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KAUR DAMANJIT, KHANNA SHWETA. Hydrogen bonding of formamide, urea, urea monoxide and their thio-analogs with water and homodimers. J CHEM SCI 2015. [DOI: 10.1007/s12039-014-0725-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Computational study of interactions and nuclear magnetic shielding constants in linear chains of formamide clusters. J Mol Model 2014; 20:2320. [PMID: 24944093 DOI: 10.1007/s00894-014-2320-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
We investigated the energetic, structural, dielectric, and nuclear magnetic shielding properties of linear n-formamide clusters, with n up to 6, to quantitatively characterize cooperative effects in model biological systems. The geometries of the complexes were optimized at the MP2 and DFT/B3LYP levels by using the pc-2 and pc-3 basis sets, while the nuclear magnetic shielding constants were calculated by employing pcS-n type basis sets, which have been optimized specifically for density functional calculations of these properties. The interaction energies show the cooperative effect, which favors the successive addition of monomers. In addition, by analyzing structural changes in the intermolecular C=O, C-N and hydrogen O⋯H bonds, as well as in the average dipole moments as cluster size increases, we found that the cooperative interaction far exceeds that expected for electrostatic interactions. Such non-pairwise-additive effects are also reflected in the changes of the nuclear magnetic shielding constants. In particular, the negativity of O shielding decreases around 23% from the monomer to the 6-formamide chain. It is possible to note the decrease in the shielding of H and in the deshielding of O as a result of their hydrogen bonding. However, the results obtained show that these variations in the extremes of formamide chains tend to zero, and the respective shielding values tend to stabilize as the number of monomers increases in the chain. Also, the cooperative effect increases in the middle of the chains, by decreasing the shielding for all atoms except that of O, which decreases its deshielding. These results could serve to guide improvements in current conventional models for simulating hydrogen bonded systems.
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Hydrogen bonded networks in formamide [HCONH2]n (n = 1 − 10) clusters: A computational exploration of preferred aggregation patterns#. J CHEM SCI 2012. [DOI: 10.1007/s12039-011-0193-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.
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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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Wu Q, Ayers PW, Zhang Y. Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies. J Chem Phys 2009; 131:164112. [DOI: 10.1063/1.3253797] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Albrecht M, Rice CA, Suhm MA. Elementary Peptide Motifs in the Gas Phase: FTIR Aggregation Study of Formamide, Acetamide, N-Methylformamide, and N-Methylacetamide. J Phys Chem A 2008; 112:7530-42. [DOI: 10.1021/jp8039912] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Merwe Albrecht
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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Cabaleiro-Lago EM, Rodríguez-Otero J, Peña-Gallego Á. Computational Study on the Characteristics of the Interaction in Naphthalene···(H2X)n=1,2 (X = O, S) Clusters. J Phys Chem A 2008; 112:6344-50. [DOI: 10.1021/jp8021979] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
| | - Jesús Rodríguez-Otero
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
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Tatchen J, Kleinschmidt M, Marian CM, Parac M, Grimme S. Quantum Chemical Investigation of Spin-Forbidden Transitions in Dithiosuccinimide. ACTA ACUST UNITED AC 2008. [DOI: 10.1524/zpch.217.3.205.20464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The vertical and adiabatic electronic spectra of dithiosuccinimide have been investigated by means of multi-reference Møller–Plesset perturbation theory and combined densitiy functional/multi-reference configuration interaction methods. Geometries of the electronic ground state and several low-lying excited states have been optimised at the level of time-dependent density functional theory. We have determined spin-orbit coupling for correlated wavefunctions utilising a non-empirical spin-orbit mean-field approach. Because of the two thiocarbonyl groups present in the molecule, dithiosuccinimide exhibits a dense spectrum of low-lying valence states. The first two excited singlet states (S
1 and S
2) originate from n → π* excitations. Nearby, three triplet states are located, two n → π* states (T
1 and T
2), and a π → π* triplet excitation (T
3). The experimentally observed strong absorption band with maximum at 3.96 eV arises from the π → π* excited 1
B
2 (S
3) state. Computed radiative lifetimes are presented for the experimentally known phosphorescence from the n → π* excited T
1 state. Further, we find nearly equal probabilities for the spin-forbidden S
0 → T
2 and the spin-allowed S
0 → S
1 transitions in absorption. On these grounds, we assign band number 3 in the spectra measured by Meskers et al. [J. Phys. Chem.
99 (1995) 1134] to this spin-forbidden transition.
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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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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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Kowal AT. First-principles calculation of geometry and anharmonic vibrational spectra of thioformamide and thioformamide-d2. J Chem Phys 2006; 124:14304. [PMID: 16409033 DOI: 10.1063/1.2139995] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The equilibrium geometry of thioformamide HCSNH2 has been determined at the MP2 and CCSD(T) electron correlation levels under C(s) symmetry constraints using triple-zeta basis sets up to cc-pVTZ. All optimized planar structures are true minima on the potential-energy surface and are characterized by the C-N bond length within 1.353-1.343 A, C-S distances of 1.656-1.628 A, and NCS angle between 125.7 degrees and 125.9 degrees . The wave number of the NH2 out-of-plane wagging mode computed in the harmonic approximation shows stronger dependence on the basis set rather than the electron correlation level and varies from 85.9 cm(-1) at CCSD(T)cc-pVDZ level to 335 cm(-1) at MP2/aug-cc-pVTZ level. Anharmonic vibrational spectra of HCSNH2 and HCSND2 have been determined directly from the potential-energy surfaces computed at MP2 level in triple-zeta valence (TZV)(2df,2p) and TZV+(2df,2p) basis sets using vibrational self-consistent-field (VSCF) and correlation-corrected VSCF (CC-VSCF) methods. CC-VSCF wave numbers of fundamental, first overtone, and most intense combination transitions are reported for thioformamide and those of fundamentals for thioformamide-d2. The NH2 wagging (nu12) mode is strongly anharmonic and its fundamentals have been computed at 406.9 cm(-1) [TZV(2df,2p)] and 399.5 cm(-1) [TZV+(2df,2p)], which is remarkably close to the experimental energy of 393 cm(-1). Anharmonically computed fundamentals of this mode in thioformamide-d2, 299.7 cm(-1) [TZV(2df,2p)] and 299.6 cm(-1) [TZV+(2df,2p)], are only approximately 7 cm(-1) higher than the transition energy (293 cm(-1)) observed in the gas phase spectrum of HCSND2. The first overtone of the NH2 wagging mode of thioformamide (nu12 (02)) has been calculated by CC-VSCF procedure at 830.8 cm(-1) [TZV(2df,2p)] and 880.0 cm(-1) [TZV+(2df,2p)], which implies "negative" (nu12 (02)>2*nu12 (01)) anharmonicity of this mode.
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Affiliation(s)
- Andrzej T Kowal
- Department of Chemistry, Wrocław University of Technology, Wyb. St. Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Maeyama T, Negishi Y, Tsukuda T, Yagi I, Mikami N. Electron localization in negatively charged formamide clusters studied by photodetachment spectroscopy. Phys Chem Chem Phys 2006; 8:827-33. [PMID: 16482324 DOI: 10.1039/b514656a] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Size-dependent features of the electron localization in negatively charged formamide clusters (FAn-, n = 5-21) have been studied by photodetachment spectroscopy. In the photoelectron spectra for all the sizes studied, two types of bands due to different isomers of anions were found. The low binding energy band peaking around 1 eV is assigned to the solvated electron state by relative photodetachment cross-section measurements in the near-infrared region. It is suggested that nascent electron trapping is dominated by formation of the solvated electron. The higher energy band originates from the covalent anion state generated after a significant relaxation process, which exhibits a rapid increase of electron binding energy as a function of the cluster size. A unique behavior showing a remarkable band intensity of the higher energy band was found only for n = 9.
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Affiliation(s)
- Toshihiko Maeyama
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
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Hobza P, Zahradník R, Müller-Dethlefs K. The World of Non-Covalent Interactions: 2006. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060443] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.
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Abstract
Properties of neat liquid formamide (HCONH2) have been studied by the combination of gradient-corrected density-functional theory, norm-conserving pseudopotentials, and the adaptive finite-element method. The structural and dynamical quantities have been calculated through molecular dynamics simulations under the Born-Oppenheimer approximation. Satisfactory agreement with experimental data was obtained for both intramolecular and intermolecular properties. Our results are also compared with those of the empirical potential functions to clarify their accuracies.
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Affiliation(s)
- Eiji Tsuchida
- Research Institute for Computational Sciences, AIST Tsukuba Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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Kobko N, Dannenberg JJ. Cooperativity in Amide Hydrogen Bonding Chains. Relation between Energy, Position, and H-Bond Chain Length in Peptide and Protein Folding Models. J Phys Chem A 2003. [DOI: 10.1021/jp0365209] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Nadya Kobko
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10021
| | - J. J. Dannenberg
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10021
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George L, Sanchez-García E, Sander W. Matrix Isolation Infrared and ab Initio Study of Formic Acid−Acetylene Interaction: Example of H···π and C−H···O Interaction. J Phys Chem A 2003. [DOI: 10.1021/jp034158s] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lisa George
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Elsa Sanchez-García
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Sabzyan H, Noorbala MR. Ab initio and DFT study of carbon monoxide cyclic oligomers, (CO)2 to (CO)6. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00029-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gálvez O, Gómez PC, Pacios LF. Variation with the intermolecular distance of properties dependent on the electron density in cyclic dimers with two hydrogen bonds. J Chem Phys 2003. [DOI: 10.1063/1.1545678] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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