On the role of London dispersion forces in biomolecular structure determination

100 Years of the Lennard-Jones Potential

It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic and molecular interactions, where applications range from descriptions of intermolecular forces to molecules, clusters, and condensed matter.

Biopolymers as a Potential Alternative for the Retention of Pollutants from Vinasse: An In Silico Approach

Vinasse, a waste from the bioethanol industry, presents a crucial environmental challenge due to its high organic matter content, which is difficult to biodegrade. Currently, no sustainable alternatives are available for treating the amount of vinasse generated. Conversely, biopolymers such as cellulose, carboxymethylcellulose, and chitosan are emerging as an interesting alternative for vinasse control due to their flocculating capacity against several organic compounds. This study seeks to determine the thermodynamic behavior of in silico interactions among three biopolymers (cellulose, carboxymethylcellulose, and chitosan) regarding 15 organic compounds found in vinasse. For this, the Particle Mesh Ewald (PME) method was used in association with the Verlet cutoff scheme, wherein the Gibbs free energy (ΔG) was calculated over a 50 ns simulation period. The findings revealed that cellulose showed a strong affinity for flavonoids like cyanidin, with a maximum free energy of -84 kJ/mol and a minimum of -55 kJ/mol observed with phenolic acids and other flavonoids. In contrast, chitosan displayed the highest interactions with phenolic acids, such as gallic acid, reaching -590 kJ/mol. However, with 3-methoxy-4-hydroxyphenyl glycol (MHPG), it reached an energy of -70 kJ/mol. The interaction energy for flavonoid ranged from -105 to -96 kJ/mol. Finally, carboxymethylcellulose (CMC) demonstrated an interaction energy with isoquercetin of -238 kJ/mol, while interactions with other flavonoids were almost negligible. Alternatively, CMC exhibited an interaction energy of -124 kJ/mol with MHPG, while it was less favorable with other phenolic acids with minimal interactions. These results suggest that there are favorable interactions for the interfacial sorption of vinasse contaminants onto biopolymers, indicating their potential for use in the removal of contaminants from the effluents of the bioethanol industry.

Comparison of Density-Functional Theory Dispersion Corrections for the DES15K Database

While density-functional theory (DFT) remains one of the most widely used tools in computational chemistry, most functionals fail to properly account for the effects of London dispersion. Hence, there are many popular post-self-consistent methods to add a dispersion correction to the DFT energy. Until now, the most popular methods have never been compared on equal footing due to not being implemented in the same electronic structure packages. In this work, we performed a large-scale benchmarking study, directly comparing the accuracy of the exchange-hole dipole moment (XDM), D3BJ, D4, TS, MBD, and MBD-NL dispersion models when applied to the recent DES15K database of nearly 15,000 molecular complexes at both expanded and compressed geometries. Our study showed similarly good performance for all dispersion methods (except TS) when applied to neutral complexes. However, they all performed worse for ionic complexes, particularly those involving dications of alkaline earth metals, due to systematic overbinding by the base PBE0 density functional. Investigation of the largest outliers also revealed that only the MBD and MBD-NL methods demonstrate surprising errors for complexes involving alkali metal cations at compressed geometries where they tended to significantly overbind. As we would expect minimal dispersion binding for such complexes, we further investigated the origins of these errors for the potential energy curve of a model cation-π complex. Overall, there is little choice between the XDM, D3BJ, D4, MBD, and MBD-NL dispersion methods for most systems. However, the MBD-based methods are not recommended for complexes involving organic species and alkali or alkaline earth metal cations, for example when modeling Li+ intercalation into graphite.

Discovery, implications and initial use of semi-synthetic organisms with an expanded genetic alphabet/code

Much recent interest has focused on developing proteins for human use, such as in medicine. However, natural proteins are made up of only a limited number of canonical amino acids with limited functionalities, and this makes the discovery of variants with some functions difficult. The ability to recombinantly express proteins containing non-canonical amino acids (ncAAs) with properties selected to impart the protein with desired properties is expected to dramatically improve the discovery of proteins with different functions. Perhaps the most straightforward approach to such an expansion of the genetic code is through expansion of the genetic alphabet, so that new codon/anticodon pairs can be created to assign to ncAAs. In this review, I briefly summarize more than 20 years of effort leading ultimately to the discovery of synthetic nucleotides that pair to form an unnatural base pair, which when incorporated into DNA, is stably maintained, transcribed and used to translate proteins in Escherichia coli. In addition to discussing wide ranging conceptual implications, I also describe ongoing efforts at the pharmaceutical company Sanofi to employ the resulting 'semi-synthetic organisms' or SSOs, for the production of next-generation protein therapeutics. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Probing the Size Limit of Dispersion Energy Donors with a Bifluorenylidene Balance: Magic Cyclohexyl

We report the synthesis of 14 2,2'-disubstituted 9,9'-bifluorenylidenes as molecular balances for the quantification of London dispersion interactions between various dispersion energy donors. For all balances, we measured ΔG_Z/E at 333 K using ¹H NMR in seven organic solvents. For various alkyl and aryl substituents, we generally observe a preference for the "folded" Z-isomer due to attractive London dispersion interactions. The cyclohexyl-substituted system shows the largest Z-preference in this study with ΔG_Z/E = -0.6 ± 0.05 kcal mol^-1 in all solvents, owing to the rotational freedom of cyclohexyl groups paired with their large polarizability that maximizes London dispersion interactions. On the other hand, rigid and sterically more demanding substituents like tert-butyl unexpectedly favor the unfolded E-isomer. This is a result of the close relative position in which the functional groups are positioned in this molecular balance. This close proximity is the reason for the increase of Pauli repulsion in the Z-isomers with large rigid substituents (tert-butyl, adamantyl, and diamantyl) which leads to an equilibrium shift toward the unfolded E-form. While we were able to reproduce most of our experimental trends qualitatively using contemporary computational chemistry methods, quantitative accuracy of the employed methods still needs further improvement.

The periodic table and the physics that drives it

Mendeleev's introduction of the periodic table of elements is one of the most important milestones in the history of chemistry, as it brought order into the known chemical and physical behaviour of the elements. The periodic table can be seen as parallel to the Standard Model in particle physics, in which the elementary particles known today can be ordered according to their intrinsic properties. The underlying fundamental theory to describe the interactions between particles comes from quantum theory or, more specifically, from quantum field theory and its inherent symmetries. In the periodic table, the elements are placed into a certain period and group based on electronic configurations that originate from the Pauli and Aufbau principles for the electrons surrounding a positively charged nucleus. This order enables us to approximately predict the chemical and physical properties of elements. Apparent anomalies can arise from relativistic effects, partial-screening phenomena (of type lanthanide contraction) and the compact size of the first shell of every l-value. Further, ambiguities in electron configurations and the breakdown of assigning a dominant configuration, owing to configuration mixing and dense spectra for the heaviest elements in the periodic table. For the short-lived transactinides, the nuclear stability becomes an important factor in chemical studies. Nuclear stability, decay rates, spectra and reaction cross sections are also important for predicting the astrophysical origin of the elements, including the production of the heavy elements beyond iron in supernova explosions or neutron-star mergers. In this Perspective, we critically analyse the periodic table of elements and the current status of theoretical predictions and origins for the heaviest elements, which combine both quantum chemistry and physics.

What is “many-body” dispersion and should I worry about it?

“Many-body” dispersion can refer to two distinct phenomena, here termed electronic and atomic many-body effects, both of which cause the dispersion energy to be non-additive.

Exploring London Dispersion and Solvent Interactions at Alkyl-Alkyl Interfaces Using Azobenzene Switches

Interactions on the molecular level control structure as well as function. Especially interfaces between innocent alkyl groups are hardly studied although they are of great importance in larger systems. Herein, London dispersion in conjunction with solvent interactions between linear alkyl chains was examined with an azobenzene-based experimental setup. Alkyl chains in all meta positions of the azobenzene core were systematically elongated, and the change in rate for the thermally induced Z→E isomerization in n-decane was determined. The stability of the Z-isomer increased with longer chains and reached a maximum for n-butyl groups. Further elongation led to faster isomerization. The origin of the intramolecular interactions was elaborated by various techniques, including ¹ H NOESY NMR spectroscopy. The results indicate that there are additional long-range interactions between n-alkyl chains with the opposite phenyl core in the Z-state. These interactions are most likely dominated by attractive London dispersion. This work provides rare insight into the stabilizing contributions of highly flexible groups in an intra- as well as an intermolecular setting.

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.

A double exponential potential for van der Waals interaction

Van der Waals (vdw) interaction is an important force between atoms and molecules. Many potential functions have been proposed to model vdw interaction such as the Lennard-Jones (L-J) potential. To overcome certain drawbacks of existing function forms, this work proposes a double exponential (DE) potential that contains a repulsive exponential term and an attractive exponential term. This potential decays faster than the L-J potential and has a soft core. The DE potential is very flexible and its two exponential parameters can be adjusted continuously to mimic many potential functions. Combined with the isotropic periodic sum (IPS) method, the DE potential can efficiently and accurately describe non-bonded interactions and is convenient for alchemical free energy calculation.

A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User

This account is written for general users of density functional theory (DFT) methods as well as experimental researchers who are new to the field and would like to conduct such calculations. Its main emphasis lies on how to find a way through the confusing ‘zoo’ of DFT by addressing common misconceptions and highlighting those modern methods that should ideally be used in calculations of energetic properties and geometries. A particular focus is on highly popular methods and the important fact that popularity does not imply accuracy. In this context, we present a new analysis of the openly available data published in Swart and co-workers’ famous annual ‘DFT poll’ (http://www.marcelswart.eu/dft-poll/) to demonstrate the existing communication gap between the DFT user and developer communities. We show that despite considerable methodological advances in the field, the perception of some parts of the user community regarding their favourite approaches has changed little. It is hoped that this account makes a contribution towards changing this status and that users are inspired to adjust their current computational protocols to accommodate strategies that are based on proven robustness, accuracy, and efficiency rather than popularity.

A physically grounded damped dispersion model with particle mesh Ewald summation

Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.

π-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds?

The results from absolutely localized molecular orbital (ALMO)-energy decomposition analysis (EDA) and ALMO-charge transfer analysis (CTA) at M06-2X/cc-pVTZ level reveal that double-proton transfer (DPT) reactions through base pairing H-bonds have nonignorable effects on the stacking energies of dinucleotide steps, which introduces us to a novel stabilization (or destabilization) factor in the DNA duplex. Thus, intra- and inter-strand base stacking interactions are coalesced with each other mediated by H-bridged quasirings between base pairs. Changes in stacking energies of dinucleotide steps depending on the positions of H atoms are due to variations in local aromaticities of individual nucleobases, manifesting π-cooperativity effects. CT analyses show that dispersion forces in dinucleotide steps can lead to radical changes in the redox properties of nucleobases, in particular those of adenine and guanine stacked dimers in a strand. Besides Watson-Crick rules, novel base pairing rules were propounded by considering CT results. According to these, additional base pairing through π-stacks of nucleobases in dinucleotide steps does not cause any intrinsic oxidative damage to the associated nucleobases throughout DPT.

The expanded genetic alphabet

All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.

Role of Polarization in Halogen Bonds

A classical point-charge self-consistent polarization model has been used to investigate the role of polarization in the CF3Cl:OH2 complex. The polarised electron densities of the monomers component are shown to be a good representation of the electron densities of complexes, especially CF3Cl. The point-charge model overestimates the polarization of the water molecule, which is likely because exchange repulsion is unaccounted for in the classical model calculations.

Effect of counterions on the protonation state in a poly(G)-poly(C) radical cation

The proton transfer process from a guanine to its complementary cytosine in a B-form d[GG] radical cation is investigated theoretically. The d[GG] radical cation is optimized by the ONIOM + PCM method. In this two-layer ONIOM method, the high layer consists of the π-stacked complementary base pairs with a hole charge, which is treated at the B97D/6-31G(d) level. The low layer includes the sugar-phosphate backbone and sodium ions, which is treated with the Amber99SB/Parmbsc0 force field. Our calculations reveal that the stabilization of the deprotonated state in d[GG] oligomers is related to the location of sodium ions. When sodium ions are located near phosphate groups, the proton prefers bonding with the guanine, and 80% of the hole charge is delocalized on the guanine residues. When sodium ions are placed in the major groove, the deprotonated state is favorable, and 70% of the hole charge localizes on the corresponding guanine-cytosine pair. According to the natural bond orbital analysis, the N-H···N hydrogen bond between the guanine-cytosine pair provides an important contribution to the stabilization of the deprotonated state. Stabilization of this hydrogen bond is very sensitive to the d[GG] oligomer configuration. In summary, the proton transfer process in a guanine-cytosine pair of poly(G)-poly(C) radical cations is largely affected by the arrangement of counterions.