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1.
ACS Omega ; 7(15): 12753-12764, 2022 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-35474790

RESUMO

A two-pronged computational approach was taken to study the promiscuity of the SAM+-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl-, Br-, I-, NCO-, NCS-). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico. The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H2O molecules at the reactive site favors the reaction of NCS- over Cl- and Br- in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H2O molecules to the N terminus of NCS- greatly increases its reactivity, while H2O molecules attached to Cl- slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.

2.
J Phys Chem A ; 124(19): 3795-3804, 2020 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-32310651

RESUMO

Dative bonds between identical atoms of the same formal oxidation state are formed as geometric and electronic constraints turn an otherwise lone pair into a bond. Calculations at the B3LYP/6-31+g(d,p) level supported by additional atoms in molecules (AIM) and electron localization function (ELF) analyses on selected germanium polycations are used to prove the concept. The electron density (ρ) is not equally shared between the two atoms of such a homonuclear dative bond (HDB), and the associated charge transfer results in formal charges contradicting chemical convention.

3.
Chem Sci ; 8(1): 524-529, 2017 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-28451199

RESUMO

A pseudo-enantiomeric pair of optically switchable helicenes containing a catalytic 4-N-methylaminopyridine (MAP) bottom unit and a C2-symmetric, (10R,11R)-dimethoxymethyl-dibenzosuberane top template was synthesized. They underwent complementary photoswitching at 290 nm (P/M', <1/>99) and 340 nm (P/M', 91/9) and unidirectional thermo-rotation at 130 °C (P/M', >99/<1). They were utilized to catalyze enantiodivergent Steglich rearrangement of O- to C-carboxylazlactones, with formation of either enantiomer with up to 91% ee (R) and 94% ee (S), respectively.

4.
J Phys Chem A ; 121(2): 505-514, 2017 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-28004936

RESUMO

The degradation of S-adenosyl methionine (SAM) to homoserine-γ-lactone (HSL) and methyltioadenine (MTA) in water is studied with MD simulations. The AM1 Hamiltonian is used for the quantum part and the flexible AMBER force field for the H2O molecules. The MD simulations predict the free energy barrier for the degradation reaction to be between 109 and 112 kJ mol-1 and an overall gain in free energy of -26 kJ mol-1. The high barrier and the low energy gain of this reaction can be linked to interactions among the carboxylate group of the SAM molecule and solvent H2O molecules, which are not observed on the product side. Hence, the H2O molecules effectively slow down the reaction that otherwise would be much faster.

5.
J Org Chem ; 80(12): 6222-37, 2015 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-25992883

RESUMO

[2,3]-Wittig rearrangements of sugar-derived dihydropyran allyl propargyl ethers located at the 2- or 4-position have been studied as useful means for extending the carbon chains of the 4- or 2-position with chirality transfer. The stereochemical course of these reactions depends on the following factors: (1) deprotonation of pro-R or pro-S-H, (2) equilibration of the lithiated stereogenic carbanion, (3) conformational inversion during the rearrangement, and (4) concerted [2,3]- or [1,2]-Wittig rearrangement. In some cases, a stepwise mechanism that involves the allyl-C-O bond cleavage is shared as the first step by both the [2,3]- and [1,2]-Wittig rearrangements. The stereochemical courses of the rearrangements are compared among the lithiated reactants to determine the reaction pathways. These mechanisms in the polyoxygenated dihydropyran ring system were further supported by DFT calculations.

6.
Phys Chem Chem Phys ; 16(48): 26658-71, 2014 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-25384675

RESUMO

The formation of CH3Cl from (CH3)3SCl in various solvents has been studied based on M05/6-311+G(2d,p) DFT calculations to quantify the influence of the solvent on the stability of sulfonium cations. Four different pathways (one SN1, one backside and two frontside attacks for SN2) as well as the formation of different ion pairs (tripod, seesaw, and linear) are discussed to investigate the origin of the kinetic solvent effect (KSE) and the contribution of ion pairs to the overall reaction. Ion pairs are formed only in solvents with a permittivity ε lower than 28, but the reaction proceeds via a standard SN2 mechanism with a backside attack in all solvents. The formation of ion pairs does not change the order of the rate law, but it strongly influences the KSE, which can distinguish between reactions starting from free ions and those starting from ion pairs, in contrast to standard kinetic analysis.


Assuntos
Cloreto de Metila/química , Sulfetos/química , Compostos de Sulfônio/química , Íons/química , Cinética , Modelos Moleculares , Solventes/química
7.
Org Biomol Chem ; 12(37): 7297-309, 2014 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-25110957

RESUMO

Several chemical properties of Lewis base-allenoate adducts (LB·allenoate), such as solvent effect, basicity, nucleophilicity and cycloaddition, are studied to provide a detailed foundation for the analysis of LB-catalyzed reactions of allenoates. The zwitterionic LB·allenoates formed between methyl allenoate and Lewis bases, such as N-heterocyclic carbenes (NHCs), phosphines, amines and aza-heterocycles, are studied at the M06-2X/6-31+G* level. The addition of the LBs to the allenoate can yield Z- or E-type adducts. The formation of the Z-type adducts is more favorable in the gas phase due to electrostatic interactions. The yield of the E-type adducts increases with the permittivity of the solvent. The lowest barriers for the addition and the most stable adducts are observed with NHCs as catalysts. It is also shown that the α-carbon atom of the allenic moiety in LB·allenoate is more nucleophilic than the γ-carbon atom. Aza-arenes, phosphines and NHCs stabilize the [3 + 2]-ylides formed by the cycloaddition of LB·allenoate to ethylene; therefore, these LBs thermodynamically support the [3 + 2] cycloadditions. The detailed analysis of [3 + 2]-, [2 + 4]-, [2 + 2]- and [2 + 2 + 2]-cycloadditions with enones/ketones shows that the amine-catalyzed reactions follow the kinetically preferred path, and that the exergonic formation of the P-ylide favors the [3 + 2] cycloaddition in the phosphine-catalyzed reaction. The thermodynamically preferred pathway is followed with NHCs whereas the high stability of NHC·allenoate adducts reduces the overall catalytic efficiency of NHCs.


Assuntos
Bases de Lewis/química , Naftalenos/química , Teoria Quântica , Ciclização , Estrutura Molecular , Termodinâmica
8.
Complement Ther Med ; 22(1): 141-7, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24559829

RESUMO

OBJECTIVES: Complementary and alternative therapies in treating atopic dermatitis are not uncommon. However, substantial evidence and consensus on treating atopic dermatitis is lacking. The aim of this study is to investigate the characteristics and utilization of traditional Chinese medicine in patients with atopic dermatitis. DESIGN: We retrospectively collected patients with atopic dermatitis at the Chang Gung Memorial Hospital in Taiwan between 2002 and 2011. Patients' demographic data, duration and frequency of treatment, serum total immunoglobulin E levels, and traditional Chinese medicine treatment principles and prescription were analyzed. RESULTS: There were 4145 patients (8.8%) received traditional Chinese medicine therapy between 2002 and 2011. Among them, 2841 (68.54%) chose TCM only and 1304 (31.46%) chose to combine TCM and WM therapies. Those who chose combination therapy were younger, and needed more times of visit and longer duration of treatment. The most frequent comorbid conditions accompany atopic dermatitis were allergic rhinitis (46.06%) and asthma (21.46%). Among the 87,573 prescriptions written for Chinese medicine, the most frequently prescribed herbal formula and single herb were Xiao-Feng-San (Eliminate Wind Powder) (16.98%) and Bai-Xian-Pi (Cortex Dictamni) (12.68%), respectively. The most commonly used therapeutic principles of herbal formulas and single herbs were releasing exterior (20.23%) and clearing heat (41.93%), respectively. CONCLUSION: Our hospital-based study characterized the utilization patterns of traditional Chinese medicine in atopic dermatitis patients. This information could be used as references for clinical application and provide valuable information for future clinical trials.


Assuntos
Dermatite Atópica/epidemiologia , Dermatite Atópica/terapia , Prescrições de Medicamentos/estatística & dados numéricos , Medicamentos de Ervas Chinesas/uso terapêutico , Medicina Tradicional Chinesa , Adolescente , Adulto , Criança , Pré-Escolar , Comorbidade , Feminino , Hospitais , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Taiwan , Adulto Jovem
9.
J Org Chem ; 79(4): 1700-11, 2014 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-24437625

RESUMO

Allenoates and enones form cyclopentenes via a phosphine-catalyzed [3 + 2] cycloaddition while the amine-catalyzed [2 + 4] cycloaddition yields dihydropyrans or pyrans. The difference between these catalysts is studied with M06-2X/6-31+G* calculations. The addition of the catalyst to the allenoate is the first step in both pathways followed by the reaction with the enone. The formation of the [3 + 2] phosphorus-ylide is exergonic, and hence, the [3 + 2] cycloaddition is kinetically favored over the [2 + 4] addition. Amines do not stabilize [3 + 2] ammonium-ylides. However, electron-withdrawing groups on the enone enable [2 + 4] cycloadditions. The strength of the electron-withdrawing group further controls the α/γ regioselectivity of the [2 + 4] cycloaddition, and the analysis of the HOMO-LUMO interactions explains why only E-dihydropyrans from the direct γ-[2 + 4] cycloaddition have been observed in experiments. The quantum calculations further reveal a new path to the α-[2 + 4] product starting with an intermediate Rauhut-Currier reaction. This new path is kinetically favored over the direct amine-catalyzed α-[2 + 4] cycloaddition.

10.
J Chem Phys ; 138(21): 214102, 2013 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-23758353

RESUMO

A constrained reduced-dimensionality algorithm can be used to efficiently locate transition states and products in reactions involving conformational changes. The search path (SP) is constructed stepwise from linear combinations of a small set of manually chosen internal coordinates, namely the predictors. The majority of the internal coordinates, the correctors, are optimized at every step of the SP to minimize the total energy of the system so that the path becomes a minimum energy path connecting products and transition states with the reactants. Problems arise when the set of predictors needs to include weak coordinates, for example, dihedral angles, as well as strong ones such as bond distances. Two principal constraining methods for the weak coordinates are proposed to mend this situation: static and dynamic constraints. Dynamic constraints are automatically activated and revoked depending on the state of the weak coordinates among the predictors, while static ones require preset control factors and act permanently. All these methods enable the successful application (4 reactions are presented involving cyclohexane, alanine dipeptide, trimethylsulfonium chloride, and azafulvene) of the reduced dimensionality method to reactions where the reaction path covers large conformational changes in addition to the formation/breaking of chemical bonds. Dynamic constraints are found to be the most efficient method as they require neither additional information about the geometry of the transition state nor fine tuning of control parameters.

11.
Phys Chem Chem Phys ; 14(1): 138-47, 2012 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-22073399

RESUMO

Density functional theory has been used to investigate the properties of organic high spin molecules. The M05/cc-pVDZ calculations predict a septet ground state for the 2,3,6,7,10,11-hexahydro-1,4,5,8,9,12-hexaoxocoronene-2,3,6,7,10,11-hexayl radical (coronene-6O). The computations show further that the formation of intermolecular carbon-carbon bonds yields a singlet ground state for the dimer rather than a possible tridectet state as expected from the monomer's multiplicity. A benzene molecule placed between coronene-6O molecules leads to the desired high-spin cluster, but the overall stability of the cluster is low. A chromium atom inserted between two peripheral C(6) rings of coronene-6O yields a sandwich structure with the expected tridectet ground state and a binding energy which is 15 times larger than the corresponding tridectet dimer stabilized by a benzene molecule. The presented DFT calculations suggest that a chromium atom can effectively link organic polyradicals to larger magnetic units.

12.
Phys Chem Chem Phys ; 13(28): 12758-69, 2011 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-21691635

RESUMO

A series of model calculations was done to analyze the delocalization of the proton in the linking hydrogen bond of the (Dih)(2)H(+) cation (Dih: 4,5-dihydro-1H-imidazole). Standard quantum chemical calculations (B3LYP/D95+(d,p)) predict a low barrier hydrogen bond (LBHB) and thereby a delocalized proton in the NHN(+) hydrogen bridge. Explicit quantum calculations on the proton indicate that the delocalization of the proton does not provide enough energy to stabilize a permanent LBHB. Additional Born-Oppenheimer Molecular Dynamics (BOMD) simulations indicate further that the proton is localized at either side of the NHN(+) bridge and that a central proton position is the result of temporal averaging. The possibility of the proton to tunnel from one side to the other side of the NHN(+) bridge increases with the temperature as the trajectory of the (Dih)(2)H(+) cation runs through regions where the thermal excitation of Dih ring vibrations creates equal bonding opportunities for the proton on both sides of the bridge (vibrationally assisted proton tunneling). The quantum calculations for the proton in (Dih)(2)H(+) suggest further a broad peak for the 1 ← 0 transition with a maximum at 938 cm(-1) similar to that observed for LBHBs. Moreover, the asymmetric NHN(+) bridge in a thermally fluctuating environment is strong enough to create a significant peak at 1828 cm(-1) for the 2 ← 0 transition, while contributions from the 2 ← 1 are expected to be weak for the same reason.


Assuntos
Aminas/química , Prótons , Teoria Quântica , Algoritmos , Ligação de Hidrogênio , Imidazóis/química , Modelos Moleculares , Conformação Molecular , Simulação de Dinâmica Molecular , Espectrofotometria Infravermelho , Temperatura
13.
Chem Asian J ; 6(8): 2080-91, 2011 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-21656688

RESUMO

Symplectin is a photoprotein containing the dehydrocoelenterazine (DCL) chromophore, which links to a cysteine residue through a covalent bond with the emission of blue light. This study focuses on the stereochemical process of the emerging stereogenic centers. Two isomeric fluorinated DCL analogs (2,4-diF- and 2,6-diF-DCL) were employed owing to their different bioluminescence activities, these being 200% and 20% compared to natural DCL, respectively. Each of these diF-DCLs was found to exchange with the natural DCL in symplectin at pH 6.0. The emerging stereogenic carbons were racemic at the binding sites. Changing the pH of this storage form to the protein's optimum solubility pH (pH 7.8) resulted in 2,4-diF-DCL-bound symplectin luminescence, and the spent solutions were then analyzed and coelenteramide-390-CGLK-peptide and coelenteramine were detected after a peptidase digestion. The same analysis of the 2,6-diF-DCL-bound symplectin, on the other hand, afforded coelenteramine only but no coelenteramide. When the racemic storage diF-DCLs moved to the active site at pH 7.8, a change in the chirality with the 390-Cys residue resulted. Model experiments using L-cysteine-containing CGLK-peptide supported two diastereoisomers from each diF-DCL. The significant difference in the luminescence from these two chromophores is attributed to a plausible mechanism including the dynamically variable stereogenic center emerging at the storage and then the active site on the symplectin. It is concluded that such dynamic chirality plays a significant role in the symplectoteuthis bioluminescence.


Assuntos
Decapodiformes/química , Imidazóis/química , Substâncias Luminescentes/química , Proteínas Luminescentes/química , Pirazinas/química , Sequência de Aminoácidos , Animais , Benzenoacetamidas/química , Benzenoacetamidas/metabolismo , Sítios de Ligação , Dicroísmo Circular , Cisteína/química , Cisteína/metabolismo , Decapodiformes/metabolismo , Imidazóis/metabolismo , Luminescência , Substâncias Luminescentes/metabolismo , Proteínas Luminescentes/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Pirazinas/metabolismo , Estereoisomerismo
14.
J Comput Chem ; 32(12): 2716-26, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21671242

RESUMO

Density functional theory has been used to calculate the thermodynamic properties and molecular orbitals of pillar[n]quinones. Pillar[n]quinones are expected to be effective electron acceptors and the ability to accept more than one electron increases with the size of the interior cavity. Pillar[5]quinone and pillar[7]quinone show a great intramolecular charge transfer upon the electron excitation from highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) as indicated by a large difference of electron distributions between their HOMO and LUMO and a notable dipole moment difference between the ground and first triplet excited state. The aggregation of pillar[n]quinones leads to tubular dimeric structures joined by 2n CH···O nonclassical hydrogen bonds (HBs) with binding energies about 2 kcal/mol per HB. The longitudinal extension of the supramolecular self-assembly of pillar[n]quinone may be adjustable through forming and breaking their HBs by controlling the surrounding environment. The tunability of the diameter of the tubular structures can be achieved by changing the number of quinone units in the pillar[n]quinone. The electrostatic potential maps of pillar[n]quinones indicate that the positive charge in the interior cavity decreases as the number of quinone units increases. Chloride and bromide anions are chosen to examine the noncovalent anion-π interactions between pillar[n]quinones and captured anions. The calculations show that the better compatibility of the effective radius of the anions with the interior dimension of pillar[n]quinone leads to larger stabilization energy. The selectivity of spatial matching and specific interaction of pillar[n]quinone is believed to possibly serve as a candidate for ionic and molecular recognition.

15.
J Comput Chem ; 31(9): 1853-9, 2010 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-20082386

RESUMO

The observation of the Asp-His-Ser triad (Asp: aspartate, His: histidine, Ser: serine) triad both in mammalian and bacterial proteases suggests a special efficiency. A series of B3LYP/D95*(d,p) calculations on various [X-H(beta)Y](-) dyads (as part of the [X-H(beta)Y-H(alpha)Ac](-) model triad, HAc: acetic acid) made from eight different anions X(-) and 15 different coupling elements H(beta)Y was done to analyze the molecular origin of this efficiency. The X(-) anion acts merely as an electron density donor independent of its chemical nature, and the evolutionary selection of Asp for the catalytic triad therefore seems to be caused by the pH of the triads environment. As the linking proton H(beta) moves from Y(-) to X(-), electron density is effectively moved from X(-) to Y(-) thereby increasing the proton affinity (PA) of the [X-HY](-) dyad, which finally leads to the deprotonization of the HAc molecule. The degree to which the position of H(alpha) controls the PA is dominantly determined by the coupling element HY. The model calculations indicate that 4-methyl-1H-imidazole (HMim) is a very efficient coupling element, which suggest that the evolutionary convergence to the Asp-His-Ser is not only controlled by the ready availability of the imidazole motive in His but also by its high efficiency.


Assuntos
Ácido Aspártico/química , Histidina/química , Serina Endopeptidases/química , Serina/química , Motivos de Aminoácidos , Ácido Aspártico/metabolismo , Histidina/metabolismo , Cinética , Modelos Químicos , Modelos Moleculares , Teoria Quântica , Serina/metabolismo , Serina Endopeptidases/metabolismo
16.
Phys Chem Chem Phys ; 9(2): 299-310, 2007 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-17186073

RESUMO

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.

17.
J Chem Inf Comput Sci ; 44(2): 635-42, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15032545

RESUMO

A number of recently released numerical libraries including Automatically Tuned Linear Algebra Subroutines (ATLAS) library, Intel Math Kernel Library (MKL), GOTO numerical library, and AMD Core Math Library (ACML) for AMD Opteron processors, are linked against the executables of the Gaussian 98 electronic structure calculation package, which is compiled by updated versions of Fortran compilers such as Intel Fortran compiler (ifc/efc) 7.1 and PGI Fortran compiler (pgf77/pgf90) 5.0. The ifc 7.1 delivers about 3% of improvement on 32-bit machines compared to the former version 6.0. Performance improved from pgf77 3.3 to 5.0 is also around 3% when utilizing the original unmodified optimization options of the compiler enclosed in the software. Nevertheless, if extensive compiler tuning options are used, the speed can be further accelerated to about 25%. The performances of these fully optimized numerical libraries are similar. The double-precision floating-point (FP) instruction sets (SSE2) are also functional on AMD Opteron processors operated in 32-bit compilation, and Intel Fortran compiler has performed better optimization. Hardware-level tuning is able to improve memory bandwidth by adjusting the DRAM timing, and the efficiency in the CL2 mode is further accelerated by 2.6% compared to that of the CL2.5 mode. The FP throughput is measured by simultaneous execution of two identical copies of each of the test jobs. Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks.

18.
J Org Chem ; 68(9): 3626-33, 2003 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-12713371

RESUMO

The model compounds of tryptophan tryptophylquinone (TTQ), o-benzoquinone (OBQ), 3-methyl-6,7-dihydro-1H-6,7-indoledione (MIQ), and 3-methyl-4-(3-methyl-1H-2-indolyl)-6,7-dihydro-1H-6,7-indoledione (IIQ), all of which are characteristic of o-quinone groups, have been studied with density functional theory. The dihedral angle of the two indole rings (chi) of IIQ is calculated to be 49.6 degrees for the global minimum. Another local minimum, 0.74 kcal/mol higher in energy, with a chi value of 123.5 degrees is also fully optimized. The transition state connecting the two minima, with a chi value of 97.9 degrees, has been located and the rotation barrier is 1.71 kcal/mol. A scan of the potential energy surface along this dihedral angle showed that the difference of the total energy was within 1.0 kcal/mol at a range of the dihedral angle from 30 degrees to 75 degrees. Hence, IIQ is flexible for the rotation of inter-indole rings. The origin of regioselectivity for the condensation reactions of the models MIQ and IIQ with NH(3) has been elucidated. It is shown that the energy difference between the two different types of carbinolamine intermediates (Delta E) and their corresponding transition structures (Delta E(++)) should be responsible for the regioselectivity. To assess the effect of the fused ring on regioselectivity of the condensation reaction, a series of models were designed. A good linear correlation has been found between the energy difference of the two different carbinolamine intermediates (Delta E) and that of the corresponding transition states (Delta E(++)), suggesting that the factors that stabilize the carbinolamine intermediate also favor the stability of the corresponding transition structure. The pair, 6-amino-6-hydroxy-8-methyl-6H-quinolin-5-one and 5-amino-5-hydroxy-8-methyl-5H-quinolin-6-one (7/8), deviates from the correlation and represents some anomalous behavior, which may be due to their structural particularity. It also has been shown that the tricyclic models, which consist of OBQ and two fused heterocyclic rings, represent more regioselectivity in contrast to the bicyclic systems. Moreover, the fused electron-donating pyrrole and the fused electron-withdrawing pyridine or pyrimidine show a somewhat synergistic effect on each other via the medial OBQ molecule. The barrier of the condensation reaction for pyrrolo[2,3-f]quinoline-4,5-dione is calculated to be ca. 22 kcal/mol. This is lower than that for MIQ (ca. 33 kcal/mol) and IIQ (ca. 32 kcal/mol) by as much as 10.0 kcal/mol, explaining reasonably the larger catalytic effect of pyrroloquinolinequinone (PQQ) relative to TTQ.


Assuntos
Indolquinonas/química , Modelos Teóricos , Triptofano/análogos & derivados , Triptofano/química , Fenômenos Químicos , Físico-Química , Estrutura Molecular , Relação Estrutura-Atividade , Termodinâmica
19.
J Org Chem ; 68(9): 3663-72, 2003 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-12713376

RESUMO

Myers-Saito cyclizations of a series of enyne-allenes and enyne-butatrienes have been studied by density functional methods. The pure DFT method, BPW91, in conjunction with the 6-311 basis set is demonstrated to be suitable to study these systems. Geometry optimizations and harmonic frequency calculations were applied for every reactant, transition structure, as well as product. It has been shown that the cyclic structure of reactant lowers significantly the critical distance and reaction barrier. For the Myers-Saito product of (5Z)-1,2,3,5-cyclononatetraen-7-yne (10R), the confinement of ring leads to an essential change of the biradical character from sigma-pi type to sigma-sigma type. The through-bond coupling is therefore involved in this product as in the Bergman products. With the enlargement of the ring, the geometrical distortion weakens the through-bond coupling and raises the stability of the products. As a consequence, 1,5-didehydroindene (10P) presents a particularly long critical distance and lower thermodynamic stability. Detailed comparisons of the reactivities of 10R, (Z)-1-cyclononene-3,8-diyne (13R), and (Z)-1-cyclodecene-3,9-diyne (14R) that represent the core structure of a category of natural antitumor drugs have also been made. It reveals that the reactivity of these three systems is quite similar, despite the fact that the thermochemical properties of the prototypical Myers-Saito and Bergman cyclizations are significantly different from each other.

20.
J Chem Inf Comput Sci ; 42(3): 673-81, 2002.
Artigo em Inglês | MEDLINE | ID: mdl-12086529

RESUMO

One of the most frequently used packages for electronic structure research, GAUSSIAN 98, is compiled on Linux systems with various hardware configurations, including AMD Athlon (with the "Thunderbird" core), AthlonMP, and AthlonXP (with the "Palomino" core) systems as well as the Intel Pentium 4 (with the "Willamette" core) machines. The default PGI FORTRAN compiler (pgf77) and the Intel FORTRAN compiler (ifc) are respectively employed with different architectural optimization options to compile GAUSSIAN 98 and test the performance improvement. In addition to the BLAS library included in revision A.11 of this package, the Automatically Tuned Linear Algebra Software (ATLAS) library is linked against the binary executables to improve the performance. Various Hartree-Fock, density-functional theories, and the MP2 calculations are done for benchmarking purposes. It is found that the combination of ifc with ATLAS library gives the best performance for GAUSSIAN 98 on all of these PC-Linux computers, including AMD and Intel CPUs. Even on AMD systems, the Intel FORTRAN compiler invariably produces binaries with better performance than pgf77. The enhancement provided by the ATLAS library is more significant for post-Hartree-Fock calculations. The performance on one single CPU is potentially as good as that on an Alpha 21264A workstation or an SGI supercomputer. The floating-point marks by SpecFP2000 have similar trends to the results of GAUSSIAN 98 package.

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