Studies of (CH3OH)n(n=3—12) and [Na(CH3OH)n]+(n=3—6)via ab initio and ABEEMσπ/MM†

doi:10.7503/cjcu20160307

Abstract

Abstract:

The stable structures, charge distributions and binding energies of cyclic methanol cluster(CH₃OH)_n(n=3—12) and [Na(CH₃OH)_n]⁺(n=3—6) were studied via ab initio and the atom bond electronegativity equalization fluctuating charge force field(ABEEMσπ/MM). Based on the ab initio results, the ABEEMσπ/MM fluctuating charge potential function were constructed and the related parameters were determined for the above systems. The results show that the structures, binding energies and other properties from ABEEMσπ/MM are in consistent with the ab initio calculation, and better than the OPLS/AA force field. The average absolute deviation(AAD) of bond length is less than 0.004 nm, and the relative root mean square deviations(RRMSDs) of bond length, bond angle and binding energy are less than 3.8%, 1.7% and 6.8%, respectively. The linear correlation coefficients of the charge distributions of ABEEMσπ/MM and ab initio calculation are all above 0.99.

Key words: Ab initio, ABEEMσπ, /MM, Methanol, Sodium ion, Molecular interaction

CLC Number:

O641

TrendMD:

YU Yongbo,LIU Cui,GONG Lidong. Studies of (CH₃OH)_n(n=3—12) and [Na(CH₃OH)_n]⁺(n=3—6)via ab initio and ABEEMσπ/MM^†[J]. Chem. J. Chinese Universities, 2016, 37(8): 1468.

Figures/Tables 12

Table 1 ABEEMσπ/MM parameters(χ*, 2η*, σ, ε) of (CH3OH)n and Na+(CH3OH)n

Code	χ^*	2η^*	σ	ε
C	3.150	4.700	3.500	0.066
H(—H₃C)	2.455	13.038	2.500	0.030
O	3.300	4.327	3.120	0.170
H(—HO)	2.060	6.300	1.450	0.010
σ(C—H)	6.010	42.350
σ(C—O)	6.920	49.780
σ(O—H)	6.050	62.180
Olp	4.035	5.730
Na⁺	8.101	14.510	3.330	0.003

Table 2 Parameters of klp,H

Interaction site	A	B	C	D
lp of O in methanol and H	0.5509	0.0462	1.12963	0.01638
lp of O in methanol and Na⁺	0.8660	0.2220	1.83031	0.02248

Fig.1 Stable geometry of cyclic (CH3OH)n(n=3—6) optimized via ab initio and ABEEMσπ/MM

Table 3 ROH, RO…H, RO…O and ∠O1—H1—O2 of cyclic (CH3OH)n(n=3—6)

n	R_OH/nm				R_O…H/nm
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	ONIOM^c	QM^a	ABEEMσπ/MM	OPLS/AA^b	ONIOM^c
3	0.0978	0.0947	0.0967	0.0984	0.1883	0.1897	0.1838
4	0.0986	0.0950	0.0972	0.0991	0.1740	0.1772	0.1759
5	0.0988	0.0950	0.0973	0.0991	0.1706	0.1741	0.1758
6	0.0989	0.0948	0.0973	0.0990	0.1694	0.1731	0.1780
AAD		0.0036	0.0014	0.0004		0.0030	0.0051
RRMSD		3.72%	1.43%	0.43%		1.76%	3.18%
n	R_O…O/nm				∠O1—H1—O2/(°)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	ONIOM^c	QM^a	ABEEMσπ/MM	OPLS/AA^b	ONIOM^c
3	0.2775	0.2812	0.2747	0.2799	150.24	150.93	155.37	153.00
4	0.2712	0.2709	0.2719	0.2754	168.12	168.11	168.56	168.70
5	0.2692	0.2690	0.2728	0.2752	175.65	175.62	174.45	174.50
6	0.2681	0.2679	0.2751	0.2752	176.71	176.63	176.63	176.70
AAD		0.0011	0.0035	0.0049		0.20	1.71	1.13
RRMSD		0.68%	1.54%	1.93%		0.21%	1.57%	0.91%

Fig.2 Charge linear correlation diagram of (CH3OH)n(n=3—6) via ab initio and ABEEMσπ/MM

Table 4 Binding energy(ΔEn) of cyclic methanol cluster(CH3OH)n(n=3—6) applied by MP2, ABEEMσπ/MM, OPLS/AA, PHH3 and cluster approaches

n	Δ $E n a$ /(kJ·mol^-1)
n	QM^b	ABEEMσπ/MM	OPLS/AA^c	Cluster approach a^d	Cluster approach b^d	PHH3^e
3	61.24	63.41	55.05	64.83	66.92	59.11
4	112.11	115.41	89.70	124.98	131.88	98.27
5	151.57	169.50	146.72	174.52	186.51	132.30
6	188.85	189.35	215.77	221.08	237.76
AAD		5.97	15.09	17.91	27.32
RRMSD		6.71%	13.11%	15.25%	23.20%

Table 4 Binding energy(ΔEn) of cyclic methanol cluster(CH3OH)n(n=3—6) applied by MP2, ABEEMσπ/MM, OPLS/AA, PHH3 and cluster approaches

n	Δ $E n a$ /(kJ·mol^-1)
n	QM^b	ABEEMσπ/MM	OPLS/AA^c	Cluster approach a^d	Cluster approach b^d	PHH3^e
3	61.24	63.41	55.05	64.83	66.92	59.11
4	112.11	115.41	89.70	124.98	131.88	98.27
5	151.57	169.50	146.72	174.52	186.51	132.30
6	188.85	189.35	215.77	221.08	237.76
AAD		5.97	15.09	17.91	27.32
RRMSD		6.71%	13.11%	15.25%	23.20%

Table 5 ROH, RO…H, RO…O and ∠O1—H1—O2 of cyclic (CH3OH)n(n=7—12)

n	R_OH/nm			R_O…H/nm
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
7	0.0953	0.0951	0.0972	0.1881	0.1874	0.1803
8	0.0953	0.0951	0.0971	0.1877	0.1867	0.1830
9	0.0953	0.0951	0.0971	0.1879	0.1868	0.1840
10	0.0953	0.0951	0.0970	0.1882	0.1873	0.1866
11	0.0953	0.0946	0.0970	0.1878	0.1878	0.1882
12	0.0953	0.0947	0.0966	0.1881	0.1888
AAD		0.0004	0.0017		0.0007	0.0037
RRMSD		0.43%	1.80%		0.43%	2.39%
n	R_O…O/nm			∠O1—H1—O2/(°)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
7	0.2832	0.2824	0.2773	175.54	178.39	176.43
8	0.2828	0.2817	0.2799	174.55	177.89	175.08
9	0.2830	0.2818	0.2809	174.55	177.69	175.11
10	0.2832	0.2823	0.2834	175.07	177.45	174.95
11	0.2829	0.2824	0.2849	175.14	178.05	174.24
12	0.2831	0.2834		175.24	177.51
AAD		0.0008	0.0026		2.81	0.6
RRMSD		0.30%	1.14%		1.62%	0.38%

Table 6 ΔEn of cyclic (CH3OH)n(n=7—12)

n	Δ $E n a$ /(kJ·mol^-1)			n	Δ $E n a$ /(kJ·mol^-1)
n	QM^b		ABEEMσπ/MM	OPLS/AA^c	QM^b	ABEEMσπ/MM	OPLS/AA^c
7	220.04	222.92	295.11	11	353.63	328.97	672.65
8	252.85	241.31	378.54	12	390.16	373.98
9	283.95	266.22	473.34	AAD		14.26	192.16
10	323.20	310.62	574.83	RRMSD		5.08%	72.55%

Table 6 ΔEn of cyclic (CH3OH)n(n=7—12)

n	Δ $E n a$ /(kJ·mol^-1)			n	Δ $E n a$ /(kJ·mol^-1)
n	QM^b		ABEEMσπ/MM	OPLS/AA^c	QM^b	ABEEMσπ/MM	OPLS/AA^c
7	220.04	222.92	295.11	11	353.63	328.97	672.65
8	252.85	241.31	378.54	12	390.16	373.98
9	283.95	266.22	473.34	AAD		14.26	192.16
10	323.20	310.62	574.83	RRMSD		5.08%	72.55%

Table 7 Comparison of charge distributions for cyclic (CH3OH)n(n=7—12)*

n	y=Ax+B^a	R	S	U_max	q_O/a.u.
n	y=Ax+B^a	R	S	U_max	ab initio	ABEEM
7	y=1.0923x-2.7971×10^-6	0.9933	0.0233	0.0431	-0.3590	-0.3675
8	y=1.0867x-8.7182×10^-6	0.9937	0.0226	0.0386	-0.3595	-0.3666
9	y=1.0829x-1.3304×10^-6	0.9936	0.0225	0.0434	-0.3594	-0.3654
10	y=1.0837x-1.7028×10^-6	0.9939	0.0222	0.0422	-0.3593	-0.3664
11	y=1.0791x-6.1424×10^-6	0.9940	0.0219	0.0445	-0.3596	-0.3653
12	y=1.0796x-1.4995×10^-8	0.9936	0.0225	0.0441	-0.3593	-0.3645
AAD					0.0066

Table 8 RM…O, ∠M—O1—C1, ∠O1—M—O2 and ΔEn of [Na(CH3OH)n]+(n=3—6)

n	R_M…O/nm			∠M—O1—C1/(°)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
3	0.2310	0.2334	0.2365	128.43	127.19	100.17
4	0.2346	0.2374	0.2398	125.33	123.65	100.65
5	0.2342	0.2377	0.2397	129.03	126.66	100.37
6	0.2338	0.2346	0.2402	134.96	134.34	106.25
AAD		0.0024	0.0057		1.48	27.58
RRMSD		1.10%	2.43%		1.24%	21.34%
n	∠O1—M—O2/(°)			Δ $E n c$ /(kJ·mol^-1)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
3	119.87	119.88	119.99	250.59	226.68	520.79
4	104.82	105.00	109.47	309.99	297.16	602.51
5	98.97	98.81	110.66	367.76	378.08	651.70
6	93.81	93.79	110.64	423.10	457.84	686.82
AAD		0.09	8.32		20.45	277.60
RRMSD		0.12%	10.02%		6.58%	80.78%

Table 8 RM…O, ∠M—O1—C1, ∠O1—M—O2 and ΔEn of [Na(CH3OH)n]+(n=3—6)

n	R_M…O/nm			∠M—O1—C1/(°)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
3	0.2310	0.2334	0.2365	128.43	127.19	100.17
4	0.2346	0.2374	0.2398	125.33	123.65	100.65
5	0.2342	0.2377	0.2397	129.03	126.66	100.37
6	0.2338	0.2346	0.2402	134.96	134.34	106.25
AAD		0.0024	0.0057		1.48	27.58
RRMSD		1.10%	2.43%		1.24%	21.34%
n	∠O1—M—O2/(°)			Δ $E n c$ /(kJ·mol^-1)
n	QM^a	ABEEMσπ/MM	OPLS/AA^b	QM^a	ABEEMσπ/MM	OPLS/AA^b
3	119.87	119.88	119.99	250.59	226.68	520.79
4	104.82	105.00	109.47	309.99	297.16	602.51
5	98.97	98.81	110.66	367.76	378.08	651.70
6	93.81	93.79	110.64	423.10	457.84	686.82
AAD		0.09	8.32		20.45	277.60
RRMSD		0.12%	10.02%		6.58%	80.78%

Fig.3 Stable geometry of [Na(CH3OH)n]+(n=3—6) optimized via ab initio and ABEEMσπ/MM

Fig.4 Charge linear correlation diagram of [Na(CH3OH)n]+(n=3—6) via ab initio and ABEEMσπ/MM

References 38

[1]	Mountain R D., Int. J Thermophys., 2007, 28, 536—543
[2]	Yizhak M., Chem Rev., 2009, 109, 1346—1370
[3]	Jun S., Isao Y., Koji A., Langmuir,2010, 26, 8030—8035
[4]	Medhekar N V., Ramasubramaniam A., Ruoff R S., Shenoy V B., ACS Nano,2010, 4, 2300—2306
[5]	Marcus Y., Pure Appl Chem., 2010, 82, 1889—1899
[6]	Boyd S L., Boyd R J., J. Chem. Theory Comput., 2007, 3, 54—61
[7]	Pires M M., de Turi V F., J. Chem. Theory Comput., 2007, 3, 1073—1082
[8]	Reddy A S., Sastry G N., J. Phys. Chem A,2005, 109, 8893—8903
[9]	Rai D., Kulkarni A D., Gejji S P., Pathak R K., J. Chem Phys., 2011, 135, 024307
[10]	Ponder J W., Case D A., Adv. Protein Chem., 2003, 66, 27—85 doi: 10.1016/S0092-8674(03)00035-7 URL pmid: 12553913
[11]	Hart K., Foloppe N., Baker C M., Denning E J., Nilsson L., MacKerell A D., New Phytologist,2012, 8, 348—362 doi: 10.3969/j.issn.1005-2860.2012.12.002 URL
[12]	Christen M., Hunenberger P H., Bakowies D., Baron R., Bürgi R., Geerke D P., Heinz T N., Kastenholz M A., Kräutler V., Oostenbrink C., Peter C., Trzesniak D., Gunsteren W. F V., J. Comput Chem., 2005, 26, 1719—1751
[13]	Kaminski G A., Friesner R A., J. Phys. Chem B,2001, 105, 6474—6487
[14]	Do H., Besley N A., J. Chem Phys., 2012, 137, 134106
[15]	Huang Z G., Yu L., Dai Y M., Struct Chem., 2010, 21, 565—572
[16]	Kazachenko S., Bulusu S., Thakkar A J., J. Chem Phys., 2013, 138, 224303
[17]	Morrone J A., Tuckerman M E., Chem. Phys Lett., 2003, 370, 406—411
[18]	Zeng Y P., Hu J M., Yuan Y., Zhang X B., Ju S G., Chem. Phys Lett., 2012, 538, 60—66
[19]	Jorgensen W L., Bigot B., Chandrasekhar J., J. Am. Chem Soc., 1982, 104, 4584—4591
[20]	Forck R M., Dauster I., Buck U., Zeuch T., J. Phys. Chem A,2011, 115, 6068—6076
[21]	Chen A A., Pappu R V., J. Phys. Chem B,2007, 111, 11884—11887
[22]	Yang Z Z., Wang C S., J. Phys. Chem A,1997, 101, 6315—6321
[23]	Yang Z Z., Cui B Q., J. Chem. Theory Comput., 2007, 3, 1561—1568
[24]	Yang Z Z., Wu Y., Zhao D X., J. Chem Phys., 2004, 120, 2541—2557
[25]	Zhao D X., Liu C., Wang F F., Yu C Y., Gong L D., Liu S B., Yang Z Z., J. Chem. Theory Comput., 2010, 6, 795—804
[26]	Gong L D., Sci. China Chem., 2012, 55(12), 2471—2484
[27]	Lu L N., Liu C., Gong L D., Chem. Res. Chinese Universities,2013, 29(2), 344—350
[28]	Liu L L., Yang Z Z., Chem. J. Chinese Universities,2015, 36(11), 2179—2188
[29]	Gong L D., Ren W H., Zhang Y L., Li W B., Yang Z Z., Sci. Sinica Chim., 2016, 46, 114—125
[30]	Frisch M.J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., et al., Gaussian 09, D.01, Gaussian Inc., Wallingford CT, 2013
[31]	Dennington R., Keith T., Millam J., GaussView, Version 5, Semichem Inc., Shawnee Mission, KS, 2009
[32]	Meher B R., Kumar M. V S., Bandyopadhyay P., Indian J Phys., 2009, 83, 81—90
[33]	Yang Z Z., Cui B Q., J. Chem. Theory Comput., 2007, 3, 1561—1568
[34]	Zhao D X., Liu C., Wang F F., Yu C Y., Gong L D., Liu S B., Yang Z Z., J. Chem. Theory Comput., 2010, 6, 795—804
[35]	Yang Z Z., Wang J J., Zhao D X., J. Comput Chem., 2014, 35, 1690—1706
[36]	Haynes W.M., Lide D. R., CRC Handbook of Chemistry and Physics, 95th Edition, Boca Raton, CRC Press, 2014, 9—40
[37]	Buck U., Siebers J G., J. Chem Phys., 1998, 108, 20—32
[38]	Hagemeister F C., Gruenloh C J., Zwier T S., J. Phys. Chem A,1998, 102, 82—94

Studies of (CH₃OH)_n(n=3—12) and [Na(CH₃OH)_n]⁺(n=3—6)via ab initio and ABEEMσπ/MM^†

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 12

References 38

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	ZHOU Zixuan, YANG Haiyan, SUN Yuhan, GAO Peng. Recent Progress in Heterogeneous Catalysts for the Hydrogenation of Carbon Dioxide to Methanol [J]. Chem. J. Chinese Universities, 2022, 43(7): 20220235.
[2]	LIU Jie, LI Jinsheng, BAI Jingsen, JIN Zhao, GE Junjie, LIU Changpeng, XING Wei. Constructing a Water-blocking Interlayer Containing Sulfonated Carbon Tubes to Reduce Concentration Polarization in Direct Methanol Fuel Cells [J]. Chem. J. Chinese Universities, 2022, 43(11): 20220420.
[3]	XU Wenzhe, ZHANG Hao. Supramolecular Interactions-mediated Nanodrug Nucleation [J]. Chem. J. Chinese Universities, 2022, 43(10): 20220264.
[4]	XU Xiaolong, FANG Lining, LIU Changyu, LIU Minchao, JIA Jianbo. Preparation of Z-type g-C₃N₄/Pt/TiO₂ Nanotube Array Composite Electrode and Its Performance of Photoelectric Oxidation of Methanol [J]. Chem. J. Chinese Universities, 2021, 42(9): 2926.
[5]	LI Xinyi, LIU Yongjun. Theoretical Insights into the Cleavage of β-Hydroxy Ketone Catalyzed by Artificial Retro-aldolase RA95.5-8F [J]. Chem. J. Chinese Universities, 2021, 42(7): 2306.
[6]	PENG Qin, FANG Yeguang, ZHANG Tengshuo, CUI Ganglong, FANG Weihai. Theoretical Study on the Excited State Properties and Photophysical Mechanism of Selenothymine and Adenine Base Pairs in DNA Environment [J]. Chem. J. Chinese Universities, 2021, 42(7): 2136.
[7]	MA Zhuoyuan, WANG Dayang. Status and Prospect of Surface Wettability of Molecular Self-assembled Monolayers [J]. Chem. J. Chinese Universities, 2021, 42(4): 1031.
[8]	LI Jian, YU Mingming, SUN Yuan, FENG Wenhua, FENG Zhaochi, WU Jianfeng. Effect of Aqueous Solution pH on the Oxidation of Methane to Methanol at Low Temperature [J]. Chem. J. Chinese Universities, 2021, 42(3): 776.
[9]	SUN Quanhu, LU Tiantian, HE Jianjiang, HUANG Changshui. Advances in the Study of Heteratomic Graphdiyne Electrode Materials [J]. Chem. J. Chinese Universities, 2021, 42(2): 366.
[10]	WANG Man, WANG Xin, ZHOU Jing, GAO Guohua. Efficient Synthesis of Dimethyl Carbonate via Transesterification of Methanol and Ethylene Carbonate Catalyzed by Poly（ionic liquid）s [J]. Chem. J. Chinese Universities, 2021, 42(12): 3701.
[11]	GUO Shujia, WANG Sen, ZHANG Li, QIN Zhangfeng, WANG Pengfei, DONG Mei, WANG Jianguo, FAN Weibin. Regulating the Acid Sites Distribution in ZSM-5 Zeolite and Its Catalytic Performance in the Conversion of Methanol to Olefins [J]. Chem. J. Chinese Universities, 2021, 42(1): 227.
[12]	SUN Weixin, LIU Jia, WANG Jiazheng, ZHANG Yimiao, JIN Lei, ZHOU Jianzhang, YANG Fangzu, WU Deyin, TIAN Zhongqun. Preparation of Platinum-modified Uniform Gold Nanopillar Electrodes and Photoelectrocatalytic Oxidation of Methanol [J]. Chem. J. Chinese Universities, 2020, 41(12): 2788.
[13]	WANG Yanyan, LIU Huizhen, HAN Buxing. Advances in CO₂ Hydrogenation to Methanol by Heterogeneous Catalysis [J]. Chem. J. Chinese Universities, 2020, 41(11): 2393.
[14]	CHEN Danyi, ZHANG Fumei, HE Dan, ZHANG Zimei, ZHONG Fen, WEN Simiaomiao, LIU Qixing, ZHOU Haifeng. Synthesis of Chiral Phenylbenzothiazole Methanol via Transfer Hydrogenation Catalyzed by Ruthenium Complexes^† [J]. Chem. J. Chinese Universities, 2020, 41(10): 2264.
[15]	YIN Jiao, ZHANG Guoqiang, YAN Lifei, JIA Dongsen, ZHENG Huayan, LI Zhong. Influence of Structure Evolution of CuY Catalyst During the Reaction Process on Its Catalytic Performance for Oxidative Carbonylation of Methanol^† [J]. Chem. J. Chinese Universities, 2019, 40(7): 1510.