پیوندهای مفید
آمار
| تعداد نشریات | 21 |
| تعداد شماره‌ها | 610 |
| تعداد مقالات | 9,028 |
| تعداد مشاهده مقاله | 67,082,862 |
| تعداد دریافت فایل اصل مقاله | 7,656,349 |
Calculation of cartesian internal molecular coordinates | ||
| International Journal of Nonlinear Analysis and Applications | ||
| مقاله 20، دوره 15، شماره 4، تیر 2024، صفحه 217-220 اصل مقاله (376.55 K) | ||
| نوع مقاله: Research Paper | ||
| شناسه دیجیتال (DOI): 10.22075/ijnaa.2023.30754.4479 | ||
| نویسندگان | ||
| Arezo Moradi* 1؛ Aida Azuji2 | ||
| 1Department of Statistics, Faculty of Basic Science, University of Kurdistan, Sanandaj, Iran | ||
| 2Department of Biophysics, North Tehran Branch, Islamic Azad University, Tehran, Iran | ||
| تاریخ دریافت: 28 بهمن 1401، تاریخ بازنگری: 29 اردیبهشت 1402، تاریخ پذیرش: 06 خرداد 1402 | ||
| چکیده | ||
| For the solution of a variety of problems which concern molecular structures, it is often necessary to calculate the Cartesian coordinates of the atoms from a set of geometric parameters. In order to fully utilize symmetry operations in the calculation of Cartesian coordinates, it is necessary to construct the molecule within a primary coordinate system. This is accomplished by introducing a set of four dummy atoms, by which unit vectors are specified. One atom is placed at the origin and the others at unit distances along each of the three Cartesian axes. in this framework according to the attachment procedures described below. The atoms of a molecule are positioned through the use of a secondary coordinate system. A base coordinate system is defined by the positions of three atoms, numbered 1, 2, and 3. The origin is taken at Atom 1, the negative x-axis passes through Atom 2, and Atom 3 lies in the first or second quadrant of the xy plane. In order to define the angles, the following conventions are adopted: for a general atom j, the atom to which it was attached is called $j^{\prime}$, and the atom to which $j^{\prime}$ was attached is called $j^{\prime \prime}$, and the atom to which $j^{\prime \prime}$ was attached is called $j^{\prime \prime \prime}$. Two special cases where these definitions do not suffice are atoms attached to Atom 1 and to Atom 2. Where j is attached to Atom 2, Atom 1 is taken as $j^{\prime \prime}$ and Atom 3 as $j^{\prime \prime \prime}$. Where j is attached to Atom 1, Atom 2 is taken as $j^{\prime \prime}$ and Atom 3 as $j^{\prime \prime \prime}$. The program described is being used extensively for specifying molecular structures for electron diffraction investigations. Other current uses are in programs for x-ray diffraction of polymers, for estimating magnitudes of energy via postulated force field functions, and in molecular orbital calculations. | ||
| کلیدواژه‌ها | ||
| Calculation؛ Cartesian Coordinates؛ Internal Molecular Coordinates | ||
| مراجع | ||
|
[1] M. Brehm, M. Thomas, S. Gehrke, and B. Kirchner, TRAVIS—A free analyzer for trajectories from molecular simulation, J. Chem. Phys. 152 (2020), no. 16, 164105. [2] M. Ernst, F. Sittel, and G. Stock, Contact-and distance-based principal component analysis of protein dynamics, J. Chem. Phys. 143 (2015), no. 24, 12B640 1. [3] M. Ernst, S. Wolf, and G. Stock, Identification and validation of reaction coordinates describing protein functional motion: Hierarchical dynamics of T4 lysozyme, J. Chem. Theory Comput. 13 (2017), no. 10, 5076–5088. [4] S.R. Hare, L.A. Bratholm, D.R. Glowacki, and B.K. Carpenter, Low dimensional representations along intrinsic reaction coordinates and molecular dynamics trajectories using interatomic distance matrices, Chem. Sci. 10 (2019), no. 43, 9954–9968. [5] A. Hospital, J.R. Goni, M. Orozco, and J.L. Gelpı, Molecular dynamics simulations: advances and applications, Adv. Appl. Bioinf. Chem. 8 (2015), 37–47. [6] F. Martın-Garcıa, E. Papaleo, P. Gomez-Puertas, W. Boomsma, and K. Lindorff-Larsen, Comparing molecular dynamics force fields in the essential subspace, PLoS One 10 (2015), no. 3, e0121114. [7] F. Sittel, T. Filk, and G. Stock, Principal component analysis on a torus: Theory and application to protein dynamics, J. Chem. Phys. 147 (2017), no. 24, 244101. [8] F. Sittel, A. Jain, and G. Stock, Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates, J. Chem. Phys. 141 (2014), no. 1, 07B605 1. [9] H.B. Thompson, Calculation of cartesian coordinates and their derivatives from internal molecular coordinates, J. Chem. Phys. 47 (1967), no. 9, 3407–3410. [10] D. Vlachakis, E. Bencurova, N. Papangelopoulos, and S. Kossida, Current state-of-the-art molecular dynamics methods and applications, Adv. Protein Chem. Struct. Biol. 94 (2014), 269–313. | ||
|
آمار تعداد مشاهده مقاله: 20,816 تعداد دریافت فایل اصل مقاله: 238 |
||