Tyrosine-glycine revisited : resolving the discrepancy between theory and experiment

LFH acknowledges the Engineering and Physical Sciences Research Council for studentship support through the Doctoral Training Account scheme.Energies of 20 conformers of the Tyr-Gly dipeptide were computed using DSD-PBEP86-D3BJ/aug-cc-VTZ, with geometries from M06-2X/6-31+G* and B97-D/6-31+G*. At 0 K, these energies support the earlier finding from MP2/6-31+G*//B3LYP/6-31+G*, that the most stable conformer is folded and H-bonded. However, when free-energy corrections at 400 K are added, non-H-bonded conformers are the most stable. This supports an earlier spectroscopic study in which H-bonded conformers were absent. Of the four most stable conformers at 400 K, two were not matched with spectra in the experimental study, but we argue that all four can in fact be plausibly assigned to the experimental spectra.PostprintPeer reviewe

Towards a symmetric reversible single-molecule switch : amino-imino-cyclo-n-enes

The research data supporting this publication can be accessed at https://doi.org/10.17630/4908b94e-d478-4d1a-8f05-0d85851abab8.We propose cyclic 5- and 7-ring structures with alternating single and double bonds and adjacent imino and amino groups as candidates for switches in molecular electronics, with amino-imino tautomerisation as the switching mechanism. Due to the C2V-symmetric transition state, the molecules exhibit a symmetric double-well potential with identical energies for the two states, which is a desirable property for a functioning molecular switch. Calculations at the double hybrid mPW2PLYP-D2/def2-TZVP level show barriers of 1.07 and 0.52 eV for the 5-ring and 7-ring, respectively (zero-point corrected: 0.97 and 0.41 eV, respectively). The corresponding 9-ring structure is not suitable as a molecular switch, due to ring puckering and the existence of multiple minima. Attachment of ethyne groups to the nitrogens and the opposite carbon, as models for molecular wires, only slightly changes the barrier heights. The 5- and 7-ring structures are promising switch candidates for further investigation.Publisher PDFPeer reviewe

A computational study of TyrGly hydration

Twenty-two conformers of the neutral tyrosine-glycine (TyrGly) dipeptide have been studied at the mPW2PLYP-D2/def2-TZVP level in the gas phase, in implicit solvent and with one explicit water molecule. Implicit solvation brings the conformers closer in energy, whereas explicit monosolvation significantly extends the range of stability of the complexes. Thus, interaction with a single water molecule preferentially stabilises some conformers over others. The most stable conformer in the gas phase remains the most stable in implicit solvation and explicit monosolvation, though the third most stable conformer in the gas phase is nearly iso-energetic in implicit solvation. The two most stable monohydrated complexes are based on the folded most stable conformer in the gas phase and only differ slightly in the orientation of the water molecule. The water molecule increases the foldedness of these structures by bridging the carboxylic acid group and phenyl OH.PostprintPostprintPeer reviewe

Halogen-bonded guanine base pairs, quartets and ribbons

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).Publisher PDFPeer reviewe

Stacking with the unnatural DNA base 6-ethynylpyridone

The authors are grateful to EaStCHEM for computational support via the EaStCHEM Research Computing Facility.It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:A-containing duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair.PostprintPostprintPeer reviewe

DNA base stacking involving adenine and 2-aminopurine

The potential energy surfaces of stacked structures consisting of adenine (A) and 2-aminopurine (2AP) have been investigated in the gas phase. Both face-to-back (the double ring system of one base exactly on top of that of the other one) and face-to-face (one base flipped by 180°) A/A, 2AP/2AP and A/2AP stacks were considered. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level of theory. For each type of stack, between five and nine minima were located, usually connected by low barriers of 1-2 kcal/mol. This shows the large conformational flexibility of these stacked base pairs. The double-ring system in A and 2AP affords multiple minima with similar twist angles, making the potential energy surface of stacks comprising of purine bases more complex than those of pyrimidine stacks. The locations of the stationary points on the potential energy surface differ for the three different systems; thus, the replacement of A by 2AP in a base stack changes its potential energy landscape.Publisher PDFPeer reviewe

Competition between hydrogen and halogen bonding in halogenated 1-methyluracil: water systems

The competition between hydrogen- and halogen-bonding interactions in complexes of 5-halogenated 1-methyluracil (XmU; X = F, Cl, Br, I or At) with one or two water molecules in the binding region between C5-X and C4=O4 is investigated with M06-2X/6-31+G(d). In the singly-hydrated systems, the water molecule forms a hydrogen bond with C4=O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5-X exist only for X = Br, I and At. Structures with two waters forming a bridge between C4=O and C5-X (through hydrogen- and halogen-bonding interactions) exist for all halogens except F. The absence of a halogen-bonded structure in singly-hydrated ClmU is therefore attributed to the competing hydrogen-bonding interaction with C4=O4. The halogen-bond angle in the doubly-hydrated structures (150-160°) is far from the expected linearity of halogen bonds, indicating that significantly non-linear halogen bonds may exist in complex environments with competing interactions.PostprintPeer reviewe

Corrigendum : Competition between hydrogen and halogen bonding in halogenated 1-methyluracil:water systems

This article corrects: Competition between hydrogen and halogen bonding in halogenated 1-methyluracil:water systems, Volume 37, Issue 8, 763-770. Article first published online: 15 January 2016.PostprintPeer reviewe

Predicting melting points of organic molecules : applications to aqueous solubility prediction using the General Solubility Equation

In this work we make predictions of several important molecular properties of academic and industrial importance to seek answers to two questions: 1) Can we apply efficient machine learning techniques, using inexpensive descriptors, to predict melting points to a reasonable level of accuracy? 2) Can values of this level of accuracy be usefully applied to predicting aqueous solubility? We present predictions of melting points made by several novel machine learning models, previously applied to solubility prediction. Additionally, we make predictions of solubility via the General Solubility Equation (GSE) and monitor the impact of varying the logP prediction model (AlogP and XlogP) on the GSE. We note that the machine learning models presented, using a modest number of 2D descriptors, can make melting point predictions in line with the current state of the art prediction methods (RMSE ≥ 40 oC). We also find that predicted melting points, with an RMSE of tens of degrees Celsius, can be usefully applied to the GSE to yield accurate solubility predictions (log10S RMSE < 1) over a small dataset of druglike molecules.PostprintPostprintPeer reviewe