The Role of Hydrogen Bond in Designing Molecular Optical Materials

Unveiling GruPol: Predicting Electric and Electrostatic Properties of Macromolecules via the Building Block Approach

Understanding electrostatics and electric properties of macromolecules is crucial in uncovering the intricacies of their behavior and functionality. The precise knowledge of these properties enhances our ability to manipulate and engineer macromolecules for diverse applications, spanning from drug design to materials science. Having that in mind, we present here the GruPol database approach to characterize and accurately predict dipole moments, static polarizabilities, and electrostatic potential of proteins and their subunits. The method involves partitioning of the electron density, calculated at the M06-HF/aug-cc-pVDZ level of theory, of small peptides into predefined building blocks that are averaged over the database. By manipulating and positioning these building blocks, GruPol enables the description of proteins assembled from over nearly 100 residual entries, allowing for efficient and precise computation of the above-mentioned properties across a broad range of proteins. The database enables the user to include solvent effects as well as define protonation states on the protein's backbone to account for pH variations. The precision of the proposed scheme is benchmarked against experimental data for myoglobin species.

A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium

Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH₂ , CHCH₃ , NH₂ , COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizable-continuum model calculations.

Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules

CONTEXT

Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well.

METHODS

Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).

Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules

The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.

Ultrafast Vibrational Response of Activated C-D Bonds in a Chloroform-Platinum(II) Complex

The vibrational response of the activated C-D bond in the chloroform complex [Pt(C₆H₅)₂(btz-N,N')·CDCl₃, where btz = 2,2'-bi-5,6-dihydro-4H-1,3-thiazine] is studied by linear and nonlinear two-dimensional infrared (2D-IR) spectroscopy. The change of the C-D stretching vibration of metal-coordinated CDCl₃ relative to the free solvent molecule serves as a measure of the non-classical Pt···D-C interaction strength. The stretching absorption band of the activated C-D bond displays a red shift of 119 cm^-1 relative to uncoordinated CDCl₃, a strong broadening, and an 8-fold enhancement of spectrally integrated absorption. The infrared (IR) absorption and 2D-IR line shapes are governed by spectral diffusion on 200 fs and 2 ps time scales, induced by the fluctuating solvent CDCl₃. The enhanced vibrational absorption and coupling to solvent forces are assigned to the enhanced electric polarizability of the activated C-D bond. Density functional theory calculations show a significant increase of C-D bond polarizability of CDCl₃ upon coordination to the 16 valence electron Pt(II) complex.

How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies

Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.

Inorganic Salts of N-phenylbiguanidium(1+)-Novel Family with Promising Representatives for Nonlinear Optics

Seven inorganic salts containing N-phenylbiguanide as a prospective organic molecular carrier of nonlinear optical properties were prepared and studied within our research of novel hydrogen-bonded materials for nonlinear optics (NLO). All seven salts, namely N-phenylbiguanidium(1+) nitrate (C2/c), N-phenylbiguanidium(1+) perchlorate (P-1), N-phenylbiguanidium(1+) hydrogen carbonate (P21/c), bis(N-phenylbiguanidium(1+)) sulfate (C2), bis(N-phenylbiguanidium(1+)) hydrogen phosphate sesquihydrate (P-1), bis(N-phenylbiguanidium(1+)) phosphite (P21), and bis(N-phenylbiguanidium(1+)) phosphite dihydrate (P21/n), were characterised by X-ray diffraction (powder and single-crystal X-ray diffraction) and by vibrational spectroscopy (FTIR and Raman). Two salts with non-centrosymmetric crystal structures-bis(N-phenylbiguanidium(1+)) sulfate and bis(N-phenylbiguanidium(1+)) phosphite-were further studied to examine their linear and nonlinear optical properties using experimental and computational methods. As a highly SHG-efficient and phase-matchable material transparent down to 320 nm and thermally stable to 483 K, bis(N-phenylbiguanidium(1+)) sulfate is a promising novel candidate for NLO.

Engineered Ionene/PNIPAM Hybrid Dual-Response Material Generating Tunable and Unique Optical Modes for Adaptive Solar Transmittance Modulation

A hybrid smart window exhibiting dual chromic response properties based on an ionene/polymer material is successfully engineered. Thermochromic poly(N-isopropylacrylamide) is integrated with an electrochromic viologen-tethered ionene, also acting as an electrolyte, to produce a smart window that can adaptively control solar visible light transmittance in response to multiple stimuli. This new blend allows the formation of unique reversible optical states, namely, "clear", "amber", "cloudy", and "grainy" states, which are passively triggered by environmental temperature and actively induced by external potential or simultaneously by both. This hybrid material shows tunability in terms of its electrochemical and optical properties, switching kinetics, and coloration efficiency and can also achieve a nearly absolute zero-transmissive state. With the material's excellent solubility and film-forming ability, the smart device can be fabricated with much flexibility and ease. Finally, this device has an all-in-one layer configuration, creating a more compact and simplified design. With all these properties combined, the development of a next-generation multifunctional smart window device, which can efficiently control incoming solar light for energy-saving in buildings and also provide visual comfort, is possible.

Accurate Atom-Dipole Interaction Model for Prediction of Electro-optical Properties: From van der Waals Aggregates to Covalently Bonded Clusters

This work aims at the accurate estimation of the electro-optical properties of atoms and functional groups in organic crystals. A better understanding of the nature of building blocks and the way they interact with each other enables more efficient prediction of self-assembly, and thus physical properties in condensed matter. We propose a modified version of an atom-dipole interaction model that is based on atomic dipole moments calculated from the quantum theory of atoms in molecules. The method is very reliable for the prediction of various optical and electric properties in diverse chemical environments, ranging from hydrocarbon molecules bonded by dispersive interactions to polar rings connected by hydrogen bonds, or even polymeric structures whose monomers are covalently linked. Distributed polarizabilities and electrostatic potentials are compared to those obtained using a complete quantum-mechanical approach on finite-size aggregates. Our electrostatic approximation recovers isotropic polarizabilities with an accuracy of ca. 5 au and electrostatic potentials of ca. 0.05 au, even in the worst-case scenario in which polarization and charge-transfer effects are large. Functional groups are highly exportable, estimating the properties of small peptides and polyaromatics with a maximum deviation as low as ca. 15%.

Crystal structure, vibrational frequencies and polarizability distribution in hydrogen-bonded salts of pyromellitic acid

Structural features of moderate-to-strong O—H...O hydrogen bonds are related to the frequencies of O—H stretching vibrations and to the electric polarizability distribution in the donor and acceptor functional groups for crystals synthesized from the 1,2,4,5-benzenetetracarboxylic (pyromellitic) acid, namely: bis(3-aminopyridinium) dihydrogen pyromellitate tetrahydrate, (1); bis(3-carboxypyridinium) dihydrogen pyromellitate, (2); bis(3-carboxyphenylammonium) dihydrogen pyromellitate dihydrate, (3); and bis(4-carboxyphenylammonium) dihydrogen pyromellitate, (4). A combination of single-crystal X-ray diffraction, powder Raman spectroscopy and first-principle calculations in both crystalline and gaseous phases has shown that changes in the O—H...O hydrogen-bond geometry can be followed by changes in the corresponding spectral modes. Vibrational properties of moderate hydrogen bonds can be estimated from correlations based on statistical analysis of several compounds [Novak (1974).Struct. Bond.18, 177–216]. However, frequencies related to very short O—H...O bonds can only be predicted by relationships built from a subset of structurally similar systems. Moreover, the way in which hydrogen bonds affect the polarizability of donor and acceptor groups depends on their strength. Moderate interactions enhance the polarizability and make it more anisotropic. Shorter hydrogen bonds may decrease the polarizability of a group as a consequence of the volume restraint implied by the neighbour molecule within a hydrogen-bonded aggregate. This is significant for evaluation of the electric susceptibility in crystals and, therefore, for estimation of refractive indices and birefringence.

Polarization of Electron Density Databases of Transferable Multipolar Atoms

Polarizability is a key molecular property involved in either macroscopic (i.e., dielectric constant) and microscopic properties (i.e., interaction energies). In rigid molecules, this property only depends on the ability of the electron density (ED) to acquire electrostatic moments in response to applied electric fields. Databases of transferable electron density fragments are a cheap and efficient way to access molecular EDs. This approach is rooted in the relative conservation of the atomic ED between different molecules, termed transferability principle. The present work discusses the application of this transferability principle to the polarizability, an electron density-derived property, partitioned in atomic contributions using the Quantum Theory of Atoms In Molecules topology. The energetic consequences of accounting for in situ deformation (polarization) of database multipolar atoms are investigated in detail by using a high-quality quantum chemical benchmark.

Experimental and Computational Perspectives on Bis(Creatininium) Succinate: An Efficient Organic Nonlinear Optical Material

In this work, combined experimental and computational investigations of a promising organic nonlinear optical (NLO) material, bis(creatininium) succinate (BCS), are reported. The optical quality single crystals of BCS were grown with the dimensions of 12×2×2 mm3. Single crystal X-ray diffraction analysis reveals that BCS crystallized in the orthorhombic system with non-centrosymmetric (NCS) space group F2dd. Vibrational modes of various BCS functional groups were confirmed by using FTIR and FT-Raman spectrum. UV-Vis-NIR spectrum shows that BCS crystal has low near-UV cut-off wavelength at 261 nm and optical transparency window in the visible and near-IR (261–1100 nm) region. Photoconductivity study has been carried out magnificently for grown crystals. The nonlinear optical property such as nonlinear refractive index (n2) and nonlinear absorption coefficient (β) have been investigated by z-scan technique. Density functional theory (DFT) studies were carried out to probe Mulliken charge analysis, frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) mapping and first order hyperpolarizability (β) for the optimized molecular structure. Experimental and computed vibrations were correlated well. All these characterization results endorse BCS as a suitable NLO candidate and are discussed in this work.