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Egorov GI, Makarov DM. Effect of high pressure and temperature on the volume properties of the liquid-phase mixture of {water (1) + formamide (2)}. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.01.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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Venkataramanan NS. Cooperativity of intermolecular hydrogen bonds in microsolvated DMSO and DMF clusters: a DFT, AIM, and NCI analysis. J Mol Model 2016; 22:151. [DOI: 10.1007/s00894-016-3022-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/27/2016] [Indexed: 01/30/2023]
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3
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Biswas S, Mallik BS. Aqueous solvation of an amide molecule from first principles molecular simulations: Structure, hydrogen bond dynamics and spectral signature. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Chebaane A, Hammami F, Nasr S, Bahri M, Bellissent-Funel MC. H-Bonding network in fully deuterated N-methylformamide-water mixtures as studied by neutron scattering. Complementarity to X-ray study. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:5. [PMID: 25627916 DOI: 10.1140/epje/i2015-15005-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/06/2014] [Accepted: 12/22/2014] [Indexed: 06/04/2023]
Abstract
In complementarity with X-ray scattering and as extension of our previous publication, neutron scattering measurements are combined to DFT calculation to investigate the structural features of N-methylformamide-water mixtures (NMF-water) for three water molar fractions x w = 0.5 , 0.66 and x w = 0.75 . The recorded data at atmospheric pressure and room temperature are analyzed to yield the structure factor, the molecular form factor and the pair correlation function. Neutron investigations corroborate the X-ray ones and clearly show that liquid order in solutions is well accounted for by a tetramer. In this cluster, an NMF molecule is connected to three water molecules by one N-D···O and two O-D···O hydrogen bonds.
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Affiliation(s)
- Abir Chebaane
- Laboratoire Physico-Chimie des Matériaux, Département de Physique, Faculté des Sciences de Monastir, Tunis, 5000, Tunisie
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Garbuio V, Cascella M, Sole RD, Marsili M, Pulci O. Excited state properties of formamide in water solution: An ab initio study. J Chem Phys 2012; 137:164317. [DOI: 10.1063/1.4763980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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6
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Okada M, Ibuki K, Ueno M. Temperature Effect on the Reorientational Correlation Time of Water in Formamide– and N,N-Dimethylformamide–Water Mixtures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20110233] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaki Okada
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University
| | - Kazuyasu Ibuki
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University
| | - Masakatsu Ueno
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University
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7
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Chebaane A, Hammami F, Bahri M, Nasr S. Intramolecular and intermolecular interactions in N-methylformamide–water mixture: X-ray scattering and DFT calculation study. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2011.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Lu JF, Wu YF, Yu ZY, Lin XJ. DFT study of ionization potentials and electron affinities of formamide and its methylation derivatives. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2011. [DOI: 10.1134/s003602441108019x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Angelina EL, Peruchena NM. Strength and Nature of Hydrogen Bonding Interactions in Mono- and Di-Hydrated Formamide Complexes. J Phys Chem A 2011; 115:4701-10. [DOI: 10.1021/jp1105168] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emilio L. Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
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Nagaraju M, Narahari Sastry G. Effect of alkyl substitution on H-bond strength of substituted amide-alcohol complexes. J Mol Model 2010; 17:1801-16. [DOI: 10.1007/s00894-010-0886-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/20/2010] [Indexed: 11/28/2022]
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11
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Chen A, Pu X, He S, Guo Y, Wen Z, Li M, Wong NB, Tian A. Solvent effects on isolated formamide and its monohydrated complex: observations from PCM study. NEW J CHEM 2009. [DOI: 10.1039/b902149c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Zhang G, Ji A, Chen D. Origin of blue and red shifts of C–H and C–N stretching vibrations in formamide–HF/H2O/H2S/NH3 complexes. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.12.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Panuszko A, Gojło E, Zielkiewicz J, Śmiechowski M, Krakowiak J, Stangret J. Hydration of Simple Amides. FTIR Spectra of HDO and Theoretical Studies. J Phys Chem B 2008; 112:2483-93. [PMID: 18247601 DOI: 10.1021/jp7099509] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Emilia Gojło
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Jan Zielkiewicz
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Joanna Krakowiak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
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Elola MD, Ladanyi BM. Computational study of structural and dynamical properties of formamide-water mixtures. J Chem Phys 2007; 125:184506. [PMID: 17115764 DOI: 10.1063/1.2364896] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A molecular dynamics simulation study of structural and dynamical properties in liquid mixtures of formamide and water is presented. Site-site radial pair distribution functions, local mole fractions, pair energy distributions, and tetrahedral orientational order are the quantities analyzed to investigate the local structure in the simulated mixtures, along with a review of the intermolecular structure in terms of the distribution of hydrogen bonds. Our results indicate that there is a substitution of formamide molecules by water in the hydrogen bonds and a formation of a common hydrogen bond network. By analyzing the extent of tetrahedral order in the liquid as a function of composition, it is observed that whereas the tetrahedral network of liquid water is progressively lost by increasing the formamide concentration, the water structure within the first coordination shell is preserved and somewhat enhanced. The hydrogen-bond mean lifetimes were estimated by performing a time integration of the autocorrelation functions of bond occupation numbers. The lifetimes associated with hydrogen bonds between water, formamide, and interspecies pairs are found to increase with increasing formamide concentration. The lifetimes of the water hydrogen bonds show the largest variations, supporting the picture of an enhancement of the water structure among the nearest neighbors within the first coordination shell. We have used two different force field models for water, SPC/E [J. C. Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] and TIP4P/2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)]. Our results for structural and dynamical properties yield very small differences between those models, the TIP4P/2005 predicting a slightly more structured liquid and, consequently, exhibiting a slightly slower translational and librational dynamics.
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Affiliation(s)
- M Dolores Elola
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
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Liu Y, Liu W, Li H, Yang Y, Cheng S. Computational study of hydrogen bonding interaction between formamide and nitrosyl hydride. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Parreira RL, Valdés H, Galembeck SE. Computational study of formamide–water complexes using the SAPT and AIM methods. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.09.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Saladino R, Crestini C, Busiello V, Ciciriello F, Costanzo G, Di Mauro E. Origin of informational polymers. Differential stability of 3'- and 5'-phosphoester bonds in deoxy monomers and oligomers. J Biol Chem 2005; 280:35658-69. [PMID: 16036914 DOI: 10.1074/jbc.m504537200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To survive, an informational macromolecule must solve the major problem set by its very polymeric nature: instability. This is especially true in prebiotic terms because of the presumed initial absence of protective structures (proteins, lipids, etc.). We have analyzed the stability of the beta-glycosidic and of the 3'- and 5'-phosphoester bonds in both deoxy monomers and deoxy oligomers under a large set of conditions. The results show a strong dependence of the relative stability of these bonds on the physico-chemical environment. A set of conditions has been identified in which the stability of polymers becomes comparable with that of the precursor monomers. In certain instances the stability of the 5'-phosphoester bond is even higher in the polymer than in the mononucleotide.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento AgroBiologia and AgroChimica, Università della Tuscia, Via San Camillo De Lellis, Viterbo 01100, Italy
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18
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Lu JF, Zhou ZY, Wu QY, Zhao G. Density functional theory study of the hydrogen bonding interaction in formamide dimer. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Fu A, Li H, Du D, Zhou Z. Density Functional Study on the Reaction Mechanism of Proton Transfer in 2-Pyridone: Effect of Hydration and Self-Association. J Phys Chem A 2005; 109:1468-77. [PMID: 16833466 DOI: 10.1021/jp0453764] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton-transfer mechanism in the isolated, mono, dehydrated forms and dimers of 2-pyridone and the effect of hydration or self-assistance on the transition state structures corresponding to proton transfer from the keto form to the enol form have been investigated using B3LYP and BH-LYP hybrid density functional methods at the 6-311++G (2d, 2p) basis set level. The barrier heights for both H2O-assisted and self-assisted reactions are significantly lower than that of the bare tautomerization reaction from 2-pyridone to 2-hydroxypyridine, implying the importance of the superior catalytic effect of H2O and (H2O)2 and the important role of 2-pyridone itself for the intramolecular proton transfer. Long-range solvent effects have also been taken into account by using the continuum model (Onsager model and polarizable continuum model (PCM)) of water. The tautomerization energies and the potential energy barriers are increased both for the water-assisted and for the self-assisted reaction because of the bulk solvent, which imply that the tautomerization of PY becomes less favorable in the polar solvent.
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Affiliation(s)
- Aiping Fu
- Department of Chemistry, Qufu Normal University, Shandong, Qufu 273165, PR China.
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Liang W, Li H, Hu X, Han S. Proton Transfer of Formamide + nH2O (n = 0−3): Protective and Assistant Effect of the Water Molecule. J Phys Chem A 2004. [DOI: 10.1021/jp047248l] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wanchun Liang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
| | - Haoran Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xingbang Hu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
| | - Shijun Han
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
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21
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Zhang HT, Zhou ZY, Shi Y. Density Functional Theory Study of the Hydrogen-Bonding Interaction of 1:1 Complexes of Alanine with Water. J Phys Chem A 2004. [DOI: 10.1021/jp040044k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai-tao Zhang
- Department of Chemistry, Qufu Normal University, Shandong, Qfnu, 273165, People's Republic of China, and State Key Laboratory Crystal Materials, Shandong University, Shandong, Jinan, 250100, People's Republic of China
| | - Zheng-yu Zhou
- Department of Chemistry, Qufu Normal University, Shandong, Qfnu, 273165, People's Republic of China, and State Key Laboratory Crystal Materials, Shandong University, Shandong, Jinan, 250100, People's Republic of China
| | - Yun Shi
- Department of Chemistry, Qufu Normal University, Shandong, Qfnu, 273165, People's Republic of China, and State Key Laboratory Crystal Materials, Shandong University, Shandong, Jinan, 250100, People's Republic of China
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Fu AP, Du DM, Zhou ZY. Theoretical study on the hydrogen bond interaction between diacetamide and methanol. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Fu A, Li H, Zhou Z, Feng D. Study of the diacetamide–water dimer with ab initio and density functional theory methods. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2003.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Fu AP, Li HL, Du DM, Zhou ZY. Theoretical study on the reaction mechanism of proton transfer in formamide. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.10.070] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Pal SK, Zhao L, Xia T, Zewail AH. Site- and sequence-selective ultrafast hydration of DNA. Proc Natl Acad Sci U S A 2003; 100:13746-51. [PMID: 14603035 PMCID: PMC283492 DOI: 10.1073/pnas.2336222100] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water molecules in the DNA grooves are critical for maintaining structural integrity, conformational changes, and molecular recognition. Here we report studies of site- and sequence-specific hydration dynamics, using 2-aminopurine (Ap) as the intrinsic fluorescence probe and with femtosecond resolution. The dodecamer d[CGCA(Ap)ATTTGCG]2 was investigated, and we also examined the effect of a specific minor groove-binding drug, pentamidine, on hydration dynamics. Two time scales were observed: approximately 1 ps (bulk-like) and 10-12 ps (weakly bound type), consistent with layer hydration observed in proteins and DNA. However, for denatured DNA, the cosolvent condition of 40% formamide hydration is very different: it becomes that of bulk (in the presence of formamide). Well known electron transfer between Ap and nearby bases in stacked assemblies becomes inefficient in the single-stranded state. The rigidity of Ap in the single strands is significantly higher than that in bulk water and that attached to deoxyribose, suggesting a unique role for the dynamics of the phosphate-sugar-base in helix formation. The disparity in minor and major groove hydration is evident because of the site selection of Ap and in the time scale observed here (in the presence and absence of the drug), which is different by a factor of 2 from that observed in the minor groove-drug recognition.
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Affiliation(s)
- Samir Kumar Pal
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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