Application of potential constants: Empirical determination of molecular energy components for diatomic molecules

The potential (force) constant of a diatomic molecule is applied to determine the molecular energy components such as the electronic kinetic (T) and electrostatic potential (V) energies. The theoretical framework of the method is constructed from T and V representations of the quantum mechanical virial theorem. To confirm the utility of the method developed here, the calculated molecular energy components of diatomic molecules are compared with available Hartree-Fock data. It is concluded that the present method is simple and powerful for evaluating the molecular energy components of various diatomic molecules.     

Dielectric properties of water clusters containing CO and NO molecules. Computational experiment

The absorption of CO and NO molecules by (H₂O)₂₀ clusters was studied by the method of molecular dynamics. In general, the clusters containing CO molecules are more stable mechanically, while the clusters with NO molecules are more stable against heating. The mobility of NO molecules in such clusters is higher than that of CO molecules. The total dipole moment, the static dielectric permeability, the number of active electrons in the clusters, and the specific number of hydrogen bonds between water molecules possess peak values when the number of doping molecules i = 6. IR absorption spectra mostly acquire a smooth shape at i > 6. Capture of CO and NO molecules by water cluster operates as anti-greenhouse effect.     

Vibrational spectra, structure, and proton conduction in hydrous tin dioxide

SnO₂ · nH₂O (hydrous tin dioxide, HTD, n = 1.5) and SnO₂ · nD₂O (deuterated hydrous tin dioxide, DHTD) samples were studied by IR and Raman spectroscopy. The using of these spectroscopic methods elucidated some structural features of the hydrogen-bond network in HTD, where two types of water molecules and two types of hydroxide groups are present. Type 1 water molecules and hydroxide groups are found to be linked to one another by weak hydrogen bonds, as in liquid water. Type 2 water molecules and hydroxide groups are linked to type 1 water molecules and hydroxide groups by rather strong hydrogen bonds. The existence of these strong hydrogen bonds is interpreted as arising from the effect of tin ions on some water molecules and hydroxide groups. Proton conductivity in HTD was found by the impedance method to be a nearly linear function of n. The break of the line at n = 1.3 corresponds to the percolation threshold. The roles of type 1 and type 2 water molecules and hydroxide groups in the generation of proton conduction in HTD are discussed.     

Clusterization of water molecules on crystalline β-AgI surface. Computer experiment

The free energy and the work of formation of the clusters of water molecules from the vapor on the ideal continuous crystalline surface of silver iodide at 260 and 300 K are calculated with the Monte Carlo method for a bicanonical statistical ensemble. Long-range electrostatic and polarization interactions with the surface are calculated with the two-dimensional Ewald method. It is shown that the adsorption of water molecules is accompanied by their intense clusterization. At negative Celsius temperatures, hydrogen-bonded molecules form the chains on the crystal surface. The closure of chains into rings begins with the clusters containing five molecules. As cluster sizes increase, the competition between five-and six-membered cycles is ended in favor of six-membered cycles. The substrate field stimulates the formation of six-membered cycles. Entropic effects strongly level the influence of clusterization on the probability of adsorption. Within the size interval 1 < N < 15, there are two clusterization barriers whose heights are negligible and equal to about 2k _B T. The presence of a substrate lowers the vapor pressure of clusterization by more than an order of magnitude.     

Quantitative characteristics of structure inhomogeneity of water

Inhomogeneity of the local surroundings of molecules was studied for water models obtained by the molecular dynamic method. For all 3456 molecules in an independent unit cell, the volume of the Voronoi polyhedron (VVP) constructed around the oxygen atom, the tetrahedricity index (T), and the potential energy of the molecule (E _pot) were calculated. Based on the values of these parameters, the molecules were grouped into two classes. The first class included molecules for which this parameter was smaller than a certain critical value; the second included molecules for which the parameter exceeded the critical value. The critical value was chosen (for each configuration) such that each class contained exactly 50% of all molecules. Then it was investigated how many molecules belonged to each of these classes among the four nearest neighbors of the given sort. Deviation from the value obtained for random distribution of molecules of two sorts can serve as a measure of structure inhomogeneity, which shows itself as the tendency of a molecule to be surrounded by alike molecules. Since approximately half of all molecules are donors (and acceptors) for two hydrogen bonds at room temperature (a ₂ d ₂ type of coordination), a similar procedure is applicable to types of coordination of molecules. Molecules with a ₂ d ₂ coordination can be assigned to one class, while all other molecules can be considered as belonging to the other. Inhomogeneity of structure is most conspicuous for distribution of molecules with low and high values of the VVP (this is especially true of the surroundings of molecules with small values of VVP). The environment of molecules with high values of E _pot and of molecules with surroundings other than a ₂ d ₂ is nearly random.     

Molecular beam diagnostics with internal state selection: Velocity distribution and dimer formation in a supersonic Na/Na2 beam

The velocity distribution parallel and perpendicular to the molecular beam axis has been determined for molecules in well defined quantum states using TOF — via optical pumping and the Doppler-shift method. It has been found that the flow velocity as well as the speed ratio changes with the internal energy of the molecule. The flow velocity increases with increasing internal energy at low pd values (p is the pressure in the oven, d is the nozzle diameter) while the opposite is true at high pd values. The parallel speed ratio is smaller for molecules in vibrationally excited states and the perpendicular velocity distribution shows excessive tails that are more pronounced for molecules in higher lying levels. The population of individual levels has been monitored via laser induced fluorescence. It does not change monotonically with pd. The population distribution is not in thermal equilibrium and can only be approximately described by a temperature of T_υ, ≈ 150 K. On the basis of these results a simple model for the influence of the recombination of atoms on the expansion is derived: Molecules are initially neither formed in the υ = 0 vibrational level nor with high internal excitation but probably with ? 1000 cm^?1 of internal energy. The recombination leads to fast atoms and molecules. It is the incomplete deceleration of these fast particles together with an efficient quenching process for the internal energy that determines the flow velocity of molecules in individual quantum states at low pd values. At high pd values the acceleration of molecules with much internal energy is incomplete because those molecules have necessarily made only few collisions.     

An alternative way to analyze the electron distribution in ab initio calculations

An alternative method is proposed to analyze the electron distribution in molecules. Explicit formulae are given to calculate the number of electrons N(S) in a sphere with radius S and the spherically averaged electron density ?_o(S) around any center for gaussian-type functions. Also the formulae for the number of electrons in a parallelepiped are given. The calculated electron number in a sphere and in a parallelepiped can be compared with experimental values determined by X-ray analysis. The plots of N(S) and ?_o(S) against S are one-dimensional ways to represent the electron distribution in molecules. Several examples of possible applications are shown for some hydrides.     

Recherches sur la structure électronique de composés soufrés (méthode L.C.A.O. améliorée)

Improved L.C.A.O. method primitively built for conjugated molecules holding only atoms of second row in the periodic classification is extended to molecules holding atoms of the third row. The application is done for thiophen, thioketones, SO₂ and SO₃. d orbitals are not introduced in this study. Discussion about results shows that d orbitals must be introduced when the sulphur atom is strongly positively charged like in sulphur oxides.     

Ab initio calculation of the first order term of the intermolecular energy near the van der Waals minimum

The first order term of the intermolecular energies between two hydrogen molecules and between Li⁺ and H₂ has been computed by three different methods: two of them are based on a perturbative procedure, including or neglecting the overlap between the orbitals of the interacting molecules or atoms in the calculation of the electrostatic and exchange terms. We can then study the effect of the overlap on each of these terms. The third method is the SCF supermolecule treatment which provides results in very good agreement with the perturbative procedure including the overlap. TheT configuration in the case of two hydrogen molecules and theC _2v configuration for Li⁺+H₂ are stable with respect to the first order term.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center ofRps. viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteriaRhodopseudomonas (Rps.)viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises theE _LUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease theE _LUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacteriochlorophyll (ABChl b). It is insufficient to treat the whole protein surrounding as a homogeneous dielectric medium.     

Defective disordered crystal structure of (2-hydroxyphenyl)diphenylphosphineoxide

A disordered defective crystal structure of (2-hydroxyphenyl)diphenylphosphineoxide (I) has been studied by XRD method. The rhombic structure of I (space group Pna2₁, a = 18.271 Å, b = 8.337 Å, c = 19.629 Å, Z = 8) was solved by a direct method and refined by a full-matrix LSM having taken into account its crystal packing defects (by introducing two additional independent low-populated molecules) to R = 0.060 for all 3517 independent reflections measured (a CAD-4 autodiffractometer, λMoK _α. There are two independent molecules A and B with population 0.90 and two additional independent molecules C and D with population 0.10 in the structure of I.     

New pathway to triammine complexes of chromium(III): Crystal structure of 1-chloro-2,3-diaquo-4,5,6-triamminechromium(III) chloride

A new synthetic method to triammine complexes of Cr(III) is reported, via a hydrolytic process from tetrammine complexes. The crystal and molecular structure of 1 -chloro - 2,3 - diaquo - 4,5,6 - triamminchromium(III) chloride are described. The crystals are orthorombic, space group Pnma, with a = 13.230(2), b = 10.545(1), c = 6.754(1) Å, V = 942.3(3), Z = 4. Least-squares refinement of the structure based on 529 observations led to final discrepancy indices of R = 0.047 and R_w = 0.056. The Cr atom is bonded to two water molecules, three ammonia molecules and one chlorine atom in a distorted octahedral coordination showing a trans chloro-aquo configuration.     

Stark quantum beat spectroscopy of polyatomic molecules

We derive analytical expressions for Stark quantum beat signals of polyatomic molecules and discuss them with regard to molecular and geometrical parameters. The general treatment is specified for near prolate asymmetric rotor molecules and a method for determining rotational constants and all components of the dipole moment of electronically excited polyatomic molecules is presented. The method is tested and illustrated for the vibrationlessS ₁ state of deuterated propynal (HC ≡ CCDO,C _s symmetry) and its lowest frequency non-totally symmetric state 12¹. The results of the vibrationless state are compared with structural data reported in the literature. For the 12¹ state we obtainA=1.5004(43) cm^?1,B=0.16131(34) cm^?1,C=0.14623(34) cm^?1, and the components of the electric dipole moment in the molecular plane μ _a =?0.88(2)D, μ _b =1.03(2)D. Furthermore, it is shown that the modulation depth of Stark quantum beat signals can be utilized to quantify the contribution of the individual components of the transition moment to the total emission.     

Fast atom bombardment mass spectrometry of Mycobacterial glycopeptidolipid antigens: Structural characterization by charge remote fragmentation

Mycobacteria contain species- and type-specific antigens. Among them, glycopeptidolipids are present in medically relevant organisms belonging to Mycobacterium avium or M. fortuitum complexes. Fast-a tom bombardment mass spectrometry of glycopeptidolipids has proven to be difficult. In this article the cationization method with a metanitrobenzyl alcohol matrix, doped with sodium iodide, is described for analyzing these molecules. The molecular weight of the intact glycopeptidolipids was successfully determined and, using mass-analyzed ion kinetic energy spectrometry, the complete sequences of the peptide and saccharide moieties were elucidated. Moreover, the two structural variants present in these molecules were clearly differentiated. Application of the method showed that the same structural variant occurs in the glycopeptidolipids from two serologically related species of the M. fortuitum complex.     

Synthesis and crystal structure of triaqua(18-crown-6)calcium bis(perchlorate) 18-crown-6 monohydrate

A complex [Ca(18C6)(H₂O)₃]²⁺(ClO ₄ ^? · 18C6 · H₂O is synthesized and studied by X-ray diffraction analysis. The structure (space group P2₁/n, a = 11.570 Å, b = 16.024 Å, c = 22.225 Å, β = 98.89°, Z = 4) is solved by a direct method and refined by the full-matrix least-squares method in the anisotropic approximation to R = 0.075 for 5305 independent reflections (CAD4 automated diffractometer, λMoK _α radiation). In the complex cation of the host-guest type, the Ca²⁺ cation lies in the cavity of the 18-crown-6 ligand and is coordinated by all the six O atoms and three O atoms of three water molecules. In a crystal, the alternating complex anions, 18C6 molecules, and water molecules are joined by hydrogen bonds into broad infinite chains along the y axis. The disordered ClO ₄ ^? anions are bonded to these chains on the side through hydrogen bonds.     

The polar tensors,effective charges and separation ratios of overlapped bands in methanes

The separation ratios for the overlapped bands of CH₃D, CD₃H and CH₂D₂ molecules have been obtained by a method based on the differences in molecular and electronic symmetry point groups. The signs of all the ∂P/∂Q_i elements are established. Also, the atomic polar tensors and effective charges are calculated using the intensities of all five CH_xD_4−x molecules.     

Failure of the CNDO/2 method for predicting the conformations in some systems with “localized” bonds

Results from the literature show that the CNDO/2 method fails to represent adequately the conformational properties of the molecules H_mA-BH_n and their substituted derivatives, when both atoms A and B bear one or two lone pairs. This is in contradiction with the claim that the CNDO/2 method is generally valid for molecules which may be considered as having only “localized” bonds.     

Study on the difference in adsorption thermodynamics for water on swelling and non-swelling clays with implications for prevention and treatment of pneumoconiosis

Excessive inhalation of mineral dust can cause irreversible damage such as diffuse fibrosis of lung tissue. Water-based dust reduction technology can effectively control the dust concentration. The study of the interaction of water-clay mineral dust is helpful to the prevention and treatment of pneumoconiosis by water-based dust removal technology. To better understand the underlying adsorption mechanisms of water molecules on clay mineral dust, the detailed adsorption thermodynamics analysis is necessary. In this paper, we research the thermodynamics of adsorption of water molecules on swelling clay of montmorillonite and non-swelling clay of illite. First, the adsorption isotherms of water molecules on montmorillonite and illite at 293–313 K were measured by gravimetric method. Then, the key thermodynamic variables, including entropy change (ΔS), surface potential (Ω), isosteric heat of adsorption (Q_st) and variation of Gibbs free energy (ΔG), were analyzed. Results illustrate that the adsorption amount for water molecules on illite is one order of magnitude smaller than that on montmorillonite, suggesting that swelling clay plays a dominant role in water molecules adsorption process. For water molecules adsorption on montmorillonite, the contribution of secondary adsorption to total adsorption (a₂/a) is always less than 30%. For water molecules adsorption on illite, the contribution of primary adsorption to total adsorption (a₁/a) is greater than a₂/a at the low pressure region, while a₂/a can exceed 60% at the high pressure region. The difference in the uptakes of water molecules adsorption on non-swelling and swelling clays is mainly resulted from the difference in primary adsorption on two clays. The Henry’s constant (K_AA) for montmorillonite is in the range of 21.37–75.08 mmol/g/kPa, which is evidently larger than the K_AA values of 0.34–0.98 mmol/g/kPa for illite. Compared with non-swelling clay, the adsorption spontaneity degree for water molecules on swelling clay is higher, and the interaction of swelling clay-water molecules is stronger. Meanwhile, the movement of adsorbed water molecules in swelling clay is more confined than that in non-swelling clay. These findings can offer meaningful guidelines for the prevention and treatment of pneumoconiosis.     

Gas phase hydrogen / deuterium exchange in electrospray ionization mass spectrometry as a practical tool for structure elucidation

Two methods for gas phase hydrogen/deuterium exchange have been developed for the analysis of small molecules. Hydrogen/deuterium exchange has been implemented by making simple modifications to the plumbing for the nebulizer and curtain gases on a nebulization-assisted electrospray ion source. The nebulizer gas exchange method has demonstrated deuterium exchange levels of 84–97% for a variety of molecules representing a wide range of structural classes containing up to 51 potentially exchangeable hydrogens; this allowed determination of the number of exchangeable hydrogens for all of the molecules studied containing ≤ 25 labile hydrogens (M _r ≤ 3000). ND₃ gas consumption is minimized in the nebulizer method by toggling the nebulizer from air to ND₃ for only a few scans of the total sample elution period. The curtain gas exchange method is more variable, yielding exchange levels of 32–98% for the same set of molecules; this was still sufficient to allow determination of > 70% of the molecules studied containing ≤ 25 labile hydrogens. Gas consumption is minimized in the curtain method by replacing ≤ 10% of the curtain gas flow with ND₃. Neither the nebulizer nor curtain exchange method requires the use of deuterated or aprotic solvents at typical 2 μL/min flow rates.     

Vibronic effects in elastic scattering of electrons

A method for obtaining general equations for the scattered intensities from vibronic systems is given. The approximate formulas obtained are used to calculate the effects on the electron diffraction pattern for molecules with doubly degenerate electronic E terms interacting with e-type vibrations (Ee-type of problem). The results of the approximate calculations are compared to more precise results, based on numerical solution of the vibronic problem.