K. Kholmurodov, Sagille A. Ibragimova, Pavel P. Gladishev, A. Vannikov, A. Tameev, T. Zelenyak
The perovskites with general formula ABX3 have been widely used as for materials with their unique properties (ferroelectric, piezoelectric, dielectric, catalytic and so on). Hybrid organolead halide perovskites are a class of semiconductors with ABX3 (X = Cl, Br, and I) structures consisting of lead cations in 6-fold coordination (B site), surrounded by an octahedron of halide anions (X site, face centered) together with the organic components in 12-fold cub octahedral coordination. These hybrid perovskites have a direct band gap, a large absorption coefficient as well as high charge carrier mobility that represent a very attractive characteristic of cost-effective solar cells. Basically, these crystals are inorganic solids of CaTiO3 type held together by bonds that are either ionic or partially ionic and partially covalent. In spite of the partially covalent character of the Ti-O bond, the system is modeled by a two-body central force interatomic potential (the form of the Vashishta and Rahman interatomic potential), which has been used successfully for many materials with a perovskite structure. In the present work using molecular dynamics (MD) simulation method we investigate the dynamical and structural behavior of CaTiO3 perovskite at normal pressure and temperature conditions. The MD calculations were performed on a system of 16,000 particles (3200Ca + 3200Ti + 96,00O), initially in an orthorhombic-Pbnm structure. The orthorhombic MD box had edges Lx = 53.4 A, Ly = 53.4 A and Lz = 61.12 A, which provided a density matching the experimental value of ρ = 4 g/cm3. Starting with this structure and using proposed interatomic potentials the MD system stabilizes at room temperature in its initial configuration. The aim of the present study to explore the effect of potential function representations on structural equilibrium properties for the perovskite models including hybrid halide ones outlined above. Concerning the perovskite equilibrium state we elucidate the role of potential function modification on the atomic pair correlation and structural re-organization. The details of the interatomic potential representation have to be crucially important for obtaining of correct analysis data in crystallic, liquid and amorphous phases including perovskite systems.
{"title":"Molecular Dynamics Simulations of Perovskites: The Effect of Potential Function Representation on Equilibrium Structural Properties","authors":"K. Kholmurodov, Sagille A. Ibragimova, Pavel P. Gladishev, A. Vannikov, A. Tameev, T. Zelenyak","doi":"10.4236/OJPC.2015.54012","DOIUrl":"https://doi.org/10.4236/OJPC.2015.54012","url":null,"abstract":"The perovskites with general formula ABX3 have been widely used as for materials with their unique properties (ferroelectric, piezoelectric, dielectric, catalytic and so on). Hybrid organolead halide perovskites are a class of semiconductors with ABX3 (X = Cl, Br, and I) structures consisting of lead cations in 6-fold coordination (B site), surrounded by an octahedron of halide anions (X site, face centered) together with the organic components in 12-fold cub octahedral coordination. These hybrid perovskites have a direct band gap, a large absorption coefficient as well as high charge carrier mobility that represent a very attractive characteristic of cost-effective solar cells. Basically, these crystals are inorganic solids of CaTiO3 type held together by bonds that are either ionic or partially ionic and partially covalent. In spite of the partially covalent character of the Ti-O bond, the system is modeled by a two-body central force interatomic potential (the form of the Vashishta and Rahman interatomic potential), which has been used successfully for many materials with a perovskite structure. In the present work using molecular dynamics (MD) simulation method we investigate the dynamical and structural behavior of CaTiO3 perovskite at normal pressure and temperature conditions. The MD calculations were performed on a system of 16,000 particles (3200Ca + 3200Ti + 96,00O), initially in an orthorhombic-Pbnm structure. The orthorhombic MD box had edges Lx = 53.4 A, Ly = 53.4 A and Lz = 61.12 A, which provided a density matching the experimental value of ρ = 4 g/cm3. Starting with this structure and using proposed interatomic potentials the MD system stabilizes at room temperature in its initial configuration. The aim of the present study to explore the effect of potential function representations on structural equilibrium properties for the perovskite models including hybrid halide ones outlined above. Concerning the perovskite equilibrium state we elucidate the role of potential function modification on the atomic pair correlation and structural re-organization. The details of the interatomic potential representation have to be crucially important for obtaining of correct analysis data in crystallic, liquid and amorphous phases including perovskite systems.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"110-121"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The conformations of four β-amino acids in a model peptide environment were investigated using Hartree-Fock (HF) and density functional theory (DFT) methods in gas phase and with solvation. Initial structures were obtained by varying dihedral angles in increments of 45° in the range 0° - 360°. Stable geometries were optimized at both levels of theory with the correlation consistent double-zeta basis set with polarization functions (cc-pVDZ). The results suggest that solvation generally stabilizes the conformations relative to the gas phase and that intramolecular hydrogen bonding may play an important role in the stability of the conformations. The β3 structures, in which the R-group of the amino acid is located on the carbon atom next to the N-terminus, are somewhat more stable relative to each other than the β2 structures which have the R-group on the carbon next to the carbonyl.
{"title":"A Theoretical Study of β-Amino Acid Conformational Energies and Solvent Effect","authors":"Victor F. Waingeh, F. Ngassa, Jie Song","doi":"10.4236/OJPC.2015.54013","DOIUrl":"https://doi.org/10.4236/OJPC.2015.54013","url":null,"abstract":"The conformations of four β-amino acids in a model peptide environment were investigated using Hartree-Fock (HF) and density functional theory (DFT) methods in gas phase and with solvation. Initial structures were obtained by varying dihedral angles in increments of 45° in the range 0° - 360°. Stable geometries were optimized at both levels of theory with the correlation consistent double-zeta basis set with polarization functions (cc-pVDZ). The results suggest that solvation generally stabilizes the conformations relative to the gas phase and that intramolecular hydrogen bonding may play an important role in the stability of the conformations. The β3 structures, in which the R-group of the amino acid is located on the carbon atom next to the N-terminus, are somewhat more stable relative to each other than the β2 structures which have the R-group on the carbon next to the carbonyl.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"122-131"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
An explanation is given for the thermal equilibrium in the biosphere, which is based in the equality between the thermal energy received from the sun and the thermal energy reemitted from the atmosphere to the space. In order to understand the origin of the energy that gives rise to the processes and phenomena taking place in the biosphere, it is necessary to take into account the free energy represented by the product of temperature times the change in entropy, T△S, whose magnitude can be attributed to the variation experimented by the wavelengths (or, consequently, the frequencies) of the radiations composing the radiation spectrum received from the sun compared with the radiation spectrum reemitted from the biosphere into the space. A simple discussion allows to predict that the entropy increase driving the processes is connected with a spontaneous conversion of high frequency radiations (with lower “content” of entropy) in radiations of lower frequencies (with higher “content” of entropy). A consequence of this is that high frequency radiations would correspond to more ordered states and, therefore, to less probable states than those corresponding to radiations of lower frequencies.
{"title":"Some Ideas about the Thermal Equilibrium in the Biosphere and the Entropy Variation Ascribed to Changes in the Radiations Wavelengths","authors":"J. Velasco","doi":"10.4236/OJPC.2015.54011","DOIUrl":"https://doi.org/10.4236/OJPC.2015.54011","url":null,"abstract":"An explanation is given for the thermal equilibrium in the biosphere, which is based in the equality between the thermal energy received from the sun and the thermal energy reemitted from the atmosphere to the space. In order to understand the origin of the energy that gives rise to the processes and phenomena taking place in the biosphere, it is necessary to take into account the free energy represented by the product of temperature times the change in entropy, T△S, whose magnitude can be attributed to the variation experimented by the wavelengths (or, consequently, the frequencies) of the radiations composing the radiation spectrum received from the sun compared with the radiation spectrum reemitted from the biosphere into the space. A simple discussion allows to predict that the entropy increase driving the processes is connected with a spontaneous conversion of high frequency radiations (with lower “content” of entropy) in radiations of lower frequencies (with higher “content” of entropy). A consequence of this is that high frequency radiations would correspond to more ordered states and, therefore, to less probable states than those corresponding to radiations of lower frequencies.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"106-109"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A crystal is a highly organized arrangement of atoms in a solid, wherein a unit cell is periodically repeated to form the crystal pattern. A unit cell is composed of atoms that are connected to some of their first neighbors by chemical bonds. A recent rule, entitled the even-odd rule, introduced a new way to calculate the number of covalent bonds around an atom. It states that around an uncharged atom, the number of bonds and the number of electrons have the same parity. In the case of a charged atom on the contrary, both numbers have different parity. The aim of the present paper is to challenge the even-odd rule on chemical bonds in well-known crystal structures. According to the rule, atoms are supposed to be bonded exclusively through single-covalent bonds. A distinctive criterion, only applicable to crystals, states that atoms cannot build more than 8 chemical bonds, as opposed to the classical model, where each atom in a crystal is connected to every first neighbor without limitation. Electrical charges can be assigned to specific atoms in order to compensate for extra or missing bonds. More specifically the article considers di-atomic body-centered-cubic, tetra-atomic and dodeca-atomic single-face-centered-cubic crystals. In body-centered crystals, atoms are interconnected by 8 covalent bonds. In face-centered crystal, the unit cell contains 4 or 12 atoms. For di-element crystals, the total number of bonds for both elements is found to be identical. The neutrality of the unit cell is obtained with an opposite charge on the nearest or second-nearest neighbor. To conclude, the even-odd rule is applicable to a wide number of compounds in known cubic structures and the number of chemical bonds per atom is not related to the valence of the elements in the periodic table.
{"title":"Chemical Bonds between Charged Atoms in the Even-Odd Rule and a Limitation to Eight Covalent Bonds per Atom in Centered-Cubic and Single Face-Centered-Cubic Crystals","authors":"G. Auvert, M. Auvert","doi":"10.4236/OJPC.2015.54010","DOIUrl":"https://doi.org/10.4236/OJPC.2015.54010","url":null,"abstract":"A crystal is a highly organized arrangement of atoms in a solid, wherein a unit cell is periodically repeated to form the crystal pattern. A unit cell is composed of atoms that are connected to some of their first neighbors by chemical bonds. A recent rule, entitled the even-odd rule, introduced a new way to calculate the number of covalent bonds around an atom. It states that around an uncharged atom, the number of bonds and the number of electrons have the same parity. In the case of a charged atom on the contrary, both numbers have different parity. The aim of the present paper is to challenge the even-odd rule on chemical bonds in well-known crystal structures. According to the rule, atoms are supposed to be bonded exclusively through single-covalent bonds. A distinctive criterion, only applicable to crystals, states that atoms cannot build more than 8 chemical bonds, as opposed to the classical model, where each atom in a crystal is connected to every first neighbor without limitation. Electrical charges can be assigned to specific atoms in order to compensate for extra or missing bonds. More specifically the article considers di-atomic body-centered-cubic, tetra-atomic and dodeca-atomic single-face-centered-cubic crystals. In body-centered crystals, atoms are interconnected by 8 covalent bonds. In face-centered crystal, the unit cell contains 4 or 12 atoms. For di-element crystals, the total number of bonds for both elements is found to be identical. The neutrality of the unit cell is obtained with an opposite charge on the nearest or second-nearest neighbor. To conclude, the even-odd rule is applicable to a wide number of compounds in known cubic structures and the number of chemical bonds per atom is not related to the valence of the elements in the periodic table.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"93-105"},"PeriodicalIF":0.0,"publicationDate":"2015-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular mechanics calculations, based on equations such as the one below, are used to investigate a colorectal cancer drug, 5-fluorouracil, intercalated into a clay, montmorillonite. This combination is currently being considered as a drug delivery system. The swelling of clays has been studied since the 1930s and is still not fully understood. Spartan ’14 is used for the calculations. Semi-empirical and ab initio basis set scaling is also examined since there are roughly 300 atoms involved in the full model.
{"title":"Simulation of 5-Fluorouracil Intercalated into Montmorillonite Using Spartan ’14: Molecular Mechanics, PM3, and Hartree-Fock","authors":"J. Summerfield","doi":"10.4236/OJPC.2015.53006","DOIUrl":"https://doi.org/10.4236/OJPC.2015.53006","url":null,"abstract":"Molecular mechanics calculations, based on equations such as the one below, are used to investigate a colorectal cancer drug, 5-fluorouracil, intercalated into a clay, montmorillonite. This combination is currently being considered as a drug delivery system. The swelling of clays has been studied since the 1930s and is still not fully understood. Spartan ’14 is used for the calculations. Semi-empirical and ab initio basis set scaling is also examined since there are roughly 300 atoms involved in the full model.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"49-55"},"PeriodicalIF":0.0,"publicationDate":"2015-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A calculation method for heats of formation (HOF, referred to as ∆Hf) based on the density func- tional theory (DFT) is presented in this work. Similar to Gaussian-3 theory, the atomic scheme is applied to calculate the heats of formation of the molecules. In this method, we have modified the formula for calculation of Gaussian-3 theory in several ways, including the correction for diffuse functions and the correction for higher polarization functions. These corrections are found to be significant. The average absolute deviation from experiment for the 164 calculated heats of for- mation is about 1.9 kcal·mol−1, while average absolute deviation from G3MP2 for the 149 (among the 164 molecules, 15 large-sized molecules can not be calculated at the G3MP2 level) calculated heats of formation is only about 1.9 kcal·mol−1. It indicates that the present method can be applied to predict the heats of formation of medium-sized and large-sized molecules, while the heats of formation of these molecules using Gaussian-3 theory are much difficult, even impossible, to cal- culate. That is, this method provides a choice in the calculation of ∆Hf for medium-sized and large- sized molecules.
{"title":"A Method for Calculating the Heats of Formation of Medium-Sized and Large-Sized Molecules","authors":"B. He, Hongwei Zhou, Fan Yang, Wai-Kee Li","doi":"10.4236/OJPC.2015.53008","DOIUrl":"https://doi.org/10.4236/OJPC.2015.53008","url":null,"abstract":"A calculation method for heats of formation (HOF, referred to as ∆Hf) based on the density func- tional theory (DFT) is presented in this work. Similar to Gaussian-3 theory, the atomic scheme is applied to calculate the heats of formation of the molecules. In this method, we have modified the formula for calculation of Gaussian-3 theory in several ways, including the correction for diffuse functions and the correction for higher polarization functions. These corrections are found to be significant. The average absolute deviation from experiment for the 164 calculated heats of for- mation is about 1.9 kcal·mol−1, while average absolute deviation from G3MP2 for the 149 (among the 164 molecules, 15 large-sized molecules can not be calculated at the G3MP2 level) calculated heats of formation is only about 1.9 kcal·mol−1. It indicates that the present method can be applied to predict the heats of formation of medium-sized and large-sized molecules, while the heats of formation of these molecules using Gaussian-3 theory are much difficult, even impossible, to cal- culate. That is, this method provides a choice in the calculation of ∆Hf for medium-sized and large- sized molecules.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"71-86"},"PeriodicalIF":0.0,"publicationDate":"2015-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The adsorption properties of layered double hydroxide (Mg/Al-CO3) for the removal of Congo Red (CR) dye from aqueous solution were studied. The layered double hydroxide was synthesized by co-precipitation method and characterized by X-ray diffraction (XRD), Fourier Transform Infrared spectroscopic (FTIR) and Energy-Dispersive X-ray Spectroscopic (EDX). The effects of various experimental parameters such as contact time, dye concentrations and temperature variation were investigated. The results show that the amount of Congo Red adsorbed increases with increase in temperature but decreases with increase in initial dye concentration and contact time. The data were also fitted to several kinetic models: zero-order kinetic model, first-order kinetic model, second-order kinetic model, pseudo-second-order kinetic model and third-order kinetic model respectively. The adsorption process was best defined by zero-order-kinetic model (R2 = 1). Langmuir, Freundich, Temkin and Dubinin-kaganer-Radushkevich (DPK) adsorption isotherm models were applied to analyze adsorption data with Temkin isotherm being the most applicable to the adsorption process. Thermodynamic parameters e.g. △Go, △So, △Ho and △Hx of the adsorption process were found to be endothermic, spontaneous and feasible.
{"title":"Synthesis, Characterization and Application of Mg/Al Layered Double Hydroxide for the Degradation of Congo Red in Aqueous Solution","authors":"N. Ayawei, S. Angaye, D. Wankasi, E. Dikio","doi":"10.4236/ojpc.2015.53007","DOIUrl":"https://doi.org/10.4236/ojpc.2015.53007","url":null,"abstract":"The adsorption properties of layered double hydroxide (Mg/Al-CO3) for the removal of Congo Red (CR) dye from aqueous solution were studied. The layered double hydroxide was synthesized by co-precipitation method and characterized by X-ray diffraction (XRD), Fourier Transform Infrared spectroscopic (FTIR) and Energy-Dispersive X-ray Spectroscopic (EDX). The effects of various experimental parameters such as contact time, dye concentrations and temperature variation were investigated. The results show that the amount of Congo Red adsorbed increases with increase in temperature but decreases with increase in initial dye concentration and contact time. The data were also fitted to several kinetic models: zero-order kinetic model, first-order kinetic model, second-order kinetic model, pseudo-second-order kinetic model and third-order kinetic model respectively. The adsorption process was best defined by zero-order-kinetic model (R2 = 1). Langmuir, Freundich, Temkin and Dubinin-kaganer-Radushkevich (DPK) adsorption isotherm models were applied to analyze adsorption data with Temkin isotherm being the most applicable to the adsorption process. Thermodynamic parameters e.g. △Go, △So, △Ho and △Hx of the adsorption process were found to be endothermic, spontaneous and feasible.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"56-70"},"PeriodicalIF":0.0,"publicationDate":"2015-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. G. Kunitsyn, P. Kuznetsov, E. Demchenko, O. Gimautdinova
Structure of the duplex consisting of 23 pairs of bases was studied before and after the methylation of two cytosine molecules from different chains of the duplex. The study was performed in a buffer solution using an IR Fourier spectrometer. The absorption bands corresponding to the duplex backbone were found to change their characteristics after the methylation. Firstly, the integrated intensity ratio of the absorption bands, S1044/S1085, decreased by a factor of 1.5. The absorption band at 1044 cm-1 corresponds to the COC bond of deoxyribose, and the band at 1085 cm-1 to the PO2symm.vibr bond. Secondly, a substantial shift of the absorption band 1085→1112 cm-1 (Δν = 27 cm-1) was observed. In addition, pronounced changes in the absorption region of CH stretching vibrations took place. In particular, shifting of some absorption bands assigned to the stretching vibrations of CH bonds; the 2979→2945.7 shift was equal to 33.3 cm-1. In addition to the indicated changes, some bands corresponding to the Z structure appeared in the methylated duplex. Thus, methylation of two cytosine molecules in the duplex leads to the order→order structural transition, most likely to the B→Z transition.
{"title":"Structural Study of Methylated and Non-Methylated Duplexes by IR Fourier Spectroscopy","authors":"V. G. Kunitsyn, P. Kuznetsov, E. Demchenko, O. Gimautdinova","doi":"10.4236/OJPC.2015.53009","DOIUrl":"https://doi.org/10.4236/OJPC.2015.53009","url":null,"abstract":"Structure of the duplex consisting of 23 pairs of bases was studied before and after the methylation of two cytosine molecules from different chains of the duplex. The study was performed in a buffer solution using an IR Fourier spectrometer. The absorption bands corresponding to the duplex backbone were found to change their characteristics after the methylation. Firstly, the integrated intensity ratio of the absorption bands, S1044/S1085, decreased by a factor of 1.5. The absorption band at 1044 cm-1 corresponds to the COC bond of deoxyribose, and the band at 1085 cm-1 to the PO2symm.vibr bond. Secondly, a substantial shift of the absorption band 1085→1112 cm-1 (Δν = 27 cm-1) was observed. In addition, pronounced changes in the absorption region of CH stretching vibrations took place. In particular, shifting of some absorption bands assigned to the stretching vibrations of CH bonds; the 2979→2945.7 shift was equal to 33.3 cm-1. In addition to the indicated changes, some bands corresponding to the Z structure appeared in the methylated duplex. Thus, methylation of two cytosine molecules in the duplex leads to the order→order structural transition, most likely to the B→Z transition.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"720-726"},"PeriodicalIF":0.0,"publicationDate":"2015-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the course of time, numerous rules were proposed to predict how atoms connect through covalent bonds. Based on the classification of elements in the periodic table, the rule of eight was first proposed to draw formulas of organic compounds. The later named octet rule exhibited shortcomings when applied to inorganic compounds. Another rule, the rule of two, using covalent bonds between atoms, was proposed as an attempt to unify description of organic and inorganic molecules. This rule unfortunately never managed to expand the field of application of the octet rule to inorganic compounds. In order to conciliate organic and inorganic compounds, the recently put forward even-odd and the isoelectronicity rules suggest the creation of one group of compounds with pairs of electrons. These rules compass the rule of two for covalent bonds as well as the octet rule for organic compounds and suggest transforming bonds of multi-bonded compounds in order to unify representations of both groups of compounds. The aim of the present paper is fourfold: to extend the rule of two to every atom shells; to replace the well-known octet rule by the even-odd rule; to apply the isoelectronicity rule to each atom and to reduce the influence range of the charge of an atom in a compound. According to both rules, the drawing of one atom with its single-covalent bonds is described with electron pairs and charge positions. To illustrate the rules, they are applied to 3D configurations of clusters.
{"title":"How the Even-Odd Rule, by Defining Electrons Pairs and Charge Positions, Can Be Used as a Substitute to the Langmuir-Octet Rule in Understanding Interconnections between Atoms in Ions and Molecules","authors":"G. Auvert","doi":"10.4236/OJPC.2015.52004","DOIUrl":"https://doi.org/10.4236/OJPC.2015.52004","url":null,"abstract":"In the course of time, numerous rules were proposed to predict how atoms connect through covalent bonds. Based on the classification of elements in the periodic table, the rule of eight was first proposed to draw formulas of organic compounds. The later named octet rule exhibited shortcomings when applied to inorganic compounds. Another rule, the rule of two, using covalent bonds between atoms, was proposed as an attempt to unify description of organic and inorganic molecules. This rule unfortunately never managed to expand the field of application of the octet rule to inorganic compounds. In order to conciliate organic and inorganic compounds, the recently put forward even-odd and the isoelectronicity rules suggest the creation of one group of compounds with pairs of electrons. These rules compass the rule of two for covalent bonds as well as the octet rule for organic compounds and suggest transforming bonds of multi-bonded compounds in order to unify representations of both groups of compounds. The aim of the present paper is fourfold: to extend the rule of two to every atom shells; to replace the well-known octet rule by the even-odd rule; to apply the isoelectronicity rule to each atom and to reduce the influence range of the charge of an atom in a compound. According to both rules, the drawing of one atom with its single-covalent bonds is described with electron pairs and charge positions. To illustrate the rules, they are applied to 3D configurations of clusters.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"28-38"},"PeriodicalIF":0.0,"publicationDate":"2015-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70502117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mammalian collagens exhibit weak intrinsic UV fluorescence that depends on the age and previous history of the sample. Post-translational modifications result in additional fluorescent products (e.g. DOPA, dityrosine, and advanced glycation end products (AGE)). UV radiation can cause longer wavelength fluorescent oxidative bands. These alterations can assess the extent of photolysis. We describe the ground- and excited-state oxidative transformations of newly-purchased type I calf skin collagens (samples #092014 and #072012) and a 7-year-old sample (#072005). We compare the effects of UV radiation (mainly 254 nm) and age on the photochemical reaction kinetics and fluorescence spectral distribution of type I calf skin collagen at pH 7.4. The fluorescence spectra of samples #072012 and #092014 were similar but not identical to pure tyrosine, whereas #072005 indicated significant “dark” oxidation at the expense of tyrosine. Fading of oxidized product(s) at 270/360 nm is second-order. Build-up of 325/400 nm (dityrosine) fluorescence is linear with time. Rate parameters r2 and r1 were respectively proportional to second order disappearance of ground state oxidation products and the quasi–first-order photochemical formation of dityrosine. There is a reciprocal relationship between the rates of decrease in the 270/360 nm fluorescence and concomitant increase in 325/400 nm fluorescence. Their relative rates depend on the age of the collagen sample. There is a reciprocal relationship between r1 and r2. This relationship results because both ground state autoxidation and excited state photo-dimerization proceed via a common tyrosyl radical intermediate. Water of hydration appears to play a role in generating tyrosyl radical.
{"title":"Thermal and Photochemical Effects on the Fluorescence Properties of Type I Calf Skin Collagen Solutions at Physiological pH","authors":"J. Menter, Latoya Freeman, Otega Edukuye","doi":"10.4236/OJPC.2015.52003","DOIUrl":"https://doi.org/10.4236/OJPC.2015.52003","url":null,"abstract":"Mammalian collagens exhibit weak intrinsic UV fluorescence that depends on the age and previous history of the sample. Post-translational modifications result in additional fluorescent products (e.g. DOPA, dityrosine, and advanced glycation end products (AGE)). UV radiation can cause longer wavelength fluorescent oxidative bands. These alterations can assess the extent of photolysis. We describe the ground- and excited-state oxidative transformations of newly-purchased type I calf skin collagens (samples #092014 and #072012) and a 7-year-old sample (#072005). We compare the effects of UV radiation (mainly 254 nm) and age on the photochemical reaction kinetics and fluorescence spectral distribution of type I calf skin collagen at pH 7.4. The fluorescence spectra of samples #072012 and #092014 were similar but not identical to pure tyrosine, whereas #072005 indicated significant “dark” oxidation at the expense of tyrosine. Fading of oxidized product(s) at 270/360 nm is second-order. Build-up of 325/400 nm (dityrosine) fluorescence is linear with time. Rate parameters r2 and r1 were respectively proportional to second order disappearance of ground state oxidation products and the quasi–first-order photochemical formation of dityrosine. There is a reciprocal relationship between the rates of decrease in the 270/360 nm fluorescence and concomitant increase in 325/400 nm fluorescence. Their relative rates depend on the age of the collagen sample. There is a reciprocal relationship between r1 and r2. This relationship results because both ground state autoxidation and excited state photo-dimerization proceed via a common tyrosyl radical intermediate. Water of hydration appears to play a role in generating tyrosyl radical.","PeriodicalId":59839,"journal":{"name":"物理化学期刊(英文)","volume":"05 1","pages":"21-27"},"PeriodicalIF":0.0,"publicationDate":"2015-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70501966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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