2002
DOI: 10.1063/1.1498468
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Abstract: A normal mode coordinate-based molecular optimization algorithm was implemented and its performance tested against other optimization techniques. In certain cases the method was found to be computationally simpler and numerically more stable than the optimization algorithms based on Cartesian or internal valence coordinates. The usual redundant/internal coordinate scheme provided fastest convergence for compact covalently bonded molecules, while the normal mode method was found to be more suitable for more wea… Show more

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Cited by 121 publications
(120 citation statements)
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References 29 publications
(24 reference statements)
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“…57 Density functional theory (DFT) computations at the BPW91/6-31G** level were chosen as the primary method for FF determination because the BPW91 functional 58,59 with this basis set provides good vibrational frequencies with reasonable computational cost for the amide modes of prime interest. 60 Hybrid functionals, often chosen for vibrational spectral studies, do not improve the amide I and II frequencies, which are of interest here, yet lead to much longer computational times, limiting the size of peptide we can consider at the ab initio DFT level.…”
Section: Calculationsmentioning
confidence: 99%
“…57 Density functional theory (DFT) computations at the BPW91/6-31G** level were chosen as the primary method for FF determination because the BPW91 functional 58,59 with this basis set provides good vibrational frequencies with reasonable computational cost for the amide modes of prime interest. 60 Hybrid functionals, often chosen for vibrational spectral studies, do not improve the amide I and II frequencies, which are of interest here, yet lead to much longer computational times, limiting the size of peptide we can consider at the ab initio DFT level.…”
Section: Calculationsmentioning
confidence: 99%
“…11 Although the geometries of the target octanucleotides were not changed during the calculations, the smaller fragments were relaxed with the aid of the normal mode optimization method. 29 Normal modes below 300 cm -1 were frozen, while the modes in the experimentally accessible region could relax. For the optimized fragments, harmonic force fields, dipole derivatives, and the atomic axial tensors were calculated with the Gaussian 98 suite of programs 21 and transferred 26 to the octamers.…”
Section: Calculationsmentioning
confidence: 99%
“…54,55 During the minimization modes with frequencies ω ∈ (-300, 300 cm -1 ) were frozen, which ensured only a minimal change of the geometry, but the higher frequency vibrational motions present in the experimental spectra were relaxed. Program QGRAD 53 was used for the normal mode technique, while the ab initio part of the computation was done with the GAUSSIAN 56 software. Note that for the simulation of irregular DNA geometries, such as the averaged MD structures, fragments could not be propagated and for each one unique ab inito computation was needed.…”
Section: Methodsmentioning
confidence: 99%
“…Additionally, dinucleotide fragments were made (fragment c, Figure 1) for which a lower PM3 52 level was used for calculation of the longer range force field terms. The smaller fragments were minimized in the normal coordinates 53 at the BPW91/6-31G** DFT level. 54,55 During the minimization modes with frequencies ω ∈ (-300, 300 cm -1 ) were frozen, which ensured only a minimal change of the geometry, but the higher frequency vibrational motions present in the experimental spectra were relaxed.…”
Section: Methodsmentioning
confidence: 99%
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