The full non-rigid group theory for TBA (tert-butyl alcohol)

The non-rigid molecule group theory in which the dynamical symmetry operations are defined as physical operations is applied to deduce the character Table of the full non-rigid molecule group (f-NRG) of TBA. The f-NRG of this molecule is seen to be a group of order 54 which has 27 conjugacy classes.     

Full non-rigid group theory and symmetry of melamine

The non-rigid molecule group (NRG) theory in which the dynamic symmetry operations are defined as physical operations is a new field in chemistry. Smeyers, in a series of papers, applied this notion to determine the character table of restricted NRG of some molecules. For example, Smeyers and Villa computed the r-NRG of the triple equivalent methyl rotation in pyramidal trimethylamine with inversion and proved that the r-NRG of this molecule is a group of order 648, containing two subgroups of order 324 without inversion [5]. In this work, a simple method is described, through which it is possible to calculate character tables for the symmetry group of molecules. We study the full NRG of melamine, and prove that it is a groups of order 48, with 27 and 10 conjugacy classes. Also, we compute the symmetry of melamine and prove that it is a non-abelian groups of order 6. The method can be generalized to apply to other non-rigid molecules.     

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.     

Vibrational spectra, DFT calculations, unusual structure, anomalous CH2 wagging and twisting modes, and phase-dependent conformation of 1,3-disilacyclobutane

Our previously published infrared and Raman spectra of 1,3-disilacyclobutane (13DSCB) and its 1,1,3,3-d4 isotopomer have been reexamined and partially reassigned on the basis of DFT and ab initio calculations. The calculations confirm previous microwave work that the CSiC angles in the ring are unexpectedly larger than the SiCSi angles. This may arise from the partial charges on the ring atoms. The calculations are in excellent agreement with the observed spectra in both frequency and intensity. They also demonstrate that this molecule has CH2 wagging and twisting vibrations with frequencies below 1000 cm-1, about 200 cm-1 lower than expected. These unprecedented low values can be explained by the decreased slope in the potential energy curves for these vibrations as the sideways motions of the CH2 groups result in attractive forces between the positively charged hydrogens on the carbon atoms and the negatively charged hydrogens on the silicon atoms. The theoretical calculations also confirm the previous conclusions that the individual molecules (vapor) have C2v symmetry whereas in the solid the molecules become planar with D2h symmetry. The vibrational coupling between the ring-angle bending mode and the SiH2 in-phase rocking, which is present for the C2v structure, is forbidden for D2h and hence disappears.     

A study of the internal dynamics of trimethylamine by means of the non-rigid group theory

The non-rigid molecule group theory (NRG) in which the dynamical symmetry operations are defined as physical operations is applied to determine the character table for the triple equivalent methyl rotation and pyramidal inversion in trimethylamine. The restricted NRG of this molecule is seen to be a group of order 648, formed as a product of two subgroups: the G ₃₂₄ subgroup corresponding to planar trimethylamine and the pyramidal inversion. For this purpose the structure of the r-NRG of planar trimethylamine is first deduced, i.e., the number of classes, irreducible representations, as well as their dimensions. Finally, guidelines are given to deduce systematically the symmetry eigenvectors developed on the basis of quadruple products of trigronometric functions. The r-NRG molecule group theory is seen to be used advantageously to study the internal dynamics of such small organic molecules.     

Ab initio calculation of torsion and inversion barriers of the amino group in aminopyrimidines

Calculations of the barriers to internal rotation and inversion of the amino group in substituted pyrimidines have been performed. Torsion and inversion barriers were determined by several ab initio methods: HF, HF/MP2, MP4, CISD, QCISD, QCISD(T), CCSD, and CCSD(T). DFT method also employed. Dependencies of the calculated barrier heights on the basis set and the electron correlation level and on the substitution position of the nitrogen atom in the ring were studied. We have determined that for certain molecules relatively low level calculations may eventually provide adequate results, but in general, higher level calculations are necessary.     

Normal mode analyses of methyl palmitate all-trans and disordered forms in wagging progressive region

Normal mode analyses are made for methyl palmitate molecule having all-trans or conformational disorders around the ester head group, in order to explain characteristic observed frequency shifts in the wagging progressive region between all-trans and disorder chains in triglyceride molecules. It was found that one gauche conformation at C(alpha)-C(beta) position and 90 degrees rotation of the ester head group in an alkyl chain produce frequency shifts for twisting mode as observed. For wagging modes, contamination of the disorders around the head group makes assignments change and apparent frequency shifts occur.     

Lattice-dynamical calculations for orthorhombic sulfur: a non-rigid molecular model

A lattice-dynamical calculation for orthorhombic (“α”) sulfur has been carried out with a non-rigid molecular model. A difference is observed for the lowest frequencies between the free and the packed molecule. For this reason the empirical force fields which have been fitted to the crystal should be modified, especially by lowering the torsional constants. If such a modified field is used, excellent agreement of calculated thermodynamic functions and crystallographic temperature factors with experimental data is obtained. An underestimation of nearly 2 cal mol^?1 K^?1 in the values which are currently reported for the entropy of the vapour at room temperature is also inferred.     

按非刚性转子模型计算NF3和环氧乙烷的光谱熵

NF_3和环氧乙烷(C_2H_4O)作为推进剂,曾由Sundaram按刚性转子-谐振子模型计算了其光谱熵.但由于忽略了离心力的影响,必然致使计算结果偏低(尤其在高温下).本文按Kivelson等给出的离心力校正参数τ值与离心力伸长常数D_J、D_(JK)和D_K间的关系式,由微波谱给出的数据计算了C_2H_4O的离心伸长常数(表1).改按非刚性转子—谐振子模型,采用直接加和法重新精确计算转动、振动配分函数,进而在100～2000K范围内计算了NF_3和C_2H_4O的光谱熵(表2).比较了所得结果与Sundaram的计算值     

A new far-infrared broadband absorption in non-rigid polar molecules

A new far-infrared broadband absorption has been observed for non-rigid ketone molecules in the frequency range 220 to 340 cm⁻¹. It has been found that the amplitude of this absorption increases with an increase in the flexibility of the molecule. Such an increase in the amplitude of this absorption is accompanied by a corresponding reduction in that of the Poley absorption.     

P NMR spectroscopy and discrete metallocycles from non-rigid ligands

The combination of the square-planar cis-protected Pt(II) with the 180° divergence bis(amidopyridine) bridging ligand, leads to quantitative self-assembled M₂L₂ macrocycles. The rhomboids are characterized, by multinuclear NMR and electrospray ionization mass spectroscopy. Size estimations for the rhomboid assemblies, using MM2 simulation, are given.     

An implemented potential of non-rigid water molecules for molecular dynamics simulations

The central force model for a water molecule is corrected by adding a three-body term. The present potential fits both an accurate ab initio potential energy surface and the fundamental vibrational frequencies of gas-phase water. The three-body terms allow us to reproduce the gas-phase IR spectrum by molecular dynamics simulations. Some problems connected with MD simulations of IR spectra are discussed.     

New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities

A new set of formulae is developed for the derivatives of torsion angle energy terms and is introduced into the program CHARMM. These formulae, which are based on derivatives of the torsion angle itself, avoid the singularities introduced by use of the derivatives of the torsion angle cosine. The potential energy can include any differentiable function of the torsion angle and there is no need for a special treatment for cases where planar conformations are not extrema. The resulting code is simpler than the original version and yields correct derivatives in all practical situations. Because the minimum of the torsion energy can be at any angle, the functionality of the existing energy routines is generalized. © 1996 by John Wiley & Sons, Inc.     

Far infrared investigation of aniline and 4-fluoroaniline in the vapour phase. Inversion and torsion of the amino group

Far infrared gas spectra of aniline and 4-fluoroaniline are reported and used to calculate barriers to inversion and to internal rotation of the NH₂ group. The inversional barrier increases and the torsional barrier decreases on fluorine substitution.     

The chaos-to-order transition in critical modes of shearing for polymer and nanocomposite melts

Two unusual experimental phenomena that were found for polymer melts or solutions containing the dispersed phases of Na-montmorillonite or detonation synthesis nanodiamond have been studied. These phenomena consist in the reduction of viscosity upon addition of specified amount of particles and in the formation of regular morphology by these particles in strong flows looking as a system of concentric rings. In other words, under certain conditions, there is transition to stratified shear stream and the viscosity of such a regular heterogeneous system canbe lower than that for the polymer matrix itself. Hence, both phenomena are mutually related; and the main problem here is the analysis of driving forces leading to the regular texture formation taking place in intense flows for unfilled viscoelastic polymers as well. As a preliminary explanation, the conception of the special kind of the elastic instability is discussed. This instability appears either in the regular helix-like structure formation or in the irregular elastic turbulence. The particles of the filler play a role of tracers that revealed the relief of texture.     

Dynamic model and tunneling splittings in LMH4 non-rigid hydrides

A non-rigid model for the molecules LiBH₄. NaBH₄⁺. LiCH₄⁺ is suggested on the basis of ab initio data. The model is used in numerical calculations of the levels of large-amplitude deformation-migration motion of the cation in these molecules. It is shown that the lowest states can be regarded as highly anharmonic bending vibrations, while levels above the barrier should be considered as hindered rotation of the MH₄ group. T_d symmetry is used to classify the states. Tunneling splittings of the vibrational states are 0.01–1 cm^?1.     

The 2-acetylthioethyl ester group: A versatile protective group for P-OH-groups

Phosphodiesters are bridging elements in nucleic acids. In nature and synthesis, their negative charge protects them from hydrolysis and controls their solubility profile. RNA is a promising material for gene technology but cellular uptake is low due to negative charges. Synthetic oligonucleotides were delivered into cells by a prodrug approach relying on the enzymatic release of the polyphosphodiester oligonucleotides. In synthetic chemistry, a protective group for the POH functionality is often necessary, e.g. due to solubility or chemical incompatibility. Several methods for POH protection were proposed, but often with low selectivity or harsh conditions. Here, we present the 2-acetylthioethyl group as a versatile protective group for low molecular weight or polymeric phosphodiesters, which can be cleaved under acidic conditions in water or by hydrazine in THF to release the POH-functionality, but olefins remain intact. This straightforward use allows designing various synthetic polyphosphodiesters, e.g. for flame-retardant or dispersants.     

The solubility of group I and group II fluorosulfates in fluorosulfuric acid

The solubilities at 25° of some Group I and Group II fluorosulfates in fluorosulfuric acid have been determined. The solubilities (g fluorosulfates/100 g fluorosulfuric acid) are LiSO₃F, 38.78; NaSO₃F, 80.21; KSO₃F, 63.83; RbSo₃F, 89.43; CsSO₃F, 132.4; MgSo₃F, 0.12; CaSO₃F, 16.39; SrSO₃F, 14.52 and BaSO₃F, 4.67.These results can be rationalized on the basis of lattice and solvation energy considerations. These solubility trends are consistent with those of the corresponding fluorides in hydrogen fluorides.     

The spectrum of vibration modes in soft opals

Numerous vibrational modes of spherical submicrometer particles in fabricated soft opals are experimentally detected by Brillouin light scattering and theoretically identified by their spherical harmonics by means of single-phonon scattering-cross-section calculations. The particle size polydispersity is reflected in the line shape of the low-frequency modes, whereas lattice vibrations are probably responsible for the observed overdamped transverse mode.     

The torsional barrier for the HCCH group

Ab initio calculations have been carried out to examine the torsional barrier for non-linear HCCH fragments. At the SCF level the most stable configuration is skew for all geometries studied, but this is not found when correlation is included. For acetylene bond lengths and ∠ HCC = 121.2 °, the Møller-Plesset (MP) perturbation method gives trans as the most stable structure and the resulting torsion potential agrees with that calculated from an analytic many-body-expansion (MBE) potential of Halonen, Child and Carter. When the CC bond length is increased to 1.34 Å (as in ethene) or 1.54 Å (as in ethane), the MP method is poorly convergent and unreliable. Variational (CI) calculations at 1.34 A give a minimum at the trans structure, but at 1.54 A and ∠ HCC = 110.9° a skew structure is slightly more stable than trans. The MBE potential is in poor agreement with these calculations at the longer bond lengths, and is probably in error.