Biomedical subjects

Ning-Bew Wong

Publications and source records attributed to Ning-Bew Wong.

12 recordsLinked to original sources

PubMed2006

What makes the cylinder-shaped N72 cage stable?

Recent theoretical studies have suggested that the stabilizing factors for large nitrogen cages tend to favor more five-membered rings, more three-membered rings, and cylindrical structures with large numbers of layers. One of the major issues in this study of the all-nitrogen molecule is the determination of what brings about the stabilizing factors. Herein, the cylinder-shaped molecule of N72 (D3d) has been studied in detail. The geometry and energies are examined at B3LYP/cc-pVDZ, and single-point energy calculations at MP2/cc-pVDZ are carried out for the purposes of determining relative thermodynamic stability. Natural bond order (NBO) analysis and atoms in molecules (AIM) analysis are applied to investigate the bonding properties of the cage molecule. The major result of this study is the identification of intramolecular interactions, whether it is at B3LYP/cc-pVDZ or at MP2/cc-pVDZ, as the dominant stabilizing factor for the large all-nitrogen cage. The length of the cylinder-shaped molecule is about 2.2 nm. N72 (D3d) might be one novel nanomaterial which is environment friendly, and as a beeline nanotube or a beeline "nano-bar", it is expected to impact a wide range of applications.

Journal Article↗

PubMed2006

Theoretical study on the cylinder-shaped N78 cage.

Recent theoretical studies have suggested that the stabilizing factors for large nitrogen cages tend to favor more five-membered rings, more three-membered rings and cylindrical structure with large numbers of layers. Further studies of relative stability of the all-nitrogen molecule have prompted to figure out what brings about the stabilizing factors. Herein, the cylinder-shaped molecule of N(78) (D(3h)) has been studied in detail. The geometry and energies are examined at B3LYP/cc-pVDZ and single point energy calculations at MP2/cc-pVDZ are carried out for the purposes of determining relative thermodynamic stability. NBO analysis and AIM analysis are applied to investigate the bonding properties of the cage molecule. The major result of this study is the identification of intra-molecular interactions, whether it is at B3LYP/cc-pVDZ or at MP2/cc-pVDZ, as the dominant stabilizing factor for the large all-nitrogen cage. The length of the cylinder-shaped molecule is about 2.5nm. N(78) (D(3h)) might be one novel nanomaterial which is environment-friendly and as a beeline nanotube or a beeline "nano-bar", it is expected to impact a wide range of applications.

Drug Stability↗

PubMed2006

Microsolvation effect, hydrogen-bonding pattern, and electron affinity of the uracil-water complexes U-(H2O)n (n = 1, 2, 3).

To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.

Electrons↗

PubMed2006

Theoretical investigation on the replacement of CH groups by N atoms in caged structure (CH)8.

A molecular design was performed for the caged molecule (CH)8: the replacement of CH groups by N atoms to increase the content of N as well as reduce the content of H. A series of caged molecules were obtained: (CH)xN(8-x) (0 < or = n < or = 8). The studied aspects are as follows: (i) molecular geometries and electronic structures, (ii) the analysis of the electronic structure using natural bond orbital (NBO) and atoms in molecules (AIM), and (iii) some physicochemical properties of studied molecules, such as the dipole moments, IR vibrational spectra, NMR chemical shifts, heats of formation, and relative specific impulses, were provided. Our studies show that these molecules should be a kind of potential and novel energetic material. Our work provides some useful information for the experimental study of these molecules. The effect of the substitution of N atoms for CH groups on the properties of this kind of caged molecule is presented.

Journal Article↗

PubMed2006

Theoretical study on "multilayer" nitrogen cages.

The relative stabilities of nonisomers are investigated. Twenty-two species of nitrogen cage molecules N(2n) (N6 (D(3h)), N8 (Oh), N10 (D(5h)), N12 (D(6h)), N12 (D(3d)), N16 (D(4d)), N18 (D(3h)), N20 (Ih), N24 (D(3d)), N24 (D(4h)), N24 (D(6d)), N30 (D(3h)), N30 (D(5h)), N32 (D(4d)), N36 (D(3d)), N40 (D(4h)), N42 (D(3h)), N48 (D(4d)), N48 (D(3d)), N54 (D(3h)), N56 (D(4h)), and N60 (D(3d))), which are divided into four sets, have been studied in detail. The geometries and varieties of energies are examined extensively, and NBO analysis and AIM analysis are applied to investigate the bonding properties of the cage molecules. The introducing of the concept of "layer" can well assist in explaining why one nonisomer molecule is more stable than another one. The results show that the lengths of bonds, on both sides of which are five-membered rings (referred to as pentagons), are the shortest and the orbital energies are the lowest. The nonlocalized electron numbers of orbitals, on at least one side of which is a triangle, are the greatest. Pentagons play a major role in the stability of a cage molecule, and the three-membered rings (referred to as triangles) play the second one. The layers in nitrogen cage molecules also contribute to the relative stabilities.

Energy Transfer↗

PubMed2006

Modeling of hydrogen bonds in monohydrated 2,4-dithiothymine: an ab initio and AIM study.

Twelve tautomers of 2,4-dithiothymine are calculated at the MP2/6-31+G(d) level, and the most stable one is referred to the di-keto form (P12). Then four H-bonded complexes between P12 and water are optimized at the MP2/6-31+G(d) level of theory. The calculation of vibrational frequencies and natural bond orbital analysis are also carried out at the same level to investigate the hydrogen bonds involved in all the systems. Within all the four complexes, three types of hydrogen bonds are formed, in which the O-H...S and N-H...O bonds are the normal bonds with the X-H bond elongation and red shift of the corresponding stretch frequencies, while the C-H...O interaction is an improper, blue-shifting hydrogen bond accompanied with the contraction of the C-H bond and a blue shift of the C-H stretch frequency. The topological properties are investigated with the atoms-in-molecules (AIM) theory. The NMR chemical shielding for the isolated and the four monohydrated 2,4-dithiothymine are calculated using the "gauge-including atomic orbital" (GIAO) method. The 1H chemical shifts are influenced by the formation of hydrogen bonds.

Hydrogen Bonding↗

PubMed2005

Ab initio computational insight into the ion-pair S(N)2 reaction of lithium isothiocyanate and methyl fluoride in the gas phase and in acetone solution.

The ion-pair S(N)2 reaction LiNCS + CH3F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction pathways in the title reaction are proposed. The inversion mechanism through a six-membered-ring transition-state structure is the most favorable. Methyl thiocyanate should form preferentially in the gas phase and the more stable methyl isothiocyanate will be the main product in CH3COCH3. The retardation of the reaction in CH3COCH3 solution was attributed to the differences in the solvation free energies in the separated reactants and transition structures. All of the theoretical results are consistent with the experiment.

Acetone↗

PubMed2005

Theoretical study on the bromomethane-water 1:2 complexes.

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.

Journal Article↗

PubMed2005

Anion-tri-s-triazine bonding: a case for anion recognition.

An ab initio study of the possible interaction between several anions (F(-), Cl(-), N(3)(-), N(4)(-), and N(5)(-)) and tri-s-triazine molecule, an electron-deficient aromatic ring, has been carried out at the B3LYP and MP2 levels of theory. Minima are located corresponding to hydrogen bonding, pi-pi stacking, and reactive complexes. This novel mode of bonding suggests the development of new cyclophane-type receptors for the recognition of anions.

Journal Article↗

PubMed2005

Prototropic tautomerism of imidazolone in aqueous solution: a density functional approach using the combined discrete/self-consistent reaction field (SCRF) models.

A systematic investigation of the proton transfer in the keto-amino/enol tautomerization of imidazolone was undertaken. Calculations in aqueous solution were performed using both combined discrete/self-consistent reaction field (SCRF) and SCRF methods. Complexes containing one to three water molecules around the hydrophilic site of imidazolone were used for the combined discrete/SCRF calculations. The DFT results predict that the barrier height for non-water-assisted intramolecular proton transfer is very high (214.8 kJmol(-1)). Hydrogen bonding between imidazolone and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process through a eight-member ring formed by imidazolone and two water molecules is found to be more efficient and the calculated barrier height is ca. 61 kJmol(-1).

Hydrogen Bonding↗

PubMed2002

Templating effect of hydrogen-passivated silicon nanowires in the production of hydrocarbon nanotubes and nanoonions via sonochemical reactions with common organic solvents under ambient conditions.

A new type of well-structured, hydrocarbon nanomaterial including nanotubes and onions, with interlayer spacing ranging from 3.4 to 5.8 A, was discovered by reacting SiNWs with common organic solvents in a laboratory sonicator under ambient conditions (room temperature and atmospheric pressure).

Journal Article↗

PubMed2002

Formation of silicon carbide nanotubes and nanowires via reaction of silicon (from disproportionation of silicon monoxide) with carbon nanotubes.

One-dimensional silicon-carbon nanotubes and nanowires of various shapes and structures were synthesized via the reaction of silicon (produced by disproportionation reaction of SiO) with multiwalled carbon nanotubes (as templates) at different temperatures. A new type of multiwalled silicon carbide nanotube (SiCNT), with 3.5-4.5 A interlayer spacings, was observed in addition to the previously known beta-SiC (cubic zinc blende structure) nanowires and the biaxial SiC-SiO(x) nanowires. The SiCNT was identified by high-resolution transmission microscopy (HRTEM), elemental mapping, and electron energy loss spectroscopy (EELS). The multiwalled SiCNT was found to transform to a beta-SiC crystalline structure by electron beam annealing under TEM.

Journal Article↗