of free host 1 is in following order: cone (most stable) > partial-cone > 1,3-alternate conformer. For two different kinds of complexation mode, the potassium cation in the crown-ether moiety (cr) has much better complexation efficiency than in the benzene-rings (bz) pocket for all three kinds of conformation of host molecule 1. The relative stability of complex (1+K+) in the cr-binding mode is in following order: partial-cone (most stable) ~ cone > 1,3-alternate conformer.

Full Geometry Optimizations of Bond-Stretch Isomers of C₂₀²⁺ Fullerene Dication by the Hybrid Density Functional B3LYP Methods

Lee, Ji-Hyun,Lee, Chang-Hoon,Park, Sung-S.,Lee, Kee-Hag Korean Chemical Society 2011 Bulletin of the Korean Chemical Society Vol.32 No.1

We studied the relative stability and atomic structure of five $C_{20}^{2+}$ isomers obtained by two-electron ionization of a $C_{20}$ cage (the smallest fullerene). All the isomers are bond-stretch isomers, i.e., they differ in bond length. In particular, in one of the isomers with Ih symmetry, all the bond lengths are equal. Full geometry optimizations of the dipositive ion $C_{20}^{2+}$ were performed using the hybrid density functional (B3LYP/6-31G(d)) methods. All isomers were found to be true minima by frequency analysis at the level of B3LYP/6-31G(d) under the reinforced tight convergence criterion and a pruned (99,590) grid. The zero-point correction energy for the cage bond-stretch isomers was in the increasing order $D_{2h}<C_{2h}<C_2<T_h<I_h$ of $C_{20}^{2+}$. The energy difference among the isomers of cage dipositive ions was less than that among neutral cage isomers. Our results suggest that these isomers show bond-stretch isomerism and that they have an identical spin state and an identical potential energy curve. Although the predominant electronic configurations of the isomers are similar, the frontier orbital characteristics are different, implying that we could anticipate an entirely different set of characteristic chemical reactions for each type of HOMO and LUMO.

Full Geometry Optimizations of Bond-Stretch Isomers of C20^2+ Fullerene Dication by the Hybrid Density Functional B3LYP Methods

Jihyun Lee,이창훈,Sung S. Park,Kee Hag. Lee 대한화학회 2011 Bulletin of the Korean Chemical Society Vol.32 No.1

We studied the relative stability and atomic structure of five C_20^2+ isomers obtained by two-electron ionization of a C_20 cage (the smallest fullerene). All the isomers are bond-stretch isomers, i.e., they differ in bond length. In particular, in one of the isomers with Ih symmetry, all the bond lengths are equal. Full geometry optimizations of the dipositive ion C_20^2+ were performed using the hybrid density functional (B3LYP/6-31G(d)) methods. All isomers were found to be true minima by frequency analysis at the level of B3LYP/6-31G(d) under the reinforced tight convergence criterion and a pruned (99,590) grid. The zero-point correction energy for the cage bond-stretch isomers was in the increasing order D_2h < C_2h < C_2 < Th < Ih of C_20^2+ The energy difference among the isomers of cage dipositive ions was less than that among neutral cage isomers. Our results suggest that these isomers show bond-stretch isomerism and that they have an identical spin state and an identical potential energy curve. Although the predominant electronic configurations of the isomers are similar, the frontier orbital characteristics are different,implying that we could anticipate an entirely different set of characteristic chemical reactions for each type of HOMO and LUMO.

DFT Study for Cage-annulated p-tert-Butylcalix[4]crown-ether Complexed with Potassium Ion

최종인,김광호,Seong Jun Park 대한화학회 2008 Bulletin of the Korean Chemical Society Vol.29 No.7

Using DFT B3LYP/6-31+G(d,p)//B3LYP/6-31G(d,p) calculation method, stable molecular structures were optimized for the p-tert-butylcalix[4]arene functionalized at lower rim by cage-annulated crown ether (1) in two different conformers and their potassium-ion complexes. Cone conformer of free host 1 was slightly more stable than partial-cone conformer. For two different kinds of complexation mode, the potassium ion in benzene-rings (bz) pocket showed comparable complexation efficiency with the cation in cage-annulated crown-ether (cr) for the cone and partial-cone conformers of 1. The complex (1•K+) in the cr-binding mode for the partial-cone conformer was more stable than the cone conformer for B3LYP/6-31G(d,p) geometry optimization. However, 1(cone)•K+(cr) showed lower single-point energy than the 1(pc)•K+(cr) for B3LYP/6- 31+G(d,p) calculation method.

Frontier Orbitals of Fifteen C₂₀H₁₇(OH)₃ Regioisomers: Hybrid DFT B3LYP Study

Lee, Seol,Lee, Ji Young,Lee, Kee Hag Korean Chemical Society 2013 Bulletin of the Korean Chemical Society Vol.34 No.8

The hybrid density-functional (B3LYP/6-31G(d,p)) method was used to analyze the substitution effect on the $C_{20}H_{20}$ cage based on calculation of the frontier orbitals of fifteen $C_{20}H_{17}(OH)_3$ derivatives. All substitution products were geometrically optimized without constraints and confirmed by frequency analysis. The results suggest that the cis-1 cis-1 cis-2 regioisomer is the most stable isomer, which implies that hydrogen bonding exerts a stronger effect on the relative energies of the trihydroxide than long-range interactions. Thus, this supports the experimental result in which the bisvicinal tetrol was of particular preparative-synthetic interest. While the LUMO of each of the $C_{20}H_{17}(OH)_3$ regioisomers was equivalently delocalized over the void within the cage, the HOMO was limitedly delocalized on substituents and carbons in close proximity to the substituents. The characteristics of the HOMO of each of the regioisomers vary based on the substitution sites. This indicates that the 15 regioisomers of each $C_{20}H_{20}$ trisubstituted derivative might undergo an entirely different set of characteristic chemical reactions with electrophilic reagents. The results further suggest that the penta-substituted OH groups on the surface of the fullerene cage are more likely to be localized on a pentagon than to be homogeneously delocalized.

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: Water-assisted mechanism and cluster-continuum model

Wu, Yong,Jin, Lu,Xue, Ying,Xie, Dai Qian,Kim, Chan Kyung,Guo, Yong,Yan, Guo Sen Wiley Subscription Services, Inc., A Wiley Company 2008 Journal of computational chemistry Vol.29 No.8

<P>The hydrolysis reaction of N,N-dimethyl-N′-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine (DMPFA), a model compound of the antivirus drug amidine-3TC (3TC = 2′, 3′-dideoxy-3′-thiacytidine), is investigated by the hybrid density functional theory B3LYP/6-31+G (d,p) method. The hydrolysis reaction of the title compound is predicted to undergo via two pathways, each of which is a stepwise process. Path A is the addition of H<SUB>2</SUB>O to the C&n.dbond;N double bond in the amidine group to form a tetrahedral structure in its first step, and then the transfer of the H atom of hydroxyl leads to the corresponding products via four possible channels. Path B simultaneously involves the nucleophilic attack of H<SUB>2</SUB>O to the C atom of the C&n.dbond;N bond and the proton transfer to the N atom of amino group leading to the cleavage of the C&n.bond;N single bond in the amidine group. The results indicate that path A is more favorable than path B in the gas phase. Moreover, to simulate the title reaction in aqueous solution, water-assisted mechanism and the cluster-continuum model, based on the SCRF/CPCM model, are taken into account in our work. The results indicate that it is rational for two water molecules served as a bridge to assist in the first step of path A and that cytosine rather than the cytosine-substituted formamide should be released from the tetrahedral intermediate via s six-membered cycle transition state (channel 2). Our calculations exhibit that the process toward the tetrahedral intermediate is the rate-determining step both in the gas phase and in aqueous solution. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008</P> <B>Graphic Abstract</B> <P> <img src='wiley_img/01928651-2008-29-8-JCC20883-gra001.gif' alt='wiley_img/01928651-2008-29-8-JCC20883-gra001'> </P>