Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

Topological analysis off charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case off packing polymorphism

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H---O and C-H---pi interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in PI (Z' = 2) and Form B crystallizes in P2(1)/n (Z = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms.

Performance study of high operating temperature HgCdTe mid wave infrared detector through numerical modeling

The design of present generation uncooled Hg1-xCdxTe infrared photon detectors relies on complex heterostructures with a basic unit cell of type (n) under bar (+)/pi/(p) under bar (+). We present an analysis of double barrier (n) under bar (+)/pi/(p) under bar (+) mid wave infrared (x = 0.3) HgCdTe detector for near room temperature operation using numerical computations. The present work proposes an accurate and generalized methodology in terms of the device design, material properties, and operation temperature to study the effects of position dependence of carrier concentration, electrostatic potential, and generation-recombination (g-r) rates on detector performance. Position dependent profiles of electrostatic potential, carrier concentration, and g-r rates were simulated numerically. Performance of detector was studied as function of doping concentration of absorber and contact layers, width of both layers and minority carrier lifetime. Responsivity similar to 0.38 A W-1, noise current similar to 6 x 10(-14) A/Hz(1/2) and D* similar to 3.1 x 10(10)cm Hz(1/2) W-1 at 0.1 V reverse bias have been calculated using optimized values of doping concentration, absorber width and carrier lifetime. The suitability of the method has been illustrated by demonstrating the feasibility of achieving the optimum device performance by carefully selecting the device design and other parameters. (C) 2010 American Institute of Physics. doi:10.1063/1.3463379]

Halogen Bonding in 2,5-Dichloro-1,4-benzoquinone: Insights from Experimental and Theoretical Charge Density Analysis

Experimental charge density distribution in 2, 5-dichloro-1, 4-benzoquinone has been carried out using high resolution X-ray diffraction data at 90 K to quantitatively evaluate the nature of C-Cl center dot center dot center dot O=C halogen bond in molecular crystals. Additionally, the halogen bond is studied from geometrical point of view and the same has been visualized using Hirshfeld surface analysis. The obtained results from experimental charge density analysis are compared with periodic quantum calculations using B3LYP 6-31G(d,p) level of theory. The topological values at bond critical point, three-dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C-Cl center dot center dot center dot O=C halogen bond in crystalline lattice.

Charge Density Analysis of a Pentaborate Ion in an Ammonium Borate: Toward the Understanding of Topological Features in Borate Minerals

Structural and charge density distribution studies have been carried out on a single crystal data of an ammonium borate, [C(10)H(26)N(4)][B(5)O(6)(OH)(4)](2), synthesized by solvothermal method. Further, the experimentally observed geometry is used for the theoretical charge density calculations using the B3LYP/6-31G** level of theory, and the results are compared with the experimental values. Topological analysis of charge density based on the Atoms in Molecules approach for B-O bonds exhibit mixed covalent/ionic character. Detailed analysis of the hydrogen bonds in the crystal structure in the ammonium borate provides insights into the understanding of the reaction pathways that net atomic charges and electrostatic potential isosurfaces also give additional such systems. could result in the formation of borate minerals. The input to evaluate chemical and physical properties in such systems.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

DFT study of structure and vibrational spectra of ceramide 3: comparison to experimental data

The Fourier transform Raman and infrared (IR) spectra of the Ceramide 3 (CER3) have been recorded in the regions 200-3500 cm(-1) and 680-4000 cm(-1), respectively. We have calculated the equilibrium geometry, harmonic vibrational wavenumbers, electrostatic potential surfaces, absolute Raman scattering activities and IR absorption intensities by the density functional theory with B3LYP functionals having extended basis set 6-311G. This work is undertaken to study the vibrational spectra of CER3 completely and to identify the various normal modes with better wavenumber accuracy. Good consistency is found between the calculated results and experimental data for the IR and Raman spectra.

Intermolecular charge transfer and vibrational analysis of hydrogen bonding in acetazolamide

In the present work the structural and spectral characteristics of acetazolamide have been studied by methods of infrared, Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) employing B3LYP with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. Based on these results, we have discussed the correlation between the vibrational modes and the structure of the dimers of acetazolamide. The calculated vibrational spectra of three dimers of acetazolamide have been compared with observed spectra, and the assignment of observed bands was carried out using potential energy distribution. The observed spectra agree well with the values computed from the OFT. A comparison of observed and calculated vibrational spectra clearly shows the effect of hydrogen bonding. The frequency shifts observed for the different dimers are in accord with the hydrogen bonding in acetazolamide. Natural bond orbital (NBO) analyses reflect the charge transfer interaction in the individual hydrogen bond units and the stability of different dimers of acetazolamide. (C) 2012 Elsevier B.V. All rights reserved.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

Microwave Spectroscopic and Atoms in Molecules Theoretical Investigations on the ArPropargyl Alcohol Complex: ArHO, Ar, and ArC Interactions

The structure of the Arpropargyl alcohol (ArPA) complex is determined from the rotational spectra of the parent complex and its two deuterated isotopologues, namely ArPA-D(OD) and ArPA-D(CD). The spectra confirm a geometry in which PA exists in the gauche form with Ar located in between OH and CCH groups. All a, b and c types of transitions show small splitting due to some large-amplitude motion dominated by COH torsion, as in the monomer. Splittings in a- and b-type transitions are of the order of a few kilohertz, whereas splitting in the c-type transitions is relatively larger (0.92.6 MHz) and decreases in the order ArPA>ArPA-D(CD)>ArPA-D(OD). The assignments are well supported by ab initio calculations. Atoms in molecules (AIM) and electrostatic potential calculations are used to explore the nature of the interactions in this complex. AIM calculations not only reveal the expected OHAr and Ar interactions in the Argauche-PA complex, but also novel CAr (of CH2OH group) and OHAr interactions in the Artrans-PA complex. Similar interactions are also present in the Armethanol complex.

The X-C center dot center dot center dot Y (X = O/F, Y = O/S/F/Cl/Br/N/P) `carbon bond' and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C center dot center dot center dot Y interaction, which could be called `carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the `hydrophobic interactions'.

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Characterization of Interactions Involving Bromine in 2,2-Dibromo2,3-dihydroinden-1-one via Experimental Charge Density Analysis

Experimental and theoretical charge density analyses on 2,2-dibromo-2,3-dihydroinden-1-one have been carried out to quantify the topological features of a short CBr....O halogen bond with nearly linear geometry (2.922 angstrom, angle CBr....O = 172.7 degrees) and to assess the strength of the interactions using the topological features of the electron density. The electrostatic potential map indicates the presence of the s-hole on bromine, while the interaction energy is comparable to that of a moderate OH....O hydrogen bond. In addition, the energetic contribution of CH.....Br interaction is demonstrated to be on par with that of the CBr....O halogen bond in stabilizing the crystal structure.

``Conformational Simulation'' of Sulfamethizole by Molecular Complexation and Insights from Charge Density Analysis: Role of Intramolecular S center dot center dot center dot O Chalcogen Bonding

Intramolecular S center dot center dot center dot O chalcogen bonding and its potential to lock molecular conformation have been examined in the crystal forms of sulfamethizole, a sulfonamide antibiotic. Molecular complexes of sulfamethizole, including salts and cocrystal, have been synthesized, and their crystal structures were analyzed in order to examine the possible conformational preferences of the molecule in various ionic states and supramolecular environments (neutral/cocrystal, anionic salt, and cationic salt forms). The electrostatic potential mapped on Hirshfeld surfaces generated for these crystal forms provides insights into the possible binding modes of the drug in different environments. Further, the observed conformation locking feature has been rationalized in terms of the experimental charge density features of the intramolecular S center dot center dot O chalcogen bonding in sulfamethizole. The study quantitatively illustrates and rationalizes an intriguing case of a local minimum of molecular conformation being exclusively preferred over the global minimum, as it facilitates more efficient intermolecular interactions in a supramolecular environment.

The X-C---Y (X = O/F, Y = O, S, F, Cl, Br, N, P,) Carbon bond and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.