1
|
Zhao G, Liu S, Qi J, Yang L, Qiu X, Liu G. The structure-property relationship of p-alkoxyl benzohydroxamic acids towards wolframite flotation: Theoretical and experimental investigations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
|
2
|
Brandès S, Sornosa-Ten A, Rousselin Y, Lagrelette M, Stern C, Moncomble A, Cornard JP, Meyer M. Conformational and structural studies of N-methylacetohydroxamic acid and of its mono- and bis-chelated uranium(VI) complexes. J Inorg Biochem 2015; 151:164-75. [PMID: 26116424 DOI: 10.1016/j.jinorgbio.2015.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 12/18/2022]
Abstract
The thermodynamics and kinetics of the cis/trans isomerism of N-methylacetohydroxamic acid (NMAH) and its conjugated base (NMA(-)) have been reinvestigated in aqueous media by (1)H NMR spectroscopy. Hindered rotation around the central C-N bond due to electronic delocalization becomes slow enough on the NMR time scale to observe both rotamers in equilibrium in D2O at room temperature. By properly assigning the methyl group resonances, evidence for the prevalence of the E over the Z form is unambiguously provided [K300=[E]/[Z]=2.86(2) and 9.63(5) for NMAH and NMA(-), respectively], closing thereby a long-lasting dispute about the most stable conformer. To that end, calculations of the chemical shifts by density functional theory (DFT), which accurately reproduced the experimental data, turned out to be a much more reliable method than the direct computation of the relative energy for each conformer. The Z ⇌ E interconversion dynamics was probed at 300 K in D2O by 2D exchange-correlated spectroscopy (EXSY), affording the associated rate constants [kZE=9.0(2) s(-1) and kEZ=3.14(5) s(-1) for NMAH, kZE=0.96(3) s(-1) and kEZ=0.10(2) s(-1) for NMA(-)] and activation barriers at 300 K [ΔG(≠)ZE=68.0 kJ mol(-1) and ΔG(≠)EZ=70.6 kJ mol(-1) for NMAH, ΔG(≠)ZE=73.6 kJ mol(-1) and ΔG(≠)EZ=79.2 kJ mol(-1) for NMA(-)]. For the first time, mono- and bis-chelated uranium(VI) complexes of NMA(-) have been isolated. Crystals of [UO2(NMA)(NO3)(H2O)2] and [UO2(NMA)2(H2O)] have been characterized by X-ray diffractometry, infrared and Raman spectroscopies.
Collapse
Affiliation(s)
- Stéphane Brandès
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France
| | - Alejandra Sornosa-Ten
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France
| | - Yoann Rousselin
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France
| | - Mickael Lagrelette
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France
| | - Christine Stern
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France
| | - Aurélien Moncomble
- Laboratoire de Spectrochimie Infrarouge et Raman (LASIR), UMR 8516, CNRS, Université de Lille - Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France
| | - Jean-Paul Cornard
- Laboratoire de Spectrochimie Infrarouge et Raman (LASIR), UMR 8516, CNRS, Université de Lille - Sciences et Technologies, 59655 Villeneuve d'Ascq Cedex, France
| | - Michel Meyer
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), UMR 6302, CNRS, Université de Bourgogne Franche-Comté, 9 avenue Alain Savary, BP 47870, 21078 Dijon Cedex, France.
| |
Collapse
|
3
|
Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 752] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| |
Collapse
|
4
|
SATNAMI MANMOHANL, KARBHAL INDRAPAL, DEWANGAN HITESHK. O-Nucleophilicity of Hydroxamate Ions for Cleavage of Carboxylate and Phosphate Esters in Cationic Micelles. INT J CHEM KINET 2014. [DOI: 10.1002/kin.20852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- MANMOHAN L. SATNAMI
- School of Studies in Chemistry; Pt. Ravishankar Shukla University; Raipur 492 010 India
| | - INDRAPAL KARBHAL
- School of Studies in Chemistry; Pt. Ravishankar Shukla University; Raipur 492 010 India
| | - HITESH K. DEWANGAN
- School of Studies in Chemistry; Pt. Ravishankar Shukla University; Raipur 492 010 India
| |
Collapse
|
5
|
Chahkandi B, Tayyari SF, Bakhshaei M, Chahkandi M. Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: a DFT study. J Mol Graph Model 2013; 44:120-8. [PMID: 23792209 DOI: 10.1016/j.jmgm.2013.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 04/05/2013] [Accepted: 04/05/2013] [Indexed: 11/30/2022]
Abstract
Investigation of tautomerism and transition states in a derivative of 1,3,4-oxadiazole (A, B, C and D) in the gas phase and in solution and in a micro hydrated environment with 1-3 water molecules was performed by calculations at the DFT-B3LYP/6-311++G(d,p) level of theory. The solvent effect is taken into account via the self-consistent reaction field (SCRF) method. The geometries of four possible tautomers of 5-amino-1,3,4-oxadiazole-2(3H)-one were optimized in the gas phase and solution with polarized continuum model (PCM). It was found that in the gas phase and different solvents, A and C tautomers are the most stable and unstable forms, respectively. The results show that the tautomeric interconversion C to D has the lowest Gibbs free energy changes and so the highest equilibrium constant in the gas phase and solution. The equilibrium and rate constants of intermolecular tautomerism in the absence and presence of 1-3 molecules of water were also calculated. The calculated results show that the presence of water molecules considerably reduces the barrier energy of the various reactions. Therefore, this water-assisted tautomerism can be performed fast, especially, with the assistance of two molecules of water.
Collapse
Affiliation(s)
- Behzad Chahkandi
- Department of Chemistry, Shahrood Branch, Islamic Azad University, Shahrood, Iran.
| | | | | | | |
Collapse
|
6
|
Toward the accurate calculation of pKa values in water and acetonitrile. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:882-91. [PMID: 23567870 DOI: 10.1016/j.bbabio.2013.03.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 02/25/2013] [Accepted: 03/26/2013] [Indexed: 11/27/2022]
Abstract
We present a simple approach for the calculation of accurate pKa values in water and acetonitrile based on the straightforward calculation of the gas-phase absolute free energies of the acid and conjugate base with use of only a continuum solvation model to obtain the corresponding solution-phase free energies. Most of the error in such an approach arises from inaccurate differential solvation free energies of the acid and conjugate base which is removed in our approach using a correction based on the realization that the gas-phase acidities have only a small systematic error relative to the dominant systematic error in the differential solvation. The methodology is outlined in the context of the calculation of a set of neutral acids with water as the solvent for a reasonably accurate electronic structure level of theory (DFT), basis set, and implicit solvation model. It is then applied to the comparison of results for three different hybrid density functionals to illustrate the insensitivity to the functional. Finally, the approach is applied to the comparison of results for sets of neutral acids and protonated amine cationic acids in both aqueous (water) and nonaqueous (acetonitrile) solvents. The methodology is shown to generally predict the pKa values for all the cases investigated to within 1 pH unit so long as the differential solvation error is larger than the systematic error in the gas-phase acidity calculations. Such an approach is rather general and does not have additional complications that would arise in a cluster-continuum method, thus giving it strength as a simple high-throughput means to calculate absolute pKa values. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Collapse
|
7
|
Ahmed AA. Energetic and vibrational assignment of tautomerizm of (Hydroxyphosphino)silanethione: A theoretical study. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Chanapiwat P, Ruangpornvisuti V. An ONIOM investigation on anion recognition of alkali-metal complexes with diurea calix[4]arene receptor. J Mol Model 2011; 18:2613-20. [PMID: 22080288 DOI: 10.1007/s00894-011-1284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 10/17/2011] [Indexed: 11/25/2022]
Abstract
The ONIOM(B3LYP/6-31G(d):AM1) optimized structures of complexes of diurea calix[4]arene receptor (L) with alkali metals Li(+), Na(+) and K(+) and their complexes with halide ions F(-), Cl(-), Br(-), oxygen-containing anions HCO(3)(-), HSO(4)(-) and CH(3)COO(-) ions were obtained. Binding energies and thermodynamic properties of complex receptors LiL(+), NaL(+) and KL(+) with these anions were determined. The binding stabilities according to binding energies of LiL(+), NaL(+) and KL(+) associated with anions computed either at the ZPVE-corrected ONIOM(B3LYP/6-31G(d):AM1) or BSSE-corrected B3LYP/6-31 + G(d,p)//ONIOM(B3LYP/6-31G(d):AM1) are in the same order: F(-) >> CH(3)COO(-) ≈ HCO(3)(-) > Br(-) ≈ HSO(4)(-) ≈ Cl(-). All the receptors LiL(+), NaL(+) and KL(+) were found to be selective toward fluoride ion.
Collapse
Affiliation(s)
- Pornpan Chanapiwat
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | |
Collapse
|
9
|
Pavan MV, Lassiani L, Berti F, Stefancich G, Ciogli A, Gasparrini F, Mennuni L, Ferrari F, Escrieut C, Marco E, Makovec F, Fourmy D, Varnavas A. New Anthranilic Acid Based Antagonists with High Affinity and Selectivity for the Human Cholecystokinin Receptor 1 (hCCK1-R). J Med Chem 2011; 54:5769-85. [DOI: 10.1021/jm200438b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michela V. Pavan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, P.le Europa 1, 34127 Trieste, Italy
| | - Lucia Lassiani
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, P.le Europa 1, 34127 Trieste, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Giorgio Stefancich
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, P.le Europa 1, 34127 Trieste, Italy
| | - Alessia Ciogli
- Department of Chemistry and Technology of Biologically Active Substances, University “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Gasparrini
- Department of Chemistry and Technology of Biologically Active Substances, University “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Laura Mennuni
- Rottapharm—Madaus SpA, Via Valosa di Sopra 7, 20052 Monza, Italy
| | - Flora Ferrari
- Rottapharm—Madaus SpA, Via Valosa di Sopra 7, 20052 Monza, Italy
| | - Chantal Escrieut
- Université de Toulouse 3, EA 4552, I2MC, 1 Avenue Jean Poulhès, 31432 Toulouse, France
| | - Esther Marco
- Université de Toulouse 3, EA 4552, I2MC, 1 Avenue Jean Poulhès, 31432 Toulouse, France
| | | | - Daniel Fourmy
- Université de Toulouse 3, EA 4552, I2MC, 1 Avenue Jean Poulhès, 31432 Toulouse, France
| | - Antonio Varnavas
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, P.le Europa 1, 34127 Trieste, Italy
| |
Collapse
|
10
|
Shirai S, Goto Y, Mizoshita N, Ohashi M, Tani T, Shimada T, Hyodo SA, Inagaki S. Theoretical Studies on Si−C Bond Cleavage in Organosilane Precursors during Polycondensation to Organosilica Hybrids. J Phys Chem A 2010; 114:6047-54. [DOI: 10.1021/jp101242g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soichi Shirai
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Yasutomo Goto
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Norihiro Mizoshita
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Masataka Ohashi
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Takao Tani
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Toyoshi Shimada
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Shi-aki Hyodo
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| | - Shinji Inagaki
- Toyota Central R&D Laboratories, Inc., Nagakute, Aichi 480-1192, Japan, Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama 332-0012, Japan, and Department of Chemical Engineering, Nara National College of Technology, Yamatokoriyama, Nara 639-1080, Japan
| |
Collapse
|
11
|
Sałdyka M. Isomerical and structural determination of N-hydroxyurea: a matrix isolation and theoretical study. Phys Chem Chem Phys 2010; 12:15111-8. [DOI: 10.1039/c0cp00709a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Tavakol H. Computational study of simple and water-assisted tautomerism of hydroxamic acids. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.09.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Šille J, Šramko M, Garaj V, Remko M. Gas phase and solution state stability of complexes L…M, where M=Cu2+, Ni2+, or Zn2+ and L=R−C(O)NHOH (R=H, NH2, CH3, CF3, or Phenyl). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
14
|
Dissanayake DP, Senthilnithy R. Thermodynamic cycle for the calculation of ab initio pKa values for hydroxamic acids. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
15
|
Molecular structures of 8,8′-dithioureido-2,2′-binaphthalene derivatives and their anions recognition: an ONIOM investigation. Struct Chem 2009. [DOI: 10.1007/s11224-009-9466-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
16
|
Ding F, Smith JM, Wang H. First-Principles Calculation of pKa Values for Organic Acids in Nonaqueous Solution. J Org Chem 2009; 74:2679-91. [DOI: 10.1021/jo802641r] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Feizhi Ding
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Jeremy M. Smith
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| | - Haobin Wang
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003
| |
Collapse
|
17
|
Ho J, Coote ML. pKa Calculation of Some Biologically Important Carbon Acids - An Assessment of Contemporary Theoretical Procedures. J Chem Theory Comput 2009; 5:295-306. [DOI: 10.1021/ct800335v] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junming Ho
- ARC Centre of Excellence for Free-Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Free-Radical Chemistry and Biotechnology, Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
| |
Collapse
|
18
|
Vrček IV, Kos I, Weitner T, Biruš M. Acido-Base Behavior of Hydroxamic Acids: Experimental and Ab Initio Studies on Hydroxyureas. J Phys Chem A 2008; 112:11756-68. [DOI: 10.1021/jp804925b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivana Vinković Vrček
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Kovačića 1, 10000 Zagreb, Croatia
| | - Ivan Kos
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Kovačića 1, 10000 Zagreb, Croatia
| | - Tin Weitner
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Kovačića 1, 10000 Zagreb, Croatia
| | - Mladen Biruš
- University of Zagreb, Faculty of Pharmacy and Biochemistry, Kovačića 1, 10000 Zagreb, Croatia
| |
Collapse
|
19
|
Remko M, Fitz D, Rode BM. Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure and properties of L-arginine and zwitterionic L-arginine. J Phys Chem A 2008; 112:7652-61. [PMID: 18652440 DOI: 10.1021/jp801418h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of L-arginine is examined. The effects of metal ions (Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+)) and water on structures of Arg x M(H2O)m , m = 0, 1 complexes have been determined theoretically by employing the density functional theories (DFT) and using extended basis sets. Of the three stable complexes investigated, the relative stability of the gas-phase complexes computed with DFT methods (with the exception of K(+) systems) suggests metallic complexes of the neutral L-arginine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of arginine in the presence of the metal cations Li(+), Na(+), K(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), and Zn(2+) were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to arginine is exhibited by the Cu(2+) cation. The computed Gibbs energies DeltaG(o) are negative, span a rather broad energy interval (from -150 to -1500 kJ/mol), and are appreciably lowered upon hydration.
Collapse
Affiliation(s)
- Milan Remko
- Department of Pharmaceutical Chemistry, Comenius University, Odbojarov 10, SK-832 32 Bratislava, Slovakia.
| | | | | |
Collapse
|
20
|
Pinisakul A, Kritayakornupong C, Ruangpornvisuti V. Molecular modeling of nitrosamines adsorbed on H-ZSM-5 zeolite: an ONIOM study. J Mol Model 2008; 14:1035-41. [PMID: 18648862 DOI: 10.1007/s00894-008-0346-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Binding energies of nitrosamine compounds, N-nitrosamine (NA), N-methyl-N-nitrososamine (NMA), N-ethyl-N-nitrososamine (NEA), N,N-dimethyl-N-nitrosoamine (NDMA), N-ethyl-N-methyl-N-nitrosoamine (NEMA) and N,N-diethyl-N-nitrosoamine (NDEA) on the H-ZSM-5 zeolite were obtained using the ONIOM(B3LYP/6-31G(d):AM1) approach. Based on amino and imino isomers of nitrosamines, there are two adsorption configurations on the H-ZSM-5 for NA (as NA_a and NA_i), NMA (as NMA_a and NMA_i) and NEA (as NEA_a and NEA_i). The relative binding energies of nitrosamines are in order: NA_a > NMA_a approximately NEA_a > NA_i > NMA_i approximately NEA_i > NEMA approximately NDEA > NDMA. The order of adsorption selectivity for nitrosamines of the H-ZSM-5 is NA_a approximately NA_i >> NMA_a approximately NEA_a > NDMA approximately NMA_i approximately NEMA > NDEA approximately NEA_i. The selective recognition of the NA by the H-ZSM-5 was obviously found.
Collapse
Affiliation(s)
- Anawat Pinisakul
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi, 126 Pracha-utis Rd., Thung-kru, Bangkok 10140, Thailand
| | | | | |
Collapse
|
21
|
Senthilnithy R, Weerasinghe S, Dissanayake D. Stability of hydroxamate ions in aqueous medium. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
22
|
Politzer P, Murray JS, Concha MC. Computational characterization of the hydroxylamino (NHOH) group. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
23
|
Yu A, Liu Y, Li Z, Cheng JP. Computation of pKaValues of Substituted Aniline Radical Cations in Dimethylsulfoxide Solution. J Phys Chem A 2007; 111:9978-87. [PMID: 17760427 DOI: 10.1021/jp072456+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A newly developed computation strategy was used to calculate the absolute pKa values of 18 substituted aniline radical cations in dimethylsulfoxide (DMSO) solution with the error origin elucidated and deviation minimized. The B3LYP/6-311++G(2df,2p) method was applied and was found to be capable of reproducing the gas-phase proton-transfer free energies of substituted anilines with a precision of 0.83 kcal/mol. The IEF-PCM solvation model with gas-phase optimized structures was adopted in calculating the pKa values of the substituted neutral anilines in DMSO, regenerating the experimental results within a standard deviation of 0.4 pKa unit. When the IEF-PCM solvation model was applied to calculate the standard redox potentials of anilide anions, it showed that the computed values agreed well with experiment, but the redox potentials of substituted anilines were systematically overestimated by 0.304 eV. The cause of this deviation was found to be related to the inaccuracy of the calculated solvation free energies of aniline radical cations. By adjusting the size of the cavity in the IEF-PCM method, we derived a reliable procedure that can reproduce the experimental pKa values of aniline radical cations within 1.2 pKa units to those from experiment.
Collapse
Affiliation(s)
- Ao Yu
- College of Chemistry, Nankai University, State Key Laboratory of Elemento-organic Chemistry, Tianjin 300071, China
| | | | | | | |
Collapse
|
24
|
|
25
|
Leung K. Ab initio molecular dynamics study of the hydration of the formohydroxamate anion. Biophys Chem 2006; 124:222-8. [PMID: 16678963 DOI: 10.1016/j.bpc.2006.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/29/2006] [Accepted: 04/01/2006] [Indexed: 11/19/2022]
Abstract
We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.
Collapse
Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415, Albuquerque, NM 87185, United States.
| |
Collapse
|
26
|
|
27
|
Ruangpornvisuti V, Wanno B. Molecular model for host–guest interaction of tetraamino-tert-butylthiacalix[4]arene and tetraamino-tert-butylcalix[4]arene receptors with carboxylate and dicarboxylate guests: an ONIOM study. J Mol Model 2006; 13:65-77. [PMID: 16738872 DOI: 10.1007/s00894-006-0122-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
Geometry optimizations of tetraamino-tert-butylthiacalix[4]arene (tatbtc4a) and tetraamino-tert-butylcalix[4]arene (tatbc4a) complexes with acetate, oxalate,malonate, succinate, glutarate, adipate, and pimelate were carried out using the integrated MO:MO method. Thermodynamic quantities, preorganization energies and complexation energies of these complexes were obtained at the ONIOM(B3LYP/6-31G(d):AM1) level of theory. The relative stabilities of the tatbtc4a and tatbc4a complexes with carboxylate guests are reported. The complexes tatbtc4a/malonate and tatbc4a/oxalate were found to be the most stable species. The selectivity of the tatbtc4a receptor toward to malonate with respect to oxalate, in terms of selectivity coefficient, K(oxalatemalonate) is 9.90×10(2).
Collapse
Affiliation(s)
- Vithaya Ruangpornvisuti
- Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University,Bangkok, 10330, Thailand.
| | | |
Collapse
|
28
|
|
29
|
Theoretical study of conversion reactions of ketone to hydroxyalkylene in cluster models of zeolite H-ZSM-5. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.molcata.2005.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
30
|
Ghosh KK, Satnami ML, Sinha D. Dephosphorylation of paraoxon by hydroxamate ions in micellar media. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.10.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
31
|
Wanno B, Ruangpornvisuti V. Theoretical investigation of geometrical conformation, protonation of tetraamino-p-tert-butylthiacalix[4]arene and complexation with zinc: a comparative theoretical method. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
32
|
Ruangpornvisuti V. Recognition of carboxylate and dicarboxylates by azophenol–thiourea derivatives: a theoretical host–guest investigation. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
33
|
Li P, Bu Y, Ai H, Cao Z. Acid−Base Behavior Study of Glycinamide Using Density Functional Theory. J Phys Chem A 2004. [DOI: 10.1021/jp037567x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ping Li
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China, and Chemistry Group, Heze Medical College, Heze 274030, P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China, and Chemistry Group, Heze Medical College, Heze 274030, P. R. China
| | - Hongqi Ai
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China, and Chemistry Group, Heze Medical College, Heze 274030, P. R. China
| | - Zhaohua Cao
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, Department of Chemistry, Qufu Normal University, Qufu 273165, P. R. China, and Chemistry Group, Heze Medical College, Heze 274030, P. R. China
| |
Collapse
|
34
|
Fu Y, Liu L, Li RQ, Liu R, Guo QX. First-Principle Predictions of Absolute pKa's of Organic Acids in Dimethyl Sulfoxide Solution. J Am Chem Soc 2003; 126:814-22. [PMID: 14733556 DOI: 10.1021/ja0378097] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MP2/6-311++G(d,p) and B3LYP/6-311++G(2df,p) methods were found to be able to predict the gas-phase acidities of various organic acids with a precision of 2.2 and 2.3 kcal/mol. A PCM cluster-continuum solvation method was developed that could predict the solvation free energies of various neutral, cationic, and anionic organic species in DMSO with a precision of about 2.0 kcal/mol. Using these carefully tested methods, we successfully predicted the pKa's of 105 organic acids in DMSO with a precision of 1.7-1.8 pKa units. We also predicted the pKa's of a variety of organosilanes in DMSO for the first time using the newly developed methods. This study was one of the first that employed first-principle methods for calculating pKa's of unrelated compounds in organic solutions.
Collapse
Affiliation(s)
- Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | | | | | | | | |
Collapse
|
35
|
Senent ML, Niño A, Muñoz Caro C, Ibeas S, García B, Leal JM, Secco F, Venturini M. Deprotonation sites of acetohydroxamic acid isomers. A theoretical and experimental study. J Org Chem 2003; 68:6535-42. [PMID: 12919013 DOI: 10.1021/jo0341564] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theoretical (ab initio calculations) and experimental (NMR, spectrophotometric, and potentiometric measurements) investigations of the isomers of acetohydroxamic acid (AHA) and their deprotonation processes have been performed. Calculations with the Gaussian 98 package, refined at the MP2(FC)/AUG-cc-pVDZ level considering the molecule isolated, indicate that the Z(cis) amide is the most stable form of the neutral molecule. This species and the less stable (Z)-imide form undergo deprotonation, giving rise to two stable anions. Upon deprotonation, the E(trans) forms give three stable anions. The ab initio calculations were performed in solution as well, regarding water as a continuous dielectric; on the basis of the relative energies of the most stable anion and neutral forms, calculated with MP2/PCM/AUG-cc-pVDZ, N-deprotonation of the amide (Z or E) structure appeared to be the most likely process in solution. NMR measurements provided evidence for the existence of (Z)- and (E)-isomers of both the neutral and anion forms in solution. Comparisons of the dynamic NMR and NOESY (one-dimensional) results obtained for the neutral species and their anions were consistent with N-deprotonation, which occurred preferentially to O-deprotonation. The (microscopic) acid dissociation constants of the two isomers determined at 25 degrees C from the pH dependence of the relevant chemical shifts, pK(E) = 9.01 and pK(Z) = 9.35, were consistent with the spectrophotometric and potentiometric evaluations (pK(HA) = 9.31).
Collapse
Affiliation(s)
- María L Senent
- Departamento de Astrofísica Molecular e Infrarroja, Serrano 113b, Madrid 28006, Spain
| | | | | | | | | | | | | | | |
Collapse
|
36
|
|