The pair correlation energy of bonding electrons is used and analyzed in the cal- culation of CH and CY (Y = F, O, N) bonding electron pairs in CH3X (X = F, OH, NH2) isoelec- tronic systems based on intra- and interpa...The pair correlation energy of bonding electrons is used and analyzed in the cal- culation of CH and CY (Y = F, O, N) bonding electron pairs in CH3X (X = F, OH, NH2) isoelec- tronic systems based on intra- and interpair correlation energy results at both MP2-OPT2/6- 311++G(d) and MP2-OPT2/cc-pVtz levels with MELD program. Comparison of two set results shows that cc-pVtz and 6-311++G(d) give more correlation energy of valence electrons and innermost core electron pairs, respectively in these systems, resulting that the total correlation energy with cc-pVtz basis of each system is larger than that with 6-311++G(d). Investigations of pair correlation energy show that with the decrease of electronegativity of X atom and the increase of H atoms in these CH3X (X = F, OH, NH2) systems, the pair correlation energy of 1sC2 of the C atoms is transferable, and the correlation energy of CH bonding electron pair with little changes is of approximate transferability, while those of CY (CF, CO, CN) bonding electron pair decrease in a large extent from CH3F through CH3OH to CH3NH2 molecules. It is suggested that the study of pair correlation energy of bonding electrons will further deepen the understanding of electron corre- lation effect from traditional chemical bonding concept.展开更多
As Lewis proposed his octet rule, itself inspired by Abegg’s rule, that a molecule is stable when all its composing atoms have eight electrons in their valence shell, it perfectly applied to the vast majority of know...As Lewis proposed his octet rule, itself inspired by Abegg’s rule, that a molecule is stable when all its composing atoms have eight electrons in their valence shell, it perfectly applied to the vast majority of known stable molecules. Only a few stable molecules were known that didn’t fall under this rule, such as PCl5 and SF6, and Lewis chose to leave them aside at the time of his research. With further advances in chemistry, more exceptions to this rule of eight have been found, usually with the central atom of the structure having more or less than eight electrons in its valence shell. Theories have been developed in order to modify the octet rule to suit these molecules, defining these as hyper- or hypo-valent molecules and using other configurations for the electrons. The present paper aims to propose a representation rule for gaseous single-bonded molecules that makes it possible to reconcile both;molecules following the octet theory and those which do not. In this representation rule, each element of the molecule is subscripted with two numbers that follow a set of simple criteria. The first represents the number of valence electrons of the element;while the second is calculated by adding the first number to the number of the element’s covalent bonds within the molecule. The latter is equal to eight for organic molecules following the octet rule. Molecules being exceptions to the octet rule are now encompassed by this new even-odd rule: they have a valid chemical structural formula in which the second number is even but not always equal to eight. Both rules—octet and even-odd—are discussed and compared, using several well-known gaseous molecules having one or several single-bonded elements. A future paper will discuss the application of the even-odd rule to charged molecules.展开更多
Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometrie...Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.展开更多
The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculati...The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^（＊＊） basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis（NBO） was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick（WC） edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.展开更多
The ion-pair compound [H2（teta）]^2＋·[Ni（CN）4]^2-·2H2O （C20H42N8NiO2, teta = meso- 5,7,7,12,14,14-hexamethyl- 1,4,8,11-tetraazacyclotetradecane） was synthesized and characterized by single-crystal X-ra...The ion-pair compound [H2（teta）]^2＋·[Ni（CN）4]^2-·2H2O （C20H42N8NiO2, teta = meso- 5,7,7,12,14,14-hexamethyl- 1,4,8,11-tetraazacyclotetradecane） was synthesized and characterized by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P211n with a = 10.0784（10）, b = 9.5411（7）, c = 14.1010（14）А, β= 106.752（2）°, V= 1298.4（2）A^3, Mr = 485.33, Z= 2, De= 1.241 g/cm^3,μ（MoKα） = 0.778 mm^-1 and F（000） = 524. The structure was refined to R = 0.0391 and wR = 0.0870 for 2614 observed reflections with I 〉 2σ（I）. The title compound contains one [Ni（CN）4]^2- anion, one protonated macrocyclic tetraamine cation [H2（teta）]^2＋ and two water molecules. There are multiform hydrogen bonds in the compound to link the different components and stabilize the crystal structure.展开更多
The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal ...The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal growth temperature (OGT) rather than with the G + C content. Paired and unpaired nucleotides in mesophiles were compared to those in thermophiles. OGT exhibited a relationship with paired nucleotides but not with unpaired nucleotides. The total number of paired as well as unpaired nucleotides in mesophiles was very similar to that in thermophiles. However, the components in base pairs in mesophiles significantly differed from those in thermophiles. As compared with mesophiles, the number of G·C base pairs in thermophiles was high whereas that of A·U base pairs was low. In this study, we showed that hydrogen bonds are important for stabilizing 16S rRNAs at high temperatures.展开更多
The paper discusses the researches that formed the basis of the study of the transition of “ordering-phase separation” and the reasons for such transition occurrence. Experimental results have presented what diffusi...The paper discusses the researches that formed the basis of the study of the transition of “ordering-phase separation” and the reasons for such transition occurrence. Experimental results have presented what diffusion pairs are and how they occur in binary and multicomponent alloys. The paper illustrates that the chemical bonds between atoms are realized on the principle of pair interaction in both solid and liquid states of the alloy. The process of separating a multi-component ABC alloy into diffusion pairs A/B, A/C, and B/C occurs in a liquid solution, where the diffusion mobility of atoms is very high, and the resistance of the environment is relatively low. The driving force of such a process is the chemical attraction between like and unlike atoms, that is, the tendency to phase separation and the tendency to ordering. Quenching the liquid alloy into the water fixes a microstructure consisting of microscopic areas corresponding in composition to one or another diffusion pairs. The paper shows what exactly should be done so that such a branch of science as Materials Science could get rid of the empirical approach when creating new alloys.展开更多
基金Supported by the National Natural Science Foundation of China (No. 20173027 and No. 29873023)
文摘The pair correlation energy of bonding electrons is used and analyzed in the cal- culation of CH and CY (Y = F, O, N) bonding electron pairs in CH3X (X = F, OH, NH2) isoelec- tronic systems based on intra- and interpair correlation energy results at both MP2-OPT2/6- 311++G(d) and MP2-OPT2/cc-pVtz levels with MELD program. Comparison of two set results shows that cc-pVtz and 6-311++G(d) give more correlation energy of valence electrons and innermost core electron pairs, respectively in these systems, resulting that the total correlation energy with cc-pVtz basis of each system is larger than that with 6-311++G(d). Investigations of pair correlation energy show that with the decrease of electronegativity of X atom and the increase of H atoms in these CH3X (X = F, OH, NH2) systems, the pair correlation energy of 1sC2 of the C atoms is transferable, and the correlation energy of CH bonding electron pair with little changes is of approximate transferability, while those of CY (CF, CO, CN) bonding electron pair decrease in a large extent from CH3F through CH3OH to CH3NH2 molecules. It is suggested that the study of pair correlation energy of bonding electrons will further deepen the understanding of electron corre- lation effect from traditional chemical bonding concept.
文摘As Lewis proposed his octet rule, itself inspired by Abegg’s rule, that a molecule is stable when all its composing atoms have eight electrons in their valence shell, it perfectly applied to the vast majority of known stable molecules. Only a few stable molecules were known that didn’t fall under this rule, such as PCl5 and SF6, and Lewis chose to leave them aside at the time of his research. With further advances in chemistry, more exceptions to this rule of eight have been found, usually with the central atom of the structure having more or less than eight electrons in its valence shell. Theories have been developed in order to modify the octet rule to suit these molecules, defining these as hyper- or hypo-valent molecules and using other configurations for the electrons. The present paper aims to propose a representation rule for gaseous single-bonded molecules that makes it possible to reconcile both;molecules following the octet theory and those which do not. In this representation rule, each element of the molecule is subscripted with two numbers that follow a set of simple criteria. The first represents the number of valence electrons of the element;while the second is calculated by adding the first number to the number of the element’s covalent bonds within the molecule. The latter is equal to eight for organic molecules following the octet rule. Molecules being exceptions to the octet rule are now encompassed by this new even-odd rule: they have a valid chemical structural formula in which the second number is even but not always equal to eight. Both rules—octet and even-odd—are discussed and compared, using several well-known gaseous molecules having one or several single-bonded elements. A future paper will discuss the application of the even-odd rule to charged molecules.
基金This project was financially supported by the Natural Science Foundation of Fujian Province (E0200014) the Provincial Education Foundation of Fujian and the Test Foundation of Jinan University
文摘Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.
基金Project supported by the National Key Research and Development Project(No.2016YFB0201404)
文摘The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^（＊＊） basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis（NBO） was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick（WC） edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.
文摘The ion-pair compound [H2（teta）]^2＋·[Ni（CN）4]^2-·2H2O （C20H42N8NiO2, teta = meso- 5,7,7,12,14,14-hexamethyl- 1,4,8,11-tetraazacyclotetradecane） was synthesized and characterized by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P211n with a = 10.0784（10）, b = 9.5411（7）, c = 14.1010（14）А, β= 106.752（2）°, V= 1298.4（2）A^3, Mr = 485.33, Z= 2, De= 1.241 g/cm^3,μ（MoKα） = 0.778 mm^-1 and F（000） = 524. The structure was refined to R = 0.0391 and wR = 0.0870 for 2614 observed reflections with I 〉 2σ（I）. The title compound contains one [Ni（CN）4]^2- anion, one protonated macrocyclic tetraamine cation [H2（teta）]^2＋ and two water molecules. There are multiform hydrogen bonds in the compound to link the different components and stabilize the crystal structure.
文摘The number of base pairs in the 16S rRNA secondary structures of 51 bacterial sequences was counted, and the number of hydrogen bonds was estimated. The number of hydrogen bonds was highly correlated with the optimal growth temperature (OGT) rather than with the G + C content. Paired and unpaired nucleotides in mesophiles were compared to those in thermophiles. OGT exhibited a relationship with paired nucleotides but not with unpaired nucleotides. The total number of paired as well as unpaired nucleotides in mesophiles was very similar to that in thermophiles. However, the components in base pairs in mesophiles significantly differed from those in thermophiles. As compared with mesophiles, the number of G·C base pairs in thermophiles was high whereas that of A·U base pairs was low. In this study, we showed that hydrogen bonds are important for stabilizing 16S rRNAs at high temperatures.
文摘The paper discusses the researches that formed the basis of the study of the transition of “ordering-phase separation” and the reasons for such transition occurrence. Experimental results have presented what diffusion pairs are and how they occur in binary and multicomponent alloys. The paper illustrates that the chemical bonds between atoms are realized on the principle of pair interaction in both solid and liquid states of the alloy. The process of separating a multi-component ABC alloy into diffusion pairs A/B, A/C, and B/C occurs in a liquid solution, where the diffusion mobility of atoms is very high, and the resistance of the environment is relatively low. The driving force of such a process is the chemical attraction between like and unlike atoms, that is, the tendency to phase separation and the tendency to ordering. Quenching the liquid alloy into the water fixes a microstructure consisting of microscopic areas corresponding in composition to one or another diffusion pairs. The paper shows what exactly should be done so that such a branch of science as Materials Science could get rid of the empirical approach when creating new alloys.
