Computational Chemistry-Molecular Modelling

Course code: CH-638

ASSIGNMENT

Submitted to
Dr. Zahid Rashid
Department of Chemistry
Quaid-e-Azam University
Islamabad

Submitted by
Ayesha Wasim
Registration No: 02062413028
MPhil Organic Chemistry
Fall 2024 (1st Semester)
Quaid-e-Azam University
Islamabad

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Contents
Abstract:................................................................................................................................... 3
Introduction:............................................................................................................................. 3
Hartree-Fock Theory............................................................................................................ 3
Density Functional Theory................................................................................................... 3
Compound used for Analysis................................................................................................4
Methodology:........................................................................................................................... 5
Geometry Optimization:...........................................................................................................5
Optimized Bond Lengths (in Angstrom)...............................................................................5
Optimized Angles (in Degrees).............................................................................................6
Optimized Dihedral Angles (in Degrees)..............................................................................6
FT-IR Spectroscopy:.................................................................................................................6
IR Frequencies obtained from HF.........................................................................................6
IR Frequencies obtained from DFT......................................................................................7
Comparison with Experimental data.....................................................................................8
Reasons for Differences in IR frequencies............................................................................8
Single Point Energy:.................................................................................................................9
Single Point Energy obtained from HF.................................................................................9
Single Point Energy obtained from DFT............................................................................10
UV-Vis Spectroscopy:............................................................................................................ 11
UV-Vis Spectrum obtained from HF...................................................................................12
UV-Vis spectrum using DFT.................................................................................................. 13
NMR Spectrum:..................................................................................................................... 14
NMR using Hartree Fock........................................................................................................14
NMR using DFT.....................................................................................................................17
Conclusion:.........................................................................................................................18
References:............................................................................................................................. 18

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Abstract:

The target compound, 4-Phenylbenzaldehyde, was characterized using both Hartree-Fock

(HF) and Density Functional Theory (DFT) with the 6-31+G(d,p) basis set and the B3LYP
functional for the theoretical calculations. The optimized geometric parameters, including
bond lengths, angles, and dihedral angles were studied, both HF and DFT methods.
Additionally, Hartree-Fock and Density Functional Theory was used to perform UV-Vis
spectroscopy simulations, determining the excitation energies and oscillator strengths for the
10 lowest energy excited states of the molecule. Furthermore, NMR spectrum and FTIR
spectrum covering chemical shift values and vibrational frequencies were also determined.

Introduction:

Hartree-Fock Theory

The Hartree–Fock (HF) approach is an approximation technique used in computational

physics and chemistry to determine the energy and wave function of a quantum many-body
system in a stationary state. The electronic Hamiltonian is employed with a single
determinant wavefunction in a contemporary ab initio electronic structure computation on a
closed shell molecule. Molecular orbitals, ψ, which are expressed as linear combinations of
contracted Gaussian basis functions, φ, are used to produce this wavefunction, ψ. To fit
Slater-type orbitals (STOs), the contracted Gaussian functions are made out of primitive
Gaussian functions. Using the nonlinear variational technique, the exponential parameters in
the STOs are optimized by computations on tiny molecules, and those values are
subsequently applied to other molecules. The Hartree-Fock technique frequently makes the
assumption that a single Slater determinant can accurately represent the system's N-body
wave function. A set of N-coupled equations for the N spin orbitals can be obtained by
applying the variational technique. The system's energy and Hartree-Fock wave function are
obtained by solving these equations.

Density Functional Theory

In physics, chemistry, and materials science, density-functional theory (DFT) is a

computational quantum mechanical modelling technique used to study the electronic

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structure (or nuclear structure) (essentially the ground state) of many-body systems,
specifically atoms, molecules, and condensed phases. The fundamental variable in DFT is the
one-body density rather than the many-body wave function. Density-functional theory is
computationally viable even for enormous systems since the density n(r) is a function of only
three spatial coordinates (instead of the 3N coordinates of the wave function). According to
this theory, functionals that is, functions of another function—can be used to ascertain the
characteristics of a many-electron system. These are functionals of the spatially dependent
electron density in the context of DFT.

Compound used for Analysis

The compound on which the calculations were performed is 4-Phenylbenzaldehyde. It

consists of 24-atom, 96-electron, neutral system consisting of carbon, hydrogen and oxygen
atoms. 2-Phenylbenzaldehyde (also known as 2-biphenylcarboxaldehyde) is an aromatic
aldehyde. It is used as a key intermediate in the synthesis of various organic compounds,
including pharmaceuticals, agrochemicals, and dyes. It can be used in the formulation of
perfumes and flavours due to its aromatic properties. It serves as a precursor in the synthesis
of advanced materials and specialty polymers. Used as a starting material for the synthesis of
certain drugs, including those with anti-inflammatory and antimicrobial properties. The
picture below shows the 3-D structure of 4-phenylbenzaldehyde

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 Figure 1 Optimized Structure of 4-Phenylbenzaldehyde

Methodology:

The 6-31+G(d,p) basis set for the carbon (C), hydrogen (H), and oxygen (O) atoms was used
in the calculations on the target molecule utilizing the Hartree Fock (HF) and Density
Functional Theory (DFT) approaches. This is a triple-zeta quality split-valence basis set that
includes diffused functions, one set of d-type polarization functions for C and O, and one set
of p-type polarization functions for H respectively. The Guassian-6.0.16 quantum chemistry
package's implementation of the B3LYP functional was also used for the DFT calculations.
Both HF and DFT were utilized to determine the vibrational infrared frequencies of the target
structure (4-phenyl benzaldehyde) and to optimize its geometry. The excitation energies and
oscillator strengths of ten lowest energy excited groups were also determined using DFT.
The target structure (4-phenyl benzaldehyde) was optimized geometrically and its vibrational
infrared frequencies were calculated using both HF and DFT. Additionally, using the TD-
SCF (Time-Dependent Self-Consistent Field) approach, DFT was utilized to determine the
excitation energies and oscillator strengths of ten lowest energy excited states. The H-NMR
and C-NMR spectra were also obtained using both HF and DFT. Their chemical shift values
were obtained by running NMR of optimized SiMe4 and then subtracting isotropic values of
C and H from isotropic values of SiMe4 respectively.

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Results and Discussion:

Geometry Optimization:

The tables below show a comparison of some of the optimized parameters (bond length, angle
and dihedral angle) that were obtained using both, HF and DFT.

Optimized Bond Lengths (in Angstrom)

Bond Length Hartree Fock (HF) Density Functional Theory
(DFT)
C=O (22-24) 1.1923 Å 1.1116 Å
C=C (10-11) 1.3868 Å 1.3976 Å
C-H (10-19) 1.0754 1.086 Å

The above values shows that the optimized bond lengths obtained in DFT are slightly larger
than the HF values.
Optimized Angles (in Degrees)
Angle Hartree Fock (HF) Density Functional Theory
(DFT)
A (23,22,24) 120.302° 120.2572 °
A (4,5,15) 119.9294° 120.2572 °
A (4,5,6) 120.5221 124. 5211 °

Optimized Dihedral Angles (in Degrees)

Dihedral Angle Hartree Fock (HF) Density Functional Theory
(DFT)
D(3,4,22,24) 179.9869 ° 179.8479
D(12,7,8,17) 178.8304 ° 178.4431

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The dihedral values in DFT is slightly lower than the ones obtained via Hartree-Fock.

FT-IR Spectroscopy:

The target compound was characterized in gas phase for FT-IR Spectroscopy using both HF
and DFT and the results obtained from each method are discussed below.

IR Frequencies obtained from HF

The obtained FT-IR spectrum using the HF method is shown below.

Figure 2 FTIR Spectrum using HF

A strong intense peak observed at 1977.15 cm-1 C=O stretches. The C=C stretches of the
aromatic ring are observed at 1324.17 cm -1 and 1300.11 cm-1. Furthermore, the sp2 hybridised
C-H stretch of benzene ring is observed at 3375 cm-1. while the sp2 C-H stretch of the
aldehyde group is observed at 3141.88 cm-1.

IR Frequencies obtained from DFT

The following FT-IR spectrum was obtained using DFT calculations.

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 Figure 3 FTIR Spectrum using DFT

A strong intense peak observed at 1435.15 cm-1 C=O stretches. The C=C stretches of the
aromatic ring are observed at 978.17 cm -1 and 990.21 cm-1. Furthermore, the sp2 hybridised C-
H stretch of benzene ring is observed at 3095 cm-1. while the sp2 C-H stretch of the aldehyde
group is observed at 1599.88 cm-1.

Comparison with Experimental data

In general, the IR frequencies obtained from DFT are more accurate as they are closer to the
experimentally observed values while those obtained from HF are much higher. For example,
experimentally the C-O stretches are observed in the. The C=O stretch from DFT also lies
close to the expected 1600-1800 cm-1 region whereas a higher frequency is obtained from HF
calculations.
Reasons for Differences in IR frequencies

The observed discrepancy in infrared (IR) frequencies between Hartree-Fock (HF)

calculations and experimental values, compared to the more accurate results obtained from
Density Functional Theory (DFT), can be attributed to several factors:

• Electron Correlation Effects: HF calculations treat electrons in a mean-field

approximation without accounting for dynamic electron correlation. As a result, HF
tends to overestimate the stability of the system, leading to higher vibrational
frequencies than observed experimentally whereas DFT includes a more realistic

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 treatment of electron-electron correlation through the exchange-correlation functional.
This helps capture dynamic correlation effects that are absent in HF, leading to more
accurate vibrational frequencies.

• Zero-Point Energy (ZPE) Differences: HF often underestimates zero-point energy,

contributing to the overestimation of vibrational frequencies while DFT can provide
more accurate predictions of zero-point energy, leading to better agreement with
experimental vibrational frequencies.
• Dispersion Interactions: Some DFT functionals incorporate dispersion corrections,
improving the description of dispersion interactions that are important in vibrational
frequencies. HF, lacking dispersion corrections, may not account for these interactions
as effectively.
• System-Specific Considerations: The choice of DFT functional can significantly
impact results. Certain functionals might be more suitable for specific systems or
types of interactions. HF may perform well for certain systems but is generally less
accurate than DFT for a wide range of molecular properties.

These effects are important for accurate theoretical determination of equilibrium geometries,
vibrational frequencies, and electrical properties, thus leading to differences in the values
obtained.

Single Point Energy:

a Single Point Energy (SPE) calculation is used to determine the electronic energy of a
molecular system at a fixed geometry without performing any structural optimization. The
target molecule shows following results for single point energy.

Single Point Energy obtained from HF

The following diagram represents the energy levels for some of the molecular orbitals
(M.O’s) involved in the transitions via HF-method. The value of LUMO 48 is smaller than
the HOMO 49. The energy of HOMO is ionization energy of the target molecule. The
LOMO’s energy is multiplied by -1 gives the electron affinity value of the target molecules.

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 Figure 4 Some Values of M.Os obtained via ESP by H-F

The given below results shows electron density mapped with Single point Energy via Hartree
Fock Method.

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 Figure 5 Electrostatic potential mapped via ESP

The red site shows the attack of electrophile which can be mapped on oxygen as its
nucleophilic in nature. While a nucleophile will attack on carbonyl carbon.

Single Point Energy obtained from DFT

The following diagram represents the energy levels for some of the molecular orbitals
(M.O’s) involved in the transitions via DFT-method. The value of LUMO 48 is smaller than
the HOMO 49.

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 Figure 6 Some values of M.Os mapped out with DFT

Figure 7 Pictorial representation of M.Os mapped out via ESP by DFT

The above picture is pictorial representation of molecular orbitals obtained by applying DFT

UV-Vis Spectroscopy:

UV-Vis was performed by employing benzene as solvent for both Hartree-Fock and DFT.

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UV-Vis Spectrum obtained from HF

The obtained UV-Vis spectrum showing the various transitions for the target compound is
shown below.

Figure 8 UV-Vis Spectrum by HF

The excitation energies, wavelengths and oscillator strengths for the 3 energy excited states
are listed in the following tables.

Excited State 1 Excitation Wavelength Oscillator

Energy Strength
44 -> 49(0.50871) 4.8397 eV 256.18 nm f=0.0004
44 -> 54(0.16352)

Excited State 2 Excitation Wavelength Oscillator

Energy Strength
45 -> 49 (-0.11361) 5.0687 eV 244.61 nm f = 0.5943
45 -> 61 (-0.10254)

Excited State 3 Excitation Wavelength Oscillator

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 Energy Strength
46 -> 49 (0.55314) 5.5367 eV 214.31 nm f = 0.0370
47 -> 49 (0.10112)

The magnitude of the oscillator strength (f) is an indication of the intensity of the transition
occurring. Thus, it can be deduced from the results that the transitions for the 2 nd excited state
are the most intense while weakest transitions are observed for the 1st excited state.

Furthermore, in perfectly planar molecules, the σ and π separation in the orbitals is already
present while such distinction cannot be made in case of non-planar structures. In the
structure of 4-phenylbenzaldehyde, the benzene ring and the carbonyl group are planar.

UV-Vis spectrum using DFT

Figure 9 UV-Vis Spectrum by DFT

Excited State 1 Excitation Wavelength Oscillator

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 Energy Strength
46 -> 49(0.65331) 3.6787 eV 337.03 nm f=0.0003
46 -> 52 (0.12457)

Excited State 2 Excitation Wavelength Oscillator

Energy Strength
48 -> 49(0.70146) 4.0123 eV 309.01 nm f =0.6957

Excited State 3 Excitation Wavelength Oscillator

Energy Strength
45 -> 49(0.10107) 4.4287 eV 279.96 nm f =0.0045
46 -> 49(-0.20119)

The magnitude of the oscillator strength (f) is an indication of the intensity of the transition
occurring. Thus, it can be deduced from the results that the transitions for the 2nd excited state
are the most intense while weakest transitions are observed for the 1st excited state.

NMR Spectrum:

NMR spectrum obtained for Carbon and hydrogen from both H-F and DFT are discussed
below.

NMR using Hartree Fock

The NMR spectrum calculated from HF method is discussed next:

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Figure 10CNMR by HF

Figure 11 HNMR by HF

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 Figure 12 O NMR by HF

Explanation of Chemical Shift values

Chemical shift Values can be determined by running separate NMR spectrum of optimized
SiMe4. Then subtracting the isotropic values of atoms of target molecule from SiMe4.

For example,

Isotropic Value of C (SiMe4)- Isotropic Value of Carbon 22 (Aldehydic Carbon)

203.0728 ppm – 2023ppm = 182.8428 ppm (Characteristic Aldehydic Chemical shift in C-

NMR)

Isotropic Value of H (SiMe4)- Isotropic Value of Carbon 22 (Aldehydic Hydrogen)

32.2680 ppm - 22.4905ppm = 9.8 ppm which is close to (Aldehydic hydrogen)

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NMR using DFT

Figure 13 C-NMR USING DFT

Figure 14 H-NMR using DFT

Explanation of Chemical Shift values

Chemical shift Values can be determined by running separate NMR spectrum of optimized
SiMe4. Then subtracting the isotropic values of atoms of target molecule from SiMe4.

For example,

Isotropic Value of C (SiMe4)- Isotropic Value of Carbon 22 (Aldehydic Carbon)

192.5549 – 7.8139 = 184.74 ppm (Characteristic Aldehydic Chemical shift in C-NMR)

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Isotropic Value of H (SiMe4)- Isotropic Value of Hydrogen 24 (Aldehydic Hydrogen)

31.6496 ppm - 21.3865 ppm = 10.26 ppm which is close to (Aldehydic hydrogen).

Conclusion:

Thus, the target molecule 4-Phenylbenzaldeyde was successfully characterized by performing

various HF and DFT calculations. The geometry of the structure was optimized along with
the determination of the theoretical IR frequencies of the characteristic vibrational modes as
well as the calculation of the excitation energies and oscillator strengths of 10 lowest energy
excited states in the molecule. Furthermore, NMR spectrum was also obtained by employing
both HF and DFT.

References:
Gaussian 09, Revision A.02,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci,
G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian,
A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada,
M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima,
Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr.,
J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers,
K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand,
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V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann,
O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski,
R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth,
P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels,
O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski,
and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.

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