CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.
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DOI：
10.1021/ct9000608
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发表时间：
2009-04-27
影响因子：
5.5
通讯作者：
MacKerell, Alexander D., Jr.
中科院分区：
文献类型：
--
作者：
Hatcher, Elizabeth R.;Guvench, Olgun;MacKerell, Alexander D., Jr.
对无环多元醇、无环碳水化合物和肌醇的加性全原子CHARMM力场进行了参数化。初始参数从烷烃和吡喃己糖碳水化合物转移，随后开发和优化本研究中考虑的分子所特有的参数。使用模型化合物丙酮和乙醛，非键参数羰基优化目标的溶质-水对和纯溶剂的热力学数据的量子力学相互作用数据。键和角度参数进行了调整，通过比较优化的几何形状的小分子晶体测量数据，并通过对丙酮，乙醛和甘油进行振动分析。使用自动化Monte Carlo模拟退火程序将多元醇链的C-C-C-C、C-C-C-O、C-C-OH和O-C-C-O扭转参数拟合到包括超过1500个RIMP 2/cc-pVTZ//MP2/6- 31 G（d）构象的量子力学二面角势能扫描。计算的凝聚相的数据，包括晶格参数和密度，核磁共振质子-质子耦合，密度和水溶液的扩散系数的比较，实验数据验证了优化的参数。这些化合物的参数开发被证明是特别具有挑战性的，因为无环糖和多元醇的灵活性，以及所有化合物的邻位羟基之间的分子内氢键。新优化的添加剂CHARMM力场参数预计是实用的原子水平的详细模拟的无环多元醇，无环碳水化合物和肌醇在溶液中。
Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution.
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影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
3
作者：
Guvench, Olgun;Greene, Shannon N.;Kamath, Ganesh;Brady, John W.;Venable, Richard M.;Pastor, Richard W.;Mackerell, Alexander D., Jr.
通讯作者：
Mackerell, Alexander D., Jr.
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
4.4
作者：
FELLER, SE;ZHANG, YH;BROOKS, BR
通讯作者：
BROOKS, BR
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML