Interaction Energies Of Complexes Research Articles

Non-covalent interaction, biological activity prediction, topology and molecular docking studies on adenine derivative

The schiff base 4-(((9H-purin-6-yl)imino)methyl)-2‑methoxy-6-nitrophenol (A5NV) was synthesized and characterized by FTIR, UV, 1H13C–NMR spectral analysis. The experimental FTIR, UV, 1H, 13CNMR spectra were compared with the corresponding predicted by B3LYP/cc-pVDZ calculations. The local energy decomposition analsyis (LED) confirms the A5NV-H2O complex interaction energy, which is -7.17 kcal/mol. The A5NV is a optical material, because it is showed good absorption wavelength, which is 260, 316, and 432 nm. The titled compound is biologically active compound, because calculated HOMO and LUMO energy gap is very low, which is 2.70 eV. In molecular electrostatic potential analsyis confirms the A5NV molecule electrophilic and nucleophilic attacking sites. Inter and intra molecular interadctions and hyper conjucative interactions were calculated by NBO analysis. Condensed fukui functions, local softness, and mulliken charges also calculated. The pharmacological analysis like ADMET properties were calculated. Based on the antimicrobial activity, the synthesized compound showed moderate activity. Using molecular docking study the protein-lignad interactions were investigated.

Interactions between Paracetamol and Formaldehyde: Theoretical Investigation and Topological Analysis.

In this work, noncovalent interactions including hydrogen bonds, C···C, N···O, and van der Waals forces between paracetamol and formaldehyde were investigated using the second-order perturbation theory MP2 in conjunction with the correlation consistent basis sets (aug-cc-pVDZ and aug-cc-pVTZ). Two molecular conformations of paracetamol were considered. Seven equilibrium geometries of dimers were found from the result of the interactions with formaldehyde for each conformation of paracetamol. Interaction energies of complexes with both ZPE and BSSE corrections range from -7.0 to -21.7 kJ mol-1. Topological parameters (such as electron density, its Laplacian, and local electron energy density at the bond critical points) of the bonds from atoms in molecules theory were analyzed in detail. The natural bond orbital analysis showed that the stability of complexes was controlled by noncovalent interactions including O-H···O, N-H···O, C-H···O, C-H···N, C-H···H-C, C···C, and N···O. The red- and blue-shifted hydrogen bonds could both be observed in these complexes. The properties of these interactions were also further examined in water using a polarized continuum model. In water, the stability of the complex was slightly reduced as compared to that in the gas phase.

Intermolecular interactions between the heavy-atom analogues of acetylene T2H2 (T = Si, Ge, Sn, Pb) and HCN

The intermolecular interactions between the heavy-atom analogues of acetylene T2H2 (T = Si, Ge, Sn, Pb) and HCN have been investigated by theoretical calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level. The global energy minimum of T2H2 is the butterfly structure A, and another energy minimum is the planar structure B. Both structures A and B exhibit the dual behavior when binding with HCN. The various hydrogen bond (HB), dihydrogen bond (DB) and tetrel bond (TB) complexes can be found according to the MEP maps of T2H2. One TB and three HB complexes formed between structure A and HCN can be located for Si2H2 and Ge2H2. One TB, two HB and one DB complexes formed between structure A and HCN can be located for Sn2H2 and Pb2H2. Four TB and one HB complexes formed between structure B and HCN can be located for all the T2H2. The geometries and binding strengths of the complexes are compared and analyzed. The interactions in these complexes are generally weak, and the interaction energies of these complexes range from -0.53 to -8.23 kcal/mol. The interaction energies of the TB complexes are larger than those of the corresponding HB and DB complexes for structure A···HCN systems. The relative binding strength of the four TB complexes exhibits different order for different structure B···HCN systems, which is consistent with the MEP maps of the isolated monomers.

Hydrogen-bonding interactions involving the Imidazol-2‑ylidene and its Heavy-atom analogues

The hydrogen-bonded complexes formed between the imidazol-2‑ylidene and its heavier congeners C2H4N2T: (T = C, Si, Ge, Sn, Pb) and the three selected electron acceptors (HF, HCN and C2H2) have been optimized at the aug-cc-pVTZ level, and the nature of these complexes has been investigated by natural bond orbital (NBO), atoms in molecules (AIM) and energy decomposition analyses. The complexes can be classified into type-A structure and type-B structure according to the location of the electron acceptors. The electron acceptors are around T atoms of C2H4N2T: for the type-A complexes, and the electron acceptors are above the five-membered ring (π-system) of C2H4N2T: for the type-B complexes. The electron-donating ability of T atoms becomes weaker, and that of π-systems becomes stronger when T atoms become heavier for C2H4N2T:, which is consistent with the molecular electrostatic potentials (MEP) maps of C2H4N2T:. For a given C2H4N2T:, the Eint values of the type-A complexes go in the order HF > HCN > C2H2, and the Eint values of the type-B complexes go in the order HF ≈ HCN > C2H2. The contribution of electrostatic energy to the interaction energy of complexes becomes smaller for the type-A complexes when the T atoms become heavier. The interaction energies are dominated by the electrostatic energies for all the type-B complexes involving HF, and the interaction energies are dominated by the dispersion energies for most type-B complexes involving HCN and C2H2. The relaxed potential energy surface scans were performed for some selected complexes involving HF and HCN to examine the difference in binding behavior between HF and HCN.

Theoretical aspects of cooperativity and hydrogen bond in complexes of adenine and two formaldehyde molecules

AbstractIn the present work, we use quantum chemical calculations to investigate the strength, origin and role of hydrogen bonds as well as their cooperativity in complexes of adenine with two formaldehyde molecules. Eight stable structures of complexes are determined on potential energy surface at the B3LYP/aug‐cc‐pVDZ level of theory. The interaction energies of complexes with ZPE and BSSE corrections range from ‐4.45 to ‐9.45 kcal.mol‐1. The NBO and AIM analyses indicate that the strength of complexes is mainly governed by the N‐H‧‧‧O hydrogen bonds predominating O=C‧‧‧O and C‐H‧‧‧O/N intermolecular interactions. Besides, the C‐H‧‧‧O/N contacts are blue shifting hydrogen bonds, while the red shift of N‐H stretching frequency occurs in N‐H‧‧‧O hydrogen bonds in the complexes investigated. Noticeably, it is found that the positive cooperativity makes an increase in the complex stability and the C‐H blue shift of stretching frequency in C‐H‧‧‧O hydrogen bonds upon complexation.

Hexaconazole exposure ravages biosynthesis pathway of steroid hormones: revealed by molecular dynamics and interaction.

Widespread application of hexaconazole for agriculture purpose poses a threat to human health by disrupting normal endocrine homeostasis. To avoid adverse health effects on human, it is crucial to identify the effects of hexaconazole on key enzymes responsible for steroidal hormone synthesis. In view of this, present study was conducted to investigate the interaction mechanisms of hexaconazole with key enzymes in comparison with their food drug administration (FDA) approved inhibitor by molecular docking and molecular dynamics simulations. Results indicate that hexaconazole contacts with the active site of the key enzymes required for steroidal hormonal synthesis. Results pertaining to root-mean-square deviation, root-mean-square calculation, radius of gyration, hydrogen bonding and solvent accessible surface area exhibited that the interaction pattern and stability of interaction of hexaconazole was similar to enzyme specific inhibitor. In addition, ligand and enzyme complex interaction energy of hexaconazole was almost similar to key enzyme and FDA-approved enzyme specific inhibitor complex. This study offers a molecular level of understanding of hexaconazole with different enzymes required for steroidal hormonal synthesis. Findings of the study clearly suggest that hexaconazole has efficacy to stably interact with various enzyme required to progress the pathway of hormonal synthesis. If incessant exposure of hexaconazole occurs during agricultural work it may lead to ravage hormonal synthesis or potent endocrine disruption. The result of binding energy and complex interaction energy is depicted in the graphical abstract.

Unravelling the non-covalent interactions in certain n-propyl amine – Ether systems through acoustic and DFT studies at 303.15 K

Ultrasonic study of four binary liquid mixtures, containing n-propyl amine (NPA) as the common component and four structurally different ethers [tetrahydrofuran (THF), 1, 4 dioxane (DIOX), anisole (ANI) and diphenyl ether (DPE)] as varying components is carried out over the entire mole fraction range at 303.15 K and at experimental pressure of 101 kPa. The acoustical and excess thermo acoustic parameters reveal the existence of H-bonded interactions in the four systems and the influence of non-covalent interactions on the constitutional arrangement of ether molecules. It is found that the H-bonded interactions with NPA are stronger in aromatic ethers (ANI, DPE) systems than those in alicyclic ethers systems (THF, DIOX), presented in the manuscript. The optimized molecular geometries of dimers of pure components and the amine-ether complexes are obtained through Density Functional Theory (DFT) method. The values of dipole moments and interaction energies reveal that the stabilization arises due to C-H---π, C-H---O and C-H---N non-covalent interactions (NCI) besides the classical N-H---O H-bonding. The independent gradient model (IGM) analysis of the four systems shows structural dependent on the strength of the interactions. δginter descriptors obtained from pro-molecular IGM method presented against sign(λ2)ρ show the variation of interaction energies of complexes of NPA with structure of ethers.

Analysis of electrostatic interaction energies in complexes of IFIT5 proteins with RNA via UBDB+EPMM method

Analysis of electrostatic interaction energies in complexes of IFIT5 proteins with RNA <i>via</i> UBDB+EPMM method

Benchmark of the Extension of Frozen-Density Embedding Theory to Nonvariational Correlated Methods: The Embedded-MP2 Case.

The extension of the frozen-density embedding theory for nonvariational methods [J. Chem. Theory Comput. 2020, 16, 6880] was utilized to evaluate intermolecular interaction energies for complexes in the Zhao-Truhlar basis set. In the applied method (FDET-MP2-FAT-LDA), the same auxiliary system is used to evaluate the correlation energy by means of the second-order Møller-Plesset perturbation theory (MP2), as in our previous work [J. Chem. Phys. 2019, 150, 121101]. Local density approximation is used for ExcTnad[ρA,ρB] in both cases. Additionally, the contribution to the energy due to the neglected correlation potential was evaluated and analyzed. The domain of applicability of the local density approximation for ExcTnad[ρA,ρB] was determined based on deviations from the interaction energies from the conventional MP2 calculations. The local density approximation for ExcTnad[ρA,ρB] performs well for hydrogen- or dipole-bound complexes. The relative errors in the interaction energy lie within 3-30%. While for charge-transfer complexes, this approximation fails consistently, and for other types of complexes, the performance of this approximation is not systematic. The sources of error are discussed in detail.

The coulombic σ-hole model describes bonding in CX3IY- complexes completely.

Contrary to recent reports, the σ-hole interaction energies of complexes between the carbon tetrahalides CX3I (X = F, Cl, Br, I) and halide anions Y- (Y = F, Cl, Br, I) are described very well by the simple Coulombic σ-hole concept if it is applied properly. There is no need to invoke charge transfer, which in any case is not uniquely distinguishable from polarization.

Does alkali cation binding to aromatic ring retard the fluxional haptotropic migration? Evidences from density functional study

DFT calculations were performed on the sandwich complexes of naphthalene (MNC) with alkali metal cation $$(\hbox {Li}^{+}/\hbox {Na}^{+}/\hbox {K}^{+})$$ on one $${\uppi }$$ face and the tripodal $$\hbox {Cr(CO)}_{3}$$ moiety on the other with a view to explore the role of cation on haptotropic migration. Cation binding not only enhances the complex interaction energy but also delicately affects the fluxionality in the molecule by increasing the barrier to haptotropic shift of $$\hbox {Cr(CO)}_{3}$$ . The competing nature of the bifacial acids with sandwiched aromatic ring is established. In line with Pearson’s HSAB principle, LiNC system with highest interaction energy is found to be the most stable one among all the systems under study. Synopsis:DFT calculations were performed on the sandwich complexes of naphthalene with alkali metal cation $$(\hbox {Li}^{+}/ \hbox {Na}^{+}/ \hbox {K}^{+})$$ on one $${\uppi }$$ face and the tripodal $$\hbox {Cr(CO)}_{3}$$ moiety on the other with a view to explore the role of cation on haptotropic migration.

Arrangement and nature of intermolecular hydrogen bonding in complex biomolecular systems: modeling the vitamin C---L-alanine interaction

Vitamin C is known as an essential dietary supplement and implicated in diverse biological processes. We present here a theoretical study on the nature of hydrogen bonding of vitamin C in biological systems. For this reason, the complexes of vitamin C (VC) with neutral and zwitterionic L-alanine (as the simplest chiral amino acid) were studied at the MP2/6-311++G(d,p) level of theory. In the gas phase, neutral L-alanine leads to more stable complexes than the zwitterionic forms while the reverse is true in the aqueous phase. The complexes are formed via two hydrogen bond interactions, which result in a ring-like hydrogen-bonded networks. The nature of H-bonds was characterized in terms of natural bond orbital and quantum theory of atoms in molecule analyses (QTAIM). The H-bonds in the studied complexes were electrostatic in nature; however, in the case of shorter and directional H-bonds and ionic interactions, contributions of covalent character were also non-negligible. Natural energy decomposition analysis of hydrogen-bonded complexes reveals that the charge transfer and electrical components are the largest contributors for the interaction energies of complexes. Natural resonance theory analysis suggests higher resonance weight for charge-assisted interactions of vitamin C---alanine (zwitterionic) complexes, where the total interaction energy is considerably higher than that of neutral alanine.

Transition Metal Cation−π Interactions: Complexes Formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ Binding with Benzene Molecules

A computational investigation of the structures and interaction energies of complexes formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ binding with benzene (Bz) molecules is performed employing high level ab initio quantum chemical methods, such as the second-order perturbation theory (MP2), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods, along with the 6-311++G(2d,2p) and 6-311++G(d,p) basis sets. As far as we know, the present work is the first to study the structures and energetics of Bz-M2+ and Bz-M2+-Bz type complexes (M = Co, Ni, Cu, and Zn). Relativistic effects are also investigated via Douglas-Kroll-Hess second-order scalar relativistic computations for the complexes considered. Our results demonstrate that there are strong bindings between transition metal cations and benzene molecules. The computed interaction energies, including relativistic energy corrections, for the Bz-M2+ type complexes at the CCSD(T)/6-311++G(2d,2p) level are -131.9 (Bz-Fe2+), -172.6 (Bz-Co2+), -189.8 (Bz-Ni2+), -181.1 (Bz-Cu2+), and -158.2 (Bz-Zn2+) kcal mol-1. Similarly, interaction energies for the Bz-M2+-Bz type complexes at the CCSD(T)/6-311++G(d,p) level are -206.4 (Bz-Fe2+-Bz), -213.4 (Bz-Co2+-Bz), -249.7 (Bz-Ni2+-Bz), -258.6 (Bz-Cu2+-Bz), and -235.2 (Bz-Zn2+-Bz) kcal mol-1. Further, our results also demonstrate that the relativistic effects are very important in accurate computations of interaction energies. The predicted relativistic energy corrections to interaction energies, using the ωB97X-D functional, are between -1.9 and -7.7 kcal mol-1. The transition metal cation-π interactions investigated in this study prove significantly larger binding energies compared to arbitrary π-π interactions and main group cation-π interactions. We believe that the present study may open new avenues in cation-π interactions.

Dispersion Interactions and the Stability of Amine Dimers.

Weak, intermolecular interactions in amine dimers were studied by using the combination of a dispersionless density functional and a function that describes the dispersion contribution to the interaction energy. The validity of this method was shown by comparison of structural and energetic properties with data obtained with a conventional density functional and the coupled cluster method. The stability of amine dimers was shown to depend on the size, the shape, and the relative orientation of the alkyl substituents, and it was shown that the stabilization energy for large substituents is dominated by dispersion interactions. In contrast to traditional chemical explanations that attribute stability and condensed matter properties solely to hydrogen bonding and, thus, to the properties of the atoms forming the hydrogen bridge, we show that without dispersion interactions not even the stability and structure of the ammonia dimer can be correctly described. The stability of amine dimers depends crucially on the interaction between the non‐polar alkyl groups, which is dominated by dispersion interactions. This interaction is also responsible for the energetic part of the free energy interaction used to describe hydrophobic interactions in liquid alkanes. The entropic part has its origin in the high degeneracy of the interaction energy for complexes of alkane molecules, which exist in a great variety of conformers, having their origin in internal rotations of the alkane chains.

Nature of the interaction between ammonia derivatives and carbon disulfide. A theoretical investigation

AbstractThe interactions between NH3, its methylated and chlorinated derivatives and CS2 are investigated by ab initio CCSD(T) and density functional BLYP‐D3 methods. The CCSD(T)/aug‐cc‐pVTZ calculated interaction energies of complexes characterized by the S···N chalcogen bonds range between −1.71 and −2.78 kcal mol−1. The S···N bonds are studied by atoms in molecules, natural bond orbital, and noncovalent interaction methods. The lack of correlation between the interaction energies of methylated amines complexes and the electrostatic potential results from the lone pair effect in aliphatic amines. Different structures of CS2 complexed with ammonia derivatives, stabilized by other than the S···N chalcogen bonds, are also predicted. These structures are characterized by interaction energies ranging between 1.15 and 3.46 kcal mol−1. The results show that the complexing ability of CS2 is not very high but this molecule is able to attack the electrophilic or nucleophilic sites of a guest molecule.

Comparison of noncovalent interactions of zigzag and armchair carbon nanotubes with heterocyclic and aromatic compounds: Imidazole and benzene, imidazophenazines, and tetracene

We study non-covalent functionalization of SWCNT by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2–F4). MP2 and DFT/M05-2X quantum-chemical methods are used to determine the structures and the interaction energies of complexes formed by F1–F4 with the zigzag(10,10) and armchair(6,6) nanotubes. The calculations show that for small diameter nanotubes the binding energies with zigzag nanotubes are stronger than with armchair nanotubes. But above the diameter of 1.4nm the interaction energies for the armchair nanotubes become larger than for the zigzag nanotubes. Experimental measurements demonstrates that the ratio of the integral intensity of the resonance Raman bands assigned to the RBM modes of semiconducting nanotubes to the integral intensity of the metallic nanotubes increases for supernatant of SWCNT:F4 (1,2,3-triazole-[4,5-d]-phenazine) hybrids solved in 1-Methyl-2-pyrrolidone as compared to this ratio in sediment samples. It demonstrates that the linear heterocyclic compounds can be used for separating SWCNTs with different electron-conduction types.

Synthesis, Antibacterial Activity, Interaction with Nucleobase and Molecular Docking Studies of 4-Formylbenzoic Acid Based Thiazoles.

Synthesis, characterization and investigation of antibacterial activity of ten novel Schiff base derivatives of 4-formylbenzoic acid is presented. Their structures were determined using 1H and 13CNMR, EI(+)-MS and elemental analyses. Additionally, DFT calculations of interaction energies in complexes of the novel drugs and DNA bases are carried out. Design and synthesis of thiazole derivatives with benzoic acid scaffold to obtain compounds with an improved antibacterial activity. The examined compounds were screened in vitro for antibacterial activity using the broth microdilution method. Geometrical parameters of the investigated complexes were optimized within the Density Functional Theory (DFT) approximation using the B3LYP functional and the 6-311G** basis set. The docking simulations were performed using the FlexX docking module. Among the derivatives, compound 4b showed very strong bacterial activity against staphylococci, MIC 1.95-3.91 µg/ml, micrococci, MIC 0.98 µg/ml, and Bacillus spp., MIC 7.81-15.62 µg/ml. The compounds 4c, 4d, 4e and 4j also showed high bioactivity against staphylococci, MIC 3.91-31.25 µg/ml, and micrococci, MIC 0.98-15.62 µg/ml. Interaction energy values for investigated guanine complexes are about 2 kcal/mol lower than for the corresponding cytosine complexes. Molecular docking studies of all compounds on the active sites of bacterial enzymes indicated gyrase B as possible target. To conclude, an efficient and economic method for the synthesis of thiazoles containing benzoic acid moiety has been developed. The results of antibacterial screenings reveal that some obtained compounds show high to very strong antibacterial activity. The DFT calculations showed that interaction of the obtained drugs with guanine is stronger than with cytosine. Molecular docking studies of all compounds on the active sites of bacterial enzymes indicated gyrase B as possible target.

Cationic P⋯N interaction in XH3P+⋯NCY complexes (X = H, F, CN, NH2, OH; Y = H, Li, F, Cl) and its cooperativity with hydrogen/lithium/halogen bond

The geometries, interaction energies and bonding properties of cationic pnicogen bond (CPB) interactions are studied in binary XH3P+⋯NCY (X=H, F, CN, NH2, OH; Y=H, Li, F, Cl) complexes by means of MP2/aug-cc-pVTZ calculations. Interaction energies of these binary complexes span a large range, from −16.36kcal/mol in (NH2)H3P+⋯NCF to −71.36kcal/mol in FH3P+⋯NCLi complex. The spin–spin coupling constant across P⋯N interaction depends considerably on the nature of X and Y substituents. The characteristic of CPB interactions is analyzed in terms of parameters derived from quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. The charge transfer from the nitrogen base to the cationic acid stabilizes these pnicogen–bonded complexes. For a given XH3P+, the net charge transfer value increases as the interaction energy of the complex becomes more negative, i.e., NCLi>NCCl>NCH>NCF. Moreover, mutual influence between the CPB and hydrogen/halogen/lithium bond is studied in the ternary XH3P+⋯NCY⋯NCH complexes. The results indicate that the formation of a Y⋯N interaction tends to strengthen CPB in the ternary systems.

A theoretical investigation of the energetics and spectroscopic properties of the gas-phase linear proton-bound cation-molecule complexes, XCH(+)-N2 (X = O, S).

The structural features, spectroscopic properties, and interaction energies of the linear proton-bound complexes of OCH(+) and its sulfur analog SCH(+) with N2 were investigated using the high-level ab initio methods MP2 and CCSD(T) as well as density functional theory with the aug-cc-pVXZ (X = D, T) basis sets. The rotational constants along with the vibrational frequencies of the cation-molecule complexes are reported here. A comparison of the interaction energies of the OCH(+)-N2 and SCH(+)-N2 complexes with those of the OCH(+)-CO and OCH(+)-OC complexes was also performed. The energies of all the complexes were determined at the complete basis set (CBS) limit. CS shows higher proton affinity at the C site than CO does, so the complex OCH(+)-N2 is relatively strongly bound and has a higher interaction energy than the SCH(+)-N2 complex. Symmetry-adapted perturbation theory (SAPT) was used to decompose the total interaction energies of the complexes into the attractive electrostatic interaction energy (E elst), induction energy (E ind), dispersion energy (E disp), and repulsive exchange energy (E exch). We found that the ratio of E ind to E disp is large for these linear proton-bound complexes, meaning that inductive effects are favored in these complexes. The bonding characteristics of the linear complexes were elucidated using natural bond orbital (NBO) theory. NBO analysis showed that the attractive interaction is caused by NBO charge transfer from the lone pair on N to the σ*(C-H) antibonding orbital in XCH(+)-N2 (X = O, S). The quantum theory of atoms in molecules (QTAIM) was used to analyze the strengths of the various bonds within and between the cation and molecule in each of these proton-bound complexes in terms of the electron density at bond critical points (BCP). Graphical Abstract Linear proton-bound complexes of OCH(+)-N2 and SCH(+)-N2. In these complexes, inductive effect is favored over dispersive effect. The attractive interaction is the NBO charge transfer from N-lone pair of N2 to CH σ* antibonding orbital of XCH(+) (X = O, S).

Development of force field parameters for cyclopentane-modified peptide nucleic acids

CHARMM force field parameters were developed for cyclopentane-modified peptide nucleic acid (cpPNA) analogs. As in the original force field parameterization, a self-consistent step-wise optimization approach was taken that involved the iterative adjustments of internal and external parameters until convergence was obtained. The geometry parameters such as standard bond lengths and bond angles were obtained by reproducing ab initio gas-phase geometries of model compounds. The internal force constants used for stretch and bend deformations were optimized to fit the calculated vibrational spectra. Torsional parameters were modified to fit the rotational barriers about single bonds in model compounds. The partial atomic charges were optimized based on interaction energies of complexes between water and the model compound. Our parameterization accurately reproduced high-level quantum mechanical calculations. The parameters were validated by series of molecular dynamics simulations of cpPNA in explicit water. Together with the existing force field for nucleic acids, these parameters will enable simulations of cpPNA complexes with RNA and DNA.