Hydrogen bonding in liquid methanol, methylamine, and methanethiol studied by molecular-dynamics simulations

Ab Initio Molecular Dynamics Simulations of Amino Acids and Their Ammonia-Based Analogues in Ammonia

α-Amino acids are the fundamental building blocks for complex molecular structures within the water-based biochemistry of Earth. In a hypothetical ammonia-based biochemistry, α-amino amidines may serve an equivalent role. In this study, we explore the basic properties of α-amino amidines in comparison to α-amino acids solvated in ammonia, utilizing ab initio molecular dynamics simulations. The investigation of the time-resolved molecular dipole moment reveals, in intricate detail, the relationship among the conformation, state, and magnitude of the dipole moment. Moreover, it allows for the tracking of proton-transfer reactions. In ammonia, α-amino acids tend to adopt an anionic state, with the zwitterionic state still being accessible. In contrast, the α-amino amidines remain neutral. Grotthuss diffusion is induced by the deprotonation of zwitterionic alanine. The charge transferred upon solvation serves as an indicator for the interaction strength between the solute and solvent. It is much stronger for α-amino acids, while, on average, the α-amino amidines exchange no charge with ammonia. The analyses reveal that in terms of structure, anionic α-amino acids behave very similarly to neutral α-amino amidines.

On the complex hydrogen-bond network structural dynamics of liquid methanol: Chains, rings, bifurcations, and lifetimes

Solvation plays a pivotal role in chemistry to effectively steer chemical reactions. While liquid water has been extensively studied, our molecular-level knowledge of other associated liquids capable of forming H-bond networks, such as liquid methanol, remains surprisingly scarce. We use large-scale ab initio molecular dynamics simulations to comprehensively study the structural, dynamical, and electronic properties of bulk methanol under ambient conditions. Methanol is an interesting species in the liquid state since it can only donate one H-bond while a significant fraction accepts two H-bonds, which imprints one-dimensional linear and cyclic H-bonding patterns subject to significant bifurcations. After validation of radial distribution functions and the self-diffusion coefficient with respect to experimental data, we carried out detailed analyses of the H-bond network topology in terms of chain-like, ring-like, and branched H-bonded aggregates, including lifetime assessment. The analysis revealed that nearly all methanol molecules are actively engaged in filamentary H-bonding, predominantly forming branched linear chains with a significant contribution arising from tetrameric to hexameric rings-in stark contrast to the compact three-dimensional H-bond network of water. Five-membered rings turned out to be the most long-lived cyclic structures with an intermittent lifetime of 4 ps, while rings consisting of only three methanol molecules as well as very large cyclic structures are merely transient motifs. Detailed analyses of the effective electric molecular dipoles disclose a pronounced sensitivity of non-additive polarization and charge transfer effects of the individual methanol molecules to the particular H-bond network structure they are a member of, including its topology, be it linear or cyclic.

Microscopic Structure of Neat Linear Alkylamine Liquids: An X-Ray Scattering and Computer Simulation Study

Linear amines, from propylamine to nonylamine, are studied under ambient conditions by X-ray scattering and molecular dynamics simulations of various force field models. The major finding is that the prepeak in alkylamines is about 1 order of magnitude weaker than that in alkanols, hence suggesting much weaker hydrogen bonding-induced clustering of the amine groups than for the hydroxyl groups. Computer simulation studies reveal that the OPLS-UA model reproduces the prepeak, but with larger amplitudes, while the GROMOS-UA and CHARMM-AA force fields show almost no prepeak. Simulations of all models show the existence of hydrogen-bonded clusters, equally confirmed by the prominent prepeak of the structure factor between the nitrogen atoms. The hydrogen bond strength, as modeled by the Coulomb association in classical force field models, is about the same order of magnitude for both systems. Then, one may ask what is the origin of the weaker prepeak in alkylamines? Simulation data reveal that the existence of the prepeak is controlled through the cancellation of the positive contributions from the charged group correlations by the negative contributions from the cross charged-uncharged correlations. The C2v symmetry of the amine headgroup hinders clustering, which favors cross correlations with the tail atoms. This is opposite to alkanols where the symmetry of the hydroxyl headgroup favors clustering and hinders cross correlations with the alkyl tail. This competition between charged and uncharged atomic groups appears as a general mechanism to explain the existence of scattering prepeaks, including their position and amplitude.

Inferring the existence of hydrogen bonds directly from statistical analysis of molecular dynamics trajectories

As a demonstration of how fundamental chemical concepts can be gleaned from data using machine learning methods, we demonstrate the automated detection of hydrogen bonds by statistical analysis of molecular dynamics trajectories. In particular, we infer the existence and nature of electrostatically driven noncovalent interactions by examining the relative probability of supramolecular configurations with and without electrostatic interactions. Then, using Laplacian eigenmaps clustering, we identify hydrogen bonding motifs in hydrogen fluoride, water, and methanol. The hydrogen bonding motifs that we identify support traditional geometric criteria.

Hydrogen Bonding and Vaporization Thermodynamics in Hexafluoroisopropanol-Acetone and -Methanol Mixtures. A Joined Cluster Analysis and Molecular Dynamic Study

Binary mixtures of hexafluoroisopropanol with either methanol or acetone are analyzed via classical molecular dynamics simulations and quantum cluster equilibrium calculations. In particular, their populations and thermodynamic properties are investigated with the binary quantum cluster equilibrium method, using our in-house code Peacemaker 2.8, upgraded with temperature-dependent parameters. A novel approach, where the final density from classical molecular dynamics, has been used to generate the necessary reference isobars. The hydrogen bond network in both type of mixtures at molar fraction of hexafluoroisopropanol of 0.2, 0.5, and 0.8 respectively is investigated via the molecular dynamics trajectories and the cluster results. In particular, the populations show that mixed clusters are preferred in both systems even at 0.2 molar fractions of hexafluoroisopropanol. Enthalpies and entropies of vaporization are calculated for the neat and mixed systems and found to be in good agreement with experimental values.

Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids

Hydrogen-bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc.); hence, the lifetime of these structures is an important microscopic parameter, which can be calculated via computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short-timescale regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and be weakly dependent on criteria such as the bonding distance and angle, much similar to non-hydrogen-bonding simple liquids, while the long-timescale regime is known to have some power law dependence. Unexpectedly, all the hydrogen-bonding liquids studied herein, namely water and alcohols, display three highly hierarchical specific lifetimes, in the sub-picosecond range 0-0.5 ps. The dominant lifetime depends very strongly on the bonding-distance criterion and is related to hydrogen-bonded pairs. This mode is absent in non-H-bonding simple liquids. The secondary and tertiary mean lifetimes are related to clusters and are nearly independent of the bonding criterion. Of these two lifetimes, only the first one can be related to that of simple liquids, which poses the question of the nature of the third lifetime. The study of alcohols reveals that this third lifetime is related to the topology of the H-bonded clusters and that its distribution may also be affected by the alkyl tail surrounding the "bath". This study shows that hydrogen-bonding liquids have a universal hierarchy of hydrogen-bonding lifetimes with a timescale regularity across very different types, and which depend on the topology of the cluster structures.

Relevance of hydrogen bonded associates to the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol

2-Propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of approximately several Ångstroms, employing static and quasi-elastic neutron scattering and molecular dynamics simulation. Dynamic neutron scattering measurements were performed over an exchanged wave-vector range encompassing the pre-peak, indicative of the presence of H-bonding associates, and the main peak. The dynamics observed at the pre-peak is associated with the formation and disaggregation of the H-bonded associates and is measured to be at least one order of magnitude slower than the dynamics at the main peak, which is identified as the structural relaxation. The measurements indicate that the macroscopic shear viscosity has a similar temperature dependence as the dynamics of the H-bonded associates, which highlights the important role played by these structures, together with the structural relaxation, in defining the macroscopic rheological properties of the system. Importantly, the characteristic relaxation time at the pre-peak follows an Arrhenius temperature dependence whereas at the main peak it exhibits a non-Arrhenius behavior on approaching the supercooled state. The origin of this differing behavior is attributed to an increased structuring of the hydrophobic domains of 2-propanol accommodating a more and more encompassing H-bond network, and a consequent set in of dynamic cooperativity.

On the X-ray Scattering Pre-peak of Linear Mono-ols and the Related Microstructure from Computer Simulations

The X-ray scattering intensities (I(k)) of linear alkanols OH(CH₂)_n-1CH₃ obtained from experiments (methanol to 1-undecanol) and computer simulations (methanol to 1-nonanol) of different force field models are comparatively studied particularly in order to explain the origin and the properties of the scattering pre-peak in the k-vector range 0.3-1 Å^-1. The experimental I(k) values show two apparent features: the pre-peak position k_P decreases with increasing n, and more intriguingly, the amplitude A_P goes through a maximum at 1-butanol (n = 4). The first feature is well reproduced by all force-field models, while the second shows strong model dependence. The simulations reveal various shapes of clusters of the hydroxyl head-group from n>2. k_P is directly related to the size of the meta-objects corresponding to such clusters surrounded by their alkyl tails. The explanation of the A_P turnover at n = 4 is more involved in terms of cancellations of atom-atom structure factor S(k) contributions related to domain ordering. The flexibility of the alkyl tails tends to reduce the cross contributions, thus revealing the crucial importance of this parameter in the models. Force fields with all-atom representation are less successful in reproducing the pre-peak features for smaller alkanols, n<6, possibly because they blur the charge ordering process since all atoms bear partial charges. The analysis clearly shows that it is not possible to obtain a model-free explanation of the features of I(k).

Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters

Molecular dynamics simulations are helpful tools for a range of applications, ranging from drug discovery to protein structure determination. The successful use of this technology largely depends on the potential function, or force field, used to determine the potential energy at each configuration of the system. Most force fields encode all of the relevant parameters to be used in distinct atom types, each associated with parameters for all parts of the force field, typically bond stretches, angle bends, torsions, and nonbonded terms accounting for van der Waals and electrostatic interactions. Much attention has been paid to the nonbonded parameters and their derivation, which are important in particular due to their governance of noncovalent interactions, such as protein-ligand binding. Parametrization involves adjusting the nonbonded parameters to minimize the error between simulation results and experimental properties, such as heats of vaporization and densities of neat liquids. In this setting, determining the best set of atom types is far from trivial, and the large number of parameters to be fit for the atom types in a typical force field can make it difficult to approach a true optimum. Here, we utilize a previously described Minimal Basis Iterative Stockholder (MBIS) method to carry out an atoms-in-molecules partitioning of electron densities. Information from these atomic densities is then mapped to Lennard-Jones parameters using a set of mapping parameters much smaller than the typical number of atom types in a force field. This approach is advantageous in two ways: it eliminates atom types by allowing each atom to have unique Lennard-Jones parameters, and it greatly reduces the number of parameters to be optimized. We show that this approach yields results comparable to those obtained with the typed GAFF 1.7 force field, even when trained on a relatively small amount of experimental data.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding

Coarse-graining (CG) methodologies have been widely used to extend the time and length scales of computer simulations by averaging over the atomistic details beneath the resolution of the CG models. Despite the efficiency of CG models, important configurational information during a given process may be lost at the CG resolution. One example of this is the topology of the hydrogen bonding network in the liquid state. When the functional group that participates in hydrogen bonding (e.g., -OH in methanol) is coarse-grained into one CG site, the effective interactions of the resultant CG model are usually derived from an averaged overall trajectory and, thus, do not take into account the hydrogen bonding interactions and topologies that are present at the all-atom resolution. In order to overcome this challenge, the present study develops new ultra-coarse-grained (UCG) models that include internal states within the CG sites that participate in hydrogen bonding, where each state represents a specific configuration such as the hydrogen bonding donor or acceptor. Internal states of the UCG beads are modeled to remain in quasi-equilibrium, and the degree of mixing is controlled by utilizing the effective local density of the UCG sites. In particular, we consider two groups of UCG models with different types of hydrogen bonding motifs: chain-like and ring-like. Using five different liquid systems that contain the same fundamental functional groups as biomolecules, we demonstrate the ability of the UCG models to reproduce the structural properties that originate from the configurations beneath the resolution of the UCG model. This proposed approach can also be applied to other liquids with such specific and directional interactions, or even to complex biomolecular systems in which hydrogen bonding is critical.

Spatially Controlled Noncovalent Functionalization of 2D Materials Based on Molecular Architecture

Polymerizable amphiphiles can be assembled into lying-down phases on 2D materials such as graphite and graphene to create chemically orthogonal surface patterns at 5-10 nm scales, locally modulating functionality of the 2D basal plane. Functionalization can be carried out through Langmuir-Schaefer conversion, in which a subset of molecules is transferred out of a standing phase film on water onto the 2D substrate. Here, we leverage differences in molecular structure to spatially control transfer at both nanoscopic and microscopic scales. We compare transfer properties of five different single- and dual-chain amphiphiles, demonstrating that those with strong lateral interactions (e.g., hydrogen-bonding networks) exhibit the lowest transfer efficiencies. Since molecular structures also influence microscopic domain morphologies in Langmuir films, we show that it is possible to transfer such microscale patterns, taking advantage of variations in the local transfer rates based on the structural heterogeneity in Langmuir films. Nanoscale domain morphologies also vary in ways that are consistent with predicted relative transfer and diffusion rates. These results suggest strategies to tailor noncovalent functionalization of 2D substrates through controlled LS transfer.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.

MD simulation study of the diffusion and local structure of n-alkanes in liquid and supercritical methanol at infinite dilution

The diffusion coefficients of 14 n-alkanes (ranging from methane to n-tetradecane) in liquid and supercritical methanol at infinite dilution (at a pressure of 10.5 MPa and at temperatures of 299 K and 515 K) were deduced via molecular dynamics simulations. Values for the radial distribution function, coordination number, and number of hydrogen bonds were then calculated to explore the local structure of each fluid. The flexibility of the n-alkane (as characterized by the computed dihedral distribution, end-to-end distance, and radius of gyration) was found to be a major influence and hydrogen bonding to be a minor influence on the local structure. Hydrogen bonding reduces the flexibility of the n-alkane, whereas increasing the temperature enhances its flexibility, with temperature having a greater effect than hydrogen bonding on flexibility. Graphical abstract The flexibility of the alkane is a major influence and the hydrogen bonding is a minor influence on the first solvation shell; the coordination numbers of long-chain n-alkanes in the first solvation shell are rather low.

Experimental study of dielectric property changes in DMSO–primary alcohol mixtures under low-intensity microwaves

By applying a low-intensity microwave to DMSO–primary alcohol mixtures, distinct dielectric property changes have been observed.

Liquid 1-propanol studied by neutron scattering, near-infrared, and dielectric spectroscopy

Liquid monohydroxy alcohols exhibit unusual dynamics related to their hydrogen bonding induced structures. The connection between structure and dynamics is studied for liquid 1-propanol using quasi-elastic neutron scattering, combining time-of-flight and neutron spin-echo techniques, with a focus on the dynamics at length scales corresponding to the main peak and the pre-peak of the structure factor. At the main peak, the structural relaxation times are probed. These correspond well to mechanical relaxation times calculated from literature data. At the pre-peak, corresponding to length scales related to H-bonded structures, the relaxation times are almost an order of magnitude longer. According to previous work [C. Gainaru, R. Meier, S. Schildmann, C. Lederle, W. Hiller, E. Rössler, and R. Böhmer, Phys. Rev. Lett. 105, 258303 (2010)] this time scale difference is connected to the average size of H-bonded clusters. The relation between the relaxation times from neutron scattering and those determined from dielectric spectroscopy is discussed on the basis of broad-band permittivity data of 1-propanol. Moreover, in 1-propanol the dielectric relaxation strength as well as the near-infrared absorbance reveal anomalous behavior below ambient temperature. A corresponding feature could not be found in the polyalcohols propylene glycol and glycerol.

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

Nonadditive effects in the mixed trimers of HCl and methanethiol

Ab initio and density functional theory calculations with aug-cc-pVDZ and aug-cc-pVTZ basis sets have been performed on the HCl-CH3SH dimer and HCl-(CH3SH)2 and (HCl)2-CH3SH trimers. Structures, energetics, and infrared frequencies are calculated. The results are discussed in terms of the cooperativity effect which is a characteristic of H-bonded systems and compared to oxygen-containing analogs of the same trimers, HCl-(CH3OH)2 and (HCl)2-CH3OH, which have been published recently.

Structure of liquid and glassy methanol confined in cylindrical pores

We present a neutron scattering analysis of the density and the static structure factor of confined methanol at various temperatures. Confinement is performed in the cylindrical pores of MCM-41 silicates with pore diameters D=24 and 35 A. A change of the thermal expansivity of confined methanol at low temperature is the signature of a glass transition, which occurs at higher temperature for the smallest pore. This is evidence of a surface induced slowing down of the dynamics of the fluid. The structure factor presents a systematic evolution with the pore diameter, which has been analyzed in terms of excluded volume effects and fluid-matrix cross correlation. Conversely to the case of Van der Waals fluids, it shows that stronger fluid-matrix correlations must be invoked most probably in relation with the H-bonding character of both methanol and silicate surface.

Role of solvent in determining conformational preferences of alanine dipeptide in water

Evidence from a variety of spectroscopic probes indicates that (phi, psi) values corresponding to the left-handed polyproline II helix (P(II)) are preferred for short alanine-based peptides in water. On the basis of results from theoretical studies, it is believed that the observed preference is dictated by favorable peptide-solvent interactions, which are realized through formation of optimal hydrogen-bonding water bridges between peptide donor and acceptor groups. In the present study, we address this issue explicitly by analyzing the hydration structure and thermodynamics of 16 low-energy conformers of the alanine dipeptide (N-acetylalanine-N'-methylamide) in liquid water. Monte Carlo simulations in the canonical ensemble were performed under ambient conditions with all-atom OPLS parameters for the alanine dipeptide and the TIP5P model for water. We find that the number of hydrogen-bonded water molecules connecting the peptide group donor and acceptor atoms has no effect on the solvation thermodynamics. Instead, the latter are determined by the work done to fully hydrate the peptide. This work is minimal for conformations that are characterized by a minimal overlap of the primary hydration shells around the peptide donor and acceptor atoms. As a result, peptide-solvent interactions favor "compact" conformations that do not include P(II)-like geometries. Our main conclusion is that the experimentally observed preference for P(II) does not arise due to favorable direct interactions between the peptide and water molecules. Instead, the latter act to unmask underlying conformational preferences that are a consequence of minimizing intrapeptide steric conflicts.