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1.
J Phys Chem B ; 113(25): 8675-81, 2009 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-19485367

RESUMEN

Self-assembly at the liquid/solid interface of an electrochemically active DNA nucleobase analogue, 1H-benzoimidazole-4,7-dione (Q), has been studied by means of scanning tunneling microscopy (STM). High-resolution STM images revealed the formation of well-ordered two-dimensional (2D) supramolecular nanostructures when the Q molecules are adsorbed onto the graphite surface from a 1-octanol solution. Detailed analysis shows that the observed 2D nanostructures are mainly dominated by hydrogen-bonded Q molecules. Since Q can be considered as a molecule mimicking the nucleobase guanine (G), which is known to form Watson-Crick base pairs with its complementary nucleobase cytosine (C), we have examined the binding ability of Q with C realized by available hydrogen-bonding sites on both Q and C molecules. Upon deposition of a mixture of Q and C molecules onto a graphite surface, one might expect that hydrogen-bonded QC dimers were observed in a new 2D self-assembled structure governed by inter- and intramolecular hydrogen-bonding interactions between Q and C molecules. However, our STM experiments showed that no well-ordered structures are formed and instead phase separation occurs where large-scale homodomains are formed consisting of the individual QQ and CC dimers. To gain further insight into the possible molecular arrangements of the Q and C nucleobases in the mixture phase, the high-resolution STM images are compared with the results from ab initio density functional theory (DFT) calculations.


Asunto(s)
Bencimidazoles/química , Guanina/química , Microscopía de Túnel de Rastreo , Nanoestructuras/química , Teoría Cuántica
2.
J Chem Phys ; 130(2): 024705, 2009 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-19154048

RESUMEN

From an interplay between scanning tunneling microscopy (STM) and ab initio density functional theory (DFT) we have identified and characterized two different self-assembled adenine (A) structures formed on the Au(111) surface. The STM observations reveal that both structures have a hexagonal geometry in which each molecule forms double hydrogen bonds with three nearest neighbors. One of the A structures, with four molecules in the primitive cell, has p2gg space group symmetry, while the other one, with two molecules in the cell, has p2 symmetry. The first structure is observed more frequently and is found to be the dominating structure after annealing. Experimental as well as theoretical findings indicate that the interaction of A molecules with the gold surface is rather weak and smooth across the surface. This enabled us to unequivocally characterize the observed structures, systematically predict all structural possibilities, based on all known A-A dimers, and provisionally optimize positions of the A molecules in the cell prior to full-scale DFT calculations. The theoretical method is a considerable improvement compared to the approach suggested previously by Kelly and Kantorovich [Surf. Sci. 589, 139 (2005)]. We propose that the less ordered p2gg symmetry structure is observed more frequently due to kinetic effects during island formation upon deposition at room temperature.


Asunto(s)
Adenina/química , Oro/química , Teoría Cuántica , Algoritmos , Microscopía de Túnel de Rastreo , Modelos Moleculares , Propiedades de Superficie , Temperatura
3.
J Am Chem Soc ; 130(2): 695-702, 2008 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-18072777

RESUMEN

A novel supramolecular nanostructure formed by the coadsorption of the complementary nucleobases guanine (G) and uracil (U) at the liquid (1-octanol solvent)/solid (graphite) interface is revealed by scanning tunneling microscopy (STM). The GU supramolecular structure is distinctly different from the structures observed by STM when the individual nucleobases (NB) are adsorbed on graphite in the control experiments. Using a systematic methodology and ab initio density functional theory (DFT), an atomistic structural model is proposed for the supramolecular coadsorbed GU structure, which consists of a periodic repetition of cyclic units based on the strongest GU base pairing.


Asunto(s)
Grafito/química , Guanina/química , Nanoestructuras/química , Octanoles/química , Uracilo/química , Adsorción , Microscopía de Túnel de Rastreo
4.
Small ; 4(9): 1494-500, 2008 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-18680099

RESUMEN

Two molecular phases of the DNA base adenine (A) on a Au(111) surface are observed by using STM under ultrahigh-vacuum conditions. One of these phases is reported for the first time. A systematic approach that considers all possible gas-phase two-dimensional arrangements of A molecules connected by double hydrogen bonds with each other and subsequent ab initio DFT calculations are used to characterize and identify the two phases. The influence of the gold surface on the structure of A assemblies is also discussed. DFT is found to predict a smooth corrugation potential of the gold surface that will enable A molecules to move freely across the surface at room temperature. This conclusion remains unchanged if van der Waals interaction between A and gold is also approximately taken into account. DFT calculations of the A pairs on the Au(111) surface show its negligible effect on the hydrogen bonding between the molecules. These results justify the gas-phase analysis of possible assemblies on flat metal surfaces. Nevertheless, the fact that it is not the most stable gas-phase monolayer that is actually observed on the gold surface indicates that the surface still plays a subtle role, which needs to be properly addressed.


Asunto(s)
Adenina/química , Oro/química , Microscopía de Túnel de Rastreo , Modelos Moleculares , Conformación Molecular , Propiedades de Superficie
5.
J Chem Phys ; 129(18): 184707, 2008 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-19045423

RESUMEN

Using ultrahigh vacuum scanning tunneling microscopy (STM) and ab initio density functional theory, we have investigated in detail structures formed by cytosine on the Au(111) surface in clean ultrahigh vacuum conditions. In spite of the fact that the ground state of this DNA base on the surface is shown to be an ordered arrangement of cytosine one-dimensional branches (filaments), this structure has never been observed in our STM experiments. Instead, disordered structures are observed, which can be explained by only a few elementary structural motifs: filaments, five- and sixfold rings, which randomly interconnect with each other forming bent chains, T junctions, and nanocages. The latter may have trapped smaller structures inside. The formation of such an unusual assembly is explained by simple kinetic arguments as a liquid-glass transition.


Asunto(s)
Citosina/química , ADN/química , Oro/química , Dimerización , Cinética , Nanotecnología , Teoría Cuántica , Propiedades de Superficie
6.
J Phys Chem B ; 111(42): 12048-52, 2007 Oct 25.
Artículo en Inglés | MEDLINE | ID: mdl-17918893

RESUMEN

In this work, the self-assembly of the DNA base molecule adenine (A) is imaged with high-resolution scanning tunneling microscopy (STM) at the liquid (1-octanol)/solid (HOPG) interface at room temperature. Rather surprisingly, the STM results reveal, for the first time, the spontaneous formation of two coexisting distinct (homo- and heterochiral) domains of adenine, which are formed at the liquid/solid interface without changing any experimental conditions. Ab initio density functional theory (DFT) calculations support our STM findings and suggest the existence of various A networks of nearly similar stability that all are constructed from the most stable A dimer.


Asunto(s)
Adenina/química , 1-Octanol/química , Adsorción , Dimerización , Grafito/química , Microscopía de Túnel de Rastreo , Modelos Moleculares , Soluciones , Estereoisomerismo , Tensoactivos
11.
ACS Nano ; 5(8): 6651-60, 2011 Aug 23.
Artículo en Inglés | MEDLINE | ID: mdl-21749154

RESUMEN

Xanthine molecule is an intermediate in nucleic acid degradation from the deamination of guanine and is also a compound present in the ancient solar system that is found in high concentrations in extraterrestrial meteorites. The self-assembly of xanthine molecules on inorganic surfaces is therefore of interest for the study of biochemical processes, and it may also be relevant to the fundamental understanding of prebiotic biosynthesis. Using a combination of high-resolution scanning tunneling microscopy (STM) and density functional theory (DFT) calculations, two new homochiral xanthine structures have been found on Au(111) under ultrahigh vacuum conditions. Xanthine molecules are found to be self-assembled into two extended homochiral networks tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Our findings indicate that the deamination of guanine into xanthine leads to a very different base pairing potential and the chemical properties of the base which may be of relevance to the function of the cell and potential development of human diseases. Moreover, the adsorption of xanthine molecules on inorganic surfaces leading to homochiral assemblies may be of interest for the fundamental understanding of the emerged chirality at early stages of life.

12.
J Phys Chem B ; 113(49): 16016-20, 2009 Dec 10.
Artículo en Inglés | MEDLINE | ID: mdl-19904958

RESUMEN

All planar homopairings of the artificial nucleobase 1H-benzoimidazole-4,7-dione are reported for the first time in this study. Using the idea of binding sites discussed in our previous work and an ab initio density functional theory method we predict 13 homopairs. The stabilization energies of the homopairs vary from -0.13 to -0.69 eV. The collected data on all the planar homopairs reported here may be useful when constructing assemblies of this artificial base on various solid substrates.


Asunto(s)
Emparejamiento Base , Bencimidazoles/química , Imidazoles/química , Sitios de Unión , Dimerización , Enlace de Hidrógeno , Modelos Moleculares , Conformación Molecular , Teoría Cuántica , Termodinámica
13.
J Chem Phys ; 128(3): 034312, 2008 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-18205503

RESUMEN

We report a new full-dimensional potential energy surface (PES) for the water dimer, based on fitting energies at roughly 30,000 configurations obtained with the coupled-cluster single and double, and perturbative treatment of triple excitations method using an augmented, correlation consistent, polarized triple zeta basis set. A global dipole moment surface based on Moller-Plesset perturbation theory results at these configurations is also reported. The PES is used in rigorous quantum calculations of intermolecular vibrational frequencies, tunneling splittings, and rotational constants for (H2O)2 and (D2O)2, using the rigid monomer approximation. Agreement with experiment is excellent and is at the highest level reported to date. The validity of this approximation is examined by comparing tunneling barriers within that model with those from fully relaxed calculations.

14.
Science ; 319(5861): 312-5, 2008 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-18079368

RESUMEN

Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.

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