Biomedical subjects
Publications and source records attributed to N Sathyamurthy.
Ab initio calculations at the second-order Møller-Plesset perturbation theoretic level have been carried out to study the solvation of protonated water by phenol molecules. The results show that in addition to classical O-H...O hydrogen bonds, C-H...O, pi...H-O, and pi...H-C bonds are also formed, thus stabilizing the H3O+(C(6)H(5)OH)3 complex.
Time-independent quantum mechanical (TIQM) approach (helicity basis truncated at k = 2) has been used for computing differential and integral cross sections for the exchange reaction H- + D2 (v = 0, j = 0-4) --> HD + D- and D- + H2 (v = 0, j = 0-3) --> HD + H- in three dimensions on an accurate ab initio potential energy surface. It is shown that the j-weighted differential reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder at four different relative translational energies (Etrans = 0.55, 0.93, 1.16 and 1.48 eV) for (H-, D2) and at one relative translational energy (Etrans = 0.6 eV) by Haufler et al. for both (H-, D2) and (D-, H2) collisions. The j-weighted integral reaction cross section values are in good agreement with the crossed beam measurements by Zimmer and Linder in the Etrans range 0.5-1.5 eV and close to the guided ion beam results by Haufler et al. for (H-, D2) in the range 0.8-1.2 eV. Time-dependent quantum mechanical (TDQM) results obtained using centrifugal sudden approximation are reported in the form of integral reaction cross section values as a function of Etrans in the range 0.3-3.0 eV for both reactions in three dimensions on the same potential energy surface. The TDQM reaction cross section values decline more sharply than the TIQM results with increase in the initial rotational quantum number (j) for the D2 molecules in their ground vibrational state (v = 0) for (H-, D2) collisions. The computed j-weighted reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder for (H-, D2) collisions and guided ion beam results by Haufler et al. for both (H-, D2) and (D-, H2) collisions for energies below the threshold for electron detachment channel.
The structure and stability of different forms of salicylic acid dimer have been examined by Hartree-Fock and density functional theoretic calculations using 6-31G(d,p) and 6-311++g(d,p) basis sets. Vertical excitation energies for the monomer as well as the dimer have been computed using the time-dependent density functional theory using 6-311++G(d,p) basis set. The predicted absorption maxima for the first excited singlet state of salicylic acid monomer and the dimer of the primary form are in reasonable agreement with the experimental result. There is a slight red shift (approximately 6 nm) in the absorption maximum in going from the monomer to the dimer, in accord with the experimental observation. Configuration-interaction calculations including single excitation have been carried out to map the potential-energy profile for the intra- as well as the intermolecular proton transfer in different forms of the dimer. The barrier for proton transfer in the ground state as well as the excited states makes it clear that most of the processes take place in the primary form and largely by intramolecular proton transfer.
A three-dimensional time-dependent quantum mechanical wave packet approach is used to calculate reaction probability (P(R)) and integral reaction cross section (sigma(R)) values for both the channels of the reaction He + HD(+) (v = 1; j = 0, 1, 2, 3) --> HeH(D)(+) + D(H), over a range of translational energy (E(trans)) on the McLaughlin-Thompson-Joseph-Sathyamurthy (MTJS) potential energy surface using centrifugal sudden approximation for nonzero total angular momentum (J) values. The reaction probability plots as a function of translational energy for different J values exhibit several oscillations, which are characteristic of the system. It is shown that HeH(+) is preferred over HeD(+) for large J values and that HeD(+) is preferred over HeH(+) for small J values for all the rotational (j) states studied. The integral reaction cross section for both the channels and therefore the isotopic branching ratio for the reaction depend strongly on j in contrast to the marginal dependence shown by earlier QCT calculations. The computed results are in overall agreement with the available experimental results.
Fuller's earth (FE) has been used as an adsorbent in this work to remove mercury from aqueous solutions. For the purpose of comparison, simultaneous experiments using activated carbon (AC) have also been done. The aim of the work is to test how best FE can be used as an adsorbent for mercury. Equilibrium isotherms, such as Freundlich, Langmuir, Dubinin-Redushkevich, Temkin, Harkins-Jura, Halsey and Henderson have been tested. Kinetic studies based on Lagergren first-order, pseudo-second-order rate expressions and intra-particle diffusion studies have been done. The batch experiments were conducted at room temperature (30 degrees C) and at the normal pH (6.7+/-0.2) of the solution. It has been observed that Hg(II) removal rate is better for FE than AC, due to large dosage requirement, whereas the adsorption capacity of AC is found to be much better than FE. Hence, although FE can be used as an adsorbent, a high dosage is required, when compared to AC. Hybrid fractional error function analysis shows that the best-fit for the adsorption equilibrium data is represented by Freundlich isotherm. Kinetic and film diffusion studies show that the adsorption of mercury on FE and AC is both intra-particle diffusion and film diffusion controlled.
Hartree-Fock (HF) calculations using 6-31G*, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets show that hydrogen peroxide molecular clusters tend to form hydrogen-bonded cyclic and cage structures along the lines expected of a molecule which can act as a proton donor as well as an acceptor. These results are reiterated by density functional theoretic (DFT) calculations with B3LYP parametrization and also by second-order Møller-Plesset perturbation (MP2) theory using 6-31G* and 6-311++G(d,p) basis sets. Trends in stabilization energies and geometrical parameters obtained at the HF level using 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are similar to those obtained from HF/6-31G* calculation. In addition, the HF calculations suggest the formation of stable helical structures for larger clusters, provided the neighbors form an open book structure.
Density functional theory with B3LYP parametrization and 6-311++G(d,p) basis set has been used to investigate the structure and stability of salicylic acid-water complexes. The vertical excitation energies for these complexes have been computed using time-dependent density functional theory (with B3LYP parametrization and a 6-311++G(d,p) basis set). It is shown that the hydrogen bond between the carboxylic hydrogen and the oxygen of water is the strongest among all possible hydrogen bonds in the system. The hydrogen bond strength in salicylic acid-water complexes seems to be nearly additive. The change in absorption maximum (lambda(max)) corresponding to the vertical excitation energy for the first three excited singlet and triplet states of the complex with 1-3 water molecules is nominal (approximately 1-3 nm). But with the addition of the fourth water molecule, the lambda(max) for S(1) and T(1) decreases by approximately 17 nm and it increases for S(2) and S(3) by about the same amount. The decrease in lambda(max) for transition to the T(2) state on the addition of the fourth water molecule is only approximately 9 nm. There seems to be an intersystem crossing between the S(1) and T(3) states that could account for the observed fluorescence quenching of salicylic acid in water.
It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.
The ground-state properties of the monomer and the dimer of formic acid, acetic acid, and benzoic acid have been investigated using Hartree-Fock (HF) and density functional theory (DFT) methods using the 6-311++G(d,p) basis set. Some of the low-lying excited states have been studied using the time-dependent density functional theory (TDDFT) with LDA and B3LYP functionals and also employing complete-active-space-self-consistent-field (CASSCF) and multireference configuration interaction (MRCI) methodologies. DFT calculations predict the ground-state geometries in quantitative agreement with the available experimental results. The computed binding energies for the three carboxylic acid dimers are also in accord with the known thermodynamic data. The TDDFT predicted wavelengths corresponding to the lowest energy n-pi* transition in formic acid (214 nm) and acetic acid (214 nm) and the pi-pi* transition in benzoic acid (255 nm) are comparable to the experimentally observed absorption maxima. In addition, TDDFT calculations predict qualitatively correctly the blue shift (4-5 nm) in the excitation energy for the pi-pi* transition in going from the monomer to the dimer of formic acid and acetic acid and the red shift (approximately 19 nm) in pi-pi* transition in going from benzoic acid monomer to dimer. This also indicates that the electronic interaction arising from the hydrogen bonds between the monomers is marginal in all three carboxylic acids investigated.
A three-dimensional time-dependent quantum mechanical approach is used to calculate the reaction probability (P(R)) and the integral reaction cross section (sigma(R)) for both channels of the reaction He + HD+(v = 0, 1, 2, 3; j = 0) --> HeH(D)+ + D(H), over a range of translational energy (E(trans)) on two different ab initio potential energy surfaces (McLaughlin-Thompson-Joseph-Sathyamurthy and Palmieri et al.). The reaction probability plots as a function of translational energy exhibit several oscillations, which are characteristic of the system. The vibrational enhancement of the reaction probability and the integral reaction cross section values are reproduced qualitatively by our calculations, in accordance with the experimental results. The isotopic branching ratio for the reaction decreases in going from v = 0 to v = 1 and then becomes nearly v-independent in going from v = 1 to v =3 on both the surfaces.
The effect of spatial confinement on the properties of isoelectronic molecules HF, H2O, NH3, and CH4 has been studied by encapsulating them in a C60 fullerene cage. Second-order Møller-Plesset perturbation theoretical (MP2) calculations suggest that all the guest species are stable inside the fullerene cage. This stabilization arises from the dispersion interaction between the guest and the host. It is shown that the excitation energy (Esigma*-Esigma) for the X-H bond increases and that there is a blue shift in the stretching frequencies due to confinement.
Ab initio calculations suggest the possibility of forming boric acid clusters in the laboratory. The most stable form of the boric acid dimer contains two hydrogen bonds, similar to the carboxylic acid dimers. Though the trimer and the tetramer form extensions of this geometry, the pentamer prefers a bowl shape. Any addition of boric acid molecules to this geometry leads to bowl-shaped structures with the 15-mer forming a (3/4)buckyball and the 20-mer a full-fledged buckyball. The hexamer, on the other hand, prefers to stay planar as a hexagon-centered rosette. Any further extension of this geometry leads to planar structures as long as a pentagon is not included.
Polysilanes are potential candidates for active materials in light emitting diodes because of possible emission in the near-ultraviolet to blue region. Unfortunately, they degrade rapidly upon exposure to light because of scission of sigma bonds. Relative stability of four polysilanes, for example, poly(di-n-butylsilane) (PDBS), poly(di-n-hexylsilane) (PDHS), poly(methylphenylsilane) (PMPS), and poly[bis(p-butylphenyl)silane] (PBPS), which have been reported as active materials in light emitting diodes, have been investigated theoretically through semiempirical (AM1) and ab initio (HF/6-31g) methods and density functional theory using B3LYP parametrization. The AM1 level of calculation predicts the absorption maxima reasonably, but it fails to explain the relative stabilities of the four polysilanes in the excited state. However, calculations based on configuration interaction with single excitation and time-dependent density functional theory suggest additional stabilization in the excited states through intersystem crossing to triplets for PMPS and PBPS, consistent with the experimental observation. In contrast, no such stabilization is predicted for PDBS and PDHS. Furthermore, the existence of a stable triplet state in PMPS may also explain the visible emission observed experimentally in PMPS.
Photophysical and photochemical properties of 1-hydroxy-2-naphthoic acid (1,2-HNA) have been investigated experimentally by steady state and time domain fluorescence measurements and theoretically by Hartree-Fock (HF), configuration interaction at the single excitation (CIS) level, density functional theoretic (DFT), and semiempirical (AM1) methods. 1,2-HNA exhibits normal fluorescence that depends on its concentration, nature of the solvent, pH, temperature, and wavelength of excitation. It seems to form different emitting species in different media, akin to 3-hydroxy-2-naphthoic acid (3,2-HNA). The large Stokes shifted emission observed at pH 13 is attributed to species undergoing excited-state intramolecular proton transfer. Nonradiative transition seems to increase on protonation and decrease on deprotonation. AM1(PECI=8) calculations predict the absorption maximum (lambda(max) = 335.9 nm) in reasonable agreement with experiment (lambda(max) = 352 nm) for the neutral 1,2-HNA. They also predict a red shift in absorption on protonation and a blue shift on deprotonation as observed experimentally. CIS calculations tend to overestimate the energy gap and hence underestimate the absorption maxima between the ground and the excited electronic states of 1,2-HNA and its protonated and deprotonated forms. However, they do predict correctly that the excited state intramolecular proton transfer is likely to occur in the deprotonated form of 1,2-HNA and not in the neutral and the protonated forms. A single minimum is found in the potential energy profile for the ground state as well as the first excited state of 1,2-HNA and its protonated species. In contrast, a double minimum with a nominal barrier in between is predicted for the ground state and also the first three excited states of the deprotonated species. The keto form of the deprotonated species is found to be slightly less stable than the enol form in all the states investigated.
We present the results of a time-dependent quantum mechanical investigation using centrifugal sudden approximation in the form of reaction probability as a function of collision energy (E(trans)) in the range 0.3-3.0 eV for a range of total angular momentum (J) values and the excitation function sigma(E(trans)) for the exchange reaction H(-) + H(2) (v = 0, j = 0) --> H(2) + H(-) and its isotopic variants in three dimensions on an accurate ab initio potential energy surface published recently (J. Chem. Phys. 2004, 121, 9343). The excitation function results are shown to be in excellent agreement with those obtained from crossed beam measurements by Zimmer and Linder for H(-) + D(2) collisions for energies below the threshold for electron detachment channel and somewhat larger than the most recent results of Haufler et al. for (H(-), D(2)) and (D(-), H(2)) collisions.
Structure, stability, and hydrogen-bonding interaction in phenol, water, and phenol-water clusters have been investigated using ab initio and density functional theoretical (DFT) methods and using various topological features of electron density. Calculated interaction energies at MP2/6-31G level for clusters with similar hydrogen-bonding pattern reveal that intermolecular interaction in phenol clusters is slightly stronger than in water clusters. However, fusion of phenol and water clusters leads to stability that is akin to that of H(2)O clusters. The presence of hydrogen bond critical points (HBCP) and the values of rho(r(c)) and nabla(2)rho(r(c)) at the HBCPs provide an insight into the nature of closed shell interaction in hydrogen-bonded clusters. It is shown that the calculated values of total rho(r(c)) and nabla(2)rho(r(c)) of all the clusters vary linearly with the interaction energy.
A detailed three-dimensional time-dependent quantum dynamical study of the He+H(2) (+)(v=0-3,j=0)-->HeH(+)+H reaction is reported for different vibrational v states of H(2) (+) in its ground rotational (j=0) state over a range of translational E(trans) energies on an accurate ab initio potential energy surface published by Palmieri et al. Plots of reaction probability as a function of total energy E reveal a large number of oscillations indicating the presence of a number of reactive scattering resonances. When averaged over total angular momentum J, some of the oscillations survive, indicating that they may be amenable to experimental observation. A comparison of our present results with our earlier results on the McLaughlin-Thompson-Joseph-Sathyamurthy surface and the experimental results from different research groups reveal a good deal of agreement as well as some discrepancies between theory and experiment at the level of state-selected gas phase dynamics.
pi-pi Interaction in pyridine dimer and trimer has been investigated in different geometries and orientations at the ab initio (HF, MP2) and DFT (B3LYP) levels of theory using various basis sets (6-31G, 6-31G, 6-311++G) and corrected for basis set superposition error (BSSE). While the HF and DFT calculations show the pyridine dimer and the trimer to be unstable with respect to the monomer, the MP2 calculations show them to be clearly stable, thus emphasizing the need to include electron correlation while determining stacking interaction in such systems. The calculated MP2/6-311++G binding energy (100% BSSE corrected) of the parallel-sandwich, antiparallel-sandwich, parallel-displaced, antiparallel-displaced, T-up and T-down geometries for pyridine dimer are 1.53, 3.05, 2.39, 3.97, 1.91, 1.47 kcal/mol, respectively. The results show the antiparallel-displaced geometry to be the most stable. The binding energies for the trimer in parallel-sandwich, antiparallel-sandwich, and antiparallel-displaced geometry are found to be 3.18, 6.14, and 8.04 kcal/mol, respectively.