Comparative DFT study for molecular geometries and spectra of methyl pheophorbides-a: test of M06-2X and two other functionals

Huh, Do Sung; Choe, Sang Joon

doi:10.1142/s1088424610002410

Cited by 22 publications

(15 citation statements)

References 14 publications

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“…9, [15][16][17] This method characterizes the chlorin conformation in terms of equivalent displacements along the normal coordinates of the chlorin macrocycle. Typically, the largest static distortions of the chlorin macrocycle occur along the softest normal modes; hence, the greatest contributors to the nonplanar distortion are the lowest-frequency normal coordinates of each out-of-plane symmetry type (i.e., B1u, B2u, A2u, Eg, and A1u).…”

Section: Methodsmentioning

confidence: 99%

“…9(a)-17 Choe et al 17 reported the geometry of methyl pheophorbide-a and compared the validity of M06-2X with two other functional calculations, namely, B3LYP and LSDA. The main problem with DFT calculations is that the exact functionals for exchange and correlation are unknown, except for free electron gases.…”

Section: Introductionmentioning

confidence: 99%

“…9, [15][16][17] This study provides a wealth of theoretical data and gives insights into the geometric preferences of TPOPN-Oxide and chlorin N-oxide regioisomers.…”

Section: Introductionmentioning

confidence: 99%

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Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Choe¹

2012

Bulletin of the Korean Chemical Society

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Results of the comparisons of various density functional theory (DFT) methods with different basis sets for predicting the molecular geometry of TPOP24N-Oxide macrocycle, an oxoporphyrin N-oxide, are reported in this paper. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), and 6-311++G (d, p), are also considered. The M06-2X/6-31G* level is superior to all other density functional methods used in predicting the geometry of TPOP24N-Oxide. The geometries of regioisomeric chlorin N-oxide and oxoporphyrin N-oxide are reported using M06-2X/6-31G* method. The geometry effects of oxoporphyrin and chlorin N-oxide regioisomers are increased β-β bond lengths by N-oxidation because the bond overlap index due to charge transfers is decreased. In N-oxidation ring (II, III), angles that include β-β bond length increase as the bond overlap index of β-β bond is decreased by N-oxidation. The potential energy surfaces of chlorin N-oxide and oxoporphyrin N-oxide are explored by M06-2X/6-31G*, and single-point calculations are performed at levels up to M06-2X/6-311++G (d, p). Total and relative energies are then calculated. The results indicate that chlorin 24 N-oxides are more stable than chlorin 22 N-oxides in chlorin N-oxide regioisomers. Moreover, TPOP24N-Oxide is less stable than TPOP22N-Oxide.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Choe¹

2012

Bulletin of the Korean Chemical Society

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“…60 Geometry optimizations were performed with the M06-2X [61][62][63] functional using the 6-311++G(d,p) basis set. The M06-2X functional was chosen based on the work of Zhao and Thrular 64 that showed that the M06-2X functional describes well the cation-π interaction.…”

Section: Computational Detailsmentioning

confidence: 99%

Interaction of allylic carbocations with benzene: a theoretical model of carbocationic intermediates in terpene biosynthesis

Oliveira¹,

Esteves²

2011

J. Braz. Chem. Soc.

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Carbocátions atuam de formas diferentes quando interagem com anéis aromáticos. É interessante como na biosíntese de terpenos, os intermediários carbocatiônicos não alquilam a cadeia lateral aromática de aminoácidos presentes no sítio ativo, como seria esperado para outros carbocátions, como o cátion terc-butila. Neste trabalho, a interação entre benzeno e diferentes carbocátions alílicos é analisada, mimetizando carbocátions terpenóides, para melhor compreender como esta interação ocorreria. Cálculos em nível de teoria do funcional da densidade (DFT) mostram que para carbocátions alílicos secundários e terciários (como os encontrados na natureza), a forma não ligada da interação é mais estável energeticamente do que a alquilação do anel aromático, justificando a escolha da natureza por esses carbocátions mais estabilizados.Carbocations act in different ways when interacting with aromatic rings. It is interesting that in terpene biosynthesis, the carbocationic intermediates do not alkylate the aromatic side chain of the amino acids present in the enzymatic active site, as would be expected by other carbocations such as the tert-butyl cation. In this study, the interaction between benzene and different allylic carbocations, mimicking terpenoid cations, is analysed in order to better understand how this interaction would occur. Density-functional-theory (DFT) calculations show that for secondary and tertiary allylic carbocations (as found in nature), the non-covalent interaction is energetically favoured with respect to alkylation of the aromatic ring.Keywords: density-functional calculations, DFT, electrophilic substitution, cation-π interaction IntroductionThe study of noncovalent interactions has been gaining interest due to their broad applications in diverse fields such as ligand recognition, catalysis 1 and supramolecular chemistry.2 However, the importance of noncovalent interactions, such as π stacking, 3,4 charge-dipole 5,6 and cation-π interactions, 4,7-10 has only been recognized recently. A cation-π interaction is defined as a strong, attractive, noncovalent and quite specific interaction between a cation and a π-system.11 The cation-π interaction, which is of the same magnitude or even stronger than a typical hydrogen bond, 9,12 has a key role in protein folding, 13 selectivity of potassium channels 14 and several types of intermolecular recognition. 1,13,[15][16][17] The nature of the cation in the cation-π interaction can be metallic, 11,18 of ammonium derivatives, [19][20][21][22] which are very common in biological systems, 23,24 or carbocationic, 25-30 among others. Most of the available information for cation-π complexes has been obtained from coordinatively saturated cations, such as Na + and NH 4 + . 11,[18][19][20][21][22] In the case of carbocations, cation-π interactions are found as intermediates in many enzymatic reactions, e.g. elongation and cyclization reactions in terpene biosynthesis. [31][32][33] The study of the interaction of such cations with aromatic side chains of amino acids is...

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“…DFT has been extensively utilized to study various aspects of porphyrin and chlorin macrocycle [9][10][11][12][13][14][15][16][17][18]. DFT calculation is preferred because it includes the effects of electron correlation in model chemistry.…”

Section: Introductionmentioning

confidence: 99%

Comparison of different theory models and basis sets for the calculation of FbC-M¹⁰Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

Park

Choe

2013

J. Porphyrins Phthalocyanines

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Various density functional theory (DFT) methods with different basis sets to predict the molecular geometry of FbC-M10Iso-Bn macrocycle, a chlorin-isoimide, are compared in this study. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), 6-311++G (d, p), cc-PVDZ, cc-PVTZ, and cc-PVQZ are also considered. The examined hybrid DFT methods are in agreement with the geometry of X-ray crystallography available for comparison. B3LYP/cc-PVDZ level is particularly consistent with available X-ray crystallography in terms of predicting the geometries of FbC-M10Iso-Bn. Geometries of chlorin-imide and chlorin-isoimide isomeric pairs are described through B3LYP/cc-PVDZ method. The bond lengths of chlorin-isoimide, specifically C13–C14, C14–C15, and C2–C3, increase as bond overlap index decreases because of charge transfer. β-β bond lengths (C2–C3 bond lengths) with a three-substituent benzylcarbamoyl group also increase as bond overlap index decreases compared with other molecules. The bond lengths of chlorin-imide are smaller than those of chlorin-isoimide. Angles with β-β bond lengths, specifically C2–C3–C4 in ring A, also decrease with a three-substituent benzylcarbamoyl group; however, the angles in C1–C2–C3 increase. Potential energy on the surfaces of the chlorin-imide and chlorin-isoimide isomeric pairs is optimized by calculating the total and relative energies at B3LYP/cc-PVDZ level. Results indicate that chlorin-imides are more stable than chlorin-isoimides. Normal-coordinate structural decomposition shows that chlorin-imides exhibit greater deformation than chlorin-isoimides except for FbC-M10Iso-Ph.

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Comparative DFT study for molecular geometries and spectra of methyl pheophorbides-a: test of M06-2X and two other functionals

Cited by 22 publications

References 14 publications

Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Interaction of allylic carbocations with benzene: a theoretical model of carbocationic intermediates in terpene biosynthesis

Comparison of different theory models and basis sets for the calculation of FbC-M¹⁰Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

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Comparative DFT study for molecular geometries and spectra of methyl pheophorbides-a: test of M06-2X and two other functionals

Cited by 22 publications

References 14 publications

Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Comparison of Different Theory Models and Basis Sets in Calculations of TPOP24N-Oxide Geometry and Geometries of meso-Tetraphenyl Chlorin N-Oxide Regioisomers

Interaction of allylic carbocations with benzene: a theoretical model of carbocationic intermediates in terpene biosynthesis

Comparison of different theory models and basis sets for the calculation of FbC-M10Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

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Comparison of different theory models and basis sets for the calculation of FbC-M¹⁰Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs