Total Steric Energy Research Articles

Theoretical Analysis of Stereoelectronic Effects in the 2,4,6-Trihalo-1,3,5-trioxane and 2,4,6-Trihalo-1,3,5-trithiane Conformers

This research aimed at exploring the conformers stabilities of 2,4,6-trihalo-1,3,5-trioxane and 2,4,6-trihalo-1,3,5-trithiane molecules at the LC-wPBE/6-311+G(d, p) theory level. To this goal, estimations of the total energies and frontier orbitals energies of the axial and equatorial conformations were first done for the afore-mentioned molecules. C–E (E = O, S), C–X (X = F, Cl), and C–H bonds lengths were calculated and these variations were explained with negative hyperconjugative anomeric effects. In addition, QTAIM analysis was used to illustrate the character of these bonds. The partitioning of the total electronic energy E(tot) into Lewis EL and non-Lewis ENL parts was performed using the concept of natural bond orbital (NBO) analysis. Then, the natural Coulomb electrostatic (NCE) potential energies, total energies into Lewis components, and total steric energies were estimated. Proton chemical shift and C–H spin–spin coupling values (J(C–H)) of the studied molecules were calculated.

DFT and NBO Studies of Stability, Electronic, and Structural Features of the 2-fluoroacetaldehyde Conformers

In this investigation, the stability of the keto-enol forms and conformers of 2-fluoroacetaldehyde was investigated by LC-wPBE, B3LYP and M06-2X functionals and 6-311++G(d,p) basis set. The total energy, the energies of frontier orbitals, HOMO-LUMO gaps and total dipole moment of these molecules were estimated. These calculations show that more stability of the keto form in compared to enol form. Calculations at the LC-wPBE/6-311++G(d,p) level of theory reveal the more stability of I-conformer in compared to other conformers. Natural bond orbital (NBO) analysis was applied for illustrating the negative hyperconjugative effect on the conformers. In the basis of NBO analysis, the LP (O2) *(C-H) and LP (O2) *(C-C) interactions were responsible of the negative hyperconjugation in the examined compounds. The interaction energy, off-diagonal elements, and total steric energy values of these interactions were reported.

Bound Water and Hydroxyproline are the essential contributors to collagen molecular stability: A Computational Analysis

Being the primarily organic phase of bone, collagen type I is an important contributor to bone’s mechanical resistance to fracture. Gaining mechanistic insight into collagen stabilization mechanism is critical to developing new targets to prevent bone fracture. The role of water and hydroxyproline (Hyp) in collagen stability mechanism is still controversial. The aim of this study was to investigate the influences of Hyp and bound water on the collagen molecular stability. Four collagen like-peptide (CLP) models were compared in terms of conformational energies and hydrogen bonding types. CLP1 model represents regular collagen structure without water molecules while CLP2 model represents collagen structure without water and Hyp residue. CLPW1 and CLPW2 are the models of CLP1 and CLP2 with water molecules around them, respectively. Cumulative interpreting of four CLPs models was shed light on the factors influencing collagen stability in the frame of steric energy. Total steric energy was ordered as: CLP2 > CLP1 > CLPW2 > CLPW1, indicating that CLPW1 was the most stable collagen model. On the other hand, CLP2 was the least stable collagen model based on the steric energy comparison. In addition, the hydrogen bonding observed in the four models reveled that water molecules around the models help in binding collagen triple helix through different water bridges since they contributed extra way for binding of triple chains. Moreover, some of the observed water bridges involved directly the presence of Hyp residue. Cumulative results suggested the important role of bound water molecules and Hyp on collagen molecular stability.

Computer simulation of fatty acids

Fatty acids modified by sulfhydric collectors are investigated. Three-dimensional molecular models are constructed for these acids and the main computer parameters of the total steric energy are determined. Based on the computer design, new reagents are suggested and molecular models are constructed and the total steric energy is calculated for them.

Optimization of a molecular mechanics force field for type‐II polyoxometalates focussing on electrostatic interactions: A case study

In this study, we have focussed on type-II polyanions such as [M(7)O(24)](6-), and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type-I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed-charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4-interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM-optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta-anions interacting with organic molecules.

Study of reactor-NO2-gas diffusion in a porous glass chip by near-infrared Raman spectroscopy

We have used near-infrared (NIR) Raman spectroscopy to study a coloration reaction that occurs in nano-sized pores in a porous glass chip. This coloration reaction is a modified Saltzman reaction that produces an azo dye by selective reaction with nitrogen dioxide gas (NO2). Neither the details of the reaction mechanisms in the nano-sized pores nor the interaction between the products and the pore surface have previously been investigated. We analyzed the mechanism by measuring the Raman intensity of the azo dye produced in the pores. We found that, in the early stages of NO2 exposure, the NO2 gas reacts at the surface of the porous glass chip, while in the later stages more NO2 gas diffuses into deeper areas without reacting with the reagent. We estimated the limit of the NO2 gas diffusion distance to be about 500 μm. We also analyzed the interaction between the azo dye and the surface of the pores by comparing the Raman spectrum in the porous glass chip with that in a bulk d4-methanol solution. The azo dye is mainly adsorbed as a result of hydrogen bonding between the π-electrons of the phenyl group and the silanol of the glass surface. We also determined that the azo dye has a trans-conformation molecular structure by calculating the total steric energy. The interaction between the azo group and the silanol is weaker in the adsorbed state than in bulk, due to the steric effect of the bulky substituents around the azo group. Our proposed geometry for the azo dye adsorbed on the surface of the pores has a flatter orientation.

Atomic and electronic structures of Si-included C74 cluster studied by HREM and molecular orbital calculations

Endohedral fullerenes Si@C74 were produced by direct current and radio-frequency hybrid arc-discharge. Atomic structure analysis and structural optimization of the Si@C74 were carried out by high-resolution electron microscopy, image simulation, molecular mechanics and ab initio molecular orbital calculations. Total steric energy of the Si@C74 was the lowest in the present calculation of C60–C76 clusters. The energy gap of the Si@C74 was calculated to be 0.098 eV, and the heat of formation per carbon atom is almost the same as that of the C60 cluster.

Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH2 backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The γ global and the α, β and Δ local minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or over-estimate the relative energy of some local minima, the ID polarization energy term represents a significant correction to the total relative energy.