Symmetrizer: Algorithmic determination of point groups in nearly symmetric molecules

Symmetry is an extremely useful and powerful tool in computational chemistry, both for predicting the properties of molecules and for simplifying calculations. Although methods for determining the point groups of perfectly symmetric molecules are well‐known, finding the closest point group for a “nearly” symmetric molecule is far less studied, although it presents many useful applications. For this reason, we introduce Symmetrizer, an algorithm designed to determine a molecule's symmetry elements and closest matching point groups based on a user‐adjustable tolerance, and then to symmetrize that molecule to a given point group geometry. In contrast to conventional methods, Symmetrizer takes a bottom‐up approach to symmetry detection by locating all possible symmetry elements and uses this set to deduce the most probable point groups. We explain this approach in detail, and assess the flexibility, robustness, and efficiency of the algorithm with respect to various input parameters on several test molecules. We also demonstrate an application of Symmetrizer by interfacing it with the WebMO web‐based interface to computational chemistry packages as a showcase of its ease of integration. © 2012 Wiley Periodicals, Inc.     

三梯级和四梯级圆筒和Mbius分子的拓扑特性研究

Walba等以其卓越的工作,合成了三-THYME(C_(42)H_(72)O_(18))和四-THYME(C_(56)H_(96)O_(24))圆筒及其Mbius扭曲环带分子,被誉为拓扑学进入有机化学领域的奇迹,成为迄今为止拓扑立体化学研究的重要内容,但从拓扑学的观点探索分子图拓扑结构特性尚缺乏深入研究,本文作者考虑到一般性,曾将扭曲数T为偶数(0,2,4)的定义为Hckel型,扭曲数     

A Basis for Orbital Symmetry Rules

The influence of molecular symmetry on reaction rates is examined with an approach in which reactions are viewed as electronic transitions between states of reacants and products (described, in turn by quasiadiabatic potential surface). The moleculer Hamiltonian is used to derive selection rules for these transitions. The complete Hamilatonian has no useful symmetery. Neglect of non-Born-Oppenheimer and spin-orbit terms (and of other angular momentum coupling terms) leads to an apporixmate Hamiltonian and to selection rules which from the basis of the Woodward-Hoffmann rules. This apporch provides an alternative to the adiabatic potantial surfaces, reaction coordinates, and transition state theory used in more familiar discussions of the Woodward-Hoffmann rules. Further, it provides a particulary clear method for discussing violations of these symmetry rules, and for differentiating concerted and nonconcerted reactions.     

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.     

Nonadiabatic sudden increase of the cooperative kinetic effect at lattice energy stabilization—Microscopic mechanism of superconducting state transition: Model study of MgB2

The theory of the nonadiabatic electron–vibration interactions has been applied to the study of MgB₂ superconducting state transition. It has been shown that at nonadiabatic conditions in which the Born–Oppenheimer approximation is not valid and electronic motion is dependent not only on the nuclear coordinates but also on the nuclear momenta, the fermionic ground‐state energy of the studied system can be stabilized by nonadiabatic electron–phonon interactions at broken translation symmetry. Moreover, the new arising state is geometrically degenerate; i.e., there are an infinite number of different nuclear configurations with the same fermionic ground‐state energy. The model study of MgB₂ yields results that are in a good agreement with the experimental data. For distorted lattice, with 0.016 Å/atom of in‐plane out‐of‐phase B? B atoms displacements out of the equilibrium (E_2g phonon mode) when the nonadiabatic interactions are most effective, it has been calculated that the new arising state is 87 meV/unit cell more stable than the equilibrium–high symmetry clumped nuclear structure at the level of the Born–Oppenheimer approximation. The calculated T_c is 39.5 K. The resulting density of states exhibits two‐peak character, in full agreement with the tunneling spectra. The peaks are at ±4 meV, corresponding to the change of the π band density of states, and at ±7.6 meV, corresponding to the σ band. The superconducting state transition can be characterized as a nonadiabatic sudden increase of the cooperative kinetic effect at lattice energy stabilization (NASICKELES). © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A survey and new results on computer enumeration of polyhex and fusene hydrocarbons

After a short historic review, we briefly describe a new algorithm for constructive enumeration of polyhex and fusene hydrocarbons. In this process our algorithm also enumerates isomers and symmetry groups of molecules (which implies enumeration of enantiomers). Contrary to previous methods often based on the boundary code or its variants (which records orientation of edges along the boundary) or on the DAST code, which uses a rigid dualist graph (whose vertices are associated with faces and edges with adjacency between them), the proposed algorithm proceeds in two phases. First inner dual graphs are enumerated; then molecules obtained from each of them by specifying angles between adjacent edges are obtained. Favorable computational results are reported. The new algorithm is so fast that output of the structures is by far the most time-consuming part of the process. It thus contributes to enumeration in chemistry, a topic studied for over a century, and is useful in library making, QSAR/QSPR, and synthesis studies.     

Exploiting space‐group symmetry in fragment‐based molecular crystal calculations

Recent developments in fragment‐based methods make it increasingly feasible to use high‐level ab initio electronic structure techniques to molecular crystals. Such studies remain computationally demanding, however. Here, we describe a straightforward algorithm for exploiting space‐group symmetry in fragment‐based methods which often provides computational speed‐ups of several fold or more. This algorithm does not require a priori specification of the space group or symmetry operators. Rather, the symmetrically equivalent fragments are identified automatically by aligning the individual fragments along their principle axes of inertia and testing for equivalence with other fragments. The symmetry operators relating equivalent fragments can then be worked out easily. Implementation of this algorithm for computing energies, nuclear gradients with respect to both atomic coordinates and lattice parameters, and the nuclear hessian is described. © 2014 Wiley Periodicals, Inc.     

Practical modeling of molecular systems with symmetries

A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree‐based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree‐based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

Exhaustive and nonredundant generation of stereoisomers of a chemical compound with a specified constitution is an important tool for molecular structure elucidation and molecular design. It is known that many chemical compounds have outerplanar graph structures. In this paper we deal with chemical compounds composed of carbon, hydrogen, oxygen, and nitrogen atoms whose graphical structures are outerplanar and consider stereoisomers caused only by asymmetry around carbon atoms. Based on dynamic programming, we propose an algorithm of generating all stereoisomers without duplication. We treat a given outerplanar graph as a graph rooted at its structural center. Our algorithm first recursively computes the number of stereoisomers of the subgraph induced by the descendants of each vertex and then constructs each stereoisomer by backtracking the process of computing the numbers of stereoisomers. Our algorithm correctly counts the number of stereoisomers in O(n) time and space and correctly enumerates all of the stereoisomers in O(n3) time per stereoisomer on average and in O(n) space, where n is the number of atoms in a given structure.     

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     

Initial conformations of macrocyclic compounds with rotational symmetry generated from a molecular fragment

An algorithm is described for generating atomic Cartesian coordinates of conformations of macrocyclic molecules possessing exact rotational or rotation-reflection symmetries. A fragment representing the asymmetric unit of the molecule is suitably oriented in space, and then a symmetry operator is applied to generate the initial coordinates of the molecule. An empirical force field of interatomic interactions is used to generate equilibrium conformations. Results of calculations performed on two cyclic polylactones and one crown ether using this approach are given. They reveal that symmetric conformations of these molecules are often preferred. Since the latter conformations are probably responsible for the specialized properties of these molecules, this method should facilitate doing theoretical studies on these kinds of compounds.     

Symmetry measures of the electron density

In this communication we define electronic symmetry operation and symmetry group measures, eSOM and eSGM, respectively, develop the basic algorithms to obtain them, and give some examples of the possible applications of these new computational tools. These new symmetry measures based on the electron density have been tested in an analysis of (a) the inversion symmetry for heteronuclear diatomic molecules, for the eclipsed and staggered conformations of ethane and tetrafluoroethane, and for a series of octahedral sulfur halides; (b) the reflection symmetry of three different conformers of tetrafluoroethene; and (c) the loss of C₆ symmetry along the B_2u distortion mode of benzene and an analysis of rotational symmetry for different six‐member ring heterocycles. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Evaluating a Degree of Molecular Symmetry and Chirality

A method of evaluating a degree of molecular symmetry is suggested. The symmetry criteria calculated by this technique are useful for predicting phase transition temperatures in mesogen compounds. Methods of evaluating chirality avoiding molecular representation as a set of simplices are proposed. The efficiency of these methods is verified on model structures belonging to different symmetry groups. The new approach may be used to analyze stereochemical relationships between atoms in a molecule.     

Direct Observation of Ordered High‐Spin–Low‐Spin Intermediate States of an Iron(III) Three‐Step Spin‐Crossover Complex

A neutral mononuclear Fe^III complex [Fe^III(H‐5‐Br‐thsa‐Me)(5‐Br‐thsa‐Me)]?H₂O ( 1 ; H₂‐5‐Br‐thsa‐Me=5‐bromosalicylaldehyde methylthiosemicarbazone) was prepared that exhibited a three‐step spin‐crossover (SCO) with symmetry breaking and a 14 K hysteresis loop owing to strong cooperativity. Two ordered intermediate states of 1 were observed, 4HS–2LS and 2HS–4LS, which exhibited reentrant phase‐transition behavior. This study provides a new platform for examining multistability in SCO complexes.     

Nonrigid molecule effects in molecules with linear or nongeometrically equivalent equilibrium configurations

A theoretical study is made of the states of nonrigid molecules, extending earlier work to apply Longuet–Higgins' symmetry group of feasible permutation/inversions in two previously untreated cases. The first involves nonrigid molecule processes between different stereoisomers, that is between molecular equilibrium configurations of different geometrical shapes. The second takes into account nonrigid molecule processes in linear molecules. The theory is applied to the specific case of nonrigid molecule effects in the butyl ion C₄H (case i), and the form of the nonrigid molecule energy levels and spectra are determined. The theory is also applied to determine the nonrigid molecule energy levels in linear H₂F₂ (case ii).     

Molecular symmetry perception

An algorithm for molecular symmetry perception is presented. The method identifies the full set of molecular symmetry elements (proper and improper) and determines their coordinates. The algorithm eliminates the necessity to explore the entire graph automorphism group; as a result its computer application is extremely effective. Application to several dendrimers and fullerenes with high topological symmetry is presented.     

Mirror Symmetry Breaking by Chirality Synchronisation in Liquids and Liquid Crystals of Achiral Molecules

Spontaneous mirror symmetry breaking is an efficient way to obtain homogeneously chiral agents, pharmaceutical ingredients and materials. It is also in the focus of the discussion around the emergence of uniform chirality in biological systems. Tremendous progress has been made by symmetry breaking during crystallisation from supercooled melts or supersaturates solutions and by self‐assembly on solid surfaces and in other highly ordered structures. However, recent observations of spontaneous mirror symmetry breaking in liquids and liquid crystals indicate that it is not limited to the well‐ordered solid state. Herein, progress in the understanding of a new dynamic mode of symmetry breaking, based on chirality synchronisation of transiently chiral molecules in isotropic liquids and in bicontinuous cubic, columnar, smectic and nematic liquid crystalline phases is discussed. This process leads to spontaneous deracemisation in the liquid state under thermodynamic control, giving rise to long‐term stable symmetry‐broken fluids, even at high temperatures. These fluids form conglomerates that are capable of extraordinary strong chirality amplification, eventually leading to homochirality and providing a new view on the discussion of emergence of uniform chirality in prebiotic systems.     

Ein neues programmierbares Schema zur Bestimmung der Molekülsymmetrie

The symmetry of molecules can be determined, when their structure is known, using schemes of questions (algorithms), by means of which the existence of certain elements of symmetry is checked. In this paper, a new algorithm is presented, which renders feasible the prompt determination of symmetry point groups and visualizes relations between different types of symmetry. The application of the algorithm is demonstrated by means of a graphic scheme and a Pascal computer version.

     

Molecular torus group

Generally speaking, the highest symmetry of M?bius cyclacene molecule possesses the C₂ symmetry based on the theory of point group according to the previous works. However, based on the topology principle, the fundamental group of M?buis strip is an infinite continuous cyclic group and its border is made up of twice of the generator. Of course, the M?bius strip-like molecule is associated with a finite discrete cyclic symmetry group. For the cyclacene isomers constructed by several (n) benzene rings, these isomers include: the common cylinder Hückel cyclacene (HC-[n]) molecules, the M?bius cyclacene (MC-[n]) molecules by twisting the linear precursor one time (180°), and the multi-twisted M?bius strip-like cyclacene (M ^m C?[n]) molecules by twisting the linear precursor m times (m × 180°). The relevant results suggest that in addition to the point symmetry, there is a new kind of symmetry called the torus screw rotation (denoted as TSR). In this article, we take the M ^m C?[n] molecules as examples to discuss their TSR group and point group symmetry, and the relative symmetry adaptive atom sets as well as their atomic orbital (AO) sets. Here, the Cartesian coordinates is not quite fit for the investigation of these AOs, so it is replaced by either the torus orthogonal curvilinear coordinates (for M ^m C?[n] molecule) or the cylinder orthogonal curvilinear coordinates (for HC-[n] molecule). According to the features of cyclic group, the character table of the irreducible representation of the TSR group could be constructed easily. Some other relevant point-group symmetries maybe also belong to the molecule, so its symmetry maybe called as the torus group symmetry. For multi-twisted M?bius strip-like molecule, there are some correlations in topology characteristics.