Published in J Phys Chem B on October 06, 2005
Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res (2009) 1.43
Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B (2010) 0.93
Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput (2011) 0.85
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. J Chem Theory Comput (2012) 0.84
Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches. J Mol Model (2009) 0.83
Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res (2014) 0.81
On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies. RNA (2010) 0.79
Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. J Mol Model (2012) 0.78
RNABP COGEST: a resource for investigating functional RNAs. Database (Oxford) (2015) 0.77
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic Acids Res (2015) 0.76
Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Res (2013) 0.76
How Does Mg(2+) Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair. Biophys J (2017) 0.75
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. Phys Chem Chem Phys (2006) 2.55
Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. Nat Nanotechnol (2011) 2.51
DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J (2003) 2.12
Toward the development of "nano-QSARs": advances and challenges. Small (2009) 1.63
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J (2006) 1.54
Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J Am Chem Soc (2002) 1.54
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys J (2003) 1.46
Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers (2007) 1.41
Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys J (2003) 1.38
Theoretical studies on the mechanism of C-P bond cleavage of a model alpha-aminophosphonate in acidic condition. J Phys Chem A (2007) 1.38
Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc Natl Acad Sci U S A (2006) 1.34
Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J (2004) 1.33
Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res (2006) 1.30
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases. Biophys J (2005) 1.27
Ribosomal RNA kink-turn motif--a flexible molecular hinge. J Biomol Struct Dyn (2004) 1.23
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J Mol Biol (2005) 1.20
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure (2006) 1.17
Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc (2003) 1.14
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res (2003) 1.14
The possible covalent nature of N-H...O hydrogen bonds in formamide dimer and related systems: an ab initio study. J Phys Chem A (2006) 1.13
Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? J Phys Chem B (2010) 1.12
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B (2010) 1.11
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers (2006) 1.11
Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs. J Phys Chem B (2005) 1.10
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. RNA (2009) 1.08
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophys J (2002) 1.07
UVA light-induced DNA cleavage by isomeric methylbenz[a]anthracenes. Chem Res Toxicol (2002) 1.02
Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys Chem Chem Phys (2010) 1.02
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res (2013) 1.02
Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys (2009) 1.01
Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs. J Mol Biol (2003) 1.00
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys J (2007) 1.00
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys J (2004) 1.00
Theoretical study of the decomposition of formamide in the presence of water molecules. J Phys Chem A (2013) 0.99
Ab initio molecular dynamics study on the initial chemical events in nitramines: thermal decomposition of CL-20. J Phys Chem B (2008) 0.99
Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues. J Phys Chem B (2007) 0.99
Comprehensive study on the solvation of mono- and divalent metal cations: Li+, Na+, K+, Be2+, Mg2+ and Ca2+. J Phys Chem A (2008) 0.98
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res (2010) 0.97
Predicting water solubility and octanol water partition coefficient for carbon nanotubes based on the chiral vector. Comput Biol Chem (2007) 0.97
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res (2009) 0.97
Mineral-organic interfacial processes: potential roles in the origins of life. Chem Soc Rev (2012) 0.97
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Res (2007) 0.97
Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study. J Am Chem Soc (2004) 0.96
Cooperativity in hydrogen-bonded interactions: ab initio and "atoms in molecules" analyses. J Phys Chem A (2006) 0.96
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B (2008) 0.96
Advancing risk assessment of engineered nanomaterials: application of computational approaches. Adv Drug Deliv Rev (2012) 0.96
Two-photon absorption and first nonlinear optical properties of ionic octupolar molecules: structure-function relationships and solvent effects. J Phys Chem A (2005) 0.96
Aromaticity-controlled tautomerism and resonance-assisted hydrogen bonding in heterocyclic enaminone-iminoenol systems. J Org Chem (2007) 0.95
Theoretical studies of symmetric five-membered heterocycle derivatives of carbazole and fluorene: precursors of conducting polymers. J Phys Chem A (2006) 0.95
Unusual complexes of trapped methanol with azacryptands. CrystEngComm (2010) 0.95
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
Structures and energetics of the cation-pi interactions of Li+, Na+, and K+ with cup-shaped molecules: effect of ring addition to benzene and cavity selectivity. J Phys Chem A (2008) 0.95
Predicting water solubility of congeners: chloronaphthalenes--a case study. J Hazard Mater (2009) 0.94
Properties of the halogen-hydride interaction: an ab initio and "atoms in molecules" analysis. J Phys Chem A (2006) 0.94
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B (2008) 0.93
Novel approach for efficient predictions properties of large pool of nanomaterials based on limited set of species: nano-read-across. Nanotechnology (2014) 0.93
Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study. J Phys Chem A (2005) 0.93
Ab initio kinetic simulation of gas-phase experiments: tautomerization of cytosine and guanine. J Phys Chem B (2009) 0.93
QSAR modeling of acute toxicity by balance of correlations. Bioorg Med Chem (2008) 0.92
DNA strand breaks induced by near-zero-electronvolt electron attachment to pyrimidine nucleotides. Proc Natl Acad Sci U S A (2006) 0.92
Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view. J Phys Chem B (2007) 0.91
Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings. J Phys Chem B (2009) 0.91
How short can the H...H intermolecular contact be? New findings that reveal the covalent nature of extremely strong interactions. J Phys Chem A (2005) 0.91
Theoretical study of the kinetics and mechanism of the decomposition of trifluoromethanol, trichloromethanol, and tribromomethanol in the gas phase. J Mol Model (2008) 0.91
Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res (2012) 0.91
Molecular simulations of adsorption of RDX and TATP on IRMOF-1(Be). J Mol Model (2012) 0.91
Towards understanding mechanisms governing cytotoxicity of metal oxides nanoparticles: hints from nano-QSAR studies. Nanotoxicology (2014) 0.91
Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys (2010) 0.90
DNA deformability at the base pair level. J Am Chem Soc (2004) 0.90
Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem Rev (2012) 0.90
Theoretical study of formamide decomposition pathways. J Phys Chem A (2011) 0.90
Light-induced cytotoxicity of 16 polycyclic aromatic hydrocarbons on the US EPA priority pollutant list in human skin HaCaT keratinocytes: relationship between phototoxicity and excited state properties. Environ Toxicol (2007) 0.89
Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes. J Am Chem Soc (2004) 0.89
Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids. J Am Chem Soc (2006) 0.89
Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. J Phys Chem A (2005) 0.89
Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters. J Comput Chem (2005) 0.88
TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach. J Comput Chem (2004) 0.88
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res (2007) 0.87
Formation of a beta-pyrimidine nucleoside by a free pyrimidine base and ribose in a plausible prebiotic reaction. J Am Chem Soc (2007) 0.87
How strong can the bend be on a DNA helix from cisplatin? DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases. Inorg Chem (2003) 0.87
Novel application of the CORAL software to model cytotoxicity of metal oxide nanoparticles to bacteria Escherichia coli. Chemosphere (2012) 0.87
B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys (2013) 0.86
Electron attachment-induced DNA single strand breaks: C3'-O3' sigma-bond breaking of pyrimidine nucleotides predominates. J Am Chem Soc (2006) 0.86
Environmental toxicology and health effects associated with dinitrotoluene exposure. Rev Environ Health (2003) 0.86
Aromaticity in heterocyclic analogues of benzene: comprehensive analysis of structural aspects, electron delocalization and magnetic characteristics. Phys Chem Chem Phys (2011) 0.86
Electron density distribution in stacked benzene dimers: a new approach towards the estimation of stacking interaction energies. J Chem Phys (2005) 0.85
Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment. Chemistry (2012) 0.85
Room temperature synthesis of PbSe quantum dots in aqueous solution: stabilization by interactions with ligands. Nanoscale (2012) 0.85
The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study. J Comput Aided Mol Des (2008) 0.85
Encapsulation and selectivity of sulfate with a furan-based hexaazamacrocyclic receptor in water. Org Biomol Chem (2014) 0.85
On the role of the cis Hoogsteen:sugar-edge family of base pairs in platforms and triplets-quantum chemical insights into RNA structural biology. J Phys Chem B (2010) 0.84