CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

Photoelectron studies on intramolecularly hydrogen-bonded systems. I. The photoelectron spectra of cis- and trans-2-aminocyclopentanol, and cis- and trans-2-(N,N-dimethylamino)cyclopentanol

1976 ◽  
Vol 54 (4) ◽  
pp. 642-646 ◽  
Author(s):  
R. S. Brown
Keyword(s):  
Hydrogen Bonding ◽  
Ionization Energy ◽  
Lone Pair ◽  
Intramolecular Hydrogen Bonding ◽  
Photoelectron Spectra ◽  
Hydrogen Bonded Systems ◽  
Intramolecular Hydrogen ◽  
Cis And Trans ◽  
Infrared Data ◽  
Hydrogen Bonded

The photoelectron spectra of cis- and trans-2-aminocyclopentanol and cis- and trans-2-(N,N,-dimethylamino)cyclopentanol have been recorded and interpreted. The cis isomers exhibit N lone pair ionizations at higher ionization energy, and O lone pair ionizations at lower ionization energy than their trans isomers.The results are most consistent with the existence and observation of intramolecular hydrogen-bonding in the cis isomers. Infrared data on these systems also show that the cis isomers exist in the intramolecularly hydrogen-bonded state.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

ASSESSMENT OF THE PERFORMANCE OF THE M05-CLASS AND M06-CLASS FUNCTIONALS FOR THE STRUCTURE AND GEOMETRY OF THE HYDROGEN-BONDED AND HALOGEN-BONDED COMPLEXES

2012 ◽  
Vol 11 (06) ◽  
pp. 1165-1173 ◽  
Author(s):  
YU ZHANG ◽  
NING MA ◽  
WEIZHOU WANG
Keyword(s):  
Numerical Integration ◽  
Density Functional ◽  
Carbonic Acid ◽  
Binding Energies ◽  
Noncovalent Complexes ◽  
Good For ◽  
Better Than ◽  
Bonded Complexes ◽  
Hydrogen Bonded

The M05-class (M05 and M05-2X) and M06-class (M06, M06-2X, M06-HF, and M06-L) functionals, developed by Zhao and Truhlar, have shown better performance than popular older DFT functionals in obtaining accurate binding energies of noncovalent complexes. However, the reliability of these functionals for the structure and geometry of noncovalent systems was seldom assessed. Here, using the MP2/aug-cc-pVTZ values as a benchmark, we assessed the performance of the M05-class and M06-class functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes. The results clearly show that the M05, M06 and M06L functionals totally fail to predict the structure of the hydrogen-bonded complex formed between glycine and carbonic acid whereas the M05-2X, M06-2X, M06-HF, and even B3LYP succeed. For the geometries of a series of halogen-bonded complexes, it is found that the M05-2X functional performs slightly better than the M06-2X and M06-HF functionals and much better than the M05, M06 and M06-L functionals on average. Based on these tests, we concluded that the M05, M06 and M06-L functionals are not good for the study of the structure and geometry of the hydrogen-bonded and halogen-bonded complexes and the density functional M05-2X is the best choice. In addition, we have also assessed the integration grid errors arising from the numerical integration of these functionals for the structure and geometry of the hydrogen-bonded and halogen-bonded complexes.

Irᴵᴵᴵ as a Strategy for Preorganization in H-Bonded Motifs

2019 ◽  
Author(s):  
Barbora Balonova ◽  
Helena J. Shepherd ◽  
Christopher Serpell ◽  
Barry Blight
Keyword(s):  
Hydrogen Bonding ◽  
Metal Complexes ◽  
General Formula ◽  
Self Assembly ◽  
Structural Design ◽  
Functional Materials ◽  
Soft Materials ◽  
Thiourea Derivatives ◽  
Hydrogen Bonded Systems ◽  
Hydrogen Bonded

Here we present the synthesis and characterisation of four hydrogen bonded systems based on thiourea derivatives. These motifs are considered to be stable and desirable for supramolecular hydrogen-bonded functional materials. Interpretation of the structural design of thiourea based ligand and its incorporation into metal complexes can contribute to the understanding of preorganised self-assembly and open new pathways in design of novel soft materials. This work contributes to the unexplored library of hydrogen bonded metal complexes based on iridium. Further we examined the photoluminescence of the system of general formula [Ir(C^N)<sub>2</sub>(N^S)] and the effect of hydrogen bonding on the emission properties when combined with different <i>n</i>-heteroacenes.

Theoretical exploration of the cooperative effect in NMF–NMF–amino acid residue hydrogen bonding system

2008 ◽  
Vol 10 (36) ◽  
pp. 5607 ◽  
Author(s):  
Xichen Li ◽  
Wenlan Liu ◽  
Kening Sun ◽  
Yan Wang ◽  
Hongwei Tan ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Cooperative Effect ◽  
Bonding System ◽  
Hydrogen Bonding System
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