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[转载]Wyckoff Positions
swx0789 2016-3-6 22:42
wyckoff position 各种晶格群的表格 http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list 下面是从其他网站转的,读过后,对wyckoff position 可以有大致的了解了。 Space Groups The International Tables for Crystallography From examination of a space group in “The International Tables for Crystallography” Vol. A, you should be able to ascertain the following information: · Herman-Mauguin (HM) Symbol (Long, Short) · Point Group (HM, Schoenflies) · Locate and identify symmetry elements · Understand Wyckoff site multiplicity and symmetry · Distinguish general and special positions · Extinction conditions · Identify possible subgroups and supergroups Understanding the Herman-Mauguin Space Group Symbol Space groups are typically identified by their short Herman-Mauguin symbol (i.e. Pnma, I4/mmm, etc.). The symmetry elements contained in the short symbol are the minimum number needed to generate all of the remaining symmetry elements. This symbolism is very efficient, condensed form of noting all of the symmetry present in a given space group. We won’t go into all of the details of the space group symbol, but I will expect you to be able to determine the Crystal system, Bravais Lattice and Point group from the short H-M symbol. You should also be able to determine the presence and orientation of certain symmetry elements from the short H-M symbol and vice versa. The HM space group symbol can be derived from the symmetry elements present using the following logic. The first letter identifies the centering of the lattice, I will hereafter refer to this as the lattice descriptor : · P ® Primitive · I ® Body centered · F ® Face centered · C ® C-centered · B ® B-centered · A ® A-centered The next three symbols denote symmetry elements present in certain directions, those directions are as follows: Crystal System Symmetry Direction Primary Secondary Tertiary Triclinic None Monoclinic Orthorhombic Tetragonal / Hexagonal/ Trigonal / / Cubic / / – Axis parallel or plane perpendicular to the x-axis. – Axis parallel or plane perpendicular to the y-axis. – Axis parallel or plane perpendicular to the z-axis. – Axis parallel or plane perpendicular to the line running at 45° to the x and y axes. – Axis parallel or plane perpendicular to the long face diagonal of the ab face of a hexagonal cell. – Axis parallel or plane perpendicular to the body diagonal. For a better understanding see specific examples from class notes. However, with no knowledge of the symmetry diagram we can identify the crystal system from the space group symbol. · Cubic – The secondary symmetry symbol will always be either 3 or –3 (i.e. Ia3, Pm3m, Fd3m) · Tetragonal – The primary symmetry symbol will always be either 4, (-4), 4 1 , 4 2 or 4 3 (i.e. P4 1 2 1 2, I4/m, P4/mcc) · Hexagonal – The primary symmetry symbol will always be a 6, (-6), 6 1 , 6 2 , 6 3 , 6 4 or 6 5 (i.e. P6mm, P6 3 /mcm) · Trigonal – The primary symmetry symbol will always be a 3, (-3) 3 1 or 3 2 (i.e P31m, R3, R3c, P312) · Orthorhombic – All three symbols following the lattice descriptor will be either mirror planes, glide planes, 2-fold rotation or screw axes (i.e. Pnma, Cmc2 1 , Pnc2) · Monoclinic – The lattice descriptor will be followed by either a single mirror plane, glide plane, 2-fold rotation or screw axis or an axis/plane symbol (i.e. Cc, P2, P2 1 /n) · Triclinic – The lattice descriptor will be followed by either a 1 or a (-1). The point group can be determined from the short H-M symbol by converting glide planes to mirror planes and screw axes to rotation axes. For example: Space Group = Pnma ® Point Group = mmm Space Group = I`4c2 ® Point Group =`4m2 Space Group = P4 2 /n ® Point Group = 4/m Wyckoff Sites One of the most useful pieces of information contained in the International Tables are the Wyckoff positions. The Wyckoff positions tell us where the atoms in a crystal can be found. To understand how they work consider the monoclinic space group Pm. This space group has only two symmetry elements, both mirror planes perpendicular to the b-axis. One at y = 0 and one at y = ½ (halfway up the unit cell in the b direction). Now let’s place an atom in the unit cell at an arbitrary position, x,y,z. If we now carry out the symmetry operation associated with this space group a second atom will be generated by the mirror plane at x,-y,z. However, if we were to place the atom on one of the mirror planes (its y coordinate would have to be either 0 or ½) then the reflection operation would not create a second atom.All of the information in the proceeding paragraph is contained in Wyckoff positions section of the International Tables. Pm has three Wyckoff sites as shown in the table below: Multiplicity Wyckoff Letter Site Symmetry Coordinates 2 c 1 (1) x,y,z (2) x,-y,z 1 b m x,½,z 1 a m x,0,z The multiplicity tells us how many atoms are generated by symmetry if we place a single atom at that position. In this case for every atom we insert at an arbitrary position (x,y,z) in the unit cell a second atom will be generated by the mirror plane at x,-y,z. This corresponds to the uppermost Wyckoff position 2c. The letter is simply a label and has no physical meaning. They are assigned alphabetically from the bottom up. The symmetry tells us what symmetry elements the atom resides upon. The uppermost Wyckoff position, corresponding to an atom at an arbitrary position never resides upon any symmetry elements. This Wyckoff position is called the general position. The coordinates column tells us the coordinates of all of the symmetry related atoms (two in this case). All of the remaining Wyckoff positions are called special positions. They correspond to atoms which lie upon one of more symmetry elements, because of this they always have a smaller multiplicity than the general position. Furthermore, one or more of their fractional coordinates must be fixed. In this case the y value must be either 0 or ½ or the atom would no longer lie on the mirror plane. Generating a Crystal Structure from its Crystallographic Description Using the space group information contained in the International Tables we can do many things. One powerful use is to generate an entire crystal structure from a brief description.Consider the following description of the crystal structure of Sr 2 AlTaO 6 .Space Group = Fm`3ma = 7.80 ÅAtomic PositionsAtom X Y ZSr 0.25 0.25 0.25Al 0.0 0.0 0.0Ta 0.5 0.5 0.5O 0.24 0.0 0.0 From the space group tables we see that the atoms are located on the following Wyckoff sites Sr ® 8c Al ® 4a Ta ® 4b O ® 24e The number associated with the Wyckoff sites tells us how many atoms of that type there are in the unit cell. In this So there are 40 atoms in the unit cell, with stoichiometry Sr 8 Al 4 Ta 4 O 24 which reduces to the empirical formula Sr 2 AlTaO 6 . Since the number of atoms in the unit cell is four times the number of atoms in the formula unit, we say that Z = 4. Using the face centering generators (0,0,0), (½,½,0), (½,0,½), (0,½,½) together with the coordinates of each Wyckoff site we can generate the fractional coordinates of all atoms in the unit cell: Sr 1:(0.25,0.25,0.25), 2:(0.75,0.75,0.25), 3:(0.75,0.25,0.75), 4:(0.25,0.75,0.75) 5:(0.25,0.25,0.75), 6:(0.75,0.75,0.75), 7:(0.75,0.25,0.25), 8:(0.25,0.75,0.25) Al 1:(0.0,0.0,0.0), 2:(0.5,0.5,0.0), 3:(0.5,0.0,0.5), 4:(0.0,0.5,0.5) Ta 1:(0.5,0.5,0.5), 2:(0.0,0.0,0.5), 3:(0.0,0.5,0.0), 4:(0.5,0.0,0.0) O 1:(0.24,0.0,0.0), 2:(0.74,0.5,0.0), 3:(0.74,0.0,0.5), 4:(0.24,0.5,0.5) 5:(0.76,0.0,0.0), 6:(0.26,0.5,0.0), 7:(0.26,0.0,0.5), 8:(0.76,0.5,0.5) 9:(0.0,0.24,0.0), 10:(0.5,0.74,0.0), 11:(0.5,0.24,0.5), 12:(0.0,0.74,0.5) 13:(0.0,0.76,0.0), 14:(0.5,0.26,0.0), 15:(0.5,0.76,0.5), 16:(0.0,0.26,0.5) 17:(0.0,0.0,0.24), 18:(0.5,0.5,0.24), 19:(0.5,0.0,0.74), 20:(0.0,0.5,0.74) 21:(0.0,0.0,0.76), 22:(0.5,0.5,0.76), 23:(0.5,0.0,0.26), 24:(0.0,0.5,0.26) From these fractional coordinates you can sketch out the structure of Sr 2 AlTaO 6 . With some luck I will provide a link to a picture of the structure here, at some point in the future. We can also work out bond distances from this information. The first Al ion is octahedrally coordinated by six oxygens (1,5,9,13,17,21) and the Al-O distance is : d = 7.80′ 1/2 = 1.87Å while the first Ta ion is also surrounded by 6 oxygens (4,8,11,15,18,22) at a distance of d = 7.80′ 1/2 = 2.03Å and Sr is surrounded by 12 oxygens (1,4,6,7,9,11,14,16,17,18,23,24) at a distance of d = 7.80′ 1/2 = 2.76Å Determining a Crystal Structure from Symmetry Composition Another use is that given the stoichiometry, space group and unit cell size (which can typically be determined from diffraction techniques) and the density of a compound we can often deduce the crystal structure of relatively simple compounds. As an example consider the following information: Stoichiometry = SrTiO 3 Space Group = Pm3m a = 3.90 Å Density = 5.1 g/cm 3 To derive the crystal structure from this information the first step is to calculate the number of formula units per unit cell : Formula Weight SrTiO 3 = 87.62 + 47.87 + 3′(16.00) = 183.49 g/mol Unit Cell Volume = (3.90′10 -8 cm) 3 = 5.93′10 -23 cm 3 (5.1 g/cm 3 )′(5.93′10 -23 cm 3 )′(mol/183.49 g)′(6.022′10 23 /mol) = 0.99 Thus there is one formula unit per unit cell (Z=1), and the number of atoms per unit cell is : 1 Sr, 1 Ti and 3 O. Next we compare the number of atoms in the unit cell with the multiplicities of the Wyckoff sites. · From the multiplicities of the special positions in space group Pm3m we see that Sr must occupy either the 1a or 1b positions (otherwise there would be more than one Sr in the unit cell) · By the same reasoning Ti must also reside in either the 1a or 1b position, and, since there are no free positional parameters (x,y or z) in either 1a or 1b, the two ions cannot occupy the same site. · To maintain 3 oxygen ions in the unit cell it must reside at either site 3c or 3d. If we arbitrarily put Ti at the origin (1a), then by default Sr must go to 1b. To evaluate the prospects of putting O at either 3c or 3d we calculate the Ti-O bond distances: D (O @ 3c) = 3.90′ 1/2 = 2.76Å D (O @ 3d) = 3.90′ 1/2 = 1.95Å Of these two the latter (3d) is obviously more appropriate for a Ti-O bond (consult tables of ionic radii to convince yourself of this statement). Thus we obtain the structure of SrTiO 3 to be Space Group = Pm3ma = 3.90 ÅAtomic PositionsAtom Site X Y ZSr 1b 0.5 0.5 0.5Ti 1a 0.0 0.0 0.0O 3d 0.5 0.0 0.0
个人分类: 知识储备|3 次阅读|0 个评论
崇拜大师少一个“磕头”难道还不行吗?
热度 6 大毛忽洞 2013-10-29 23:40
崇拜大师少一个“磕头”难道还不行吗? 我从本科就看过冯端先生的《金属物理学》,因为我就是学习金属物理学的。 可以说,我就是看着冯端先生的书长大的,后来又买了冯端先生最新版全套的《金属物理学》。如果从认真读书的角度看,我可能是冯端先生著作的真正崇拜者。 我崇拜冯端先生少“磕一个头”还不行吗? http://blog.sciencenet.cn/home.php?mod=spaceuid=2321do=blogid=426572 这篇文章 2011 年就贴出来了。 虽然我的文章的题目为《原子堆垛:改正冯端《金属物理学》的1个错误》。但是,我在文章一开头就开始称呼冯端先生,而且通篇里出现的都是冯端先生,这还不够吗? 再说《金属物理学》封面的署名也冯端,而不是冯端先生。我的题目也这么做有什么不行? 我的文章一点也没有对冯端先生的不敬。 我挑出了冯端先生《金属物理学》中的一个错误,在《南大的亲们……》里,我把它称为概念关联性错误。(不大不小) 如果我拿一个错别字或是一个印刷错误来做文章,那就是别有用心了。 我在搞我的研究时,遇到了一个问题,翻看了很多书(包括冯端先生的书)都没有解决,最后还是通过阅读《国际空间群表》把问题解决了。再回过头来翻阅冯端先生的书时,才意识到那样的表述是错的。由于冯端先生使用的原子坐标和国际空间群表的不同,但是,反映到晶体里,只不过是ABABABAB…和BCBCBCBCBC…的差别,我在文章明确表示,这只是参照系的不同造成的。什么问题也没有。 我认定冯端先生的表述“ 但周围原子配列情况不完全相同 ”是错的。 在我和匿名者留言讨论时,我是强调过c/a=1.633的条件。因为这个条件也是冯端先生写在那里的。 当你( 黄秀清先生 )第一次写文章回应我时,你( 黄秀清先生 )的文章语气虽然是时髦点,但我也没有什么好激动的。我只细读了你( 黄秀清先生 )的证据(黄昆先生书的一页),没有看其他的。书页很陈旧,结果让我掉以轻心,就给你( 黄秀清先生 )留言,如下图。当有网友留言说那书页来自黄昆先生时,我立马感觉坏事了。马上写了三次道歉,如下图。 我特别声明向黄昆先生的书道歉而非向那片书页道歉。(书大于书页)。如果我向那片书页道歉,就无法再坚持我的立场了。 我看到那片书页虽然老点,但是我感觉到这片书页好像是为我准备的证据。 本来是我和你( 黄秀清先生 )讨论冯端先生《金属物理学》里的错误,现在你( 黄秀清先生 )给我提供了黄昆先生《固体物理学》里的一页。这客观上,好像是你( 黄秀清先生 )为我提供了证据。 自此,我就先不和你( 黄秀清先生 )纠缠冯端先生的《金属物理学》,因为我们没有共同语言。为此,我开始写《国际空间群表的科学价值》,为讨论黄昆先生《固体物理学》里的“ A 层原子和B层原子是不等价的,这是因为他们的几何处境不相同 ”作铺垫。 实际上,很多匿名者,连是个什么问题都不知道,发起言来还滔滔不绝。因此,需要普及点空间群啊! 说实在的,这也没有什么大不了的。不就是书里的一个错误吗! 冯端先生的《金属物理学》和黄昆先生的《固体物理学》,都是大名鼎鼎的学术著作。我挑出的那个错误,连九牛之一毫毛,沧海之一小粟也算不上。 没有必要大惊小怪的,心平气和地讨论就可以了。 我感觉已经开始向好的方向发展了,当时发言非常活跃的人,留言告诉我说他也开始推导问题了。这就对了,看明白了或计算明白了再发言多好!
个人分类: 探路和走路|3489 次阅读|8 个评论
Wyckoff positions of space group
plgongcat 2013-3-13 08:19
空间群检索网站:只需要 修改 下面的网址中的 数字序号 哦! http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum= 66
个人分类: LINKS|2664 次阅读|0 个评论
答网友晶体学问题:单斜晶系的空间群符号
热度 2 大毛忽洞 2011-4-18 11:47
答网友晶体学问题:单斜晶系的空间群符号
答网友晶体学问题:单斜晶系的空间群符号 问题在: http://blog.sciencenet.cn/home.php?mod=spaceuid=2321do=wall 回答如下: 根据你提供的信息( ICSD #33243 :单斜钒酸铋 )。 ICSD 33243 数据(摘要)如下: Structured Bi (V O4) Unit Cell 5.197 5.096 11.702 90. 90. 90.4 Space Group I 1 1 2/b SG Number 15 Atom # OX SITE x y z SOF Bi 1 +3 4 e 0 0.25 0.6337(1) 1. V 1 +5 4 e 0 0.25 0.1352(5) 1. O 1 -2 8 f 0.149(3) 0.506(8) 0.210(2) 1. O 2 -2 8 f 0.258(3) 0.379(8) 0.451(2) 1. *end for ICSD #33243 在国际空间群表里, 15 号空间群有 6 种表达方式: Uniq-b 轴有三种晶胞, Uniq-c 轴有三种晶胞,共有 6 种。 注意, 6 种晶胞对应一个空间群编号,但是 6 种晶胞的 Patterson symmetry 符号不同。例如,你的数据( ICSD #33243 )对应 I 1 1 2/b , 根据这个符号确定空间群表里的具体晶胞选择。根据 Unit Cell 的( 5.197 5.096 11.702 90. 90. 90.4 ) 信息,可以确定属于 Uniq-c 轴,对应的晶胞如下: 注意,原子坐标的数据是和晶胞数据对应的。 BiVO4 的原子环境数据如下: a=,5.197,b=,5.096,c=,11.702,Delta=,.005 1 4e-Bi, is a reference atom Cartesian = ,-2.5896,-1.274,1.5681 SP coordinates=,0,.25,.634 ,1,1,The shell structure as a cluster:,shell,No,1 d of neighbors from the reference atom =,2.3434 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,2.94 Neighbor atom:,8f-1-O Cartesian = ,-3.3726,-.0306,3.3936 SP coordinates= ,-.149,.494,.79 Neighbor atom:,8f-1-O Cartesian = ,-1.8066,-2.5174,3.3936 SP coordinates= ,.149,.006,.79 ,1,2,The shell structure as a cluster:,shell,No,2 d of neighbors from the reference atom =,2.3734 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,4.4 Neighbor atom:,8f-1-O Cartesian = ,-4.4051,-2.5174,2.4574 SP coordinates= ,-.351,.006,.71 Neighbor atom:,8f-1-O Cartesian = ,-.7741,-.0306,2.4574 SP coordinates= ,.351,.494,.71 ,1,3,The shell structure as a cluster:,shell,No,3 d of neighbors from the reference atom =,2.5292 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,4.65 Neighbor atom:,8f-2-O Cartesian = ,-3.9436,.6166,.5734 SP coordinates= ,-.258,.621,.549 Neighbor atom:,8f-2-O Cartesian = ,-1.2356,-3.1645,.5734 SP coordinates= ,.258,-.121,.549 ,1,4,The shell structure as a cluster:,shell,No,4 d of neighbors from the reference atom =,2.6084 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,2.98 Neighbor atom:,8f-2-O Cartesian = ,-3.9258,-1.9313,-.5734 SP coordinates= ,-.258,.121,.451 Neighbor atom:,8f-2-O Cartesian = ,-1.2534,-.6166,-.5734 SP coordinates= ,.258,.379,.451 ,1,5,The shell structure as a cluster:,shell,No,5 d of neighbors from the reference atom =,3.6058 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,6.93 Neighbor atom:,8f-2-O Cartesian = ,-3.9081,-4.4793,.5734 SP coordinates= ,-.258,-.379,.549 Neighbor atom:,8f-2-O Cartesian = ,-1.2712,1.9313,.5734 SP coordinates= ,.258,.879,.549 ,1,6,The shell structure as a cluster:,shell,No,6 d of neighbors from the reference atom =,3.6266 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,7.25 Neighbor atom:,4e-V Cartesian = ,-5.1703,-3.8219,1.5798 SP coordinates= ,-.5,-.25,.635 Neighbor atom:,4e-V Cartesian = ,-.0089,1.274,1.5798 SP coordinates= ,.5,.75,.635 2 4e-V, is a reference atom Cartesian = ,-2.5896,-1.274,-4.2712 SP coordinates=,0,.25,.135 ,2,1,The shell structure as a cluster:,shell,No,1 d of neighbors from the reference atom =,1.7431 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,2.85 Neighbor atom:,8f-2-O Cartesian = ,-3.8519,-.6166,-5.2776 SP coordinates= ,-.242,.379,.049 Neighbor atom:,8f-2-O Cartesian = ,-1.3273,-1.9313,-5.2776 SP coordinates= ,.242,.121,.049 ,2,2,The shell structure as a cluster:,shell,No,2 d of neighbors from the reference atom =,1.7486 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,3.02 Neighbor atom:,8f-1-O Cartesian = ,-3.3549,-2.5785,-3.3936 SP coordinates= ,-.149,-.006,.21 Neighbor atom:,8f-1-O Cartesian = ,-1.8244,.0306,-3.3936 SP coordinates= ,.149,.506,.21 ,2,3,The shell structure as a cluster:,shell,No,3 d of neighbors from the reference atom =,2.89 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,4.5 Neighbor atom:,8f-1-O Cartesian = ,-4.4229,.0306,-2.4574 SP coordinates= ,-.351,.506,.29 Neighbor atom:,8f-1-O Cartesian = ,-.7564,-2.5785,-2.4574 SP coordinates= ,.351,-.006,.29 ,2,4,The shell structure as a cluster:,shell,No,4 d of neighbors from the reference atom =,3.1239 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,4.53 Neighbor atom:,8f-2-O Cartesian = ,-3.8341,-3.1645,-6.4244 SP coordinates= ,-.242,-.121,-.049 Neighbor atom:,8f-2-O Cartesian = ,-1.3451,.6166,-6.4244 SP coordinates= ,.242,.621,-.049 ,2,5,The shell structure as a cluster:,shell,No,5 d of neighbors from the reference atom =,3.6266 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,7.25 Neighbor atom:,4e-Bi Cartesian = ,-5.1703,-3.8219,-4.2829 SP coordinates= ,-.5,-.25,.134 Neighbor atom:,4e-Bi Cartesian = ,-.0089,1.274,-4.2829 SP coordinates= ,.5,.75,.134 ,2,6,The shell structure as a cluster:,shell,No,6 d of neighbors from the reference atom =,3.652 The number of neighbor atoms, N=,2,and the number of shortest bonds formed by these atoms=,1 and the shortest bond length=,7.3 Neighbor atom:,4e-Bi Cartesian = ,-5.2059,1.274,-4.2829 SP coordinates= ,-.5,.75,.134 Neighbor atom:,4e-Bi Cartesian = ,.0267,-3.8219,-4.2829 SP coordinates= ,.5,-.25,.134 3 8f-1-O, is a reference atom Cartesian = ,-1.8066,-2.5174,3.3936 SP coordinates=,.149,.006,.79 ,3,1,The shell structure as a cluster:,shell,No,1 d of neighbors from the reference atom =,1.7486 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-V Cartesian = ,-2.5718,-3.8219,4.2712 SP coordinates= ,0,-.25,.865 ,3,2,The shell structure as a cluster:,shell,No,2 d of neighbors from the reference atom =,2.3434 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-Bi Cartesian = ,-2.5896,-1.274,1.5681 SP coordinates= ,0,.25,.634 ,3,3,The shell structure as a cluster:,shell,No,3 d of neighbors from the reference atom =,2.3734 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-Bi Cartesian = ,.0089,-1.274,4.2829 SP coordinates= ,.5,.25,.866 4 8f-2-O, is a reference atom Cartesian = ,-1.3273,-1.9313,-5.2776 SP coordinates=,.242,.121,.049 ,4,1,The shell structure as a cluster:,shell,No,1 d of neighbors from the reference atom =,1.7431 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-V Cartesian = ,-2.5896,-1.274,-4.2712 SP coordinates= ,0,.25,.135 ,4,2,The shell structure as a cluster:,shell,No,2 d of neighbors from the reference atom =,2.5293 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-Bi Cartesian = ,.0267,-3.8219,-4.2829 SP coordinates= ,.5,-.25,.134 ,4,3,The shell structure as a cluster:,shell,No,3 d of neighbors from the reference atom =,2.6084 The number of neighbor atoms, N=,1,and the number of shortest bonds formed by these atoms=,0 and the shortest bond length=,0 Neighbor atom:,4e-Bi Cartesian = ,.0089,-1.274,-7.4191 SP coordinates= ,.5,.25,-.134 更多的数据可下载: BiVO4-15-Mono-Uniq-c-AEC-1-原子输出- .005.rar BiVO4-15-Mono-Uniq-c-AEC-1-配位数-简化版-修改- .005.rar
个人分类: 晶体学和空间群|10267 次阅读|3 个评论
论文:用AFM研究DL-缬氨酸晶体的结构及其表面分子的排列
Bjqdsx 2011-1-20 10:40
摘要:利用原子力显微镜 (AFM) 成像技术来观察 DL- 缬氨酸晶体表面分子的规则排列 , 研究表明对映体分子在 DL- 缬氨酸晶体中相互配对排列 , 每个晶胞单元中包含两个对映体分子 , 属于具有中心对称结构 P1 群 , 整个晶体是消旋的 . 通过原子力显微镜对 DL- 缬氨酸晶体表面重复单元的测量结果与 X 衍射数据对比 , 发现用 AFM 观察到的 DL- 缬氨酸晶体中分子表面形貌的规整排列的距离 , 同 X 衍射得出的三斜晶系晶胞参数数据基本一致 , 由此判定该晶体属于三斜晶系而不是单斜晶系 . 探讨了利用纳米技术的研究手段在分子水平研究生命起源中的手性问题 , 在确定的晶面上通过分子周期性结构排列规律 , 对 DL- 缬氨酸晶体表面分子进行手性识别 . 关键词:单晶表面手性识别 ; 空间群 ;DL- 缬氨酸 ; 原子力显微镜 ;X 射线衍射 ; 论文附件: 用AFM研究DL_缬氨酸晶体的结构及其表面分子的排列_英文_.pdf
个人分类: 论文交流|2919 次阅读|0 个评论
空间群No12:国际空间群表和晶体学数据
热度 2 大毛忽洞 2010-4-26 10:03
空间群 No12 :国际空间群表和晶体学数据 美国有个海军,海军有个什么实验室,这个实验室有个晶体学启蒙网站。 在中国,这个网站有时可以打开,有时打不开。也不知道是谁在捣蛋,是老美在捣蛋?还是本拉登在捣蛋?还是什么第三者在捣蛋?咱中国人是不会干这种缺德的事情! 老美财大气粗,特别是老美的海军,更是财大气粗中的财大气粗。他们对于案例中涉及到的晶体结构,都给出了三维动画演示,他们的原子坐标是用矢量法表示的。 我也分析了很多的晶体结构,但是我只能给出数字表示。他们是一帮人,我就我自己。他们财大气粗,有个专门的网站,我只有靠科学网这个平台,才可以把我的结果贴出来。 为什么要贴出来呢? 为了梦中的橄榄树! 老的 PDF 数据没有给出原子坐标。 这个数据给出了原子坐标,如果没有绿色框之中的信息,数据仍然是不完备的。 这是 12 号国际空间群表的表头,我喜欢使用 No.12 和 C 2h ( 3 )符号。不幸的是,编号为 12 的空间群有很多种表达方法,这给我们解读晶体学数据(如求键络)带来很多麻烦。 No.12 空间群的点群为 C 2h ,有一个 C 2 轴,还有一个镜面 m 垂直于这个 2 次轴,还有一个反演中心 i ,加上单位元素,组成一个 4 阶点群( C 2h )。 这个唯一的对称轴 C 2 就是 UNIQUE AXIS 。 如果把晶体的对称轴 C 2 给了(置于) b 轴( Y 轴),就是所谓的 UNIQUE AXIS b ; 如果把晶体的对称轴 C 2 给了(置于) c 轴( Z 轴),就是所谓的 UNIQUE AXIS c ; 当然了,也可以把晶体的对称轴 C 2 给了(置于) a 轴( X 轴),就是所谓的 UNIQUE AXIS a ; 除了空间群表的 6 种表示外,还有其他 6 种表示符号。 C12/m1 , A12/m1 , I12/m1 ; 对应选择 UNIQUE AXIS b ; A112/m , B112/m , I112/m ;对应选择 UNIQUE AXIS c ; A2/m,C2/a,C2/m11,C2/m,F2/m,I2/m 这也是 No.12 空间群的表示符号。 教科书上单斜晶系的晶胞参数是: a ≠ b ≠ c ,α=γ= 90 o ,β≠ 90 o 。 这种写法是有条件的,即把实际晶体的 UNIQUE AXIS 给了 b 。 当然了,也可以把晶体的 UNIQUE AXIS 给了 c ,也可以把晶体的 UNIQUE AXIS 给了 a 。 相对于晶体来说, a , b , c 的安放就相当于参照坐标系的选择,可以是随意的。 国际空间群表只约定了两种: 把晶体的 UNIQUE AXIS 给了 b 和把晶体的 UNIQUE AXIS 给了 c 。 此外,国际空间群表中的 No.12 空间群,给出了 6 种原子坐标,即所谓的 CELL CHOICE ,这都是由于不同的人的习惯不同,结果弄出 6 种摆放原子的模式。无论怎么描述原子的摆放,每个原子的环境是不能变的。 如何来描述原子的环境呢? 有点法、线法和面法。各种化学键理论和电子密度理论都需要知道原子的环境。 化合物 AlCeCo 的原子环境: a=,11.098,b=,4.41,c=,4.807,Delta=,.005 1, ,4i-Co,---,4i-Ce, d===,2.4613 4i-Co,:,-5.3604,14.0361,-2.205, Z=,1 SP coordinates=,1.807,0,.146 配位原子 : ,4i-Ce,: ,-2.9939,14.7126,-2.205 SP coordinates=,1.87,0,.675 4i-Ce,:,-2.9939,14.7126,-2.205, Z=,1 SP coordinates=,1.87,0,.675 配位原子 : ,4i-Co,: ,-5.3604,14.0361,-2.205 SP coordinates=,1.807,0,.146 2, ,4i-Al,---,4i-Co, d===,2.488 4i-Al,:,.1502,-6.2931,-4.41, Z=,2 SP coordinates=,-.086,-.5,.19 配位原子 : ,4i-Co,: ,.2383,-7.4422,-6.615 SP coordinates=,-.193,-1,.146 配位原子 : ,4i-Co,: ,.2383,-7.4422,-2.205 SP coordinates=,-.193,0,.146 4i-Co,:,.2383,-7.4422,-6.615, Z=,2 SP coordinates=,-.193,-1,.146 配位原子 : ,4i-Al,: ,.1502,-6.2931,-8.82 SP coordinates=,-.086,-1.5,.19 配位原子 : ,4i-Al,: ,.1502,-6.2931,-4.41 SP coordinates=,-.086,-.5,.19 3, ,4i-Co,---,4i-Ce, d===,2.5325 4i-Co,:,2.5611,-3.2969,2.205, Z=,1 SP coordinates=,.193,1,.854 配位原子 : ,4i-Ce,: ,5.0015,-3.9735,2.205 SP coordinates=,.13,1,1.325 4i-Ce,:,5.0015,-3.9735,2.205, Z=,1 SP coordinates=,.13,1,1.325 配位原子 : ,4i-Co,: ,2.5611,-3.2969,2.205 SP coordinates=,.193,1,.854 4, ,4i-Al,---,4i-Co, d===,2.574 4i-Al,:,-3.5576,.9236,-2.205, Z=,1 SP coordinates=,.586,0,-.19 配位原子 : ,4i-Co,: ,-2.5611,3.2969,-2.205 SP coordinates=,.807,0,.146 4i-Co,:,-2.5611,3.2969,-2.205, Z=,1 SP coordinates=,.807,0,.146 配位原子 : ,4i-Al,: ,-3.5576,.9236,-2.205 SP coordinates=,.586,0,-.19 5, ,4i-Co,---,4i-Co, d===,2.7453 4i-Co,:,1.1614,2.0727,0, Z=,2 SP coordinates=,.693,.5,.854 配位原子 : ,4i-Co,: ,2.2459,3.2969,-2.205 SP coordinates=,.807,0,1.146 配位原子 : ,4i-Co,: ,2.2459,3.2969,2.205 SP coordinates=,.807,1,1.146 4i-Co,:,2.2459,3.2969,-2.205, Z=,2 SP coordinates=,.807,0,1.146 配位原子 : ,4i-Co,: ,1.1614,2.0727,-4.41 SP coordinates=,.693,-.5,.854 配位原子 : ,4i-Co,: ,1.1614,2.0727,0 SP coordinates=,.693,.5,.854 6, ,4i-Al,---,4i-Al, d===,2.9562 4i-Al,:,2.6491,-4.446,0, Z=,1 SP coordinates=,.086,.5,.81 配位原子 : ,4i-Al,: ,4.9572,-6.2931,0 SP coordinates=,-.086,.5,1.19 4i-Al,:,4.9572,-6.2931,0, Z=,1 SP coordinates=,-.086,.5,1.19 配位原子 : ,4i-Al,: ,2.6491,-4.446,0 SP coordinates=,.086,.5,.81 7, ,4i-Al,---,4i-Al, d===,3.1074 4i-Al,:,-1.2494,-.9236,-2.205, Z=,1 SP coordinates=,.414,0,.19 配位原子 : ,4i-Al,: ,1.2494,.9236,-2.205 SP coordinates=,.586,0,.81 4i-Al,:,1.2494,.9236,-2.205, Z=,1 SP coordinates=,.586,0,.81 配位原子 : ,4i-Al,: ,-1.2494,-.9236,-2.205 SP coordinates=,.414,0,.19 8, ,4i-Al,---,4i-Ce, d===,3.2007 4i-Al,:,.7582,9.8156,2.205, Z=,2 SP coordinates=,1.414,1,1.19 配位原子 : ,4i-Ce,: ,.8025,12.1352,0 SP coordinates=,1.63,.5,1.325 配位原子 : ,4i-Ce,: ,.8025,12.1352,4.41 SP coordinates=,1.63,1.5,1.325 4i-Ce,:,.8025,12.1352,4.41, Z=,2 SP coordinates=,1.63,1.5,1.325 配位原子 : ,4i-Al,: ,.7582,9.8156,2.205 SP coordinates=,1.414,1,1.19 配位原子 : ,4i-Al,: ,.7582,9.8156,6.615 SP coordinates=,1.414,2,1.19 9, ,4i-Ce,---,4i-Co, d===,3.2115 4i-Ce,:,-6.4012,9.3431,4.41, Z=,2 SP coordinates=,1.37,1.5,-.325 配位原子 : ,4i-Co,: ,-5.0453,7.4422,2.205 SP coordinates=,1.193,1,-.146 配位原子 : ,4i-Co,: ,-5.0453,7.4422,6.615 SP coordinates=,1.193,2,-.146 4i-Co,:,-5.0453,7.4422,2.205, Z=,2 SP coordinates=,1.193,1,-.146 配位原子 : ,4i-Ce,: ,-6.4012,9.3431,0 SP coordinates=,1.37,.5,-.325 配位原子 : ,4i-Ce,: ,-6.4012,9.3431,4.41 SP coordinates=,1.37,1.5,-.325 10, ,4i-Ce,---,4i-Al, d===,3.2587 4i-Ce,:,-5.0015,3.9735,-2.205, Z=,2 SP coordinates=,.87,0,-.325 配位原子 : ,4i-Al,: ,-2.6491,4.446,-4.41 SP coordinates=,.914,-.5,.19 配位原子 : ,4i-Al,: ,-2.6491,4.446,0 SP coordinates=,.914,.5,.19 4i-Al,:,-2.6491,4.446,0, Z=,2 SP coordinates=,.914,.5,.19 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,-2.205 SP coordinates=,.87,0,-.325 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,2.205 SP coordinates=,.87,1,-.325 11, ,4i-Al,---,4i-Ce, d===,3.3331 4i-Al,:,-1.2494,-.9236,2.205, Z=,2 SP coordinates=,.414,1,.19 配位原子 : ,4i-Ce,: ,1.2051,-1.3961,0 SP coordinates=,.37,.5,.675 配位原子 : ,4i-Ce,: ,1.2051,-1.3961,4.41 SP coordinates=,.37,1.5,.675 4i-Ce,:,1.2051,-1.3961,0, Z=,2 SP coordinates=,.37,.5,.675 配位原子 : ,4i-Al,: ,-1.2494,-.9236,-2.205 SP coordinates=,.414,0,.19 配位原子 : ,4i-Al,: ,-1.2494,-.9236,2.205 SP coordinates=,.414,1,.19 12, ,4i-Ce,---,4i-Al, d===,3.3744 4i-Ce,:,-.1945,3.9735,6.615, Z=,1 SP coordinates=,.87,2,.675 配位原子 : ,4i-Al,: ,1.2494,.9236,6.615 SP coordinates=,.586,2,.81 4i-Al,:,1.2494,.9236,6.615, Z=,1 SP coordinates=,.586,2,.81 配位原子 : ,4i-Ce,: ,-.1945,3.9735,6.615 SP coordinates=,.87,2,.675 13, ,4i-Co,---,4i-Ce, d===,3.469 4i-Co,:,3.9607,-8.6665,-4.41, Z=,1 SP coordinates=,-.307,-.5,.854 配位原子 : ,4i-Ce,: ,4.0045,-12.1352,-4.41 SP coordinates=,-.63,-.5,.675 4i-Ce,:,4.0045,-12.1352,-4.41, Z=,1 SP coordinates=,-.63,-.5,.675 配位原子 : ,4i-Co,: ,3.9607,-8.6665,-4.41 SP coordinates=,-.307,-.5,.854 14, ,4i-Ce,---,4i-Ce, d===,3.5393 4i-Ce,:,.8025,12.1352,-4.41, Z=,2 SP coordinates=,1.63,-.5,1.325 配位原子 : ,4i-Ce,: ,1.8131,14.7126,-6.615 SP coordinates=,1.87,-1,1.675 配位原子 : ,4i-Ce,: ,1.8131,14.7126,-2.205 SP coordinates=,1.87,0,1.675 4i-Ce,:,1.8131,14.7126,-6.615, Z=,2 SP coordinates=,1.87,-1,1.675 配位原子 : ,4i-Ce,: ,.8025,12.1352,-8.82 SP coordinates=,1.63,-1.5,1.325 配位原子 : ,4i-Ce,: ,.8025,12.1352,-4.41 SP coordinates=,1.63,-.5,1.325 15, ,4i-Ce,---,4i-Ce, d===,3.6797 4i-Ce,:,-.1945,3.9735,-2.205, Z=,1 SP coordinates=,.87,0,.675 配位原子 : ,4i-Ce,: ,2.2022,6.7657,-2.205 SP coordinates=,1.13,0,1.325 4i-Ce,:,2.2022,6.7657,-2.205, Z=,1 SP coordinates=,1.13,0,1.325 配位原子 : ,4i-Ce,: ,-.1945,3.9735,-2.205 SP coordinates=,.87,0,.675 16, ,4i-Ce,---,4i-Ce, d===,3.6885 4i-Ce,:,.8025,12.1352,-4.41, Z=,1 SP coordinates=,1.63,-.5,1.325 配位原子 : ,4i-Ce,: ,3.2128,9.3431,-4.41 SP coordinates=,1.37,-.5,1.675 4i-Ce,:,3.2128,9.3431,-4.41, Z=,1 SP coordinates=,1.37,-.5,1.675 配位原子 : ,4i-Ce,: ,.8025,12.1352,-4.41 SP coordinates=,1.63,-.5,1.325 17, ,4i-Al,---,4i-Al, d===,4.2538 4i-Al,:,2.6491,-4.446,0, Z=,2 SP coordinates=,.086,.5,.81 配位原子 : ,4i-Al,: ,3.5576,-.9236,-2.205 SP coordinates=,.414,0,1.19 配位原子 : ,4i-Al,: ,3.5576,-.9236,2.205 SP coordinates=,.414,1,1.19 4i-Al,:,3.5576,-.9236,2.205, Z=,2 SP coordinates=,.414,1,1.19 配位原子 : ,4i-Al,: ,2.6491,-4.446,0 SP coordinates=,.086,.5,.81 配位原子 : ,4i-Al,: ,2.6491,-4.446,4.41 SP coordinates=,.086,1.5,.81 18, ,4i-Ce,---,4i-Ce, d===,4.41 4i-Ce,:,-5.0015,3.9735,2.205, Z=,2 SP coordinates=,.87,1,-.325 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,-2.205 SP coordinates=,.87,0,-.325 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,6.615 SP coordinates=,.87,2,-.325 4i-Ce,:,-5.0015,3.9735,6.615, Z=,2 SP coordinates=,.87,2,-.325 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,2.205 SP coordinates=,.87,1,-.325 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,11.025 SP coordinates=,.87,3,-.325 19, ,4i-Al,---,4i-Al, d===,4.41 4i-Al,:,4.0488,-9.8156,2.205, Z=,2 SP coordinates=,-.414,1,.81 配位原子 : ,4i-Al,: ,4.0488,-9.8156,-2.205 SP coordinates=,-.414,0,.81 配位原子 : ,4i-Al,: ,4.0488,-9.8156,6.615 SP coordinates=,-.414,2,.81 4i-Al,:,4.0488,-9.8156,6.615, Z=,2 SP coordinates=,-.414,2,.81 配位原子 : ,4i-Al,: ,4.0488,-9.8156,2.205 SP coordinates=,-.414,1,.81 配位原子 : ,4i-Al,: ,4.0488,-9.8156,11.025 SP coordinates=,-.414,3,.81 20, ,4i-Co,---,4i-Co, d===,4.41 4i-Co,:,5.3604,-14.0361,2.205, Z=,2 SP coordinates=,-.807,1,.854 配位原子 : ,4i-Co,: ,5.3604,-14.0361,-2.205 SP coordinates=,-.807,0,.854 配位原子 : ,4i-Co,: ,5.3604,-14.0361,6.615 SP coordinates=,-.807,2,.854 4i-Co,:,5.3604,-14.0361,6.615, Z=,2 SP coordinates=,-.807,2,.854 配位原子 : ,4i-Co,: ,5.3604,-14.0361,2.205 SP coordinates=,-.807,1,.854 配位原子 : ,4i-Co,: ,5.3604,-14.0361,11.025 SP coordinates=,-.807,3,.854 21, ,4i-Co,---,4i-Al, d===,4.4195 4i-Co,:,-1.1614,-2.0727,0, Z=,1 SP coordinates=,.307,.5,.146 配位原子 : ,4i-Al,: ,.1502,-6.2931,0 SP coordinates=,-.086,.5,.19 4i-Al,:,.1502,-6.2931,0, Z=,1 SP coordinates=,-.086,.5,.19 配位原子 : ,4i-Co,: ,-1.1614,-2.0727,0 SP coordinates=,.307,.5,.146 22, ,4i-Co,---,4i-Al, d===,4.425 4i-Co,:,2.5611,-3.2969,2.205, Z=,2 SP coordinates=,.193,1,.854 配位原子 : ,4i-Al,: ,4.9572,-6.2931,0 SP coordinates=,-.086,.5,1.19 配位原子 : ,4i-Al,: ,4.9572,-6.2931,4.41 SP coordinates=,-.086,1.5,1.19 4i-Al,:,4.9572,-6.2931,4.41, Z=,2 SP coordinates=,-.086,1.5,1.19 配位原子 : ,4i-Co,: ,2.5611,-3.2969,2.205 SP coordinates=,.193,1,.854 配位原子 : ,4i-Co,: ,2.5611,-3.2969,6.615 SP coordinates=,.193,2,.854 23, ,4i-Al,---,4i-Co, d===,4.433 4i-Al,:,-3.2571,-11.6627,6.615, Z=,2 SP coordinates=,-.586,2,-.81 配位原子 : ,4i-Co,: ,-.8463,-8.6665,4.41 SP coordinates=,-.307,1.5,-.146 配位原子 : ,4i-Co,: ,-.8463,-8.6665,8.82 SP coordinates=,-.307,2.5,-.146 4i-Co,:,-.8463,-8.6665,4.41, Z=,2 SP coordinates=,-.307,1.5,-.146 配位原子 : ,4i-Al,: ,-3.2571,-11.6627,2.205 SP coordinates=,-.586,1,-.81 配位原子 : ,4i-Al,: ,-3.2571,-11.6627,6.615 SP coordinates=,-.586,2,-.81 24, ,4i-Al,---,4i-Co, d===,4.4891 4i-Al,:,-7.4561,4.446,0, Z=,1 SP coordinates=,.914,.5,-.81 配位原子 : ,4i-Co,: ,-3.6456,2.0727,0 SP coordinates=,.693,.5,-.146 4i-Co,:,-3.6456,2.0727,0, Z=,1 SP coordinates=,.693,.5,-.146 配位原子 : ,4i-Al,: ,-7.4561,4.446,0 SP coordinates=,.914,.5,-.81 25, ,4i-Co,---,4i-Co, d===,4.4964 4i-Co,:,-4.5687,-7.4422,2.205, Z=,2 SP coordinates=,-.193,1,-.854 配位原子 : ,4i-Co,: ,-.8463,-8.6665,0 SP coordinates=,-.307,.5,-.146 配位原子 : ,4i-Co,: ,-.8463,-8.6665,4.41 SP coordinates=,-.307,1.5,-.146 4i-Co,:,-.8463,-8.6665,4.41, Z=,2 SP coordinates=,-.307,1.5,-.146 配位原子 : ,4i-Co,: ,-4.5687,-7.4422,2.205 SP coordinates=,-.193,1,-.854 配位原子 : ,4i-Co,: ,-4.5687,-7.4422,6.615 SP coordinates=,-.193,2,-.854 26, ,4i-Ce,---,4i-Co, d===,4.5149 4i-Ce,:,-6.0121,1.3961,0, Z=,2 SP coordinates=,.63,.5,-.675 配位原子 : ,4i-Co,: ,-2.5611,3.2969,-2.205 SP coordinates=,.807,0,.146 配位原子 : ,4i-Co,: ,-2.5611,3.2969,2.205 SP coordinates=,.807,1,.146 4i-Co,:,-2.5611,3.2969,-2.205, Z=,2 SP coordinates=,.807,0,.146 配位原子 : ,4i-Ce,: ,-6.0121,1.3961,-4.41 SP coordinates=,.63,-.5,-.675 配位原子 : ,4i-Ce,: ,-6.0121,1.3961,0 SP coordinates=,.63,.5,-.675 27, ,4i-Al,---,4i-Ce, d===,4.54 4i-Al,:,2.6491,-4.446,0, Z=,1 SP coordinates=,.086,.5,.81 配位原子 : ,4i-Ce,: ,6.0121,-1.3961,0 SP coordinates=,.37,.5,1.675 4i-Ce,:,6.0121,-1.3961,0, Z=,1 SP coordinates=,.37,.5,1.675 配位原子 : ,4i-Al,: ,2.6491,-4.446,0 SP coordinates=,.086,.5,.81 28, ,4i-Co,---,4i-Co, d===,4.7517 4i-Co,:,-3.9607,8.6665,0, Z=,1 SP coordinates=,1.307,.5,.146 配位原子 : ,4i-Co,: ,-1.6379,12.8118,0 SP coordinates=,1.693,.5,.854 4i-Co,:,-1.6379,12.8118,0, Z=,1 SP coordinates=,1.693,.5,.854 配位原子 : ,4i-Co,: ,-3.9607,8.6665,0 SP coordinates=,1.307,.5,.146 29, ,4i-Ce,---,4i-Ce, d===,4.807 4i-Ce,:,-5.0015,3.9735,2.205, Z=,2 SP coordinates=,.87,1,-.325 配位原子 : ,4i-Ce,: ,-9.8085,3.9735,2.205 SP coordinates=,.87,1,-1.325 配位原子 : ,4i-Ce,: ,-.1945,3.9735,2.205 SP coordinates=,.87,1,.675 4i-Ce,:,-.1945,3.9735,2.205, Z=,2 SP coordinates=,.87,1,.675 配位原子 : ,4i-Ce,: ,-5.0015,3.9735,2.205 SP coordinates=,.87,1,-.325 配位原子 : ,4i-Ce,: ,4.6125,3.9735,2.205 SP coordinates=,.87,1,1.675 30, ,4i-Co,---,4i-Co, d===,4.807 4i-Co,:,-2.5611,3.2969,-2.205, Z=,2 SP coordinates=,.807,0,.146 配位原子 : ,4i-Co,: ,-7.3681,3.2969,-2.205 SP coordinates=,.807,0,-.854 配位原子 : ,4i-Co,: ,2.2459,3.2969,-2.205 SP coordinates=,.807,0,1.146 4i-Co,:,2.2459,3.2969,-2.205, Z=,2 SP coordinates=,.807,0,1.146 配位原子 : ,4i-Co,: ,-2.5611,3.2969,-2.205 SP coordinates=,.807,0,.146 配位原子 : ,4i-Co,: ,7.0529,3.2969,-2.205 SP coordinates=,.807,0,2.146 31, ,4i-Al,---,4i-Al, d===,4.807 4i-Al,:,-1.2494,-.9236,-2.205, Z=,2 SP coordinates=,.414,0,.19 配位原子 : ,4i-Al,: ,-6.0564,-.9236,-2.205 SP coordinates=,.414,0,-.81 配位原子 : ,4i-Al,: ,3.5576,-.9236,-2.205 SP coordinates=,.414,0,1.19 4i-Al,:,3.5576,-.9236,-2.205, Z=,2 SP coordinates=,.414,0,1.19 配位原子 : ,4i-Al,: ,-1.2494,-.9236,-2.205 SP coordinates=,.414,0,.19 配位原子 : ,4i-Al,: ,8.3646,-.9236,-2.205 SP coordinates=,.414,0,2.19 32, ,4i-Co,---,4i-Co, d===,4.8327 4i-Co,:,2.5611,-3.2969,-2.205, Z=,1 SP coordinates=,.193,0,.854 配位原子 : ,4i-Co,: ,5.0453,-7.4422,-2.205 SP coordinates=,-.193,0,1.146 4i-Co,:,5.0453,-7.4422,-2.205, Z=,1 SP coordinates=,-.193,0,1.146 配位原子 : ,4i-Co,: ,2.5611,-3.2969,-2.205 SP coordinates=,.193,0,.854
个人分类: 晶体学和空间群|21474 次阅读|4 个评论
家有小女未长成:《点群/空间群操作系统》
热度 1 大毛忽洞 2009-4-23 08:29
家有小女未长成:《点群 / 空间群操作系统》 科学探索是一件很快乐的事情, 就像是在抚养一个漂亮的小女孩。 在中国文化里: 漂亮的小女孩就是父母的掌上明珠。 只要日子还过得去, 父母就不会把掌上明珠提前嫁出去, 去给人家当童养媳。 有德性的父母, 也不会用自己的掌上明珠去交换功名利禄。 《点群 / 空间群操作系统》就是俺的掌上明珠, 虽然孩子还很小, 但是已经能吟诗作文了。 俺已经聘请了 全世界最好的老师 , 来培养小女儿《点群 / 空间群操作系统》。 白居易说:“ 杨家有女初长成,养在深闺人未识 ”。 俺有小女未长成,自然也是 养在家中人未识。 不过今天俺要介绍一下小女儿(《点群 / 空间群操作系统》), 以满足(某个)形势的需要。 我的《点群 / 空间群操作系统》,可以用来干什么呢? 1. 根据晶体结构求解化学键的空间信息 操作晶体结构参数,得到关于化学键的全部空间信息。 全部空间信息包括化学键的网络结构和层次结构。 只给出键的信息,关于价的信息,是另外一个问题。 2. 根据化学键参数求解(未知)晶体结构参数 操作化学键,得到相应的晶体(分子)结构的全部信息。 如果第一种操作称为正操作,那么第二种操作就是逆操作;反之亦然。 (这部分正在从高端空间群往低端空间群核对) 《点群 / 空间群操作系统》的应用举例(点击标题): 关于张思远的化学键理论:答网友提问 ( Y 1-x Ca x Ba 2 Cu 3 O 6+y ) C60 Fullerene’s Coordinates C60 的原子坐标:旋转矩阵 原子坐标:储氢结构 Mg2FeH6 原子坐标:储氢结构 Mg2Ni Atomic Coordinates of Zinc 20 年了,魔方转出了原子坐标 原子坐标和 Madelung 配位数 原子坐标: CsCl 的 Madelung 配位数 答网友:晒出来的是野菜,苗儿还小呢 特征标理论,回避了坐标操作矩阵 我建立《点群 / 空间群操作系统》的目的,是为了研发一个科研用的工具。 搞科学研究,无论是实验型的还是理论型的,都需要一个工具。 实验研究需要设备,好的设备都很昂贵,需要很多的钱。 俺曾经自己制造了一台土设备, 搞了12 年的超塑性研究 ,看看俺的设备,真是很土啊! 土 设备里的科学思想 (有图片和制造过程) 自制土设备是不得已而为之,是为了科研起步用的。就相当于雏鹰成长需要一个遮风挡雨的巢穴一样,这鹰一旦飞上蓝天,那巢穴就没有什么用了。如果舍不得抛弃那巢穴,那鹰就永远也飞不上蓝天。 实际上,俺的 12 年超塑性实验研究,也是从实验向理论过渡的过程。要尽可能过渡的平稳一些,尽可能前后有个呼应,以避免朝三暮四的嫌疑。 请看《 从事基础研究的三点感想 》 如果是搞炒菜型的理论研究,也需要一个工具,比较流行的就是各种各样的商业计算软件。 买商业计算软件也需要很多钱,有的软件比设备还贵。俺没有那么多的钱,怎么办呢? 还是老办法,自己动手。硬件设备自己能造,计算软件当然也可以自己做。 但是,软件比硬件设备要难一些。俺自制超塑性拉伸机的时候,从备料到出实验结果,也就 2 年的时间。而研发 《点群 / 空间群操作系统》,却花费了 10 多年的时间,当然了,这也有故意放慢速度的原因,因为步伐太快会超越了便宜计算机的技术指标。 需要提醒的是,在研制设备和研发软件的过程中,收获的是智慧。而看说明书学到的东西,一般属于知识(或是知道)的范畴。从这点看来,掌握太多的科研经费未必是什么好事! 俺有个毛病,喜欢追求“独此一家”的感觉,俺那土拉伸机全世界就那么一台,这是实话。因为很土气,没有人愿意去仿造。 俺的《点群 / 空间群操作系统》,也希望是独此一家,能做到这点,需要从最基础的东西开始推导。 下面从点群操作矩阵、坐标变换、空间群加法、全晶胞原子配对和全晶胞配位数求解等环节介绍我的《点群 / 空间群操作系统》。 1. 33 (包括 Ih 点群)点群的坐标操作矩阵 33 个点群共有 452 个对应笛卡尔坐标系的操作矩阵(当然有交叉重复的),把这些矩阵求解出来,是第一步。 通过多年 数学地 转动魔方 ,俺自认为掌握了点群操作的真谛,但是要把这 452 个矩阵都求解出来,而且要保证每个点群的矩阵都正确无误,也不是一件容易的事情。 仅仅根据点群的乘法表不能判断一个点群的操作矩阵是否正确,乘法表只能检验这些矩阵是一伙的(属于一个群)。只有通过操作空间点阵才能检验点群的操作矩阵是否完全正确。 还好,俺已经检验了每一个点群的操作矩阵,它们都是很好的矩阵,可以在俺的《 点群 / 空间群操作系统 》发挥自己的作用。 2. 坐标变换 坐标变换,本质上是一种空间变换。 实际上,晶体本身就是一种空间变换的结果。 晶体结构是通过傅立叶变换从衍射空间变换来的, 傅立叶变换的表现形式是现实空间的电子密度, 电子密度极大值的地方就是原子的坐标,电子密度极小值的地方就是原子界面。 问题是要探测衍射空间的信息,必须要用实验的衍射手段。 有没有别的非衍射实验的途径,把未知晶体变换(组装)出来? 最后讨论这个问题。 俺玩坐标(空间)变换,也有很多年了。 1986 年, ODF ( orientation distribution function )在国内和国外比较热,东北大学梁志德教授最先把 ODF 引进到国内,第一篇文章发表在上海的《理化检验》物理分册上,当时我还在念硕士研究生。 在照看实验的同时,我对欧拉角进行着思考。因为我打算要用 ODF 来解释我的超塑性实验结果。当时我画了 50 种欧拉变换的情况,即通过欧拉转动联系两个三维空间。 ODF 理论非常巧妙地把一个现实的二维(二变量)空间和一个抽象的三维欧拉空间联系起来,变换矩阵用到了量子力学的角动量理论。我把思考的结果写成 “ ODF 的物理思想 ” ,发表在 1990 年《理化检验 · 物理分册》第 4 期。因为国内第一篇关于 ODF 的文章发表在《理化检验》,因此,我也把我的文章发表在这个刊物上。可惜我没有电子版,不然就会把那公式贴出来,很漂亮的。下载我的文章需要 2 元钱,还要注册,太麻烦了。 坐标变换不是很难,对 7 个晶系,需要原子(点阵)坐标的双程坐标变换(晶体坐标系-笛卡尔坐标系)。 3. 空间群加法 点群的妙处是能把原子整体地关联在一起,例如,通过 Ih 点群的 120 个矩阵对化学键 d1 和 d2 进行操作,就得到了 C60 的 60 个原子坐标,一个不多,一个不少。只要 d1 和 d2 与实验结果相同,用 Ih 点群矩阵操作出的 60 个碳原子的坐标就必然和实验结果相同。 对于 C240 , Ih 点群只能操作出 60 个围绕 12 个五边形的原子坐标,其他的原子坐标需要某种平移操作,或者提供至少 3 个不同类的围绕六边形的原子坐标,才能用 Ih 把剩下 177 个原子坐标转动出来。 由此可见,平移操作可以用点群操作来代替。 对于晶体的 230 空间群,如果仅仅使用点群操作,也可以把任何空间群的所有原子坐标都操作出来,一个不多,一个不少。但是实现这样的目标需要一种空间的加法运算,俺把它称为空间群加法。 平移是一种几乎没有规律的操作,而点群操作就相当于是围绕某个点在转圈,一圈之后就保证了操作的完备性。 虽然有的网站给出了对应 230 空间群的操作矩阵,但是这些矩阵是在晶体坐标系下给出的,不可能用于对化学键的操作。因为在用点群操作矩阵操作化学键时,还不知道是什么晶体结构。 关于晶体坐标系中的 230 空间群操作矩阵,可参看如下网站: http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-getgen Aroyo, et. al. Zeitschrift fuer Kristallographie (2006), 221 , 1, 15-27. 《 点群 / 空间群操作系统 》使用的原子坐标,都对应于笛卡尔坐标系,这些坐标( x,y,z )可以代入任何的数学公式进行运算。当要和空间群资料进行比较时,使用坐标变换公式可以把笛卡尔坐标变换为晶体坐标系中的坐标。 4. 晶胞原子配对和全晶胞配位数 对于晶体结构已知的晶体,只要有了原子坐标,无论多么复杂,都可以使用 《 点群 / 空间群操作系统 》计算出各种键距和配位数,给出详细的化学键的网络结构和层次结构信息。 将这些数据提供给研究生,他们用余瑞璜的经验电子理论,可以求解任何复杂结构化合物的价键结构,然后再和性能相关联。 5. 关于《 点群 / 空间群操作系统 》逆操作 用点群矩阵来操作化学键,是一个挑战。特别是在不知道晶体结构的情况下,通过操作化学键把晶体构造出来。 这实际上就是在用原子来组装晶体,并且要预测组装出的晶体结构。 这里最难的问题是原子的配对价(原子和原子如何接触),也可以称为键价。 例如, Na 和 Cl 配对,根据 Brown 的键价概念,很容易提取出各向异性的信息(配位信息),然后根据配位信息选择相关的点群进行操作,就可以构造出 NaCl 的晶体结构,并且还可以给出点阵参数。 对于金属元素和金属元素配对,情况比较复杂。例如, Cu 和 Au 能形成三种金属间化合物: Au 3 Cu , AuCu , AuCu 3 另外, Cu 和 Cu 原子,也能组成晶体; Au 也一样。 化学键理论(金属键)说,金属晶体中,价电子是自由的,是电子气。但是原子(去一个价电子)还是排列规则的,这说明原子和原子的空间关系还是具有配位关系的。如何把这些配位信息和原子相关联,也就是说,如何从单个的原子导出原子和原子接触后的配位信息,然后根据配位信息选择相应的点群来操作这两个原子,就构造出了晶体结构。 当然了,也有人根据第一原理从原子出发来计算晶体结构,但是计算一个具体的结构需要一篇文章的篇幅,而且归纳出的结论还不能推广到另外的化合物,也就是说,一个化合物一篇文章。有无穷无尽的化合物,那就需要无穷无尽的文章,这说明还是没有找到规律。 关于离子晶体, Brown 已经找到了规律,就是他的键价概念。 关于金属化合物, Brown 没有涉及。 要解决金属化合物的问题,还是俺的老观点,必须从最基本的问题开始,就是 原子和原子如何接触 ? 关于这个问题,俺是从电子密度下手的,因此,需要把电子密度变换为键价的信息,这又用到了变换的思想。 实际上,原子本来就不是球型的,从点群的角度看,原子的对称性不是无穷大。 这涉及到了一个最基本,最基础的问题:原子的点群对称性问题。 又回到了点群,由此可见,点群是多么的重要啊!
个人分类: 晶体学和空间群|9983 次阅读|1 个评论

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