Density Functional Theory (DFT) and Natural Bond Orbital (NBO) Investigation of Intra/Intermolecular Hydrogen Bond Interaction in Sulfonated Nata-De Coco-Water (NDCS-(H2O)n)

2020 ◽  
Vol 17 (6) ◽  
pp. 2812-2819
Author(s):  
Sitti Rahmawati ◽  
Cynthia Linaya Radiman ◽  
Muhamad Abdulkadir Martoprawiro ◽  
Siti Nuryanti
Keyword(s):  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Density Functional ◽  
Intermolecular Hydrogen Bond ◽  
Lone Pair ◽  
Dft Method ◽  
Nbo Analysis ◽  
Hydrogen Bond Interaction ◽  
Sulfonic Group ◽  
The One

This research aim to study the conformation, hydrogen bonding network, and stability of all possible molecular interactions between sulfonated nata-de-coco membranes with water (NDCS-(H2O)n), n = 1–5) as well as associate them with results of phosphorylated nata-de-coco reported previously, to determine the potential of proton transfer within both systems. The calculations used DFT method at the B3LYP/6-311G** level as well as NBO analysis. The strongest hydrogen bonds were found among sulfonic group in NDCS-(H2O)5 and the oxygen in the water molecules. The stabilization energy of NDCS-(H2O)5 is 98.9 kcal/mol, That is much greater than that found in NDCP-(H2O)5 This suggests that the NDCS was more easily to donate its lone pair and that the hydrogen bonds between sulfonic group and water molecule were stronger, so that it was easier to transfer protons to another sulfonic group than to NDCP. The energy profile showed that barrier energy was roughly 58.1 kcal/mol and 138.6 kcal/mol for NDCS-(H2O)5 and NDCP-(H2O)5 respectively. Proton transfer in NDCS-(H2O)5 generated a lower energy-barrier than the one in NDCP-(H2O)5

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

2019 ◽  
Vol 75 (5) ◽  
pp. 554-561
Author(s):  
Jian Zhang ◽  
Xiu Li
Keyword(s):  
Proton Transfer ◽  
Density Functional ◽  
Dft Method ◽  
Intramolecular Proton Transfer ◽  
Transfer Reactions ◽  
Energy Barriers ◽  
Transfer Energy ◽  
Geometrical Structures ◽  
Proton Transfer Reactions ◽  
Mediated Catalysis

The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono- and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H—O bond rotations in which the H atom rotates 180° around the C—O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton-transfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H2O molecules is much greater than that of one H2O molecule in isomerizations of 5ClU.

scholarly journals Unsaturated and Benzannulated N-Heterocyclic Carbene Complexes of Titanium and Hafnium: Impact on Catalysts Structure and Performance in Copolymerization of Cyclohexene Oxide with CO2

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4364
Author(s):  
Lakshmi Suresh ◽  
Ralte Lalrempuia ◽  
Jonas B. Ekeli ◽  
Francis Gillis-D’Hamers ◽  
Karl W. Törnroos ◽  
...  
Keyword(s):  
Density Functional ◽  
Lone Pair ◽  
Catalytic Performance ◽  
Nbo Analysis ◽  
Cyclohexene Oxide ◽  
Group 4 ◽  
Low Co2 ◽  
And Performance ◽  
High Yields ◽  
Oxygen Lone Pair

Tridentate, bis-phenolate N-heterocyclic carbenes (NHCs) are among the ligands giving the most selective and active group 4-based catalysts for the copolymerization of cyclohexene oxide (CHO) with CO2. In particular, ligands based on imidazolidin-2-ylidene (saturated NHC) moieties have given catalysts which exclusively form polycarbonate in moderate-to-high yields even under low CO2 pressure and at low copolymerization temperatures. Here, to evaluate the influence of the NHC moiety on the molecular structure of the catalyst and its performance in copolymerization, we extend this chemistry by synthesizing and characterizing titanium complexes bearing tridentate bis-phenolate imidazol-2-ylidene (unsaturated NHC) and benzimidazol-2-ylidene (benzannulated NHC) ligands. The electronic properties of the ligands and the nature of their bonds to titanium are studied using density functional theory (DFT) and natural bond orbital (NBO) analysis. The metal–NHC bond distances and bond strengths are governed by ligand-to-metal σ- and π-donation, whereas back-donation directly from the metal to the NHC ligand seems to be less important. The NHC π-acceptor orbitals are still involved in bonding, as they interact with THF and isopropoxide oxygen lone-pair donor orbitals. The new complexes are, when combined with [PPN]Cl co-catalyst, selective in polycarbonate formation. The highest activity, albeit lower than that of the previously reported Ti catalysts based on saturated NHC, was obtained with the benzannulated NHC-Ti catalyst. Attempts to synthesize unsaturated and benzannulated NHC analogues based on Hf invariably led, as in earlier work with Zr, to a mixture of products that include zwitterionic and homoleptic complexes. However, the benzannulated NHC-Hf complexes were obtained as the major products, allowing for isolation. Although these complexes selectively form polycarbonate, their catalytic performance is inferior to that of analogues based on saturated NHC.

Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model

2009 ◽  
Vol 87 (12) ◽  
pp. 1738-1746 ◽  
Author(s):  
Ping Qian ◽  
Li-Nan Lu ◽  
Zhong-Zhi Yang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Potential Model ◽  
Lone Pair ◽  
Static Properties ◽  
Range Interaction ◽  
Hydrogen Bond Interaction ◽  
Lone Pair Electron ◽  
Dynamics Simulations

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

scholarly journals One-Pot Synthesis of Oxazolidinones and Five-Membered Cyclic Carbonates from Epoxides and Chlorosulfonyl isocyanate: Theoretical Evidence for the Asynchronous Concerted Pathway

2020 ◽  
Author(s):  
Esra Demir ◽  
Özlem Sarı ◽  
Yasin Çetinkaya ◽  
Ufuk Atmaca ◽  
Safiye Sağ Erdem ◽  
...  
Keyword(s):  
Potential Energy Surfaces ◽  
Density Functional ◽  
Cycloaddition Reaction ◽  
Reaction Times ◽  
Dft Method ◽  
Cyclic Carbonates ◽  
One Pot ◽  
Purification Method ◽  
Chlorosulfonyl Isocyanate ◽  
The One

The one-pot reaction of chlorosulfonyl isocyanate (CSI) with epoxides having substituted phenyl, benzyl and fused cyclic alkyl groups in different solvents under mild reaction conditions without additives and catalysts was studied. Oxazolidinones and five-membered cyclic carbonates were obtained with a ratio close to (1:1) in the cyclization reactions. The best reaction conversion for the synthesis of these compounds was carried out in dichloromethane (DCM). The method presented here has distinct advantageous over the existing methods such as one-pot reaction, shorter reaction times, metal-free reagent, good yields and very simple purification method. The mechanism for the cycloaddition reactions has been elucidated using density functional theory (DFT) method at the M06-2X/6-31+G(d,p) level. The investigation of the potential energy surfaces associated with two possible channels leading to oxazolidinones and five-membered cyclic carbonates revealed that the cycloaddition reaction takes place through an asynchronous concerted mechanism in gas phase and in DCM.

scholarly journals Hydrogen bonds in molecular crystals alanine and tyrosine: NBO analysis

2020 ◽  
Vol 64 (10) ◽  
pp. 1-6
Author(s):  
Tatiana G. Volkova ◽  
◽  
Iroda Mamirjon kizi Abdukhalimova ◽  
Irina O. Talanova ◽  
◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Molecular Crystals ◽  
Dft Method ◽  
Nbo Analysis ◽  
Chemical Modeling ◽  
Theoretical Concepts ◽  
Oh Groups ◽  
The Third

At present, the theoretical concepts of the hydrogen bond (H-bond) in condensed media, for example, in living systems, biomolecules, are not fully solved. Quantum chemical modeling is used as one of the methods for studying the nature and determining the strength of the H-bond. In this paper, we continue to study the system of hydrogen bonds in molecular crystals of alanine and tyrosine. The dimers of these amino acids were modeled using the DFT method using the B97D functional with bases 6-31++G**. In the framework of NBO analysis, the stabilization energies of the formed hydrogen bond and the value of the transferred charge are calculated. It is shown that in alanine dimers, the main factor affecting the h-bond stabilization energy is the geometric parameters and, first of all, (N-H...O). The binding σ-orbital of the hydrogen bond is the result of the interaction of a hybrid NBO of the lone electron pairs of an oxygen atom and a loosening σ*-NBO N−H bond. The nature of bond formation in all three cases is the same, and the charge transfer value is greater than the value of the bond criterion, which indicates the presence of hydrogen bonds in all analyzed alanine systems. In tyrosine dimers, two H-bonds are formed that are similar in nature, as well as in geometric and energy parameters. The third H-bond is very weak, and the amount of charge transfer indicates its absence. The main interaction between the molecules in the third tyrosine dimer is the H-bond between the –СОО− and –OH groups. It was found that the scheme of formation of hydrogen bonds in molecular crystals of tyrosine is somewhat different from that of alanine.

scholarly journals Spectroscopic, Electronic and Optical Properties of 4-Nitroimidazole using DFT Calculations

2020 ◽  
Vol 33 (1) ◽  
pp. 83-88
Author(s):  
S. Jeyavijayan ◽  
Palani Murugan
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Dft Method ◽  
Nbo Analysis ◽  
Spectroscopic Techniques ◽  
Functional Theory ◽  
Raman Spectroscopic ◽  
Homo Lumo ◽  
Total Energy Distribution ◽  
Ft Raman

Theoretical and experimental vibrational spectra of 4-nitroimidazole were studied by FTIR, FT-Raman spectroscopic techniques and density functional theory (DFT) method. The contributions of the different modes to each wavenumber were confirmed using total energy distribution (TED). The optimized parameters and thermodynamic properties of 4-nitroimidazole have been computed. The charge transfer interactions of the molecule were explained from the small value of HOMO-LUMO energy gap. The NBO analysis, Mulliken’s plot and MEP studies of the molecule have also been reported.

Supramolecular Structure in the Cocrystal of 3, 5-Bispyridyl-1-H-1, 2, 4-Triazole and 4,4-Oxybis(Benzoic Acid)

2013 ◽  
Vol 781-784 ◽  
pp. 531-535
Author(s):  
Ting Li ◽  
Bing Li ◽  
Xiao Yan Chen ◽  
Jun Mei Wang ◽  
Lin Sun ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Benzoic Acid ◽  
Self Assembly ◽  
Cobalt Acetate ◽  
Intermolecular Hydrogen Bonds ◽  
Hydrogen Bond Interaction ◽  
Monoclinic System ◽  
One Dimensional ◽  
Carboxylate Groups ◽  
The One

A new cocrystal (3,4-Hbpt)-(H2oba) (3,4-Hbpt =3-(3-pyridyl)-5-(4-pyridyl)- 1-H-1,2,4-triazole and H2oba=4,4-oxybis (benzoic acid)), was prepared via self-assembly in the presence of cobalt acetate as template by hydrothermal reactions. The title complex was characterized by single-crystal X-ray diffraction, elemental analysis and IR spectroscopy. Structural analysis reveals that the complex belongs to monoclinic system, space group P21/c. The two carboxylate groups from H2oba are not deprotonated and form two kinds of strong intermolecular hydrogen bonds with 3,4-Hbpt, which linking the molecules into one-dimensional chains. Furthermore, the one-dimensional chains are connected by the hydrogen bond interaction to form two-dimensional lamellar structures. Intermolecular hydrogen bonds may be effective in the stabilization of the crystal structure.

Solvent effects on the infrared spectra of anilines. VII. 2-Substituted 4-nitroanilines

1970 ◽  
Vol 23 (5) ◽  
pp. 947 ◽  
Author(s):  
LK Dyall
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Infrared Spectra ◽  
Solvent Effects ◽  
Intermolecular Hydrogen Bond ◽  
Lone Pair ◽  
Acceptor Molecule ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Ortho Substituent

Measurements of N-H stretching frequencies of 4-nitroanilines in the presence of hydrogen bond acceptors show that the ease of forming a second intermolecular hydrogen bond in the presence of an ortho substituent decreases in the order hydrogen > methyl > bromo, methoxyl > nitro. This order demonstrates the importance of repulsions between lone pair orbitals on the ortho substituent and the acceptor molecule. Weak intramolecular hydrogen bonds are detected in 2-iodo- and 2-bromo-aniline, and such bonds can be strengthened by introduction of a 4-nitro substituent.

Effects of intermolecular hydrogen bonding on the excited-state proton transfer properties of the cinnamonitrile–methanol complex

2013 ◽  
Vol 91 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Dapeng Yang ◽  
Ruiquan Qi
Keyword(s):  
Hydrogen Bonding ◽  
Excited State ◽  
Charge Transfer ◽  
Proton Transfer ◽  
Density Functional ◽  
Dft Method ◽  
Electronic Energy ◽  
Intermolecular Hydrogen Bonding ◽  
Excited State Proton Transfer ◽  
Hydrogen Bonded

The time-dependent density functional theory (TD-DFT) method was used to study the excited-state proton transfer (ESPT) properties of the hydrogen-bonded cinnamonitrile (3TPAN)–methanol (MeOH) complex (3TPAN–MeOH). The intermolecular hydrogen bonds N1···H11 in both the ground state S0 and the excited state S1 were demonstrated by the optimized geometric structures of the hydrogen-bonded 3TPAN–MeOH complex. While in the excited state S3, a new hydrogen bond H11···O1 was formed after the ESPT took place from the hydrogen-bonded MeOH molecule to the 3TPAN moiety. It was demonstrated that the electronic transitions of the S1 states for both the 3TPAN monomer (including the S3 state) and the hydrogen-bonded 3TPAN–MeOH complex should be of a localized-excited (LE) nature on the 3TPAN molecule, while the S3 state of the hydrogen-bonded 3TPAN–MeOH complex should be of charge transfer (CT) character from the hydrogen-bonded MeOH molecule (through O1···H11) to the 3TPAN moiety. The S3-state proton transfer and charge transfer due to the intermolecular hydrogen-bonding interaction should be the reasons for the remarkable redshift (0.91 eV) of the S3-state electronic energy for the hydrogen-bonded 3TPAN–MeOH complex compared with that of the 3TPAN monomer.

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