Some solved problems of the periodic system of chemical elements

Basic questions on the periodic system (PS) of chemical elements are still under discussion. Several common misconceptions will be resolved. The word “chemical element” comprises more than two concepts. The PS can be rationalized on a quantum chemical basis, namely with the aid of four concepts: (1) electron configurations of bonded atoms, (2) realistic sequences of orbital energies, (3) spatial extension of valence and Rydberg orbitals, and (4) energy gaps above the closed 1s² and np⁶ shells (n = 2–6). The PS of known elements cannot be naively extrapolated. The common discussion of the PS in textbooks of general, inorganic, and physical chemistry needs revision. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Understanding topological symmetry: a heuristic approach to its determination

An algorithm based on heuristic rules for topological symmetry perception of organic structures having heteroatoms, multiple bonds, and any kind of cycle, and configuration, is presented. This algorithm identifies topological symmetry planes and sets of equivalent atoms in the structure, named symmetry atom groups (SAGs). This approach avoids both the need to explore the entire graph automorphism groups, and to encompass cycle determination, resulting in a very effective computer processing. Applications to several structures, some of them highly symmetrical such as dendrimers, are presented.     

Fuzzy space periodic symmetries for polyynes and their cyano-compounds

In our previous papers on the molecular fuzzy symmetry, we analyzed the basic characterization in connection with the fuzzy point group symmetry. In this paper, polyynes and their cyano-derivatives are chosen as a prototype of linear molecules to probe the one-dimensional fuzzy space group of parallel translation. It is notable that the space group is an infinite group whereas the point group is a finite group. For the fuzzy point group, we focus on considering the fuzzy characterization introduced due to the difference of atomic types in the monomer through point symmetry transformation in the beginning; and then we consider the difference between the infinity of space group and the finite size of real molecules. The difference between the point group and the space group lies in the translation symmetry transformation. This is the theme of this work. Starting with a simple case, we will only analyze the one-dimensional translation transformation and space fuzzy inversion symmetry transformation in this paper. The theory of the space group is often used in solid state physics; and some of its conclusions will be referred to. More complicated fuzzy space groups will be discussed in our future papers.     

Continuous symmetry analysis of NMR chemical shielding anisotropy

Molecular symmetry is a key parameter which dictates the NMR chemical shielding anisotropy (CSA). Whereas correlations between specific geometrical features of molecules and the CSA are known, the quantitative correlation with symmetry--a global structural feature--has been unknown. Here we demonstrate a CSA/symmetry quantitative relation for the first time: We study how continuous deviation from exact symmetry around a nucleus affects its shielding. To achieve this we employed the continuous symmetry measures methodology, which allows one to quantify the degree of content of a given symmetry. The model case we use for this purpose is a population of distorted SiH(4) structures, for which we follow the (29)Si CSA as a function of the degree of tetrahedral symmetry and of square-planar symmetry. Quantitative correlations between the degree of these symmetries and the NMR shielding parameters emerge.     

Molecular dynamics with helical periodic boundary conditions

Helical symmetry is often encountered in nature and thus also in molecular dynamics (MD) simulations. In many cases, an approximation based on infinite helical periodicity can save a significant amount of computer time. However, standard simulations with the usual periodic boundary conditions (PBC) are not easily compatible with it. In the present study, we propose and investigate an algorithm comprising infinitely propagated helicity, which is compatible with commonly used MD software. The helical twist is introduced as a parametric geometry constraint, and the translational PBC are modified to allow for the helical symmetry via a transitional solvent volume. The algorithm including a parallel code was implemented within the Tinker software. The viability of the helical periodic boundary conditions (HPBC) was verified in test simulations including α‐helical and polyproline II like peptide structures. For an insulin‐based model, the HPBC dynamics made it possible to simulate a fibrillar structure, otherwise not stable within PBC. © 2014 Wiley Periodicals, Inc.     

On the use of symmetry-adapted crystalline orbitals in SCF-LCAO periodic calculations. I. The construction of the symmetrized orbitals

A computational procedure for generating space-symmetry-adapted Bloch functions (BF) is presented. The case is discussed when BF are built from a basis of local functions (atomic orbitals [AOs]). The method, which is completely general in the sense that it applies to any space group and AOs of any quantum number, is based on the diagonalization of Dirac characters. For its implementation, it does not require as an input character tables or related data, since this information is automatically generated starting from the space group symbol and the AO basis set. Formal aspects of the method, not available in textbooks, are discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 299–309, 1998     

Full spin and spatial symmetry adapted technique for correlated electronic hamiltonians: Application to an icosahedral cluster

One of the long standing problems in quantum chemistry had been the inability to exploit full spatial and spin symmetry of an electronic Hamiltonian belonging to a non‐Abelian point group. Here, we present a general technique which can utilize all the symmetries of an electronic (magnetic) Hamiltonian to obtain its full eigenvalue spectrum. This is a hybrid method based on Valence Bond basis and the basis of constant z‐component of the total spin. This technique is applicable to systems with any point group symmetry and is easy to implement on a computer. We illustrate the power of the method by applying it to a model icosahedral half‐filled electronic system. This model spans a huge Hilbert space (dimension 1,778,966) and in the largest non‐Abelian point group. The C₆₀ molecule has this symmetry and hence our calculation throw light on the higher energy excited states of the bucky ball. This method can also be utilized to study finite temperature properties of strongly correlated systems within an exact diagonalization approach. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Chemistry of superheavy elements

The number of chemical elements has increased considerably in the last few decades. Most excitingly, these heaviest, man-made elements at the far-end of the Periodic Table are located in the area of the long-awaited superheavy elements. While physical techniques currently play a leading role in these discoveries, the chemistry of superheavy elements is now beginning to be developed. Advanced and very sensitive techniques allow the chemical properties of these elusive elements to be probed. Often, less than ten short-lived atoms, chemically separated one-atom-at-a-time, provide crucial information on basic chemical properties. These results place the architecture of the far-end of the Periodic Table on the test bench and probe the increasingly strong relativistic effects that influence the chemical properties there. This review is focused mainly on the experimental work on superheavy element chemistry. It contains a short contribution on relativistic theory, and some important historical and nuclear aspects.     

The combinatorics of symmetry adaptation

A method is developed for obtaining the generating functions for the equivalence classes of orbitals wherein only orbitals within an equivalence class participate in symmetry adaptation. It is shown that using Williamson's combinatorial theorem the generating functions for the symmetry species contained in each equivalence class can be obtained. The method is illustrated with Porphindianion.     

Periodic systems of molecules as elements of Shchukarev's "supermatrix", i.e. the chemical element periodic system

Generations of Soviet scientists contributed invaluable insights into molecular classification. Unfortunately, this research is little appreciated in much of the world. Among these workers S. A. Shchukarev was of great importance. His and his followers' legacy includes a host of graphical displays showing enthalpies of formation of gaseous molecules from free atoms DeltaH(a) and standard enthalpies of formation of substances plotted on the atomic number of the central elements, on their oxidation states, their internuclear separations, and other variables for a wide range of molecules. These graphs serve as databases, from which data can be extracted, to moderate precision, visually. We discuss graphs for one very limited set, or "pleiade" (gas-phase oxides of nitrogen), and for three much broader sets, or subsystems (gas-phase fluorides of all main subgroup atoms and oxides of transition-metal atoms in gas-phase and in STP conditions). When dissolved in water, molecules lose their identities but periodicity is echoed in the acids and aquocations that are formed. We show, as an example in tabular form, that redox potentials of high-oxygen acids containing S, Se, and Te change concomitantly with DeltaH(a ) and DeltaH(f) of their hexafluorides. We present graphical evidence that three properties for cations of groups 1-3 (in the short version of the periodic chart) behave similarly and share the periodicity of the elements. One of the properties is related to the ionization potential, which is shown in a tabular example to vary concomitantly with energy of hydration. It was the ultimate goal of S. A. Shchukarev that the transformation of any one graphical database into any other, having different molecules under different conditions, would be made mathematically.     

轨道对称性匹配:MXene基体上的单原子催化以实现优异的氮还原反应

氨作为一种可被植物直接吸收用以合成其他有机物的重要成分,在化学化工及含氮化合物的生产当中起着至关重要的作用.传统工业生产氨气采用Haber-Bosch工艺,将空气中丰富的氮气转化为氨气,但该工艺需要较高的压强和温度来促进氮气分解,因此会消耗大量能源.近年来,电催化反应发展迅速.在电催化工艺中,通过控制操作电位及电解质便可提高生产效率,降低能源消耗.基于这种策略,各种针对能源环境的催化研究应运而生,如二氧化碳还原、水分解反应等.其中,对于氮还原的催化研究尤其是电催化设计领域研究相对较少.研究发现,在电催化剂中,异构掺杂及原子尺度的调控可以极大地影响催化剂的催化活性.其中,单原子催化(SAC)因其在催化活性和催化选择性上的优势受到广泛关注.MXene是一种二维过渡金属碳化物或氮化物,其优异的化学性能和稳定的表面构型可以对单原子起到良好的锚定与支撑作用,是一种更具潜力的单原子催化基体.本文基于上述思想,利用密度泛函第一性原理等模拟软件,设计并研究了以MXene为基体的28种过渡金属单原子催化体系,计算并分析了各SAC@MXene体系对氮还原反应的催化效果,从限制电势、催化路径、反应机制等方面探索了其催化性能.并对体系进行了态密度、晶体轨道哈密顿量、差分电荷密度等电子结构分析,找到了适用于MXene体系的单原子催化设计原则.通过对限制电势的计算表明,Ni@MXene和Co@MXene体系具有很低的限制电势(-0.13和-0.17 V),说明这些体系在较低的启动电压下即可发生氮还原反应.研究发现了一种新型适用于SAC@MXene氮催化体系的酶促-远端反应机制.电子结构分析得到SAC原子与MXene基体的Ti原子在催化过程中存在一种协同作用.态密度及晶体轨道哈密顿量也显示出SAC原子与MXene基体Ti之间的一种轨道对称性匹配关系,揭示了这种协同作用对催化反应的积极作用.计算的氢析出反应(HER)结果也显示,在相同化学环境下,SAC@MXene体系氮还原反应相对于氢析出反应更易发生.     

Exploitation of symmetry in periodic Self-Consistent-Field ab initio calculations: application to large three-dimensional compounds

Symmetry can dramatically reduce the computational cost (running time and memory allocation) of Self-Consistent-Field ab initio calculations for crystalline systems. Crucial for running time is use of symmetry in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the SACO (Symmetry Adapted Crystalline Orbital) basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. We here illustrate the effectiveness of this scheme, following recent advancements in the CRYSTAL code, concerning memory allocation and direct basis set transformation. Quantitative examples are given for large unit cell systems, such as zeolites (all-silica faujasite and silicalite MFI) and garnets (pyrope). It is shown that the full SCF of 3D systems containing up to 576 atoms and 11136 Atomic Orbitals in the cell can be run with a hybrid functional on a single core PC with 500 MB RAM in about 8 h.     

The use of site symmetry in constructing symmetry adapted functions

It is shown that the application of a projection operator from a given group to a function is equivalent to the successive application of projection operators from factor groups of the starting group to that function. When used with the factor groups representing the site symmetry of a position and the simplest group of interchanges of positions, this concept provides a very simple method for obtaining symmetry adapted linear combinations of basis functions.     

Comparison of the accuracy of periodic reaction field methods in molecular dynamics simulations of a model liquid crystal system

A periodic reaction field (PRF) method is a technique to estimate long‐range interactions. The method has the potential to effectively reduce the computational cost while maintaining adequate accuracy. We performed molecular dynamics (MD) simulations of a model liquid‐crystal system to assess the accuracy of some variations of the PRF method in low‐charge‐density systems. All the methods had adequate accuracy compared with the results of the particle mesh Ewald (PME) method, except for a few simulation conditions. Furthermore, in all of the simulation conditions, one of the PRF methods had the same accuracy as the PME method. © 2015 Wiley Periodicals, Inc.