scholarly journals Analysis of polarization in QM/MM modelling of biologically relevant hydrogen bonds

2008 ◽  
Vol 5 (suppl_3) ◽  
pp. 207-216 ◽  
Author(s):  
Kittusamy Senthilkumar ◽  
Jon I Mujika ◽  
Kara E Ranaghan ◽  
Frederick R Manby ◽  
Adrian J Mulholland ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Bond Formation ◽  
Basis Sets ◽  
Total Electron Density ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Total Electron ◽  
Biologically Relevant ◽  
Limited Basis

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly important for the study of chemical reactions and systems in condensed phases. Here, we have tested the accuracy of a density functional theory-based QM/MM implementation (B3LYP/6-311+G(d,p)/CHARMM27) on a set of biologically relevant interactions by comparison with full QM calculations. Intermolecular charge transfer due to hydrogen bond formation is studied to assess the severity of spurious polarization of QM atoms by MM point charges close to the QM/MM boundary. The changes in total electron density and natural bond orbital atomic charges due to hydrogen bond formation in selected complexes obtained at the QM/MM level are compared with full QM results. It is found that charge leakage from the QM atoms to MM atomic point charges close to the QM/MM boundary is not a serious problem, at least with limited basis sets. The results are encouraging in showing that important properties of key biomolecular interactions can be treated well at the QM/MM level employing good-quality levels of QM theory.

scholarly journals Theoretical Study of Hydrogen Bond Formation in Trimethylene Glycol-Water Complex

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Snehanshu Pal ◽  
T. K. Kundu
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Density Functional ◽  
Bond Formation ◽  
Proton Donor ◽  
Basis Set ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Water Complex ◽  
Trimethylene Glycol

A detailed quantum chemical calculation based study of hydrogen bond formation in trimethylene glycol- (TMG-) water complex has been performed by Hatree-Fock (HF) method, second-order Møller-Plesset perturbation theory (MP2), density functional theory (DFT), and density functional theory with dispersion function (DFT-D) using 6-31++G(d,p) basis set. B3LYP DFT-D, WB97XD, M06, and M06-2X functionals are used to capture highly dispersive hydrogen bond formation. Geometrical parameters, interaction energy, deviation of potential energy curve of hydrogen-bonded O–H from that of free O–H, natural bond orbital (NBO), atom in molecule (AIM), charge transfer, and red shift are investigated. It is observed that hydrogen bond between TMG and water molecule is stronger in case of TMG acting as proton donor compared to that of water acting as proton donor, and dilute TMG solution would inhibit water cluster formation.

Theoretical analysis of the (HNO)2, (HNO···HNS), and (HNS)2 dimers — A case of red and blue shifts of N–H stretching frequency

2010 ◽  
Vol 88 (8) ◽  
pp. 849-857 ◽  
Author(s):  
Nguyen Tien Trung ◽  
Tran Thanh Hue ◽  
Minh Tho Nguyen
Keyword(s):  
Hydrogen Bond ◽  
Quantum Chemical ◽  
Bond Formation ◽  
Blue Shift ◽  
Proton Donor ◽  
Basis Sets ◽  
Coupled Cluster ◽  
Hydrogen Bond Formation ◽  
Length Contraction ◽  
Moller Plesset

The hydrogen-bonded interactions in the simple (HNZ)2 dimers, with Z = O and S, were investigated using quantum chemical calculations with the second-order Møller–Plesset perturbation (MP2), coupled-cluster with single, double (CCSD), and triple excitations (CCSD(T)) methods in conjunction with the 6-311++G(2d,2p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets. Six-membered cyclic structures were found to be stable complexes for the dimers (HNO)2, (HNS)2, and (HNO–HNS). The pair (HNS)2 has the largest complexation energy (–11 kJ/mol), and (HNO)2 the smallest one (–9 kJ/mol). A bond length contraction and a frequency blue shift of the N–H bond simultaneously occur upon hydrogen bond formation of the N–H···S type, which has rarely been observed before. The stronger the intramolecular hyperconjugation and the lower the polarization of the X–H bond involved as proton donor in the hydrogen bond, the more predominant is the formation of a blue-shifting hydrogen bond.

scholarly journals Theoretical Researches On Binding Modes and Stability of Hydrogen Bonds Between Uracil and Formic Acid

2021 ◽  
Author(s):  
Qian Tang ◽  
Ting Huang ◽  
Ruisi Huang ◽  
Hongyu Cao ◽  
Lihao Wang ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Formic Acid ◽  
Density Functional ◽  
Implicit Solvent ◽  
Binding Modes ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Vibration Absorption

Abstract The hydrogen bond formation with formic acid would affect the complementary pair of bases between uracil and adenine, but the binding modes and spectral properties of hydrogen bonds are still obscure. Density functional theory and time-dependent density functional theory were applied to investigate the intermolecular hydrogen bonds between uracil and formic acid. The reduced density gradient (RDG), bond lengths and vibration absorption frequencies revealed that the most probable uracil-formic acid (U-FA) interaction mode formed in the position c of FA and the site 1 of U, that is, the mode 1c. The theoretical parameters in excited state complexes manifested that the variety of hydrogen bond configurations led to different degrees of strengthening or weakening of molecular interaction. In the implicit solvent (water), the formations of O-H∙∙∙O in the uracil-formic acid complexes were promoted obviously. These theoretical studies would positively affect the researches of life science and medicinal chemistry.

scholarly journals Theoretically nanoscale study on ionization of muscimol nano drug in aqueous solution

2015 ◽  
Vol 51 (1) ◽  
pp. 213-219 ◽  
Author(s):  
Farhoush Kiani ◽  
Mehran Abbaszadeh ◽  
Mohammad Pousti ◽  
Fardad Koohyar
Keyword(s):  
Density Functional ◽  
Dft Method ◽  
Acid Dissociation ◽  
Basis Sets ◽  
Acid Dissociation Constant ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Pka Values ◽  
The Density Functional Theory ◽  
Good Agreement

In the present work, acid dissociation constant (pKa) values of muscimol derivatives were calculated using the Density Functional Theory (DFT) method. In this regard, free energy values of neutral, protonated and deprotonated species of muscimol were calculated in water at the B3LYP/6-31G(d) basis sets. The hydrogen bond formation of all species had been analyzed using the Tomasi's method. It was revealed that the theoretically calculated pKa values were in a good agreement with the existing experimental pKa values, which were determined from capillary electrophoresis, potentiometric titration and UV-visible spectrophotometric measurements.

scholarly journals Stability Analysis and Frontier Orbital Study of Different Glycol and Water Complex

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Snehanshu Pal ◽  
T. K. Kundu
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Bond Formation ◽  
Proton Donor ◽  
Basis Set ◽  
Geometrical Parameters ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Formation ◽  
Water Complex ◽  
Hartree Fock

A detailed theoretical study of hydrogen-bond formation in different polyethylene glycol + water complex and dipropylene glycol + water have been performed by Hartree Fock (HF) method, second-order Møller-Plesset perturbation theory (MP2), and density functional theory (DFT) using 6-31++G(d,p) basis set. B3LYP DFT-D, WB97XD, M06, and M06-2X functionals have been used to describe highly dispersive hydrogen-bond formation appropriately. Geometrical parameters, interaction energies, deformation energies, deviation of potential energy curves of hydrogen bonded O–H from that of free O–H, frontier orbitals, and charge transfer have been studied to analyze stability and nature of hydrogen bond formation of various glycol and water complexes. It is found that WB97XD is best among all the applied DFT functionals to describe hydrogen bond interaction, and intermolecular hydrogen bonds have higher covalent character and accordingly higher strength when glycol acts as proton donor for glycol + 1 water complex system.

scholarly journals Estimation of the Efficiency of Corrosion Inhibition by Zn-Dithiocarbamate Complexes: a Theoretical Study

2021 ◽  
pp. 3323-3335
Author(s):  
Mustafa M. Kadhim ◽  
Layla A. Al. Juber ◽  
Ahmed S. M. Al-Janabi
Keyword(s):  
Electron Density ◽  
Density Functional ◽  
Room Temperature ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Total Electron Density ◽  
Functional Theory ◽  
Total Electron ◽  
Homo Lumo

    Seven Zn-dithiocarbamate complexes were suggested as corrosion inhibitors. Density functional theory (DFT) was used to predict the ability of inhibition. Room temperature conditions were applied to suggest the optimization of complexes, physical properties, and corrosion parameters. In addition, the HOMO, LUMO, dipole moment, energy gap, and other parameters were used to compare the inhibitors efficiency. Gaussian 09 software with LanL2DZ basis set was used. Total electron density (TED) and electrostatic surface potential (ESP) were utilized to show the sites of adsorption according to electron density.

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

scholarly journals Chalcogen Bond versus Weak Hydrogen Bond: Changing Contributions in Determining the Crystal Packing of [1,2,5]-Chalcogenadiazole-Fused Tetracyanonaphthoquinodimethanes

2021 ◽  
Vol 03 (02) ◽  
pp. 090-096
Author(s):  
Yusuke Ishigaki ◽  
Kota Asai ◽  
Takuya Shimajiri ◽  
Tomoyuki Akutagawa ◽  
Takanori Fukushima ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Molecular Design ◽  
Crystal Packing ◽  
Cyano Group ◽  
Density Functional Theory Calculations ◽  
Weak Hydrogen Bond ◽  
Functional Theory ◽  
Chalcogen Bond ◽  
Thiadiazole Ring

The crystal structures of a series of tetracyanonaphthoquinodimethanes fused with a selenadiazole or thiadiazole ring revealed that their molecular packing is determined mainly by two intermolecular interactions: chalcogen bond (ChB) and weak hydrogen bond (WHB). ChB between Se and a cyano group dictates the packing of selenadiazole derivatives, whereas the S-based ChB is much weaker and competes with WHB in thiadiazole analogues. This difference can be explained by different electrostatic potentials as revealed by density functional theory calculations. A proper molecular design that weakens WHB can change the contribution of ChB in determining the crystal packing of thiadiazole derivatives.

Sign in / Sign up

Export Citation Format

Share Document