Search

To improve the understanding of the structure network of chalcogenide glass, we report an investigation of the structure and vibrational property of the Ge-S-Br system chalcogenide glass. The structural origin was interpreted by the result of ab initio calculation performed on the basic units such as ethane-like(ETH) structure(Ge2S6 and Ge2Br6),edge-sharing(ES) structure Ge2S2SnBr4-n (n=0,1,2,3,4) and isolated GeSnBr4-n tetrahedron (n=0,1,2,3,4), which represent the local structure of Ge-S-Br glassy system. In addition, We have compared the experimental spectra of GeS2, GeS3Br, GeSBr2 glasses and liquid GeBr4 to the calculated main vibrational modes of basic units by ab initio calculation. The calculated vibrational modes of the GeSnBr4-n cluster are assigned by group theory. Moreover, the symmetrical stretching modes related to the Ge-S and Ge-Br bond are in accordance with the vibrational coupling theory. The variation of calculated main vibrational modes of GeSmBrn clusters reveals the structure formations of Ge-S-Br glassy system with different S/Br ratios, which can be in agreement with vibrational spectra of Ge-S-Br glass. [ABSTRACT FROM AUTHOR]

The vibrational properties of molecular crystals in the terahertz range are controlled by the interplay of intermolecular and intramolecular interactions. The resulting delocalized normal modes span a substantial number of atoms within the unit cell of the molecular crystals and cannot be easily attributed to a specific stretching or bending mode. Several compounds were studied to understand the nature of normal modes. However, a systematic analysis of saccharides is still missing. This study investigates the terahertz vibrational properties of various saccharides, including glucose, galactose, lactose, cellobiose, and cellulose. The terahertz spectra were measured using terahertz time-domain spectroscopy. The samples were carefully characterized, and the residual Fabry–Perot oscillations were removed to obtain the absorption coefficient and refractive index of the saccharides. Density functional theory simulations were used to obtain theoretical terahertz spectra, considering hydrogen bonding interactions with an enhanced version of the van der Waals non-local density functional. The results revealed differences in low-energy vibrational modes frequencies, influenced by molecular structure properties, hydrogen bonding networks, and water content. Librations and internal vibrations were identified as dominant dynamics in the saccharides, with significant mixing between intermolecular and intramolecular vibrations. This comprehensive analysis sheds light on the vibrational behavior of saccharides in the terahertz range. [ABSTRACT FROM AUTHOR]

The vibrational properties of molecular crystals in the terahertz range are controlled by the interplay of intermolecular and intramolecular interactions. The resulting delocalized normal modes span a substantial number of atoms within the unit cell of the molecular crystals and cannot be easily attributed to a specific stretching or bending mode. Several compounds were studied to understand the nature of normal modes. However, a systematic analysis of saccharides is still missing. This study investigates the terahertz vibrational properties of various saccharides, including glucose, galactose, lactose, cellobiose, and cellulose. The terahertz spectra were measured using terahertz time-domain spectroscopy. The samples were carefully characterized, and the residual Fabry–Perot oscillations were removed to obtain the absorption coefficient and refractive index of the saccharides. Density functional theory simulations were used to obtain theoretical terahertz spectra, considering hydrogen bonding interactions with an enhanced version of the van der Waals non-local density functional. The results revealed differences in low-energy vibrational modes frequencies, influenced by molecular structure properties, hydrogen bonding networks, and water content. Librations and internal vibrations were identified as dominant dynamics in the saccharides, with significant mixing between intermolecular and intramolecular vibrations. This comprehensive analysis sheds light on the vibrational behavior of saccharides in the terahertz range.

Vibrational behavior and host-guest interaction of C 7 D 14 molecule (the most representative large molecular guest hydrate) in 51268 cage of structure H hydrate. [Display omitted] • The Raman spectral confusion of 512 cage and 435663 cage have been clarified by Density Functional Theory and in situ Raman spectra, which provides a theoretical basis for the accurate determination of sH hydrate. • The stretching vibration Raman spectrum of C 7 D 14 in the 51268 cages of sH is reported for the first time, which provides a basis for regulating the formation of macromolecular hydrate. • A high precision Raman spectral resolution method of Raman wavenumber for multi-hydrocarbon supramolecular was raised. • Repulsion and attraction among guest and host molecules cooperatively stabilizes the cluster structure. • Raman spectral calibration equation for hydrate under different temperature and pressure was proposed. The formation of complex multi-guest clathrate hydrates, which are more stable than single-guest ones, has expanded the clathrate hydrate stability phase space. Multi-guest clathrate hydrate may lead to the formation of sI, sII, and sH structures, introducing a variety of possible guest occupancy and crystal composition; the occupancy of sH cages in particular remains poorly understood. We report the occupancy of methane (CH 4) in the 512 and 435663 cages of sH measured via in situ Raman spectrum and density functional theory, identifying the corresponding peak position for the C–H stretching mode at 2909.80 cm−1 and 2912.40 cm−1, respectively. The in situ Raman spectrum of C 7 D 14 in the 51268 cages of sH is also reported for the first time. Vibrational-mode analysis shows that repulsion and attraction among guest and host molecules cooperatively stabilizes the cluster structure. In addition, our work provides an accurate method of distinguishing sI and sH hydrates by in situ Raman spectroscopy, offering a spectroscopic basis for the study of crystal transformation dynamics in polymorphous clathrate hydrates. [ABSTRACT FROM AUTHOR]

Spectral gaps in the vibrational modes of disordered solids are key design elements in the synthesis and control of phononic meta-materials that exhibit a plethora of novel elastic and mechanical properties. However, reliably producing these gaps often require a high degree of network specificity through complex control optimization procedures. In this work, we present as an additional tool to the existing repertoire, a numerical scheme that rapidly generates sizeable spectral gaps in absence of any fine tuning of the network structure or elastic parameters. These gaps occur even in disordered polydisperse systems consisting of relatively few particles (N ~ 102 − 103). Our proposed procedure exploits sticky potentials that have recently been shown to suppress the formation of soft modes, thus effectively recovering the linear elastic regime where band structures appear, at much shorter length scales than in conventional models of disordered solids. Our approach is relevant to design and realization of gapped spectra in a variety of physical setups ranging from colloidal suspensions to 3D-printed elastic networks.

There are different methods to calculate the rate constant of a bimolecular reaction. In this article are described two methods to calculate the rate constant and then these methods are compared using two-channel reaction. The rate constants for each reaction channel are calculated using Transition State Theory (TST) incorporating the Winger tunneling correction and the hindered rotor approximation. Furthermore, the rate constants for the dominant channel are calculated using general equation, which takes into account the rotational energy, is derived from Rice–Ramsperger–Kassel–Marcus (RRKM) theory, using the simplified version of the statistical adiabatic channel model theory. The vibrational mode analysis is used to elucidate the relationships of the reactant region (s = −∞), the saddle point (s = 0) and the product region (s = +∞).

The degree to which DNA-linked particle crystals, particularly those composed of micrometer-scale colloids, are able to dynamically evolve or whether they are kinetically arrested after formation remains poorly understood. Here, we study a recently observed displacive transformation in colloidal binary superlattice crystals, whereby a body-centered cubic to face-centered cubic transformation is found to proceed spontaneously under some annealing conditions. Using a comprehensive suite of computer simulation tools, we develop a framework for analyzing the many displacive transformation pathways corresponding to distinct, but energetically degenerate, random hexagonal close-packed end states. Due to the short-ranged, spherically symmetric nature of the particle interactions the pathways are all barrierless, suggesting that all end states should be equally likely. Instead, we find that hydrodynamic correlations between particles result in anisotropic mobility along the various possible displacive pathways, strongly selecting for pathways that lead to the fcc-CuAu-I configuration, explaining recent experimental observations. This finding may provide clues for discovering new approaches for controlling structure in this emerging class of materials. [ABSTRACT FROM AUTHOR]

The recently presented ab initio calculations for the reaction system of CH3Cl + OH (Dehestani and Shojaie, Int J Quantum Chem, in press) are applied to the vibrational mode analysis. Extending previous work, we use the vibrational mode analysis to elucidate the relationships of the reactants, the transition state, the intermediates (IM), and the products. The extensive investigation shows that the reaction mechanism is reliable. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011 [ABSTRACT FROM AUTHOR]

All species involved in the multi-channel reaction of CH3O2 with HO2 have been investigated using density functional theory (DFT). The molecular geometries for various species are optimized employing the B3LYP method implementing the 6-311++G** basis set. The relative energies of all species are calculated at the same level theory. The results show that there are two kinds of channels: singlet and triplet. The singlet channel involves four intermediates and six transition states. The triplet channel includes two intermediates and two transition states. There are four kinds of reaction products: CH3OOH + 1O2, CH3OH + O3, CH4 + 2O2, and CH3OOH + 3O2. The vibrational mode analysis is used to elucidate the relationships of the intermediates, the transition states, and the products. The extensive investigation shows that the reaction mechanism is reliable. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [ABSTRACT FROM AUTHOR]

Abstract: The decomposition reaction pathways of m-pyridyl radical have been investigated extensively with gaussian 94 package using B3LYP method at 6-311++G** basis sets. Connections of the transition states and products are confirmed by IRC calculations, and subsequently the geometries and vibrational frequencies of various species were calculated. With the relative energies after ZPVE correction, the potential energy surface was drawn out. All reaction channels are investigated with the vibrational mode analysis and electron population analysis to reveal the reaction mechanism. HCN, HCCCCH and HCCH are the principal products. [Copyright &y& Elsevier]

Abstract: All species involving the reaction system of CH3O2+NO→CH3O+NO2 have been optimized extensively using gaussian94 package at the B3LYP/6-311++G** level, and four singlet and two triplet intermediates, three singlet and a triplet transition states were found in gas phase. The overall profile of potential energy surface was drawn out. By vibrational mode analysis and population analysis we found that a singlet channel CH3O2+NO→TS3→IM4→CH3O+NO2 and a triplet channel CH3O2+NO→3IM1→3TS1→3IM1→CH3O+NO2 are energetically most favorable. [Copyright &y& Elsevier]

All species involved in the multi-channel reaction of CH3CCH with H have been investigated using density functional theory. The molecular geometries for various species are optimized employing B3LYP method implementing 6-311++G** basis sets. The potential energy surface is drawn out for this reaction. The vibrational mode analysis is used to elucidate the relationships of the transition states, intermediate and the products. The extensive investigation shows that the reaction mechanism is reliable. [Copyright &y& Elsevier]

The isomerization reaction channels of phosphaalkynes R–C&z.tbnd6;P (R=-BH2, -CH3, -NH2, -OH) were investigated extensively using gaussian 94 program package at the B3LYP/6-311G** level. The overall profile of potential energy surface was drawn out. The vibrational mode analysis was employed to elucidate the reaction mechanism, and to find out stable species. This theoretical work will be helpful for experimental works to detect and synthesize these phosphaalkynes. [Copyright &y& Elsevier]

The decomposition reaction pathways of p-pyridyl were investigated extensively at the B3LYP/6-311++G** level. With the relative energies after zero-point energy correction, the potential energy surface was drawn out. The vibrational frequencies for all species were predicted and the reaction mechanism was elucidated utilizing vibrational frequencies and vibrational mode analysis. The primary products of p-pyridyl decomposition reactions are cyanide, butadiyne and 3,4-pyridyne. [Copyright &y& Elsevier]

All species involving the reaction system of CF3Br+O (3P, 1D) has been optimized extensively using Gaussian94 procedure at the B3LYP/6-311++G** level. The overall profile of potential energy surface was drawn out. We used the vibrational mode analysis to elucidate the reaction mechanism, and used electron population analysis to study the geometry of five intermediates and three transition states. Intermediate CF3OBr has the lowest internal energy on the potential energy surface, and CF2O+BrF are the end products. [Copyright &y& Elsevier]

The decomposition reaction pathways of o-pyridyl were investigated extensively at the B3LYP/6-311G** level. With the relative energies after zero-point energy correction, the potential energy surface was drawn out. The vibrational frequencies for all species were predicted and the reaction mechanism was elucidated utilizing vibrational frequencies and vibrational mode analysis. The primary products of o-pyridyl decomposition reactions are acetylene and cyanoacetylene. [Copyright &y& Elsevier]

All species involved in the multi-channel reaction of O2 with CH3S have been optimized utilizing gaussian 94 procedure package at the B3LYP/6-311++G** level. The vibrational mode analysis is used to elucidate the relationships of the transition states, intermediates and the products. The extensive investigation shows that the reaction mechanism is reliable. [Copyright &y& Elsevier]

On the basis of full optimizations for all species involved F+CH2CO reaction system using Gaussian 94 package at B3LYP/6-311++G** level, the reaction mechanism is studied extensively.The potential energy surface is drawn out. With vibrational mode analysis and the electron population analysis, we proved that the main products are CO+CH2F, and the main reaction channel is F+CH2CO→CH2FCO→TS1→CO+CH2F. [Copyright &y& Elsevier]

Functions of protein molecules in nature are closely associated with their well-defined three-dimensional structures and dynamics in body fluid. So far, many efforts have been made to reveal the relation of protein structure, dynamics, and function, but the structural origin of protein dynamics, especially for secondary structures as building blocks of conformation transition, is still ambiguous. Here we theoretically uncover the collective vibrations of elastic poly-alanine α-helices and find vibration patterns that are distinctively different over residue numbers ranging from 20 to 80. Contrary to the decreasing vibration magnitude from ends to the middle region for short helices, the vibration magnitude for long helices takes the minimum at approximately 1/5 of helix length from ends but reaches a peak at the center. Further analysis indicates that major vibrational modes of helical structures strongly depend on their lengths, where the twist mode dominates in the vibrations of short helices while the bend mode dominates the long ones analogous to an elastic Euler beam. The helix-coil transition pathway is also affected by the alternation of the first-order mode in helices with different lengths. The dynamic properties of the helical polypeptides are promising to be harnessed for de novo design of protein-based materials and artificial biomolecules in clinical treatments., (© 2022 Wiley-VCH GmbH.)

Resonance Raman spectroscopy data of 2-aminoadenine and its deuterated species (C8-deuterated, N-deuterated and C8-, N-deuterated derivatives) in aqueous solution have been collected in the spectral region between 400 and 1800 cm, by using ultraviolet excitation wavelengths (λ = 222, 257 and 281 nm) located in the three main UV absorption bands corresponding to the strongly allowed electronic transitions of the molecule of interest. Moreover, a Raman spectrum has been recorded under off-resonance conditions with a visible excitation (λ= 488 nm). In order to assign the 2-aminoadenine in-plane vibrational bands displayed in the RRS spectra, a normal coordinate analysis has been performed by means of an empirical internal valence force field. These calculations are based on our recent normal mode analysis of adenine and guanine nucleic bases and their deuterated species, which was based on the joint use of resonance Raman spectroscopy and neutron inelastic scattering data. In the 2-aminoadenine force field proposed here, the diagonal force constants have been directly transferred from those recently obtained for adenine (and from guanine as concerns the 2-amino group), the interaction force constants (off-diagonal) then being adjusted on the basis of the actual experimental data from 2-aminoadenine and its deuterated species. The current force field is also able to assign infrared and Raman data obtained by other authors from polycrystalline samples of the pure species. [ABSTRACT FROM AUTHOR]

There are different methods to calculate the rate constant of a bimolecular reaction. In this article are described two methods to calculate the rate constant and then these methods are compared using two-channel reaction. The rate constants for each reaction channel are calculated using Transition State Theory (TST) incorporating the Winger tunneling correction and the hindered rotor approximation. Furthermore, the rate constants for the dominant channel are calculated using general equation, which takes into account the rotational energy, is derived from Rice–Ramsperger–Kassel–Marcus (RRKM) theory, using the simplified version of the statistical adiabatic channel model theory. The vibrational mode analysis is used to elucidate the relationships of the reactant region ( s = −∞), the saddle point ( s = 0) and the product region ( s = +∞). [ABSTRACT FROM AUTHOR]