Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters (English)

In: Journal of Molecular Modeling   ;  19 ,  1  ;  1-32  ;  2012

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Abstract Modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔH f for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5 % and the AUE in ΔH f decreased by about 10 %; for organic solids, the AUE in ΔH f dropped by 60 % and the reduction was 33.3 % for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol-1 in PM6 and 10.8 kcal/mol-1 in PM7 to 3.8 kcal/mol-1. The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved.

Table of contents – Volume 19, Issue 1

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1
Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
Stewart, James J. P. | 2012
33
Theoretical investigations on the structure, density, thermodynamic and performance properties of amino-, methyl-, nitroso- and nitrotriazolones
Ravi, P. / Babu, Bonige K. / Tewari, Suyra P. | 2012
49
Density functional theory study on the reaction mechanism of synthesizing 1,3-dimethyl-2-imidazolidinone by urea method
Yao, Shujuan / Chen, Huayong / Jiang, Shu / Shao, Xin / Cui, Shouxin | 2012
57
Theoretical studies on the crystal structure, thermodynamic properties, detonation performance and thermal stability of cage-tetranitrotetraazabicyclooctane as a novel high energy density compound
Zhao, Guo-zheng / Lu, Ming | 2012
65
Rectifying behavior of charge transfer complexes of tetrakis(dimethylamino)ethene with acceptor molecules: a theoretical study
Fomine, Serguei | 2012
73
MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures
Feng, Huajie / Gao, Wei / Nie, Jingjing / Wang, Jing / Chen, Xiaojuan / Chen, Liuping / Liu, Xin / Lüdemann, Hans-Dietrich / Sun, Zhenfan | 2012
83
A DFT study on the mechanisms for the cycloaddition reactions between 1−aza-2-azoniaallene cations and acetylenes
Wang, Jing-mei / Li, Zhi-ming / Wang, Quan-rui / Tao, Feng-gang | 2012
97
Electric field effect on the zigzag (6,0) single-wall BC2N nanotube for use in nano-electronic circuits
Baei, Mohammad T. / Peyghan, Ali Ahmadi / Moghimi, Masoumeh / Hashemian, Saeede | 2012
109
Characterization of the structures and dynamics of phosphoric acid doped benzimidazole mixtures: a molecular dynamics study
More, Minal / Pahari, Swagata / Roy, Sudip / Venkatnathan, Arun | 2012
119
Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3)
Poulsen, Anders / William, Anthony / Blanchard, Stéphanie / Nagaraj, Harish / Williams, Meredith / Wang, Haishan / Lee, Angeline / Sun, Eric / Teo, Ee-Ling / Tan, Evelyn et al. | 2012
131
Computational investigation on the new high energy density material of aluminum enriched 1, 1-diamino-2, 2-dinitroethylene
Bian, Liang / Shu, Yuanjie / Xu, Jinbao / Wang, Lei | 2012
139
Theoretical design study on photophysical property on oligomers based on spirobifluorene and carbazole-triphenylamine for PLED applications
Xie, Xiao-Hua / Shen, Wei / He, Rong-Xing / Li, Ming | 2012
151
Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors
Zhao, Jian-Hua / Liu, Hsuan-Liang / Elumalai, Pavadai / Chen, Wei-Hsi / Men, Lee-Chung / Liu, Kung-Tien | 2012
163
Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol
Zhao, Shu-sen / Shi, Wen-jing / Wang, Jian-long | 2012
173
Dependence of the optical absorption and Na+ binding energies of coumarin-crown ethers on the size and attachment position of ether ring: density functional investigation
Kasapbasi, Esra / Yurtsever, Mine | 2012
179
Structural and chemical basis for enhanced affinity to a series of mycobacterial thymidine monophosphate kinase inhibitors: fragment-based QSAR and QM/MM docking studies
Bueno, Renata V. / Toledo, Ney R. / Neves, Bruno J. / Braga, Rodolpho C. / Andrade, Carolina H. | 2012
193
Performance comparison of computational methods for modeling alpha-helical structures
Lupan, Alexandru / Kun, Attila-Zsolt / Carrascoza, Francisco / Silaghi-Dumitrescu, Radu | 2012
205
Anion recognition by azophenol thiourea-based chromogenic sensors: a combined DFT and molecular dynamics investigation
Wong, Ming Wah / Xie, Huifang / Kwa, Soo Tin | 2012
215
Density functional study on the adsorption of the drug isoniazid onto pristine and B-doped single wall carbon nanotubes
Saikia, Nabanita / Deka, Ramesh C. | 2012
227
A plausible explanation for enhanced bioavailability of P-gp substrates in presence of piperine: simulation for next generation of P-gp inhibitors
Singh, Durg Vijay / Godbole, Madan M. / Misra, Krishna | 2012
239
Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes
Tontapha, Sarawut / Ruangpornvisuti, Vithaya / Wanno, Banchob | 2012
247
A new interaction mechanism of LiNH2 with MgH2: magnesium bond
Yang, Xin / Li, Qingzhong / Cheng, Jianbo / Li, Wenzuo | 2012
255
Hydrogen dissociation on diene-functionalized carbon nanotubes
Beheshtian, Javad / Ahmadi Peyghan, Ali / Bagheri, Zargham | 2012
263
Probing the structural and electronic properties of aluminum-sulfur Al n S m (2 ≤ n + m ≤ 6) clusters and their oxides
Zhong, Ming-Min / Kuang, Xiao-Yu / Wang, Zhen-Hua / Shao, Peng / Ding, Li-Ping | 2012
275
A comparative study of semi-squaraine and squaraine dyes using computational techniques: tuning the charge transfer/biradicaloid character by substitution
Puyad, Avinash L. / Chaitanya, Gunturu Krishna / Prabhakar, Chetti / Bhanuprakash, Kotamarthi | 2012
289
Modeling the structure and proton transfer pathways of the mutant His-107-Tyr of human carbonic anhydrase II
Halder, Puspita / Taraphder, Srabani | 2012
299
Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase
Zhao, Xiao Ran / Wu, Yu Jie / Han, Juan / Shen, Qian Jin / Jin, Wei Jun | 2012
305
Periodic density functional theory study of the high-pressure behavior of energetic crystalline 1,4-dinitrofurazano[3, 4-b]piperazine
Wang, Wentao / Zhu, Weihua / Li, Jinshan / Cheng, Bibo / Xiao, Heming | 2012
315
Theoretical study of the decomposition of ethyl and ethyl 3-phenyl glycidate
Josa, Daniela / Peña-Gallego, Angeles / Rodríguez-Otero, Jesús / Cabaleiro-Lago, Enrique M. | 2012
321
A density functional theory analysis for the adsorption of the amine group on graphene and boron nitride nanosheets
Anota, Ernesto Chigo / Juárez, Alejandro Rodríguez / Castro, Miguel / Cocoletzi, Heriberto Hernández | 2012
329
Ab initio study of weakly bound halogen complexes: RX⋯PH3
Georg, Herbert C. / Fileti, Eudes E. / Malaspina, Thaciana | 2012
337
Conformational entropy of a polymer chain grafted to rough surfaces
Nowicki, Waldemar / Nowicka, Grażyna / Dokowicz, Marcin / Mańka, Agnieszka | 2012
349
Insight into substituent effects in Cal-B catalyzed transesterification by combining experimental and theoretical approaches
Ni, Zhong / Lin, Xianfu | 2012
359
Computer simulation based selection of optimal monomer for imprinting of tri-O-acetiladenosine in polymer matrix: vacuum calculations
Barkaline, Viatcheslav V. / Douhaya, Yana V. / Tsakalof, Andreas | 2012
371
A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3β, and CDK2/Cyclin A protein kinases
Liu, Yingting / Agrawal, Neeraj J. / Radhakrishnan, Ravi | 2012
383
Sequence selectivity of azinomycin B in DNA alkylation and cross-linking: a QM/MM study
Senthilnathan, Dhurairajan / Kalaiselvan, Anbarasan / Venuvanalingam, Ponnambalam | 2012
391
Carbon nanotube functionalization with carboxylic derivatives: a DFT study
Beheshtian, Javad / Peyghan, Ali Ahmadi / Bagheri, Zargham | 2012
397
Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione
Özdemir, Namık | 2012
407
In silico structural and functional analysis of the human TOPK protein by structure modeling and molecular dynamics studies
Kirubakaran, Palani / Karthikeyan, Muthusamy / Singh, Kh. Dhanachandra / Nagamani, Selvaraman / Premkumar, Kumpati | 2012
421
Structural phase transition of CdTe: an ab initio study
Alptekin, Sebahaddin | 2012
427
Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study
Arabieh, Masoud / Karimi-Jafari, Mohammad Hossein / Ghannadi-Maragheh, Mohammad | 2012
439
Prodrugs of fumarate esters for the treatment of psoriasis and multiple sclerosis—a computational approach
Karaman, Rafik / Dokmak, Ghadeer / Bader, Maryam / Hallak, Hussein / Khamis, Mustafa / Scrano, Laura / Bufo, Sabino Aurelio | 2012
453
A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives
Wei, Qing-guo / Shi, Wen-jing / Ren, Fu-de / Wang, Yong / Ren, Jun | 2012
465
Discovery of novel low-molecular-weight HIV-1 inhibitors interacting with cyclophilin A using in silico screening and biological evaluations
Tian, Yu-Shi / Verathamjamras, Chris / Kawashita, Norihito / Okamoto, Kousuke / Yasunaga, Teruo / Ikuta, Kazuyoshi / Kameoka, Masanori / Takagi, Tatsuya | 2012
477
Stress-induced activation of decomposition of organic explosives: a simple way to understand
Zhang, Chaoyang | 2012