Matrix-isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 4. H-bonded complexes of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water

Johan Smets, Alain Destexhe, Ludwik Adamowicz, Guido Maes

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Abstract

We continue our combined experimental and theoretical ab initio studies of hydrogen-bonded complexes involving molecules modeling cytosines by investigating the H-bond interaction of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water. The objective of the present work is theoretical and spectral characterization of the base-water complexes in the argon matrix, where the water molecule can become hydrogen bonded to the base through two H bonds with hydrogens of both bonds coming from the water molecule. For the 1-methyl-2-pyrimidone base, the ab initio calculations predict the H-bonded complex at the N 3 site to be slightly more stable than the alternative complex at the C 2=O site. Both H-bonded complexes have a second, weaker H bond between the other water OH group and the C 2=O or N 3 base site. The predicted vibrational spectra of the two complexes do not match well with the observed experimental FT-IR spectrum. Possible reasons for the discrepancies between the experiment and the theory attributed to the presence of argon are discussed. While the theory predicts two closed complexes, each containing a double hydrogen bond, from the experimental spectrum, two open complexes at the C 2=O and N 3 interaction sites are identified. H-bonding of water with N,N,1-trimethylcytosine can occur at either the N 3, C 2=O, or (CH 3) 2N site. The stability difference between the first two complexes is relatively small, and the second H bond in both complexes is considerably weaker than in the pyrimidone complexes. As results from the calculations, the H-bond interaction at the methylated amino group is much weaker than the H bonds formed with N 3 and C 2=O, and this finds conformation in the experimental matrix spectra, where the spectral signature of this complex is absent. The relative frequency shifts and the ratios between the calculated and measured frequency values for the stretching mode of the bonded water for all the complexes of both basis are discussed in relation to the earlier established correlations for similar H-bonded complexes. Water-rich matrices contain also 1:2 complexes B⋯HO(H)⋯HOH. It is found that the central H bond in these linear structures is characterized by the cooperativity factor of 1.3-1.4.

Original languageEnglish (US)
Pages (from-to)6583-6599
Number of pages17
JournalJournal of Physical Chemistry B
Volume101
Issue number33
StatePublished - Aug 14 1997

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Cytosine
tautomers
Hydrogen
isolation
Molecules
Water
hydrogen
matrices
water
molecules
Argon
Pyrimidinones
argon
spectral signatures
1-methyl-2-pyrimidone
isocytosine
interactions
Vibrational spectra
vibrational spectra
frequency shift

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Engineering(all)

Cite this

@article{89a6acab69b9466a8963d5fac080831b,
title = "Matrix-isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 4. H-bonded complexes of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water",
abstract = "We continue our combined experimental and theoretical ab initio studies of hydrogen-bonded complexes involving molecules modeling cytosines by investigating the H-bond interaction of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water. The objective of the present work is theoretical and spectral characterization of the base-water complexes in the argon matrix, where the water molecule can become hydrogen bonded to the base through two H bonds with hydrogens of both bonds coming from the water molecule. For the 1-methyl-2-pyrimidone base, the ab initio calculations predict the H-bonded complex at the N 3 site to be slightly more stable than the alternative complex at the C 2=O site. Both H-bonded complexes have a second, weaker H bond between the other water OH group and the C 2=O or N 3 base site. The predicted vibrational spectra of the two complexes do not match well with the observed experimental FT-IR spectrum. Possible reasons for the discrepancies between the experiment and the theory attributed to the presence of argon are discussed. While the theory predicts two closed complexes, each containing a double hydrogen bond, from the experimental spectrum, two open complexes at the C 2=O and N 3 interaction sites are identified. H-bonding of water with N,N,1-trimethylcytosine can occur at either the N 3, C 2=O, or (CH 3) 2N site. The stability difference between the first two complexes is relatively small, and the second H bond in both complexes is considerably weaker than in the pyrimidone complexes. As results from the calculations, the H-bond interaction at the methylated amino group is much weaker than the H bonds formed with N 3 and C 2=O, and this finds conformation in the experimental matrix spectra, where the spectral signature of this complex is absent. The relative frequency shifts and the ratios between the calculated and measured frequency values for the stretching mode of the bonded water for all the complexes of both basis are discussed in relation to the earlier established correlations for similar H-bonded complexes. Water-rich matrices contain also 1:2 complexes B⋯HO(H)⋯HOH. It is found that the central H bond in these linear structures is characterized by the cooperativity factor of 1.3-1.4.",
author = "Johan Smets and Alain Destexhe and Ludwik Adamowicz and Guido Maes",
year = "1997",
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TY - JOUR

T1 - Matrix-isolation FT-IR studies and ab initio calculations of hydrogen-bonded complexes of molecules modeling cytosine or isocytosine tautomers. 4. H-bonded complexes of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water

AU - Smets, Johan

AU - Destexhe, Alain

AU - Adamowicz, Ludwik

AU - Maes, Guido

PY - 1997/8/14

Y1 - 1997/8/14

N2 - We continue our combined experimental and theoretical ab initio studies of hydrogen-bonded complexes involving molecules modeling cytosines by investigating the H-bond interaction of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water. The objective of the present work is theoretical and spectral characterization of the base-water complexes in the argon matrix, where the water molecule can become hydrogen bonded to the base through two H bonds with hydrogens of both bonds coming from the water molecule. For the 1-methyl-2-pyrimidone base, the ab initio calculations predict the H-bonded complex at the N 3 site to be slightly more stable than the alternative complex at the C 2=O site. Both H-bonded complexes have a second, weaker H bond between the other water OH group and the C 2=O or N 3 base site. The predicted vibrational spectra of the two complexes do not match well with the observed experimental FT-IR spectrum. Possible reasons for the discrepancies between the experiment and the theory attributed to the presence of argon are discussed. While the theory predicts two closed complexes, each containing a double hydrogen bond, from the experimental spectrum, two open complexes at the C 2=O and N 3 interaction sites are identified. H-bonding of water with N,N,1-trimethylcytosine can occur at either the N 3, C 2=O, or (CH 3) 2N site. The stability difference between the first two complexes is relatively small, and the second H bond in both complexes is considerably weaker than in the pyrimidone complexes. As results from the calculations, the H-bond interaction at the methylated amino group is much weaker than the H bonds formed with N 3 and C 2=O, and this finds conformation in the experimental matrix spectra, where the spectral signature of this complex is absent. The relative frequency shifts and the ratios between the calculated and measured frequency values for the stretching mode of the bonded water for all the complexes of both basis are discussed in relation to the earlier established correlations for similar H-bonded complexes. Water-rich matrices contain also 1:2 complexes B⋯HO(H)⋯HOH. It is found that the central H bond in these linear structures is characterized by the cooperativity factor of 1.3-1.4.

AB - We continue our combined experimental and theoretical ab initio studies of hydrogen-bonded complexes involving molecules modeling cytosines by investigating the H-bond interaction of 1-methyl-2-pyrimidone and N,N-1-trimethylcytosine with water. The objective of the present work is theoretical and spectral characterization of the base-water complexes in the argon matrix, where the water molecule can become hydrogen bonded to the base through two H bonds with hydrogens of both bonds coming from the water molecule. For the 1-methyl-2-pyrimidone base, the ab initio calculations predict the H-bonded complex at the N 3 site to be slightly more stable than the alternative complex at the C 2=O site. Both H-bonded complexes have a second, weaker H bond between the other water OH group and the C 2=O or N 3 base site. The predicted vibrational spectra of the two complexes do not match well with the observed experimental FT-IR spectrum. Possible reasons for the discrepancies between the experiment and the theory attributed to the presence of argon are discussed. While the theory predicts two closed complexes, each containing a double hydrogen bond, from the experimental spectrum, two open complexes at the C 2=O and N 3 interaction sites are identified. H-bonding of water with N,N,1-trimethylcytosine can occur at either the N 3, C 2=O, or (CH 3) 2N site. The stability difference between the first two complexes is relatively small, and the second H bond in both complexes is considerably weaker than in the pyrimidone complexes. As results from the calculations, the H-bond interaction at the methylated amino group is much weaker than the H bonds formed with N 3 and C 2=O, and this finds conformation in the experimental matrix spectra, where the spectral signature of this complex is absent. The relative frequency shifts and the ratios between the calculated and measured frequency values for the stretching mode of the bonded water for all the complexes of both basis are discussed in relation to the earlier established correlations for similar H-bonded complexes. Water-rich matrices contain also 1:2 complexes B⋯HO(H)⋯HOH. It is found that the central H bond in these linear structures is characterized by the cooperativity factor of 1.3-1.4.

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