Biomedical subjects

Chin-Hui Yu

Publications and source records attributed to Chin-Hui Yu.

5 recordsLinked to original sources

PubMed2006

Correlated proton motion in hydrogen bonded systems: tuning proton affinities.

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.

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PubMed2003

Density functional study of the ring effect on the Myers-Saito cyclization and a comparison with the Bergman cyclization.

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.

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PubMed2003

Regioselectivity for condensation reactions of quinonoid models of tryptophan tryptophylquinone: a density functional theory study.

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.

Chemical Phenomena↗

PubMedDate not supplied

Recent advances in PC-Linux systems for electronic structure computations by optimized compilers and numerical libraries.

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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PubMedDate not supplied

Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries.

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.

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