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.

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 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 Theoretical Evaluation on The Interaction Between Triglycerides and Methylxanthines Using Density Functional Theory B3LYP/6-31G(d,p) and Molecular Electrostatic Potential

2020 ◽  
Vol 33 (1) ◽  
pp. 171-178
Author(s):  
N.F.M. Azmi ◽  
R. Ali ◽  
A.A. Azmi ◽  
M.Z.H. Rozaini ◽  
K.H.K. Bulat ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Basis Set ◽  
Individual Species ◽  
Interaction Energies ◽  
Binding Interaction ◽  
Functional Theory

The binding, interaction and distortion energies between the main triglycerides, palmitic-oleic-stearic (POS) in cocoa butter versus palmitic-oleic-palmitic (POP) in refined, bleached and deodorized (RBD) palm oil with cocoa′s methylxanthines (caffeine, theobromine, and theophylline) during the production of chocolate were theoretically studied and reported. The quantum mechanical software package of Gaussian09 at the theoretical level of density functional theory B3LYP/6-31G(d,p) was employed for all calculations, optimization, and basis set superposition errors (BSSE). Geometry optimizations were carried out to the minimum potential energy of individual species and binary complexes formed between the triglycerides, methylxanthines and polyphenols. The interaction energies for the optimized complexes were then corrected for the BSSE using the counterpoise method of Boys and Bernardi. The results revealed that the binding energy and interaction energy between methylxanthine components in cocoa powder with triglycerides were almost of the same magnitude (13.6-14.5 and 3.4-3.7 kJ/mol, respectively), except for the binary complex of POS-caffeine (25.1 and 10.7 kJ/mol, respectively). Based on the molecular geometry results, the hydrogen bond length and angle correlated well with the interaction energies. Meanwhile, the POS-caffeine complex with two higher and almost linear bond angles showed higher binding and interaction energies as compared to the other methylxanthines. Therefore, a donor-acceptor analysis showed that the hydrogen bond strength was proven using the molecular electrostatic potential (MEP), which resulted in parallel outcomes. The research results were believed to be one of the factors that contributed to the rheological behaviour and sensory perception of cocoa products, especially chocolate.

scholarly journals Computational Evaluation of Intermolecular Interaction in Poly(Styrene-Maleic Acid)-Water Complexes Using Density Functional Theory

2021 ◽  
Vol 21 (6) ◽  
pp. 1537
Author(s):  
Daru Seto Bagus Anugrah ◽  
Laura Virdy Darmalim ◽  
Permono Adi Putro ◽  
Liana Dewi Nuratikah ◽  
Nurwarrohman Andre Sasongko ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Maleic Acid ◽  
Density Functional ◽  
Basis Set ◽  
Water Molecules ◽  
Functional Theory ◽  
High Hydrogen

The high application of Poly(styrene-maleic acid) (PSMA) in an aqueous environment, such as biomedical purposes, makes the interaction between PSMA and water molecules interesting to be investigated. This study evaluated the conformation, the hydrogen bond network, and the stabilities of all the possible intermolecular interactions between PSMA with water (PSMA−(H2O)n, n = 1–5). All calculations were executed using the density functional theory (DFT) method at B3LYP functional and the 6–311G** basis set. The energy interaction of PSMA–(H2O)5 complex was –56.66 kcal/mol, which is classified as high hydrogen bond interaction. The Highest Occupied Molecular Orbital (HOMO) – Lowest Unoccupied Molecular Orbital (LUMO) energy gap decreased with the rise in the number of H2O molecules, representing a more reactive complex. The strongest hydrogen bonding in PSMA–(H2O)5 wasformed through the interaction on O72···O17–H49 with stabilizing energy of 50.32 kcal/mol, that analyzed by natural bond orbital (NBO) theory. The quantum theory atoms in molecules (QTAIM) analysis showed that the hydrogen bonding (EHB) value on O72···O17–H49 was –14.95 kcal/mol. All computational data revealed that PSMA had moderate to high interaction with water molecules that indicated the water molecules were easily transported and kept in the PSMA matrix.

scholarly journals Investigation into the Molecular Properties of 3-(4-Hydroxyphenyl) Prop-2-en-1-one 4-Phenyl Schiff Base and Some of Its Derivatives-DFT and Molecular Docking Studies

2021 ◽  
Vol 9 (1) ◽  
pp. 4-11
Keyword(s):  
Density Functional Theory ◽  
Staphylococcus Aureus ◽  
Hydrogen Bond ◽  
Schiff Base ◽  
Molecular Orbital ◽  
Density Functional ◽  
Molecular Properties ◽  
Basis Set ◽  
Binding Affinities ◽  
Functional Theory

The structure-property relationship is important in understanding molecular behaviors and their best-fit areas of applications. 3-(4-hydroxyphenyl) prop-2-en-1-one 4-phenyl Schiff base and some of its derivatives were optimized via the density functional theory with Becke three Lee Yang Parr correlation and 6-31G* basis set. The molecular properties calculated were the energies of the frontier molecular orbitals [highest occupied molecular orbital (EHOMO), lowest unoccupied molecular orbital (ELUMO), energy bandgap (Eg), chemical hardness (η), softness (S) and hyperpolarizabilities (β)]. The electronic transitions were calculated with the time-dependent density functional theory methods, the absorption maxima (λabs), vertical transition energies (ΔEge), oscillator strengths (f) and molecular orbital (MO) components with their percentage contributions were obtained. The anti-microbial efficacy of the molecules was tested against Staphylococcus aureus aminopeptidase S (AmpS) active site to predict the binding affinities. ADMEtox parameters of all the molecules were also investigated. Eg values ranged from 3.13 to 3.95 eV, β values ranged from 1.45 to 5.81×10-30 esu, and their binding affinities ranged from -4.57 to -6.12 kcal/mol, all were more than that of standard drug, streptomycin (-4.31 kcal/mol). The number of hydrogen bond donors and hydrogen bond acceptors were ranged from 1 to 2 and 3.75 to 5.25, respectively. Variations observed from the calculated molecular properties are the result of varying substituent groups. The molecules can be used as nonlinear optical (NLO) materials and also showed potential for being effective against Staphylococcus aureus.

THEORETICAL STUDIES ON HEATS OF FORMATION OF PYRIDINE N-OXIDES USING DENSITY FUNCTIONAL THEORY AND COMPLETE BASIS METHOD

2009 ◽  
Vol 08 (04) ◽  
pp. 541-549 ◽  
Author(s):  
ZHENG-XIN TANG ◽  
XIAO-HONG LI ◽  
RUI-ZHOU ZHANG ◽  
XIAN-ZHOU ZHANG
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Basis Set ◽  
Heats Of Formation ◽  
Functional Theory ◽  
Hydrogen Bond Formation ◽  
Substituent Group ◽  
Basis Method ◽  
Intramolecular Hydrogen ◽  
Hybrid Density Functional

The heats of formation (HOFs) for 11 pyridine N-oxide compounds are calculated by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86, PBE1PBE) methods with 6-31G** basis set and ab initio CBS-4M method. It is demonstrated that the B3PW91 method is accurate to compute the reliable HOFs for pyridine N-oxide compounds. It is also noted that the HOF is the smallest for the pyridine N-oxide which has the substituent group on the para-position, such as 4-NC–c- C 5 H 4 NO , 4- H 2 NOC – C 5 H 4 N – O , and 4- HO 2 C –c- C 5 H 4 NO . In addition, we think that the HOF of 2- HO 2 C –c- C 5 H 4 NO is much larger than that of 3- HO 2 C –c- C 5 H 4 NO and 4- HO 2 C –c- C 5 H 4 NO , which may be the result of intramolecular hydrogen bond formation and further measurements are needed to reexamine the HOFs for 2- HO 2 C –c- C 5 H 4 NO , 3- HO 2 C –c- C 5 H 4 NO , and 4- HO 2 C –c- C 5 H 4 NO .

scholarly journals Density Functional Theory (DFT) and Natural Bond Orbital (NBO) Analysis of Intermolecular Hydrogen Bond Interaction in "Phosphorylated Nata De Coco - Water"

2018 ◽  
Vol 18 (1) ◽  
pp. 173 ◽  
Author(s):  
Sitti Rahmawati ◽  
Cynthia Linaya Radiman ◽  
Muhamad Abdulkadir Martoprawiro
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Intermolecular Hydrogen Bond ◽  
Lone Pair ◽  
Basis Set ◽  
Proton Acceptor ◽  
Functional Theory

This study aims to study the conformation, the hydrogen bond network, and the stabilities of all the possible intermolecular interactions in phosphorylated nata de coco membrane with water (NDCF-(H2O)n, n = 1-5). Analysis of natural bond orbital (NBO) was performed to measure the relative strength of the hydrogen bonding interactions, charge transfer, particularly the interactions of n-σ * O-H and to take into account the effect on the stabilities of the molecular structure. All calculation were performed using density functional theory (DFT) method, at B3LYP functional level of theory and 6-311 G** basis set. The charge transfer between the lone pair of a proton acceptor to the anti-bonding orbital of the proton donor provides the substantial to the stabilization of the hydrogen bonds. Interaction between NDCF and (H2O)5 was strongest with the stabilization energy of 37.73 kcal/mol, that indicate the ease of donating lone pair electrons. The contributions of each hydrogen bond to the stability of the complex have been analyzed.

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.

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>

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