Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines

Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Li, Yang [verfasserIn] Wang, ChangSheng [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Schlagwörter:	uracils thymines binding energies hydrogen-bonded dimers hydrogen-bonded trimers hydrogen-bonded tetramers

Übergeordnetes Werk:	Enthalten in: Science in China - Asheville, NC : Science in China Press, 1995, 54(2011), 11 vom: Nov., Seite 1759-1769
Übergeordnetes Werk:	volume:54 ; year:2011 ; number:11 ; month:11 ; pages:1759-1769

Links:	Volltext

DOI / URN:	10.1007/s11426-011-4411-y

Katalog-ID:	SPR019159218

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520			\|a Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.
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allfields	10.1007/s11426-011-4411-y doi (DE-627)SPR019159218 (SPR)s11426-011-4411-y-e DE-627 ger DE-627 rakwb eng 540 550 570 ASE 35.00 bkl Li, Yang verfasserin aut Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers. uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213 Wang, ChangSheng verfasserin aut Enthalten in Science in China Asheville, NC : Science in China Press, 1995 54(2011), 11 vom: Nov., Seite 1759-1769 (DE-627)327310405 (DE-600)2043454-6 1862-2771 nnns volume:54 year:2011 number:11 month:11 pages:1759-1769 https://dx.doi.org/10.1007/s11426-011-4411-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_152 GBV_ILN_161 GBV_ILN_171 GBV_ILN_187 GBV_ILN_224 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 35.00 ASE AR 54 2011 11 11 1759-1769
spelling	10.1007/s11426-011-4411-y doi (DE-627)SPR019159218 (SPR)s11426-011-4411-y-e DE-627 ger DE-627 rakwb eng 540 550 570 ASE 35.00 bkl Li, Yang verfasserin aut Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers. uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213 Wang, ChangSheng verfasserin aut Enthalten in Science in China Asheville, NC : Science in China Press, 1995 54(2011), 11 vom: Nov., Seite 1759-1769 (DE-627)327310405 (DE-600)2043454-6 1862-2771 nnns volume:54 year:2011 number:11 month:11 pages:1759-1769 https://dx.doi.org/10.1007/s11426-011-4411-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_152 GBV_ILN_161 GBV_ILN_171 GBV_ILN_187 GBV_ILN_224 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 35.00 ASE AR 54 2011 11 11 1759-1769
allfields_unstemmed	10.1007/s11426-011-4411-y doi (DE-627)SPR019159218 (SPR)s11426-011-4411-y-e DE-627 ger DE-627 rakwb eng 540 550 570 ASE 35.00 bkl Li, Yang verfasserin aut Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers. uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213 Wang, ChangSheng verfasserin aut Enthalten in Science in China Asheville, NC : Science in China Press, 1995 54(2011), 11 vom: Nov., Seite 1759-1769 (DE-627)327310405 (DE-600)2043454-6 1862-2771 nnns volume:54 year:2011 number:11 month:11 pages:1759-1769 https://dx.doi.org/10.1007/s11426-011-4411-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_152 GBV_ILN_161 GBV_ILN_171 GBV_ILN_187 GBV_ILN_224 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 35.00 ASE AR 54 2011 11 11 1759-1769
allfieldsGer	10.1007/s11426-011-4411-y doi (DE-627)SPR019159218 (SPR)s11426-011-4411-y-e DE-627 ger DE-627 rakwb eng 540 550 570 ASE 35.00 bkl Li, Yang verfasserin aut Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers. uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213 Wang, ChangSheng verfasserin aut Enthalten in Science in China Asheville, NC : Science in China Press, 1995 54(2011), 11 vom: Nov., Seite 1759-1769 (DE-627)327310405 (DE-600)2043454-6 1862-2771 nnns volume:54 year:2011 number:11 month:11 pages:1759-1769 https://dx.doi.org/10.1007/s11426-011-4411-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_152 GBV_ILN_161 GBV_ILN_171 GBV_ILN_187 GBV_ILN_224 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 35.00 ASE AR 54 2011 11 11 1759-1769
allfieldsSound	10.1007/s11426-011-4411-y doi (DE-627)SPR019159218 (SPR)s11426-011-4411-y-e DE-627 ger DE-627 rakwb eng 540 550 570 ASE 35.00 bkl Li, Yang verfasserin aut Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers. uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213 Wang, ChangSheng verfasserin aut Enthalten in Science in China Asheville, NC : Science in China Press, 1995 54(2011), 11 vom: Nov., Seite 1759-1769 (DE-627)327310405 (DE-600)2043454-6 1862-2771 nnns volume:54 year:2011 number:11 month:11 pages:1759-1769 https://dx.doi.org/10.1007/s11426-011-4411-y lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_152 GBV_ILN_161 GBV_ILN_171 GBV_ILN_187 GBV_ILN_224 GBV_ILN_250 GBV_ILN_281 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 35.00 ASE AR 54 2011 11 11 1759-1769
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source	Enthalten in Science in China 54(2011), 11 vom: Nov., Seite 1759-1769 volume:54 year:2011 number:11 month:11 pages:1759-1769
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author	Li, Yang
spellingShingle	Li, Yang ddc 540 bkl 35.00 misc uracils misc thymines misc binding energies misc hydrogen-bonded dimers misc hydrogen-bonded trimers misc hydrogen-bonded tetramers Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
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topic_title	540 550 570 ASE 35.00 bkl Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines uracils (dpeaa)DE-He213 thymines (dpeaa)DE-He213 binding energies (dpeaa)DE-He213 hydrogen-bonded dimers (dpeaa)DE-He213 hydrogen-bonded trimers (dpeaa)DE-He213 hydrogen-bonded tetramers (dpeaa)DE-He213
topic	ddc 540 bkl 35.00 misc uracils misc thymines misc binding energies misc hydrogen-bonded dimers misc hydrogen-bonded trimers misc hydrogen-bonded tetramers
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title	Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
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title_full	Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
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title_sort	exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
title_auth	Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
abstract	Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.
abstractGer	Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.
abstract_unstemmed	Abstract Understanding the mechanisms underlying the assembly of nucleobases is a great challenge. The ability to deeply understand how nucleobases interact with themselves as well as with other molecules will allow us to gain valuable insights into how we might be able to harness these interesting biological molecules to construct complex nanostructures and materials. Uracil and thymine derivatives have been reported for use in biological applications and in self-assembling triple hydrogen bonded systems. Either uracil or thymine possesses three binding sites (Site 1, Site 2, and Site 3) that can induce strong directional N-H…O=C hydrogen bonding interaction. In this paper, theoretical calculations are carried out on the structural features and binding energies of hydrogen-bonded dimers and trimers formed by uracil and thymine bases. We find that the hydrogen bonds formed through Site 1 are the strongest, those formed through Site 3 are next, while those formed through Site 2 are the weakest. The atoms in molecules analysis show that the electron densities at the bond critical points and the corresponding Laplacians have greater values for those hydrogen bonds formed through Site 1 than through Site 2. All these results indicate that a uracil (or thymine) would interact with another uracil or thymine most likely through Site 1 and least likely through Site 2. We also find that a simple summation rule roughly exists for the binding energies in these dimers and trimers.
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title_short	Exploration on the site-preference of the hydrogen bonding interactions between uracils and/or thymines
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