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Ordóñez C, Martínez-Zapata D, Santamaria R. Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study. J Biomol Struct Dyn 2022; 40:13207-13217. [PMID: 34629032 DOI: 10.1080/07391102.2021.1987988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cristian Ordóñez
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Daniel Martínez-Zapata
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ruben Santamaria
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
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Klein J, Fleurat-Lessard P, Pilmé J. The Topological Analysis of the ELF x Localization Function: Quantitative Prediction of Hydrogen Bonds in the Guanine-Cytosine Pair. Molecules 2021; 26:molecules26113336. [PMID: 34206097 PMCID: PMC8199511 DOI: 10.3390/molecules26113336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 11/18/2022] Open
Abstract
In this contribution, we recall and test a new methodology designed to identify the favorable reaction pathway between two reactants. Applied to the formation of the DNA guanine (G) –cytosine (C) pair, we successfully predict the best orientation between the base pairs held together by hydrogen bonds and leading to the formation of the typical Watson Crick structure of the GC pair. Beyond the global minimum, some local stationary points of the targeted pair are also clearly identified.
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Affiliation(s)
- Johanna Klein
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, CC 137, 4, Place Jussieu F, CEDEX 05, 75252 Paris, France;
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, 9 Avenue Alain Savary, BP 47870, CEDEX, 21078 Dijon, France;
| | - Julien Pilmé
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, CC 137, 4, Place Jussieu F, CEDEX 05, 75252 Paris, France;
- Correspondence:
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Yam SC, Zain SM, Sanghiran Lee V, Chew KH. Correlation between polar surface area and bioferroelectricity in DNA and RNA nucleobases. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:86. [PMID: 30014219 DOI: 10.1140/epje/i2018-11696-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
We have performed computational molecular modelling to study the polarization switching and hysteresis loop behaviours of DNA and RNA nucleobases using the PM3 semi-empirical quantum mechanical approaches. All the nucleobases: adenine (A), thymine (T), guanine (G), cytosine (C), and uracil (U) were modelled. Our study indicates that all the nucleobases exhibit a zero-field polarization due to the presence of polar atoms or molecules such as amidogen and carbonyl. The shape of polarization P versus an applied electric field E hysteresis loop is square, implying typical ferroelectrics behaviour. The total energy U as a function of an applied electric field E exhibits a butterfly-like loop. The presence of zero-field polarization and ferroelectrics hysteresis loop behaviours in nucleobases may support the hypothesis of the existence of bioferroelectricity in DNA and RNA. We also found an interesting relationship between the minimum electric field required for switching [Formula: see text] and the ratio of the topological polar surface area (TPSA) to the total surface area (TSA) of a nucleobase. In particular, the [Formula: see text] of a nucleobase is inversely proportional to the TPSA/TSA ratio. This work may provide useful information for understanding the possible existence of ferroelectricity in biomaterials.
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Affiliation(s)
- See-Chuan Yam
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sharifuddin Md Zain
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Khian-Hooi Chew
- Department of Physics, Centre for Theoretical and Computational Physics, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Jia Y, Yin XB, Zhang J, Zhou S, Song M, Xing KL. Graphene oxide modified light addressable potentiometric sensor and its application for ssDNA monitoring. Analyst 2013; 137:5866-73. [PMID: 23113318 DOI: 10.1039/c2an36087j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A light addressable potentiometric sensor (LAPS) is a kind of silicon based semiconductor sensor, and surface modification is a fundamental problem for its application in biological fields. Graphene oxide (GO) based biochemically activated LAPS were proposed, called GO-LAPS. The GO-LAPS were applied to monitoring single strand DNA (ssDNA) probe immobilization and its hybridization with complementary ssDNA molecules of different chain lengths (30, 21 and 14 base pairs, respectively). It was discovered that the curves of LAPS' currents versus analyte concentrations for ssDNA probe binding and the target ssDNA hybridization were different. Explanations were proposed based on the semiconductor's surface-electric-field-effect and the electrical properties of ssDNA molecule. Moreover, comparisons between GO-LAPS and LAPS without GO modification were carried out. Enhanced response currents of GO-LAPS were reported experimentally and analyzed theoretically based on X-ray photoelectron spectroscopy (XPS) of GO-LAPS. The limitation of target ssDNA monitoring was 1 pM to 10 nM, which suggested that this LAPS based platform could be developed as a sensitive means for short chain ssDNA detection.
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Affiliation(s)
- Yunfang Jia
- College of Information Science Technology, Nankai University, 300071, China.
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Heggen B, Lan Z, Thiel W. Nonadiabatic decay dynamics of 9H-guanine in aqueous solution. Phys Chem Chem Phys 2012; 14:8137-46. [DOI: 10.1039/c2cp40300e] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Arshadi S, Bekhradnia A, Ebrahimnejad A. Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study. CAN J CHEM 2011. [DOI: 10.1139/v11-124] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.
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Affiliation(s)
- S. Arshadi
- Department of Chemistry, Payame Noor University, 1935-4697, I.R. of Iran
| | - A.R. Bekhradnia
- Pharmaceutical Sciences Research Center, Department of Medicinal Chemistry, Mazandaran University of Medical Sciences, Sari, Iran
| | - A. Ebrahimnejad
- Department of Chemistry, Payame Noor University, 1935-4697, I.R. of Iran
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Mondragón-Sánchez JA, Santamaria R, Garduño-Juárez R. Docking on the DNA G-quadruplex: A molecular electrostatic potential study. Biopolymers 2011; 95:641-50. [DOI: 10.1002/bip.21634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 11/05/2022]
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Mukherjee G, Patra N, Barua P, Jayaram B. A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets. J Comput Chem 2010; 32:893-907. [DOI: 10.1002/jcc.21671] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 07/17/2010] [Accepted: 08/12/2010] [Indexed: 11/07/2022]
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Ji Z, Santamaria R, Garzón IL. Vibrational Circular Dichroism and IR Absorption Spectra of Amino Acids: A Density Functional Study. J Phys Chem A 2010; 114:3591-601. [DOI: 10.1021/jp9108442] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhi Ji
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, 01000 México D. F., México
| | - Rubén Santamaria
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, 01000 México D. F., México
| | - Ignacio L. Garzón
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, 01000 México D. F., México
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Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA. OPEN CHEM 2008. [DOI: 10.2478/s11532-007-0068-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractWe have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H···O hydrogen bonds are replaced by N-H···S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.
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Fonseca Guerra C, van der Wijst T, Bickelhaupt FM. Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine. Chemphyschem 2007; 7:1971-9. [PMID: 16888742 DOI: 10.1002/cphc.200600216] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Substituted Watson-Crick guanine-cytosine (GC) base pairs were recently shown to yield robust three-state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson-Crick adenine-thymine (AT) base pairs? We have theoretically analyzed AT pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X=NH(-), NH(2), NH(3) (+) (N series), O(-), OH or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. Thus, we explore the trend in geometrical shape and hydrogen bond strengths in AT pairs along a series of stepwise protonations of the substituents. Introducing a charge on the substituents leads to substantial and characteristic changes in the individual hydrogen bond lengths when compared to the neutral AT pair. However, the trends along the series of negative, neutral, and positive substituents are less systematic and less pronounced than for GC. In certain instances, internal proton transfer from thymine to adenine occurs. Our results suggest that AT is a less suitable candidate than GC in the quest for chemically controlled nanoswitches.
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Affiliation(s)
- Célia Fonseca Guerra
- Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Sahu PK, Kuo CW, Lee SL. Interaction of Adenine Adducts with Thymine: A Computational Study. J Phys Chem B 2007; 111:2991-8. [PMID: 17388410 DOI: 10.1021/jp066856t] [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] [Indexed: 11/28/2022]
Abstract
The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.
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Affiliation(s)
- Prabhat K Sahu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, 621 Taiwan
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Fonseca Guerra C, van der Wijst T, Bickelhaupt FM. Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents. Chemistry 2006; 12:3032-42. [PMID: 16453355 DOI: 10.1002/chem.200501301] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have theoretically analyzed Watson-Crick guanine-cytosine (GC) base pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X = NH(-), NH(2), NH(3) (+) (N series), O(-), OH, or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. The purpose is to study the effects on structure and hydrogen-bond strength if X= H is substituted by an anionic, neutral, or cationic substituent. We found that replacing X = H by a neutral substituent has relatively small effects. Introducing a charged substituent, on the other hand, led to substantial and characteristic changes in hydrogen-bond lengths, strengths, and hydrogen-bonding mechanism. In general, introducing an anionic substituent reduces the hydrogen-bond-donating and increases the hydrogen-bond-accepting capabilities of a DNA base, and vice versa for a cationic substituent. Thus, along both the N and O series of substituents, the geometric shape and bond strength of our DNA base pair can be chemically switched between three states, thus yielding a chemically controlled supramolecular switch. Interestingly, the orbital-interaction component in some of these hydrogen bonds was found to contribute to more than 49 % of the attractive interactions and is thus virtually equal in magnitude to the electrostatic component, which provides the other (somewhat less than) 51 % of the attraction.
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Affiliation(s)
- Célia Fonseca Guerra
- Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Monajjemi M, Chahkandi B, Zare K, Amiri A. Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study. BIOCHEMISTRY (MOSCOW) 2005; 70:366-76. [PMID: 15823092 DOI: 10.1007/s10541-005-0123-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G** basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 A, respectively, at B3LYP/6-31G** level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 A). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G** and HF/6-31G** levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G** and B3LYP/6-31++G** levels, respectively. The computed B3LYP/6-31G** bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol).
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Affiliation(s)
- M Monajjemi
- Science and Research Campus, Islamic Azad University, Hesarak, Poonak, PO Box 14515-775, Tehran, Iran.
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Crespo-Hernández CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem Rev 2004; 104:1977-2019. [PMID: 15080719 DOI: 10.1021/cr0206770] [Citation(s) in RCA: 965] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Contreras JG, Madariaga ST. Structure and the energy of base pairing in non-natural bases of nucleic acids: the azaguanine-cytosine and azaadenine-thymine base pairs. Bioorg Chem 2003; 31:367-77. [PMID: 12941289 DOI: 10.1016/s0045-2068(03)00083-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Watson-Crick optimized geometries and the energies of base pairing for the natural pairs of nucleic bases: adenine-thymine (AT) and guanine-cytosine (GC) have been recalculated by ab initio methods in order to compare results to those found for the non-natural azaadenine-thymine (AAT) and azaguanine-cytosine (AGC) pairs. Geometry optimizations carried out at the HF/6-31G** level and energies obtained at MP2/6-31G**, show that AAT and AGC have hydrogen bonding patterns similar to the natural AT and GC and that the interaction energies (DeltaH0int) for the former are ca. 7 kcal/mol more stable than the latter. Accordingly, the pairs based on azapurines would be favored with respect to the natural pairs. Some possible explanations why nature does not use extensively the azabases in base pairing are given.
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Affiliation(s)
- J Guillermo Contreras
- Facultad de Ciencias Quimicas, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile.
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ARTACHO EMILIO, MACHADO MAIDER, SÁNCHEZ-PORTAL DANIEL, ORDEJÓN PABLO, SOLER JOSÉM. Electrons in dry DNA from density functional calculations. Mol Phys 2003. [DOI: 10.1080/0026897031000068587] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Reynisson J, Steenken S. DFT studies on the pairing abilities of the one-electron reduced or oxidized adenine–thymine base pair. Phys Chem Chem Phys 2002. [DOI: 10.1039/b206342e] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fonseca Guerra C, Bickelhaupt FM, Snijders JG, Baerends EJ. Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment. J Am Chem Soc 2000. [DOI: 10.1021/ja993262d] [Citation(s) in RCA: 372] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Célia Fonseca Guerra
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - F. Matthias Bickelhaupt
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - Jaap G. Snijders
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
| | - Evert Jan Baerends
- Contribution from the Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, and Theoretische Chemie, Rijksuniversiteit Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
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Dannenberg JJ, Tomasz M. Hydrogen-Bond Acid/Base Catalysis: A Density Functional Theory Study of Protonated Guanine-(Substituted) Cytosine Base Pairs as Models for Nucleophilic Attack on Mitomycin in DNA. J Am Chem Soc 2000. [DOI: 10.1021/ja993145i] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. J. Dannenberg
- Contribution from the Department of Chemistry, City University of New York, Hunter College and The Graduate School, 695 Park Avenue, New York, New York 10021
| | - Maria Tomasz
- Contribution from the Department of Chemistry, City University of New York, Hunter College and The Graduate School, 695 Park Avenue, New York, New York 10021
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Meyer M, Steinke T, Brandl M, S�hnel J. Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J Comput Chem 2000. [DOI: 10.1002/1096-987x(20010115)22:1<109::aid-jcc11>3.0.co;2-5] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Application of Molecular Orbital Theory to the Elucidation of Radical Processes Induced by Radiation Damage to DNA. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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Azaguanine: A Theoretical Study of Its Tautomerism and Protonation in the Gas Phase and Aqueous Solution. Bioorg Chem 1998. [DOI: 10.1006/bioo.1998.1113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bertran J, Oliva A, Rodríguez-Santiago L, Sodupe M. Single versus Double Proton-Transfer Reactions in Watson−Crick Base Pair Radical Cations. A Theoretical Study. J Am Chem Soc 1998. [DOI: 10.1021/ja9804417] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Bertran
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Antonio Oliva
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Luis Rodríguez-Santiago
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Mariona Sodupe
- Contribution from the Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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Rablen PR, Lockman JW, Jorgensen WL. Ab Initio Study of Hydrogen-Bonded Complexes of Small Organic Molecules with Water. J Phys Chem A 1998. [DOI: 10.1021/jp980708o] [Citation(s) in RCA: 368] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paul R. Rablen
- Contribution from the Department of Chemistry, Swarthmore College, 500 College Avenue, Swarthmore, Pennsylvania 19081-1397, and the Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Jeffrey W. Lockman
- Contribution from the Department of Chemistry, Swarthmore College, 500 College Avenue, Swarthmore, Pennsylvania 19081-1397, and the Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - William L. Jorgensen
- Contribution from the Department of Chemistry, Swarthmore College, 500 College Avenue, Swarthmore, Pennsylvania 19081-1397, and the Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
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Santamaria R, Cocho G, Corona L, González E. Molecular electrostatic potentials and Mulliken charge populations of DNA mini-sequences. Chem Phys 1998. [DOI: 10.1016/s0301-0104(97)00320-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hobza P. Chapter 7. Accurate ab initio calculations on large van der Waals clusters. ACTA ACUST UNITED AC 1997. [DOI: 10.1039/pc093257] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ab initio MP2 and DFT calculations of geometry and solution tautomerism of purine and some purine derivatives. Chem Phys 1996. [DOI: 10.1016/0301-0104(96)00184-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Donnamaria MC, Marañon J, Howard EI, Fantoni A, Grigera JR. The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water. MOLECULAR SIMULATION 1996. [DOI: 10.1080/08927029608022356] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory. Chem Phys 1996. [DOI: 10.1016/0301-0104(95)00413-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Šponer J, Leszczynski J, Hobza P. Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp952760f] [Citation(s) in RCA: 348] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, and Department of Chemistry, Jackson State University, Jackson, 39217 Mississippi
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Hutter M, Clark T. On the Enhanced Stability of the Guanine−Cytosine Base-Pair Radical Cation. J Am Chem Soc 1996. [DOI: 10.1021/ja953370+] [Citation(s) in RCA: 157] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Florián J, Leszczyński J, Scheiner S. Ab initiostudy of the structure of guanine-cytosine base pair conformers in gas phase and polar solvents. Mol Phys 1995. [DOI: 10.1080/00268979500100321] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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