Uracil Dimers Research Articles

Effects of UV and Calcium Perchlorates on Uracil Deposited on Strontium Fluoride Substrates at Mars Pressure and Temperature.

Organic matter is actively searched on Mars with current and future space missions as it is a key to detecting potential biosignatures. Given the current harsh environmental conditions at the surface of Mars, many organic compounds might not be preserved over a long period as they are exposed to energetic radiation such as ultraviolet light, which is not filtered above 190 nm by the martian atmosphere. Moreover, the presence of strong oxidizing species in the regolith, such as perchlorate salts, might enhance the photodegradation of organic compounds of astrobiological interest. Because current space instruments analyze samples collected in the upper surface layer, it is necessary to investigate the stability of organic matter at the surface of Mars. Previous experimental studies have shown that uracil, a molecule relevant to astrobiology, is quickly photolyzed when exposed to UV radiation under the temperature and pressure conditions of the martian surface with an experimental quantum efficiency of photodecomposition (φexp) of 0.30 ± 0.26 molecule·photon-1. Moreover, the photolysis of uracil leads to the formation of more stable photoproducts that were identified as uracil dimers. The present work aims to characterize the additional effect of calcium perchlorate detected on Mars on the degradation of uracil. Results show that the presence of calcium perchlorate enhances the photodecomposition of uracil with φexp = 12.3 ± 8.3 molecule·photon-1. Although some of the photoproducts formed during these experiments are common to those formed from pure uracil only, the Fourier transformation infrared (FTIR) detection of previously unseen chemical functions such as alkyne C ≡ C or nitrile C ≡ N has shown that additional chemical species are formed in the presence of calcium perchlorate in the irradiated sample. This implies that the effect of calcium perchlorate on the photolysis of uracil is not only kinetic but also related to the nature of the photoproducts formed.

On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution.

UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.

A Massively Parallel Implementation of the CCSD(T) Method Using the Resolution-of-the-Identity Approximation and a Hybrid Distributed/Shared Memory Parallelization Model.

A parallel algorithm is described for the coupled-cluster singles and doubles method augmented with a perturbative correction for triple excitations [CCSD(T)] using the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs). The algorithm bypasses the storage of four-center ERIs by adopting an integral-direct strategy. The CCSD amplitude equations are given in a compact quasi-linear form by factorizing them in terms of amplitude-dressed three-center intermediates. A hybrid MPI/OpenMP parallelization scheme is employed, which uses the OpenMP-based shared memory model for intranode parallelization and the MPI-based distributed memory model for internode parallelization. Parallel efficiency has been optimized for all terms in the CCSD amplitude equations. Two different algorithms have been implemented for the rate-limiting terms in the CCSD amplitude equations that entail and -scaling computational costs, where NO and NV denote the number of correlated occupied and virtual orbitals, respectively. One of the algorithms assembles the four-center ERIs requiring NV4 and NO2NV2-scaling memory costs in a distributed manner on a number of MPI ranks, while the other algorithm completely bypasses the assembling of quartic memory-scaling ERIs and thus largely reduces the memory demand. It is demonstrated that the former memory-expensive algorithm is faster on a few hundred cores, while the latter memory-economic algorithm shows a better strong scaling in the limit of a few thousand cores. The program is shown to exhibit a near-linear scaling, in particular for the compute-intensive triples correction step, on up to 8000 cores. The performance of the program is demonstrated via calculations involving molecules with 24-51 atoms and up to 1624 atomic basis functions. As the first application, the complete basis set (CBS) limit for the interaction energy of the π-stacked uracil dimer from the S66 data set has been investigated. This work reports the first calculation of the interaction energy at the CCSD(T)/aug-cc-pVQZ level without local orbital approximation. The CBS limit for the CCSD correlation contribution to the interaction energy was found to be -8.01 kcal/mol, which agrees very well with the value -7.99 kcal/mol reported by Schmitz, Hättig, and Tew [ Phys. Chem. Chem. Phys. 2014, 16, 22167-22178]. The CBS limit for the total interaction energy was estimated to be -9.64 kcal/mol.

Dimerization of Uracil in a Simulated Mars-like UV Radiation Environment.

The search for organic molecules at the surface of Mars is a key objective in astrobiology, given that many organic compounds are possible biosignatures and their presence is of interest with regard to the habitability of Mars. Current environmental conditions at the martian surface are harsh and affect the stability of organic molecules. For this reason, and because current and future Mars rovers collect samples from the upper surface layer, it is important to assess the fate of organic molecules under the conditions at the martian surface. Here, we present an experimental study of the evolution of uracil when exposed to UV radiation, pressure, and temperature conditions representative of the surface of Mars. Uracil was selected because it is a nucleobase that composes RNA, and it has been detected in interplanetary bodies that could be the exogenous source of this molecule by meteoritic delivery to the surface of Mars. Our results show that the experimental quantum efficiency of photodecomposition of uracil is 0.16 ± 0.14 molecule/photon. Although these results suggest that uracil is quickly photodegraded when directly exposed to UV light on Mars, such exposure produces dimers that are more stable over time than the monomer. The identified dimers could be targets of interest for current and future Mars space missions.

Plumbing Potentials for Molecules with Up To Tens of Atoms: How to Find Saddle Points and Fix Leaky Holes.

Potential energy surfaces (PESs) play an indispensable role in molecular dynamics but are notoriously difficult to flesh out properly in large-dimensional spaces. In particular, the undetected presence of PES holes, i.e., unphysical saddle points beyond which the potential energy drops arbitrarily, can have devastating effects on both classical and quantum dynamics calculations. In this study, the Crystal algorithm is developed as a tool for efficiently and accurately finding PES holes, as well as legitimate saddle points, even in very large-dimensional configuration spaces. The approach is applied to three large-dimensional PESs for molecular systems of current interest: uracil, naphthalene, and formic acid dimer. Low-lying PES holes are discovered and located for the first two systems-including naphthalene, for which no holes were previously suspected, to the best of our knowledge. Likewise, the double-well, double-proton-transfer isomerization saddle point for formic acid dimer is also located.

Benchmarking of the R-7 Anisotropic Dispersion Energy Term on the S22 Dimer Test Set.

The effects of including the anisotropic E7 term to the dispersion energy in addition to the leading E6 term are examined by using the effective fragment potential (EFP) method on the S22 test set. In this study, the full anisotropic E7 term is computed whereas the isotropic and spherical approximations are used for the E6 term. It is found that the E7 term is positive for hydrogen-bonded complexes and has a magnitude that can be as large as 50% of E6, giving rise to larger intermolecular distances than those obtained with E6 alone. The large positive value of E7 is analyzed for the hydrogen-bonded uracil dimer; it is found to originate from the large magnitude of the dynamic polarizability tensors as well as the proximity of the LMOs involved in hydrogen bonding. Conversely, E7 tends to be negative for dispersion-dominant complexes, and it has a very small magnitude for such complexes. The optimized geometries for these systems are therefore not greatly affected by the presence of the E7 term. For the mixed systems in the S22 test set, an intermediate behavior is observed. Overall, the E7 term is most important for systems with hydrogen bonding interactions and mixed systems. A full anisotropic treatment of the E6 term and higher order terms may need to be included to obtain more accurate interaction energies and geometries.

New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics.

Nucleobases spontaneously aggregate in water by forming stacked dimers and multimers. It is assumed that the main contributions to the aggregation stem from hydrophobic and base-base dispersion interactions. By studying the uracil monomer and dimer in bulk water with the first principle molecular dynamics, we discuss dimer structure and provide evidence that stacking increases the uracil-water hydrogen bonding strength and alters the hydration structure of uracil. These changes have a significant influence on the intensity and shift of the carbonyl stretching band as revealed by simulated infrared absorption spectra of the monomer and dimer and available experimental spectra. The contributions of dipole-dipole, dispersion, and water mediated forces to the stacking are discussed. The reported findings are valuable for understanding the microscopic mechanism of heteroaromatic association in water which is relevant to a large range of chemical and biological systems.

Highly accurate equilibrium structure of the C2h symmetric N1-to-O2 hydrogen-bonded uracil-dimer

The highly accurate ab initio equilibrium geometry of the hydrogen-bonded uracil dimer is derived using a composite geometry extrapolation scheme based on all-electron, complete basis set extrapolated Møller–Plesset perturbation theory using the jun-pwCV[T,Q]Z basis sets combined with a valence CCSD(T)/cc-pVTZ high-level correction. Geometrical changes on dimerization are discussed and the performance of the several density functional approximations (among others SCAN, ωB97M-V, DSD-PBEP86-D3(BJ), and DSD-PBEP86-NL) is evaluated. Orbital-optimized MP2.5 is discussed as a reduced-cost alternative to the CCSD(T) gradient in the composite scheme. A new reference interaction energy is calculated with explicitly correlated F12-CCSD(T).

Remarkable Differences in Spin Couplings for Various Self-Paired Dimers of Ring-Expansion-Radicalized Uracil: A Basis for the Design of Magnetically Anisotropic Assemblies.

The spin-coupling properties of a series of radicalized uracil (rU) dimer diradicals with different H-bonding modes is examined. Each rU has four double H-bonding sites [the amide units: two at the Watson-Crick face (upper site WC1 and lower site WC2 ), a Hoogsteen site (HO), and a minor-groove site (MI)], and ten homogeneous dimers (rU-rU) can self-pair with well-defined diradical characters and comparable stability to the native U dimers. More interestingly, all these dimers exhibit distinctly different spin-coupling characters (ferromagnetic (FM) versus antiferromagnetic (AFM) and large- versus small-magnitude spin couplings), indicative of remarkable magnetic-coupling anisotropy of rU. This observation originates from the fusion of a cyclopentadienyl radical to U, which leads to uneven spin-density distribution. In rU, the fused five-membered radical ring can spin-polarize to the edge in the minor groove, and thus dimerization of rU leads to different H-bonded structures with remarkably different magnetic couplings. The calculated larger magnetic coupling constants J are 1003.7 and 540.2 cm-1 for the WC2 -HO and MI-HO H-bonding modes between rU, which exhibit considerably large FM couplings, the MI-MI, WC1 -WC2 and WC2 -WC2 modes show moderate FM couplings (J=0.4-77 cm-1 ), and the other modes exhibit moderate or weak AFM couplings. These observations indicate that the HO and MI sites are favorable spin-coupling sites. In addition, the H-bond lengths and electronic structures of the H-bonding sites, proton transfer, and extra H-bonding interaction with the surroundings can also affect the magnetic couplings of the base pairs. Clearly, the unique magnetic coupling anisotropy of rU provides a promising application basis for the design and assembly of bio-inspired anisotropically magnetic membranes and even magnetism-tunable building blocks for novel magnetic nanoscale devices.

Ammoniated Complexes of Uracil and Transition Metal Ions: Structures of [M(Ura-H)(Ura)(NH3)]+ by IRMPD Spectroscopy and Computational Methods (M = Fe, Co, Ni, Cu, Zn, Cd).

The structures of deprotonated d-block metal dication bound uracil dimers, solvated by a single ammonia molecule, were explored in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance-mass spectrometer. The IRMPD spectra were then compared with computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6-31+G(d,p) basis set for all atoms, with the exception of Cd, for which the LANL2DZ basis set with relativistic core potentials was used. The calculations were then repeated using the def2-TZVPP basis set on all atoms and were compared to the first set of calculations. The lowest-energy structures are those in which one uracil is deprotonated at the N3 position and, aside from the Cu complex, the intact uracil is a tautomer in which the N3 hydrogen is at the O4 carbonyl oxygen. The metal displays a tetradentate interaction to the uracil moieties, with the exception of Cu, which is tridentate, and the ammonia molecule is bound directly to the metal center. In the Cu complex, a square planar geometry is observed about the metal center, consistent with Jahn-Teller distortions commonly observed in Cu(II) complexes, and the intact uracil assumes its canonical tautomer. All other metal cation complexes are five-coordinate, square pyramidal complexes, with the intact uracil adopting a tautomer in which the N3 hydrogen is on O4. The IRMPD spectroscopic data are consistent with the computed infrared spectra for the lowest-energy structures in all cases.

Massively Parallel Implementation of Explicitly Correlated Coupled-Cluster Singles and Doubles Using TiledArray Framework

A new distributed-memory massively parallel implementation of standard and explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) with canonical O(N6) computational complexity is described. The implementation is based on the TiledArray tensor framework. Novel features of the implementation include (a) all data greater than O(N) is distributed in memory and (b) the mixed use of density fitting and integral-driven formulations that optionally allows to avoid storage of tensors with three and four unoccupied indices. Excellent strong scaling is demonstrated on a multicore shared-memory computer, a commodity distributed-memory computer, and a national-scale supercomputer. The performance on a shared-memory computer is competitive with the popular CCSD implementations in ORCA and Psi4. Moreover, the CCSD performance on a commodity-size cluster significantly improves on the state-of-the-art package NWChem. The large-scale parallel explicitly correlated coupled-cluster implementation makes routine accurate estimation of the coupled-cluster basis set limit for molecules with 20 or more atoms. Thus, it can provide valuable benchmarks for the merging reduced-scaling coupled-cluster approaches. The new implementation allowed us to revisit the basis set limit for the CCSD contribution to the binding energy of π-stacked uracil dimer, a challenging paradigm of π-stacking interactions from the S66 benchmark database. The revised value for the CCSD correlation binding energy obtained with the help of quadruple-ζ CCSD computations, -8.30 ± 0.02 kcal/mol, is significantly different from the S66 reference value, -8.50 kcal/mol, as well as other CBS limit estimates in the recent literature.

Effects of single water molecule on proton transfer reaction in uracil dimer cation

Ionizing radiation to DNA induces sometimes the DNA damage. In this report, the ionization dynamics of uracil dimer (U)2 and its water complex (U)2–H2O have been investigated by means of direct ab initio molecular dynamics (AIMD) method in order to elucidate the effects of single water molecule on the reaction rate of proton transfer (PT) in DNA model base pair. The (U)2 dimer is widely used as a simplified mimetic model of Watson–Crick base pair. The static ab initio calculation showed that two conformers exist as neutral complex of (U)2–H2O. The direct AIMD calculation of ionization process of (U)2–H2O showed that the rate of PT is affected even by a single water molecule, while it was dependent on the position of H2O around (U)2. The interaction of water molecule with (U)2 affected the potential energy curve for PT. Especially, the activation barrier along the PT coordinate was significantly changed by the interaction with one H2O molecule. The effects of one H2O molecule on the PT process were discussed on the basis of theoretical results.

Why Is the Spontaneous Deprotonation of [Cu(uracil)2](2+) Complexes Accompanied by Enolization of the System?

The reaction-force formalism is applied to carry out a detailed analysis of the mechanisms behind the enolization processes undergone by the complexes formed on interaction of uracil dimers with Cu(2+) ions after spontaneous deprotonation of the resulting complexes. These enolization processes apparently involve a single proton transfer (PT) from an NH group to a carbonyl group of the same uracil moiety, which should involve a rather high activation barrier that prevents the process occurring. However, the reaction-force, chemical-potential, and electronic-flux profiles unambiguously indicate that the actual mechanism involves three low-barrier elementary steps, and this explains why enolization of the [Cu(uracil-H)(uracil)](+) complexes is a highly facile, assisted PT process. All of the observed PT processes show a typical profile for both the chemical potential and the electronic flux associated with the bond-breaking and the bond-formation processes.

Hydrogen-bonding effects on infrared spectra from anharmonic computations: uracil-water complexes and uracil dimers.

Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like frequency shifts of the order of magnitude of hundreds of cm(-1) and increases of IR intensity for bands related to vibrational modes of functional groups directly involved in the hydrogen-bonded bridges. We are actively developing a comprehensive and robust computational protocol aimed at the quantitative reproduction of the spectra of bio-organic and hybrid organic/inorganic molecular systems with a proper account of the variety of intra- and intermolecular interactions. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended our computational protocol toward hybrid models, with the harmonic part computed at the B2PLYP level, in conjunction with the maug-cc-pVTZ basis set, or by a cost-effective ONIOM B2PLYP:B3LYP focused model, where only part of the molecular system forming the hydrogen bonds is treated at the B2PLYP level of theory. In this work experimental frequencies available for a set of four uracil-water complexes have been considered as references for the computational methodologies applied to the simulation of hydrogen-bonding effects on the infrared spectrum, obtaining average uncertainties of about 22 cm(-1) for B3LYP-D3/N07D and improved description within 10 cm(-1) by hybrid B2PLYP/B3LYP-D3 approaches. The same computational schemes have been next applied to simulate fully anharmonic IR spectra of six different hydrogen-bonded uracil dimers, providing reliable support for future experimental investigations on hydrogen-bonded systems.

Quantum Chemistry Meets Spectroscopy for Astrochemistry: Increasing Complexity toward Prebiotic Molecules.

For many years, scientists suspected that the interstellar medium was too hostile for organic species and that only a few simple molecules could be formed under such extreme conditions. However, the detection of approximately 180 molecules in interstellar or circumstellar environments in recent decades has changed this view dramatically. A rich chemistry has emerged, and relatively complex molecules such as C60 and C70 are formed. Recently, researchers have also detected complex organic and potentially prebiotic molecules, such as amino acids, in meteorites and in other space environments. Those discoveries have further stimulated the debate on the origin of the building blocks of life in the universe. Many efforts continue to focus on the physical, chemical, and astrophysical processes by which prebiotic molecules can be formed in the interstellar dust and dispersed to Earth or to other planets.Spectroscopic techniques, which are widely used to infer information about molecular structure and dynamics, play a crucial role in the investigation of planetary atmosphere and the interstellar medium. Increasingly these astrochemical investigations are assisted by quantum-mechanical calculations of structures as well as spectroscopic and thermodynamic properties, such as transition frequencies and reaction enthalpies, to guide and support observations, line assignments, and data analysis in these new and chemically complicated situations. However, it has proved challenging to extend accurate quantum-chemical computational approaches to larger systems because of the unfavorable scaling with the number of degrees of freedom (both electronic and nuclear).In this Account, we show that it is now possible to compute physicochemical properties of building blocks of biomolecules with an accuracy rivaling that of the most sophisticated experimental techniques, and we summarize specific contributions from our groups. As a test case, we present the underlying computational machinery through the investigation of oxirane. We describe how we determine the molecular structure and then how we characterize the rotational and IR spectra, the most important issues for a correct theoretical description and a proper comparison with experiment. Next, we analyze the spectroscopic properties of representative building blocks of DNA bases (uracil and pyrimidine) and of proteins (glycine and glycine dipeptide analogue).Solvation, surface chemistry (dust fraction, adsorption, desorption), and inter- and intramolecular interactions, such as self-organization and self-interaction, are important molecular processes for understanding astrochemistry. Using the specific cases of uracil dimers and glycine adsorbed on silicon grains, we also illustrate approaches in which we treat different regions, interactions, or effects at different levels of sophistication.

Structures of bare and singly hydrated [M(Ura-H)(Ura)]+ (M = Mg, Ca, Sr, Ba) complexes in the gas phase by IRMPD spectroscopy in the fingerprint region

The structures of deprotonated group 2 metal dication bound uracil dimers as well as the singly hydrated dimers were explored in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy (1000–1900cm−1) in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). The IRMPD spectra were then compared to computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6–31+G(d,p) basis set for all atoms except Ba2+ and Sr2+, for which the LANL2DZ or the def2-TZVPP basis sets with relativistic core potentials were used. The lowest energy structures are those in which the one uracil is deprotonated at the N3 position while the neutral uracil is a tautomer where the N3 hydrogen is at the O4 or O2 carbonyl oxygen and the metal is tetracoordinate interacting with N3 and O4 of deprotonated uracil and either N3 and O2 or N3 and O4 of neutral uracil. In the solvated complexes, the water molecule is also coordinated to the metal ion.

Theoretical study of hydrophobicity and hydrophilicity of uracil and its dimers

The influence of hydrophilic and hydrophobic properties of the uracil elementary nucleic acids bases on its solubility and structure in aqueous solution was studied. Complexes of uracil with water molecules (from 1 to 14) were then calculated. The geometrical parameters of the hydrogen bridge of uracil and the changes in the frequency of valence vibrations of the bonds participating directly in hydrogen bond formation were calculated. It is shown that for the hydrogen bonds O(w)...HN(1) and O(w)...HN3 the hydrogen atom can tear, it may lead to tautomeric transformation of uracil. The results obtained having calculated the structure of uracil dimers, formed with the hydrogen bonds, in an isolated state and water solution, energy, dipole moments and the hydrogen bridge parameters made it possible to explain low solubility of uracil in water at room temperature. It is shown that water molecules with increase in their number are located mainly at one side of the plane of a pyrimidine uracil ring, that leads to the formation of stacking. Of two possible variants of stacking formation, the most profitable grouping is when a dipole moment of the formed dimer is equal to zero (anti-parallel stacking).

Rapid evaluation of the interaction energies for hydrogen-bonded uracil and thymine dimers, trimers and tetramers

Hydrogen bonds play an important role in the self-assembled processes of nucleic acid bases. The ability to rapidly and accurately evaluate the interaction energy for hydrogen-bonded nucleic acid base pairs and multimers is critical for correctly understanding the mechanism underlying the assembly and modeling the self-assembled processes of nucleic acid bases. In this paper, the polarizable dipole–dipole interaction model is developed and applied to hydrogen-bonded uracil and thymine base dimers, trimers and tetramers. We regard the chemical bonds NH, CH and CO in uracil and thymine as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. The parameters needed are first determined from the training dimers. Then the polarizable dipole–dipole interaction model together with the parameters is applied to a series of hydrogen-bonded uracil and thymine base dimers, trimers and tetramers. The hydrogen bond distances and the interaction energies obtained from the polarizable dipole–dipole interaction model are compared to those obtained from MP2 calculations. The calculation results show that the polarizable dipole–dipole interaction model produces the equilibrium hydrogen bond distances compared well with those yielded by the MP2/6-31G(d) method and produces the interaction energies in good agreement with those yielded by the counterpoised-corrected MP2/6-311++G(3df,2p) method, demonstrating that the polarizable dipole–dipole interaction model is reasonable and useful.

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers.

Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

Tractability gains in symmetry-adapted perturbation theory including coupled double excitations: CCD+ST(CCD) dispersion with natural orbital truncations

This work focuses on efficient and accurate treatment of the intermolecular dispersion interaction using the CCD+ST(CCD) dispersion approach formulated by Williams et al. [J. Chem. Phys. 103, 4586 (1995)]. We apply natural orbital truncation techniques to the solution of the monomer coupled-cluster double (CCD) equations, yielding substantial accelerations in this computationally demanding portion of the SAPT2+(CCD), SAPT2+(3)(CCD), and SAPT2+3(CCD) analyses. It is shown that the wholly rate-limiting dimer-basis particle-particle ladder term can be computed in a reduced natural virtual space which is essentially the same size as the monomer-basis virtual space, with an error on the order of a few thousandths of 1 kcal mol(-1). Coupled with our existing natural orbital techniques for the perturbative triple excitation contributions [E. G. Hohenstein and C. D. Sherrill, J. Chem. Phys. 133, 104107 (2010)], this technique provides speedups of greater than an order of magnitude for the evaluation of the complete SAPT2+3(CCD) decomposition, with a total error of a few hundredths of 1 kcal mol(-1). The combined approach yields tractability gains of almost 2× in the system size, allowing for SAPT2+3(CCD)/aug-cc-pVTZ analysis to be performed for systems such as adenine-thymine for the first time. Natural orbital based SAPT2+3(CCD)/aug-cc-pVTZ results are presented for stacked and hydrogen-bonded configurations of uracil dimer and the adenine-thymine dimer.